Start testing: Jun 07 13:12 UTC ---------------------------------------------------------- 55/157 Testing: integration_Run_gmx_grompp_re 55/157 Test: integration_Run_gmx_grompp_re Command: "/usr/bin/gmx" "grompp" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate_gmx "integration_Run_gmx_grompp_re" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- :-) GROMACS - gmx grompp, 2023.1 (-: Executable: /usr/bin/gmx Data prefix: /usr Working dir: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate_gmx Command line: gmx grompp Ignoring obsolete mdp entry 'title' NOTE 1 [file grompp.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file grompp.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to 2079299067 Number of degrees of freedom in T-Coupling group System is 645.00 There were 2 NOTEs GROMACS reminds you: "You're Insignificant" (Tricky) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 216 Water residues Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 0.900 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 0.900 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_gmx_grompp_re" end time: Jun 07 13:12 UTC "integration_Run_gmx_grompp_re" time elapsed: 00:00:00 ---------------------------------------------------------- 123/157 Testing: integration_Run_gmx_grompp_ppy 123/157 Test: integration_Run_gmx_grompp_ppy Command: "/usr/bin/gmx" "grompp" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_ppy "integration_Run_gmx_grompp_ppy" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- :-) GROMACS - gmx grompp, 2023.1 (-: Executable: /usr/bin/gmx Data prefix: /usr Working dir: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_ppy Command line: gmx grompp NOTE 1 [file grompp.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file grompp.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -639238274 Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file topol.top, line 484]: The bond in molecule-type Protein between atoms 1 N and 2 HN has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 243.00 There were 3 NOTEs GROMACS reminds you: "You're Insignificant" (Tricky) Generated 28 of the 28 non-bonded parameter combinations Generated 28 of the 28 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' Analysing residue names: There are: 10 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 0.900 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 0.900 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_gmx_grompp_ppy" end time: Jun 07 13:12 UTC "integration_Run_gmx_grompp_ppy" time elapsed: 00:00:00 ---------------------------------------------------------- 126/157 Testing: integration_Run_gmx_grompp_mma 126/157 Test: integration_Run_gmx_grompp_mma Command: "/usr/bin/gmx" "grompp" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_mma "integration_Run_gmx_grompp_mma" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- :-) GROMACS - gmx grompp, 2023.1 (-: Executable: /usr/bin/gmx Data prefix: /usr Working dir: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_mma Command line: gmx grompp Ignoring obsolete mdp entry 'andersen_seed' Ignoring obsolete mdp entry 'optimize_fft' Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision' Setting the LD random seed to 1591865191 Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file topol.top, line 522]: The bond in molecule-type 3-MMA between atoms 17 C2 and 18 H4 has an estimated oscillational period of 1.2e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 156.00 NOTE 2 [file grompp.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. NOTE 3 [file grompp.mdp]: This run will generate roughly 2997 Mb of data NOTE 4 [file grompp.mdp]: COM removal frequency is set to (705032704). Other settings require a global communication frequency of 100. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 100. There were 4 NOTEs GROMACS reminds you: "You're Insignificant" (Tricky) Generated 21 of the 21 non-bonded parameter combinations Generated 21 of the 21 1-4 parameter combinations Excluding 3 bonded neighbours molecule type '3-MMA' Setting gen_seed to -1075970059 Velocities were taken from a Maxwell distribution at 600 K Analysing residue names: There are: 3 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 600 K Calculated rlist for 1x1 atom pair-list as 1.052 nm, buffer size 0.152 nm Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.116 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_gmx_grompp_mma" end time: Jun 07 13:12 UTC "integration_Run_gmx_grompp_mma" time elapsed: 00:00:00 ---------------------------------------------------------- 50/157 Testing: integration_Run_csg_reupdate 50/157 Test: integration_Run_csg_reupdate Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_reupdate" "--gentable" "true" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_re.xml" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate "integration_Run_csg_reupdate" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Writing CG parameters and potential(s) Writing file: CG-CG.pot.new CG-CG potential's extrapolated core is attractive! Artifically enforcing repulsive core. Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_reupdate" end time: Jun 07 13:12 UTC "integration_Run_csg_reupdate" time elapsed: 00:00:00 ---------------------------------------------------------- 52/157 Testing: integration_Run_csg_reupdate2 52/157 Test: integration_Run_csg_reupdate2 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_reupdate" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_re.xml" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol_cg.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame_cg.dump" "--hessian-check" "no" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate2 "integration_Run_csg_reupdate2" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- I have 216 beads in 216 molecules Reading frame, timestep 0 We have CG-CG CG potential Between beads CG-CG With Function form cbspl And 4 parameters to optimize Potential range: rmin = 0.26 [nm] rcutoff = 0.3 [nm] Total number of parameters to optimize: 4 Updating parameters ****************** WARNING ***************** Hessian H NOT a positive definite! This can be a result of poor initial guess or ill-suited CG potential settings or poor CG sampling. ******************************************** However, you want to proceed despite non-positive definite H. Non-positive H does not gurantee relative entropy iterations to converge to minimum. You can turn on Hessian check by setting command line option --hessian-check=true. In this case, alternative update option is steepest descent. AA Ensemble Avg Energy :: 0.328298 CG Ensemble Avg Energy :: 5.32913 Writing CG parameters and potential(s) Writing file: CG-CG.pot.new CG-CG potential's extrapolated core is attractive! Artifically enforcing repulsive core. Writing file: CG-CG.param.new CG-CG potential's extrapolated core is attractive! Artifically enforcing repulsive core. Finished RE update! Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_reupdate2" end time: Jun 07 13:12 UTC "integration_Run_csg_reupdate2" time elapsed: 00:00:00 ---------------------------------------------------------- 65/157 Testing: integration_Run_csg_map 65/157 Test: integration_Run_csg_map Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_map" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--out" "frame.dump" "--no-map" "--force" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_map "integration_Run_csg_map" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- I have 648 beads in 216 molecules Reading frame, timestep 0 writing coarse-grained trajectory to frame.dump Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_map" end time: Jun 07 13:12 UTC "integration_Run_csg_map" time elapsed: 00:00:00 ---------------------------------------------------------- 59/157 Testing: integration_Run_csg_fmatch 59/157 Test: integration_Run_csg_fmatch Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_fmatch" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_fmatch.xml" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch "integration_Run_csg_fmatch" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- I have 648 beads in 216 molecules I have 216 beads in 216 molecules for the coarsegraining Reading frame, timestep 0 a: 0.37 ,sigma: 1 ,gamma: 0.12 Number of spline functions for the interaction CG-CG:13 You are using VOTCA! hey, somebody wants to forcematch! Using constrained Least Squares! This should be a number: -19.5494 Block No1 done! Updating file: CG-CG.force We are done, thank you very much! Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_fmatch" end time: Jun 07 13:12 UTC "integration_Run_csg_fmatch" time elapsed: 00:00:00 ---------------------------------------------------------- 67/157 Testing: integration_Run_csg_map_gro 67/157 Test: integration_Run_csg_map_gro Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_map" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" "--out" "conf_cg.gro" "--nframes" "1" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_map_gro "integration_Run_csg_map_gro" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- I have 648 beads in 216 molecules I have 216 beads in 216 molecules for the coarsegraining Reading frame, timestep 0 writing coarse-grained trajectory to conf_cg.gro Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_map_gro" end time: Jun 07 13:12 UTC "integration_Run_csg_map_gro" time elapsed: 00:00:00 ---------------------------------------------------------- 79/157 Testing: integration_Run_csg_imc_solve 79/157 Test: integration_Run_csg_imc_solve Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_imc_solve" "-i" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/imc/CG-CG.imc" "-g" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/imc/CG-CG.gmc" "-n" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/imc/CG-CG.idx" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve "integration_Run_csg_imc_solve" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_imc_solve" end time: Jun 07 13:12 UTC "integration_Run_csg_imc_solve" time elapsed: 00:00:00 ---------------------------------------------------------- 89/157 Testing: integration_Run_csg_resample_akima 89/157 Test: integration_Run_csg_resample_akima Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_resample" "--in" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_in" "--out" "table_akima" "--type" "akima" "--grid" "0:0.1:3" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample "integration_Run_csg_resample_akima" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_resample_akima" end time: Jun 07 13:12 UTC "integration_Run_csg_resample_akima" time elapsed: 00:00:00 ---------------------------------------------------------- 74/157 Testing: integration_Run_csg_stat-imc 74/157 Test: integration_Run_csg_stat-imc Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_stat" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--do-imc" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_imc.xml" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat-imc "integration_Run_csg_stat-imc" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- begin to calculate inverse monte carlo parameters # of bonded interactions: 0 # of non-bonded interactions: 1 I have 648 beads in 216 molecules I have 216 beads in 216 molecules for the coarsegraining Reading frame, timestep 0 written CG-CG.dist.new written CG-CG.imc written CG-CG.gmc written CG-CG.idx Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_stat-imc" end time: Jun 07 13:12 UTC "integration_Run_csg_stat-imc" time elapsed: 00:00:00 ---------------------------------------------------------- 56/157 Testing: integration_Run_csg_reupdate_gmx 56/157 Test: integration_Run_csg_reupdate_gmx Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_reupdate" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_re.xml" "--top" "topol.tpr" "--trj" "conf.gro" "--hessian-check" "no" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate_gmx "integration_Run_csg_reupdate_gmx" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Reading file topol.tpr, VERSION 2023.1 (single precision) I have 216 beads in 216 molecules We have CG-CG CG potential Between beads CG-CG With Function form cbspl And 4 parameters to optimize Potential range: rmin = 0.26 [nm] rcutoff = 0.3 [nm] Total number of parameters to optimize: 4 Updating parameters ****************** WARNING ***************** Hessian H NOT a positive definite! This can be a result of poor initial guess or ill-suited CG potential settings or poor CG sampling. ******************************************** However, you want to proceed despite non-positive definite H. Non-positive H does not gurantee relative entropy iterations to converge to minimum. You can turn on Hessian check by setting command line option --hessian-check=true. In this case, alternative update option is steepest descent. AA Ensemble Avg Energy :: 0.328298 CG Ensemble Avg Energy :: 5.31427 Writing CG parameters and potential(s) Writing file: CG-CG.pot.new CG-CG potential's extrapolated core is attractive! Artifically enforcing repulsive core. Writing file: CG-CG.param.new CG-CG potential's extrapolated core is attractive! Artifically enforcing repulsive core. Finished RE update! Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_reupdate_gmx" end time: Jun 07 13:12 UTC "integration_Run_csg_reupdate_gmx" time elapsed: 00:00:00 ---------------------------------------------------------- 91/157 Testing: integration_Run_csg_resample_cubic 91/157 Test: integration_Run_csg_resample_cubic Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_resample" "--in" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_in" "--out" "table_cubic" "--type" "cubic" "--grid" "0:0.1:3" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample "integration_Run_csg_resample_cubic" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_resample_cubic" end time: Jun 07 13:12 UTC "integration_Run_csg_resample_cubic" time elapsed: 00:00:00 ---------------------------------------------------------- 93/157 Testing: integration_Run_csg_resample_linear 93/157 Test: integration_Run_csg_resample_linear Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_resample" "--in" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_in" "--out" "table_linear" "--type" "linear" "--grid" "0:0.1:3" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample "integration_Run_csg_resample_linear" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_resample_linear" end time: Jun 07 13:12 UTC "integration_Run_csg_resample_linear" time elapsed: 00:00:00 ---------------------------------------------------------- 95/157 Testing: integration_Run_csg_resample_cubicfit 95/157 Test: integration_Run_csg_resample_cubicfit Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_resample" "--in" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_in" "--out" "table_cubicfit" "--type" "cubic" "--grid" "0:1:9" "--fitgrid" "0:2:9" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample "integration_Run_csg_resample_cubicfit" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- doing cubic fit 0:2:9 Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_resample_cubicfit" end time: Jun 07 13:12 UTC "integration_Run_csg_resample_cubicfit" time elapsed: 00:00:00 ---------------------------------------------------------- 69/157 Testing: integration_Run_csg_stat 69/157 Test: integration_Run_csg_stat Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_stat" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_rdf.xml" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat "integration_Run_csg_stat" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- begin to calculate distribution functions # of bonded interactions: 0 # of non-bonded interactions: 1 I have 648 beads in 216 molecules I have 216 beads in 216 molecules for the coarsegraining Reading frame, timestep 0 written CG-CG.dist.new written CG-CG.force.new Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_stat" end time: Jun 07 13:12 UTC "integration_Run_csg_stat" time elapsed: 00:00:00 ---------------------------------------------------------- 97/157 Testing: integration_Run_csg_dump 97/157 Test: integration_Run_csg_dump Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --top /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/methanol-water//topol_cg.xml > csg_dump.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump "integration_Run_csg_dump" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_dump" end time: Jun 07 13:12 UTC "integration_Run_csg_dump" time elapsed: 00:00:00 ---------------------------------------------------------- 99/157 Testing: integration_Run_csg_dump_gro 99/157 Test: integration_Run_csg_dump_gro Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --top /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/conf.gro > csg_dump_gro.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump_gro "integration_Run_csg_dump_gro" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_dump_gro" end time: Jun 07 13:12 UTC "integration_Run_csg_dump_gro" time elapsed: 00:00:00 ---------------------------------------------------------- 101/157 Testing: integration_Run_csg_dump_data 101/157 Test: integration_Run_csg_dump_data Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --top /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols_cg/spce.data > csg_dump_data.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump_data "integration_Run_csg_dump_data" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_dump_data" end time: Jun 07 13:12 UTC "integration_Run_csg_dump_data" time elapsed: 00:00:00 ---------------------------------------------------------- 115/157 Testing: integration_Run_csg_property 115/157 Test: integration_Run_csg_property Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_property --file /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_defaults.xml --print . --short --path cg.inverse.gromacs.DESC > csg_property.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property "integration_Run_csg_property" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_property" end time: Jun 07 13:12 UTC "integration_Run_csg_property" time elapsed: 00:00:00 ---------------------------------------------------------- 117/157 Testing: integration_Run_csg_property2 117/157 Test: integration_Run_csg_property2 Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_property --file /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_defaults.xml --print . --path cg.inverse.gromacs.DESC > csg_property.out2" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property "integration_Run_csg_property2" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_property2" end time: Jun 07 13:12 UTC "integration_Run_csg_property2" time elapsed: 00:00:00 ---------------------------------------------------------- 121/157 Testing: integration_Run_csg_property4 121/157 Test: integration_Run_csg_property4 Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_property --file /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/test.xml --path A.B --print C > csg_property.out4" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property "integration_Run_csg_property4" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_property4" end time: Jun 07 13:12 UTC "integration_Run_csg_property4" time elapsed: 00:00:00 ---------------------------------------------------------- 1/157 Testing: integration_votca_propertyHelp 1/157 Test: integration_votca_propertyHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tools/votca_property" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tools "integration_votca_propertyHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/tools/issues votca_property votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) Helper for parsing XML files Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --file arg xml file to parse --format arg output format [XML TXT] --level arg output from this level Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_votca_propertyHelp" end time: Jun 07 13:12 UTC "integration_votca_propertyHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 124/157 Testing: integration_Run_csg_boltzmann_ppy 124/157 Test: integration_Run_csg_boltzmann_ppy Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csg_boltzmann/csg_boltzmann" "--top" "topol.tpr" "--cg" "ppy10.xml" "--excl" "excl.txt" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_ppy "integration_Run_csg_boltzmann_ppy" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Reading file topol.tpr, VERSION 2023.1 (single precision) I have 82 beads in 1 molecules I have 10 beads in 1 molecules for the coarsegraining Writing exclusion list for atomistic molecule Protein in coarse grained representation Protein Test time = 0.07 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_boltzmann_ppy" end time: Jun 07 13:12 UTC "integration_Run_csg_boltzmann_ppy" time elapsed: 00:00:00 ---------------------------------------------------------- 72/157 Testing: integration_Run_csg_stat_angular 72/157 Test: integration_Run_csg_stat_angular Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_stat" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_angular.xml" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_angular "integration_Run_csg_stat_angular" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- begin to calculate distribution functions # of bonded interactions: 0 # of non-bonded interactions: 1 I have 648 beads in 216 molecules I have 216 beads in 216 molecules for the coarsegraining Reading frame, timestep 0 written CG-CG-CG.dist.new Test time = 0.12 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_stat_angular" end time: Jun 07 13:12 UTC "integration_Run_csg_stat_angular" time elapsed: 00:00:00 ---------------------------------------------------------- 127/157 Testing: integration_Run_csg_boltzmann_mma 127/157 Test: integration_Run_csg_boltzmann_mma Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csg_boltzmann/csg_boltzmann" "--top" "topol.tpr" "--cg" "mapping.xml" "--excl" "excl.txt" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_mma "integration_Run_csg_boltzmann_mma" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Reading file topol.tpr, VERSION 2023.1 (single precision) I have 53 beads in 1 molecules I have 11 beads in 1 molecules for the coarsegraining Writing exclusion list for atomistic molecule 3-MMA in coarse grained representation 3-MMA Test time = 0.10 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_boltzmann_mma" end time: Jun 07 13:12 UTC "integration_Run_csg_boltzmann_mma" time elapsed: 00:00:00 ---------------------------------------------------------- 85/157 Testing: integration_Run_csg_stat_imc_multi 85/157 Test: integration_Run_csg_stat_imc_multi Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_stat" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/traj.gro" "--do-imc" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/settings_imc.xml" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_imc_multi "integration_Run_csg_stat_imc_multi" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- begin to calculate inverse monte carlo parameters # of bonded interactions: 0 # of non-bonded interactions: 3 I have 200 beads in 200 molecules written LJ1-LJ1.dist.new written LJ1-LJ2.dist.new written LJ2-LJ2.dist.new written all.imc written all.gmc written all.idx Test time = 0.14 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_stat_imc_multi" end time: Jun 07 13:12 UTC "integration_Run_csg_stat_imc_multi" time elapsed: 00:00:00 ---------------------------------------------------------- 119/157 Testing: integration_Run_csg_property3 119/157 Test: integration_Run_csg_property3 Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_property --file /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/test.xml --path A.B.C --print . > csg_property.out3" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property "integration_Run_csg_property3" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.12 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_property3" end time: Jun 07 13:12 UTC "integration_Run_csg_property3" time elapsed: 00:00:00 ---------------------------------------------------------- 2/157 Testing: unit_test_calculator 2/157 Test: unit_test_calculator Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_calculator" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_calculator" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... *** No errors detected  Test time = 0.10 sec ---------------------------------------------------------- Test Passed. "unit_test_calculator" end time: Jun 07 13:12 UTC "unit_test_calculator" time elapsed: 00:00:00 ---------------------------------------------------------- 3/157 Testing: unit_test_constants 3/157 Test: unit_test_constants Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_constants" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_constants" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... *** No errors detected  Test time = 0.10 sec ---------------------------------------------------------- Test Passed. "unit_test_constants" end time: Jun 07 13:12 UTC "unit_test_constants" time elapsed: 00:00:00 ---------------------------------------------------------- 4/157 Testing: unit_test_correlate 4/157 Test: unit_test_correlate Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_correlate" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_correlate" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... *** No errors detected  Test time = 0.09 sec ---------------------------------------------------------- Test Passed. "unit_test_correlate" end time: Jun 07 13:12 UTC "unit_test_correlate" time elapsed: 00:00:00 ---------------------------------------------------------- 5/157 Testing: unit_test_crosscorrelate 5/157 Test: unit_test_crosscorrelate Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_crosscorrelate" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_crosscorrelate" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... *** No errors detected  Test time = 0.08 sec ---------------------------------------------------------- Test Passed. "unit_test_crosscorrelate" end time: Jun 07 13:12 UTC "unit_test_crosscorrelate" time elapsed: 00:00:00 ---------------------------------------------------------- 7/157 Testing: unit_test_datacollection 7/157 Test: unit_test_datacollection Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_datacollection" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_datacollection" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 6 test cases... *** No errors detected  Test time = 0.07 sec ---------------------------------------------------------- Test Passed. "unit_test_datacollection" end time: Jun 07 13:12 UTC "unit_test_datacollection" time elapsed: 00:00:00 ---------------------------------------------------------- 8/157 Testing: unit_test_edge_base 8/157 Test: unit_test_edge_base Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_edge_base" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_edge_base" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 8 test cases... Vertices 2 3 *** No errors detected  Test time = 0.07 sec ---------------------------------------------------------- Test Passed. "unit_test_edge_base" end time: Jun 07 13:12 UTC "unit_test_edge_base" time elapsed: 00:00:00 ---------------------------------------------------------- 6/157 Testing: unit_test_cubicspline 6/157 Test: unit_test_cubicspline Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_cubicspline" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_cubicspline" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 5 test cases... *** No errors detected  Test time = 0.08 sec ---------------------------------------------------------- Test Passed. "unit_test_cubicspline" end time: Jun 07 13:12 UTC "unit_test_cubicspline" time elapsed: 00:00:00 ---------------------------------------------------------- 9/157 Testing: unit_test_edgecontainer 9/157 Test: unit_test_edgecontainer Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_edgecontainer" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_edgecontainer" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 10 test cases... *** No errors detected  Test time = 0.07 sec ---------------------------------------------------------- Test Passed. "unit_test_edgecontainer" end time: Jun 07 13:12 UTC "unit_test_edgecontainer" time elapsed: 00:00:00 ---------------------------------------------------------- 81/157 Testing: integration_Run_csg_imc_solve_reg 81/157 Test: integration_Run_csg_imc_solve_reg Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_imc_solve" "-r" "1000" "-i" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/group_1.imc" "-g" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/group_1.gmc" "-n" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/group_1.idx" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve_reg "integration_Run_csg_imc_solve_reg" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.17 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_imc_solve_reg" end time: Jun 07 13:12 UTC "integration_Run_csg_imc_solve_reg" time elapsed: 00:00:00 ---------------------------------------------------------- 10/157 Testing: unit_test_elements 10/157 Test: unit_test_elements Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_elements" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_elements" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... *** No errors detected  Test time = 0.07 sec ---------------------------------------------------------- Test Passed. "unit_test_elements" end time: Jun 07 13:12 UTC "unit_test_elements" time elapsed: 00:00:00 ---------------------------------------------------------- 11/157 Testing: unit_test_filesystem 11/157 Test: unit_test_filesystem Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_filesystem" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_filesystem" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... *** No errors detected  Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "unit_test_filesystem" end time: Jun 07 13:12 UTC "unit_test_filesystem" time elapsed: 00:00:00 ---------------------------------------------------------- 12/157 Testing: unit_test_floatingpointcomparison 12/157 Test: unit_test_floatingpointcomparison Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_floatingpointcomparison" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_floatingpointcomparison" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... *** No errors detected  Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "unit_test_floatingpointcomparison" end time: Jun 07 13:12 UTC "unit_test_floatingpointcomparison" time elapsed: 00:00:00 ---------------------------------------------------------- 13/157 Testing: unit_test_graphalgorithm 13/157 Test: unit_test_graphalgorithm Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graphalgorithm" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_graphalgorithm" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 5 test cases... is single network 1 EDGE CHECK ************************************** *** No errors detected  Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "unit_test_graphalgorithm" end time: Jun 07 13:12 UTC "unit_test_graphalgorithm" time elapsed: 00:00:00 ---------------------------------------------------------- 14/157 Testing: unit_test_graph_base 14/157 Test: unit_test_graph_base Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graph_base" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_graph_base" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 8 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_graph_base" end time: Jun 07 13:12 UTC "unit_test_graph_base" time elapsed: 00:00:00 ---------------------------------------------------------- 15/157 Testing: unit_test_graph_bf_visitor 15/157 Test: unit_test_graph_bf_visitor Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graph_bf_visitor" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_graph_bf_visitor" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_graph_bf_visitor" end time: Jun 07 13:12 UTC "unit_test_graph_bf_visitor" time elapsed: 00:00:00 ---------------------------------------------------------- 16/157 Testing: unit_test_graph_df_visitor 16/157 Test: unit_test_graph_df_visitor Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graph_df_visitor" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_graph_df_visitor" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_graph_df_visitor" end time: Jun 07 13:12 UTC "unit_test_graph_df_visitor" time elapsed: 00:00:00 ---------------------------------------------------------- 17/157 Testing: unit_test_graphdistvisitor 17/157 Test: unit_test_graphdistvisitor Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graphdistvisitor" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_graphdistvisitor" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_graphdistvisitor" end time: Jun 07 13:12 UTC "unit_test_graphdistvisitor" time elapsed: 00:00:00 ---------------------------------------------------------- 18/157 Testing: unit_test_graphnode 18/157 Test: unit_test_graphnode Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graphnode" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_graphnode" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 4 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_graphnode" end time: Jun 07 13:12 UTC "unit_test_graphnode" time elapsed: 00:00:00 ---------------------------------------------------------- 19/157 Testing: unit_test_graphvisitor 19/157 Test: unit_test_graphvisitor Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graphvisitor" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_graphvisitor" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_graphvisitor" end time: Jun 07 13:12 UTC "unit_test_graphvisitor" time elapsed: 00:00:00 ---------------------------------------------------------- 20/157 Testing: unit_test_histogramnew 20/157 Test: unit_test_histogramnew Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_histogramnew" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_histogramnew" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 6 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_histogramnew" end time: Jun 07 13:12 UTC "unit_test_histogramnew" time elapsed: 00:00:00 ---------------------------------------------------------- 21/157 Testing: unit_test_identity 21/157 Test: unit_test_identity Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_identity" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_identity" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_identity" end time: Jun 07 13:12 UTC "unit_test_identity" time elapsed: 00:00:00 ---------------------------------------------------------- 22/157 Testing: unit_test_linalg 22/157 Test: unit_test_linalg Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_linalg" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_linalg" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_linalg" end time: Jun 07 13:12 UTC "unit_test_linalg" time elapsed: 00:00:00 ---------------------------------------------------------- 23/157 Testing: unit_test_name 23/157 Test: unit_test_name Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_name" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_name" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_name" end time: Jun 07 13:12 UTC "unit_test_name" time elapsed: 00:00:00 ---------------------------------------------------------- 24/157 Testing: unit_test_objectfactory 24/157 Test: unit_test_objectfactory Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_objectfactory" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_objectfactory" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_objectfactory" end time: Jun 07 13:12 UTC "unit_test_objectfactory" time elapsed: 00:00:00 ---------------------------------------------------------- 25/157 Testing: unit_test_optionshandler 25/157 Test: unit_test_optionshandler Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_optionshandler" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_optionshandler" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 6 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_optionshandler" end time: Jun 07 13:12 UTC "unit_test_optionshandler" time elapsed: 00:00:00 ---------------------------------------------------------- 26/157 Testing: unit_test_property 26/157 Test: unit_test_property Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_property" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_property" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 8 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_property" end time: Jun 07 13:12 UTC "unit_test_property" time elapsed: 00:00:00 ---------------------------------------------------------- 27/157 Testing: unit_test_reducededge 27/157 Test: unit_test_reducededge Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_reducededge" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_reducededge" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 10 test cases... Vertices 2 3 *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_reducededge" end time: Jun 07 13:12 UTC "unit_test_reducededge" time elapsed: 00:00:00 ---------------------------------------------------------- 28/157 Testing: unit_test_reducedgraph 28/157 Test: unit_test_reducedgraph Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_reducedgraph" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_reducedgraph" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 9 test cases... 4 3 2 0 *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_reducedgraph" end time: Jun 07 13:12 UTC "unit_test_reducedgraph" time elapsed: 00:00:00 ---------------------------------------------------------- 29/157 Testing: unit_test_structureparameters 29/157 Test: unit_test_structureparameters Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_structureparameters" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_structureparameters" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_structureparameters" end time: Jun 07 13:12 UTC "unit_test_structureparameters" time elapsed: 00:00:00 ---------------------------------------------------------- 30/157 Testing: unit_test_table 30/157 Test: unit_test_table Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_table" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_table" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 10 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_table" end time: Jun 07 13:12 UTC "unit_test_table" time elapsed: 00:00:00 ---------------------------------------------------------- 31/157 Testing: unit_test_thread 31/157 Test: unit_test_thread Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_thread" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_thread" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_thread" end time: Jun 07 13:12 UTC "unit_test_thread" time elapsed: 00:00:00 ---------------------------------------------------------- 32/157 Testing: unit_test_tokenizer 32/157 Test: unit_test_tokenizer Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_tokenizer" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_tokenizer" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 5 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_tokenizer" end time: Jun 07 13:12 UTC "unit_test_tokenizer" time elapsed: 00:00:00 ---------------------------------------------------------- 33/157 Testing: unit_test_random 33/157 Test: unit_test_random Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_random" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_random" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_random" end time: Jun 07 13:12 UTC "unit_test_random" time elapsed: 00:00:00 ---------------------------------------------------------- 34/157 Testing: unit_test_akimaspline 34/157 Test: unit_test_akimaspline Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_akimaspline" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_akimaspline" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_akimaspline" end time: Jun 07 13:12 UTC "unit_test_akimaspline" time elapsed: 00:00:00 ---------------------------------------------------------- 35/157 Testing: unit_test_linspline 35/157 Test: unit_test_linspline Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_linspline" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_linspline" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_linspline" end time: Jun 07 13:12 UTC "unit_test_linspline" time elapsed: 00:00:00 ---------------------------------------------------------- 36/157 Testing: unit_test_unitconverter 36/157 Test: unit_test_unitconverter Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_unitconverter" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_unitconverter" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 9 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_unitconverter" end time: Jun 07 13:12 UTC "unit_test_unitconverter" time elapsed: 00:00:00 ---------------------------------------------------------- 37/157 Testing: unit_test_NDimVector 37/157 Test: unit_test_NDimVector Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_NDimVector" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_NDimVector" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_NDimVector" end time: Jun 07 13:12 UTC "unit_test_NDimVector" time elapsed: 00:00:00 ---------------------------------------------------------- 38/157 Testing: unit_test_eigenio_matrixmarket 38/157 Test: unit_test_eigenio_matrixmarket Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_eigenio_matrixmarket" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests "unit_test_eigenio_matrixmarket" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 4 test cases... /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/tools/src/tests/DataFiles *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_eigenio_matrixmarket" end time: Jun 07 13:12 UTC "unit_test_eigenio_matrixmarket" time elapsed: 00:00:00 ---------------------------------------------------------- 39/157 Testing: integration_csg_reupdateHelp 39/157 Test: integration_csg_reupdateHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_reupdate" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_reupdateHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_reupdate, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) computes relative entropy update. Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file (only needed for RE update) RE Specific options: --options arg options file for coarse graining --gentable arg (=0) only generate potential tables from given parameters, NO RE update! --interaction arg [OPTIONAL] generate potential tables only for the specified interactions, only valid when 'gentable' is true --param-in-ext arg (=param.cur) Extension of the input parameter tables --param-out-ext arg (=param.new) Extension of the output parameter tables --pot-out-ext arg (=pot.new) Extension of the output potential tables --hessian-check arg (=1) Disable the hessian check (mostly for testing) Threading options: --nt arg (=1) number of threads Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_reupdateHelp" end time: Jun 07 13:12 UTC "integration_csg_reupdateHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 40/157 Testing: integration_csg_mapHelp 40/157 Test: integration_csg_mapHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_map" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_mapHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_map, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Convert a reference atomistic trajectory or configuration into a coarse-grained one based on a mapping xml-file. The mapping can be applied to either an entire trajectory or a selected set of frames only (see options). Examples: * csg_map --top FA-topol.tpr --trj FA-traj.trr --out CG-traj.xtc --cg cg-map.xml * csg_map --top FA-topol.tpr --trj FA-conf.gro --out CG-conf.gro --cg cg-map.xml * csg_map --top FA-topol.tpr --trj FA-traj.xtc --out FA-history.dlph --no-map * csg_map --top FA-field.dlpf --trj FA-history.dlph --out CG-history.dlph --cg cg-map.xml * csg_map --top .dlpf --trj .dlph --out .dlph --cg cg-map.xml convert HISTORY to HISTORY_CGV Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file --out arg output file for coarse-grained trajectory --vel Write mapped velocities (if available) --force Write mapped forces (if available) --hybrid Create hybrid trajectory containing both atomistic and coarse-grained Mapping options: --cg arg coarse graining mapping and bond definitions (xml-file) --map-ignore arg list of molecules to ignore separated by ; --no-map disable mapping and act on original trajectory Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_mapHelp" end time: Jun 07 13:12 UTC "integration_csg_mapHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 41/157 Testing: integration_csg_dumpHelp 41/157 Test: integration_csg_dumpHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_dumpHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_dump, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Print atoms that are read from topology file to help debugging atom naming. Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file Mapping options: --cg arg [OPTIONAL] coarse graining mapping and bond definitions (xml-file). If no file is given, program acts on original trajectory --map-ignore arg list of molecules to ignore if mapping is done separated by ; Specific options: --excl display exclusion list instead of molecule list Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_dumpHelp" end time: Jun 07 13:12 UTC "integration_csg_dumpHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 42/157 Testing: integration_csg_propertyHelp 42/157 Test: integration_csg_propertyHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_property" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_propertyHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_property, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Helper program called by inverse scripts to parse xml file. Allowed options: --help produce this help message --path arg path to part of the xml file to print --filter arg list option values that match given criteria --print arg (=.) specifies which children or root to print --file arg xml file to parse --short short version of output --with-path include path of node in output Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_propertyHelp" end time: Jun 07 13:12 UTC "integration_csg_propertyHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 43/157 Testing: integration_csg_resampleHelp 43/157 Test: integration_csg_resampleHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_resample" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_resampleHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_resample, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Change grid and interval of any sort of table files. Mainly called internally by inverse script, can also be used to manually prepare input files for coarse-grained simulations. Allowed options: --help produce this help message --in arg table to read --out arg table to write --derivative arg table to write --grid arg new grid spacing (min:step:max). If 'grid' is specified only, interpolation is performed. --type arg (=akima) [cubic|akima|linear]. If option is not specified, the default type 'akima' is assumed. --fitgrid arg specify fit grid (min:step:max). If 'grid' and 'fitgrid' are specified, a fit is performed. --nocut Option for fitgrid: Normally, values out of fitgrid boundaries are cut off. If they shouldn't, choose --nocut. --comment arg store a comment in the output table --boundaries arg (natural|periodic|derivativezero) sets boundary conditions Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_resampleHelp" end time: Jun 07 13:12 UTC "integration_csg_resampleHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 44/157 Testing: integration_csg_statHelp 44/157 Test: integration_csg_statHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_stat" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_statHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_stat, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Calculate all distributions (bonded and non-bonded) specified in options file. Optionally calculates update Eigen::Matrix3d for invere Monte Carlo. This program is called inside the inverse scripts. Unlike csg_boltzmann, big systems can be treated as well as non-bonded interactions can be evaluated. Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file Mapping options: --cg arg [OPTIONAL] coarse graining mapping and bond definitions (xml-file). If no file is given, program acts on original trajectory --map-ignore arg list of molecules to ignore if mapping is done separated by ; Specific options: --options arg options file for coarse graining --do-imc write out additional Inverse Monte Carlo data --include-intra do not exclude intramolecular neighbors --block-length arg write blocks of this length, the averages are cleared after every write --ext arg (=dist.new) Extension of the output Threading options: --nt arg (=1) number of threads Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_statHelp" end time: Jun 07 13:12 UTC "integration_csg_statHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 45/157 Testing: integration_csg_fmatchHelp 45/157 Test: integration_csg_fmatchHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_fmatch" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_fmatchHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_fmatch, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Perform force matching (also called multiscale coarse-graining) Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file --options arg options file for coarse graining --trj-force arg coarse-grained trajectory containing forces of already known interactions Mapping options: --cg arg coarse graining mapping and bond definitions (xml-file) --map-ignore arg list of molecules to ignore separated by ; --no-map disable mapping and act on original trajectory Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_fmatchHelp" end time: Jun 07 13:12 UTC "integration_csg_fmatchHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 46/157 Testing: integration_csg_gmxtopolHelp 46/157 Test: integration_csg_gmxtopolHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_gmxtopol" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_gmxtopolHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_gmxtopol, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Create skeleton for gromacs topology based on atomistic topology and a mapping file. File still needs to be modified by the user. Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file --out arg output topology (will create .top and in future also .itp) Mapping options: --cg arg coarse graining mapping and bond definitions (xml-file) --map-ignore arg list of molecules to ignore separated by ; --no-map disable mapping and act on original trajectory Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_gmxtopolHelp" end time: Jun 07 13:12 UTC "integration_csg_gmxtopolHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 47/157 Testing: integration_csg_dlptopolHelp 47/157 Test: integration_csg_dlptopolHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dlptopol" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_dlptopolHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_dlptopol, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Create a dlpoly topology template based on an existing (atomistic) topology and a mapping xml-file. The created template file needs to be inspected and amended by the user! Examples: * csg_dlptopol --top .dlpf --out .dlpf --cg cg-map.xml convert FIELD to FIELD_CGV using cg-map.xml * csg_dlptopol --top FA-dlpoly.dlpf --out CG-dlpoly.dlpf --cg cg-map.xml * csg_dlptopol --top FA-gromacs.tpr --out FA-dlpoly.dlpf --no-map Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file --out arg output topology in dlpoly format Mapping options: --cg arg coarse graining mapping and bond definitions (xml-file) --map-ignore arg list of molecules to ignore separated by ; --no-map disable mapping and act on original trajectory Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_dlptopolHelp" end time: Jun 07 13:12 UTC "integration_csg_dlptopolHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 48/157 Testing: integration_csg_densityHelp 48/157 Test: integration_csg_densityHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_density" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_densityHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_density, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Calculates the mass density distribution along a box axis or radial density profile from reference point Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file Mapping options: --cg arg [OPTIONAL] coarse graining mapping and bond definitions (xml-file). If no file is given, program acts on original trajectory --map-ignore arg list of molecules to ignore if mapping is done separated by ; Specific options:: --type arg (=mass) density type: mass or number --axis arg (=r) [x|y|z|r] density axis (r=spherical) --step arg (=0.01) spacing of density --block-length arg write blocks of this length, the averages are cleared after every write --out arg Output file --rmax arg rmax (default for [r] =min of all box vectors/2, else l ) --scale arg (=1) scale factor for the density --molname arg (=*) molname --filter arg (=*) filter bead names --ref arg reference zero point Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_densityHelp" end time: Jun 07 13:12 UTC "integration_csg_densityHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 49/157 Testing: integration_csg_imc_solveHelp 49/157 Test: integration_csg_imc_solveHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_imc_solve" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools "integration_csg_imc_solveHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_imc_solve, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Solves the linear system for IMCs Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy -r [ --regularization ] arg (=0) regularization factor -i [ --imcfile ] arg imc statefile -g [ --gmcfile ] arg gmc statefile -n [ --idxfile ] arg idx statefile Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_csg_imc_solveHelp" end time: Jun 07 13:12 UTC "integration_csg_imc_solveHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 103/157 Testing: integration_Run_gmx_grompp 103/157 Test: integration_Run_gmx_grompp Command: "/usr/bin/gmx" "grompp" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Run_gmx_grompp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- :-) GROMACS - gmx grompp, 2023.1 (-: Executable: /usr/bin/gmx Data prefix: /usr Working dir: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols Command line: gmx grompp Ignoring obsolete mdp entry 'title' NOTE 1 [file grompp.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file grompp.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -1126171682 Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 15.00 There were 2 NOTEs GROMACS reminds you: "You're Insignificant" (Tricky) Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 3 Water residues Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 0.900 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 0.900 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Test time = 0.30 sec ---------------------------------------------------------- Test Passed. "integration_Run_gmx_grompp" end time: Jun 07 13:12 UTC "integration_Run_gmx_grompp" time elapsed: 00:00:00 ---------------------------------------------------------- 51/157 Testing: integration_Compare_csg_reupdate_output 51/157 Test: integration_Compare_csg_reupdate_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.pot.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.re" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate "integration_Compare_csg_reupdate_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.pot.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.re to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_reupdate_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_reupdate_output" time elapsed: 00:00:00 ---------------------------------------------------------- 53/157 Testing: integration_Compare_csg_reupdate_output2 53/157 Test: integration_Compare_csg_reupdate_output2 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.pot.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.new.re" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate2 "integration_Compare_csg_reupdate_output2" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.pot.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.new.re to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_reupdate_output2" end time: Jun 07 13:12 UTC "integration_Compare_csg_reupdate_output2" time elapsed: 00:00:00 ---------------------------------------------------------- 54/157 Testing: integration_Compare_csg_reupdate_output3 54/157 Test: integration_Compare_csg_reupdate_output3 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.param.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.param.re" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate2 "integration_Compare_csg_reupdate_output3" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.param.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.param.re to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_reupdate_output3" end time: Jun 07 13:12 UTC "integration_Compare_csg_reupdate_output3" time elapsed: 00:00:00 ---------------------------------------------------------- 57/157 Testing: integration_Compare_csg_reupdate_gmx_output 57/157 Test: integration_Compare_csg_reupdate_gmx_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.pot.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.new.re_gmx" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate_gmx "integration_Compare_csg_reupdate_gmx_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.pot.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.new.re_gmx to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_reupdate_gmx_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_reupdate_gmx_output" time elapsed: 00:00:00 ---------------------------------------------------------- 58/157 Testing: integration_Compare_csg_reupdate_gmx_output2 58/157 Test: integration_Compare_csg_reupdate_gmx_output2 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.param.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.param.re_gmx" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate_gmx "integration_Compare_csg_reupdate_gmx_output2" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.param.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.param.re_gmx to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_reupdate_gmx_output2" end time: Jun 07 13:12 UTC "integration_Compare_csg_reupdate_gmx_output2" time elapsed: 00:00:00 ---------------------------------------------------------- 60/157 Testing: integration_Compare_csg_fmatch_output 60/157 Test: integration_Compare_csg_fmatch_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.force" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.force.fmatch" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch "integration_Compare_csg_fmatch_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.force and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.force.fmatch to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_fmatch_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_fmatch_output" time elapsed: 00:00:00 ---------------------------------------------------------- 70/157 Testing: integration_Compare_csg_stat_output1 70/157 Test: integration_Compare_csg_stat_output1 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.dist.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.rdf" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat "integration_Compare_csg_stat_output1" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.dist.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.rdf to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_stat_output1" end time: Jun 07 13:12 UTC "integration_Compare_csg_stat_output1" time elapsed: 00:00:00 ---------------------------------------------------------- 78/157 Testing: integration_Compare_csg_stat-imc_output_4 78/157 Test: integration_Compare_csg_stat-imc_output_4 Command: "/usr/bin/cmake" "-E" "compare_files" "CG-CG.idx" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.idx" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat-imc "integration_Compare_csg_stat-imc_output_4" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.01 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_stat-imc_output_4" end time: Jun 07 13:12 UTC "integration_Compare_csg_stat-imc_output_4" time elapsed: 00:00:00 ---------------------------------------------------------- 104/157 Testing: integration_Run_csg_dump_gmx_tpr 104/157 Test: integration_Run_csg_dump_gmx_tpr Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --top topol.tpr > csg_dump_tpr.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Run_csg_dump_gmx_tpr" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Reading file topol.tpr, VERSION 2023.1 (single precision) Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_dump_gmx_tpr" end time: Jun 07 13:12 UTC "integration_Run_csg_dump_gmx_tpr" time elapsed: 00:00:00 ---------------------------------------------------------- 68/157 Testing: integration_Compare_csg_map_gro_output 68/157 Test: integration_Compare_csg_map_gro_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "conf_cg.gro" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/conf_cg.gro" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_map_gro "integration_Compare_csg_map_gro_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing conf_cg.gro and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/conf_cg.gro to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_map_gro_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_map_gro_output" time elapsed: 00:00:00 ---------------------------------------------------------- 71/157 Testing: integration_Compare_csg_stat_output2 71/157 Test: integration_Compare_csg_stat_output2 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.force.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pmf" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat "integration_Compare_csg_stat_output2" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.force.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pmf to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_stat_output2" end time: Jun 07 13:12 UTC "integration_Compare_csg_stat_output2" time elapsed: 00:00:00 ---------------------------------------------------------- 106/157 Testing: integration_Run_csg_dump_gmx_tpr_excl 106/157 Test: integration_Run_csg_dump_gmx_tpr_excl Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --excl --top topol.tpr > csg_dump_tpr_excl.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Run_csg_dump_gmx_tpr_excl" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Reading file topol.tpr, VERSION 2023.1 (single precision) Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_dump_gmx_tpr_excl" end time: Jun 07 13:12 UTC "integration_Run_csg_dump_gmx_tpr_excl" time elapsed: 00:00:00 ---------------------------------------------------------- 76/157 Testing: integration_Compare_csg_stat-imc_output_2 76/157 Test: integration_Compare_csg_stat-imc_output_2 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.dist.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.dist.imc" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat-imc "integration_Compare_csg_stat-imc_output_2" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.dist.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.dist.imc to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_stat-imc_output_2" end time: Jun 07 13:12 UTC "integration_Compare_csg_stat-imc_output_2" time elapsed: 00:00:00 ---------------------------------------------------------- 108/157 Testing: integration_Run_csg_dump_gmx_tpr_cg 108/157 Test: integration_Run_csg_dump_gmx_tpr_cg Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --cg /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/../mapping.xml --top topol.tpr > csg_dump_tpr_cg.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Run_csg_dump_gmx_tpr_cg" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Reading file topol.tpr, VERSION 2023.1 (single precision) Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_dump_gmx_tpr_cg" end time: Jun 07 13:12 UTC "integration_Run_csg_dump_gmx_tpr_cg" time elapsed: 00:00:00 ---------------------------------------------------------- 66/157 Testing: integration_Compare_csg_map_output 66/157 Test: integration_Compare_csg_map_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "frame.dump" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_map "integration_Compare_csg_map_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing frame.dump and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump to a tolerance of 5e-05 Test time = 0.08 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_map_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_map_output" time elapsed: 00:00:00 ---------------------------------------------------------- 73/157 Testing: integration_Compare_csg_stat_angular_output 73/157 Test: integration_Compare_csg_stat_angular_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG-CG.dist.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG-CG.angular" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_angular "integration_Compare_csg_stat_angular_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG-CG.dist.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG-CG.angular to a tolerance of 5e-05 Test time = 0.07 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_stat_angular_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_stat_angular_output" time elapsed: 00:00:00 ---------------------------------------------------------- 77/157 Testing: integration_Compare_csg_stat-imc_output_3 77/157 Test: integration_Compare_csg_stat-imc_output_3 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.gmc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.gmc" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat-imc "integration_Compare_csg_stat-imc_output_3" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.gmc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.gmc to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_stat-imc_output_3" end time: Jun 07 13:12 UTC "integration_Compare_csg_stat-imc_output_3" time elapsed: 00:00:00 ---------------------------------------------------------- 75/157 Testing: integration_Compare_csg_stat-imc_output 75/157 Test: integration_Compare_csg_stat-imc_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.imc" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat-imc "integration_Compare_csg_stat-imc_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.imc to a tolerance of 5e-05 Test time = 0.07 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_stat-imc_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_stat-imc_output" time elapsed: 00:00:00 ---------------------------------------------------------- 88/157 Testing: integration_Compare_csg_stat-imc_multi_output_3 88/157 Test: integration_Compare_csg_stat-imc_multi_output_3 Command: "/usr/bin/cmake" "-E" "compare_files" "all.idx" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/all.idx" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_imc_multi "integration_Compare_csg_stat-imc_multi_output_3" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_stat-imc_multi_output_3" end time: Jun 07 13:12 UTC "integration_Compare_csg_stat-imc_multi_output_3" time elapsed: 00:00:00 ---------------------------------------------------------- 98/157 Testing: integration_Compare_csg_dump_output 98/157 Test: integration_Compare_csg_dump_output Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/methanol-water//csg_dump.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump "integration_Compare_csg_dump_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.01 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_dump_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_dump_output" time elapsed: 00:00:00 ---------------------------------------------------------- 100/157 Testing: integration_Compare_csg_dump_gro_output 100/157 Test: integration_Compare_csg_dump_gro_output Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump_gro.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/csg_dump_gro.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump_gro "integration_Compare_csg_dump_gro_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.01 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_dump_gro_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_dump_gro_output" time elapsed: 00:00:00 ---------------------------------------------------------- 102/157 Testing: integration_Compare_csg_dump_data_output 102/157 Test: integration_Compare_csg_dump_data_output Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump_data.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols_cg/csg_dump_data.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump_data "integration_Compare_csg_dump_data_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.01 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_dump_data_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_dump_data_output" time elapsed: 00:00:00 ---------------------------------------------------------- 105/157 Testing: integration_Compare_csg_dump_gmx_tpr_output 105/157 Test: integration_Compare_csg_dump_gmx_tpr_output Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump_tpr.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/csg_dump_tpr.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Compare_csg_dump_gmx_tpr_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.01 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_dump_gmx_tpr_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_dump_gmx_tpr_output" time elapsed: 00:00:00 ---------------------------------------------------------- 107/157 Testing: integration_Compare_csg_dump_gmx_tpr_excl_output 107/157 Test: integration_Compare_csg_dump_gmx_tpr_excl_output Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump_tpr_excl.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/csg_dump_tpr_excl.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Compare_csg_dump_gmx_tpr_excl_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.01 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_dump_gmx_tpr_excl_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_dump_gmx_tpr_excl_output" time elapsed: 00:00:00 ---------------------------------------------------------- 80/157 Testing: integration_Compare_csg_imc_solve_output 80/157 Test: integration_Compare_csg_imc_solve_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.dpot.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/imc/CG-CG.dpot.imc" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve "integration_Compare_csg_imc_solve_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing CG-CG.dpot.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/imc/CG-CG.dpot.imc to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_imc_solve_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_imc_solve_output" time elapsed: 00:00:00 ---------------------------------------------------------- 109/157 Testing: integration_Compare_csg_dump_gmx_tpr_cg_output 109/157 Test: integration_Compare_csg_dump_gmx_tpr_cg_output Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump_tpr_cg.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/csg_dump_tpr_cg.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Compare_csg_dump_gmx_tpr_cg_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.01 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_dump_gmx_tpr_cg_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_dump_gmx_tpr_cg_output" time elapsed: 00:00:00 ---------------------------------------------------------- 83/157 Testing: integration_Compare_csg_imc_solve_reg_output_3 83/157 Test: integration_Compare_csg_imc_solve_reg_output_3 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "LJ1-LJ2.dpot.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ1-LJ2.dpot.imc" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve_reg "integration_Compare_csg_imc_solve_reg_output_3" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing LJ1-LJ2.dpot.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ1-LJ2.dpot.imc to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_imc_solve_reg_output_3" end time: Jun 07 13:12 UTC "integration_Compare_csg_imc_solve_reg_output_3" time elapsed: 00:00:00 ---------------------------------------------------------- 82/157 Testing: integration_Compare_csg_imc_solve_reg_output_2 82/157 Test: integration_Compare_csg_imc_solve_reg_output_2 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "LJ1-LJ1.dpot.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ1-LJ1.dpot.imc" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve_reg "integration_Compare_csg_imc_solve_reg_output_2" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing LJ1-LJ1.dpot.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ1-LJ1.dpot.imc to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_imc_solve_reg_output_2" end time: Jun 07 13:12 UTC "integration_Compare_csg_imc_solve_reg_output_2" time elapsed: 00:00:00 ---------------------------------------------------------- 116/157 Testing: integration_Compare_csg_property_output 116/157 Test: integration_Compare_csg_property_output Command: "/usr/bin/cmake" "-E" "compare_files" "csg_property.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_property.out" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property "integration_Compare_csg_property_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_property_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_property_output" time elapsed: 00:00:00 ---------------------------------------------------------- 118/157 Testing: integration_Compare_csg_property_output2 118/157 Test: integration_Compare_csg_property_output2 Command: "/usr/bin/cmake" "-E" "compare_files" "csg_property.out2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_property.out2" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property "integration_Compare_csg_property_output2" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_property_output2" end time: Jun 07 13:12 UTC "integration_Compare_csg_property_output2" time elapsed: 00:00:00 ---------------------------------------------------------- 84/157 Testing: integration_Compare_csg_imc_solve_reg_output_4 84/157 Test: integration_Compare_csg_imc_solve_reg_output_4 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "LJ2-LJ2.dpot.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ2-LJ2.dpot.imc" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve_reg "integration_Compare_csg_imc_solve_reg_output_4" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing LJ2-LJ2.dpot.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ2-LJ2.dpot.imc to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_imc_solve_reg_output_4" end time: Jun 07 13:12 UTC "integration_Compare_csg_imc_solve_reg_output_4" time elapsed: 00:00:00 ---------------------------------------------------------- 86/157 Testing: integration_Compare_csg_stat-imc_multi_output 86/157 Test: integration_Compare_csg_stat-imc_multi_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "all.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/all.imc" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_imc_multi "integration_Compare_csg_stat-imc_multi_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing all.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/all.imc to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_stat-imc_multi_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_stat-imc_multi_output" time elapsed: 00:00:00 ---------------------------------------------------------- 120/157 Testing: integration_Compare_csg_property_output3 120/157 Test: integration_Compare_csg_property_output3 Command: "/usr/bin/cmake" "-E" "compare_files" "csg_property.out3" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_property.out3" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property "integration_Compare_csg_property_output3" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_property_output3" end time: Jun 07 13:12 UTC "integration_Compare_csg_property_output3" time elapsed: 00:00:00 ---------------------------------------------------------- 122/157 Testing: integration_Compare_csg_property_output4 122/157 Test: integration_Compare_csg_property_output4 Command: "/usr/bin/cmake" "-E" "compare_files" "csg_property.out4" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_property.out4" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property "integration_Compare_csg_property_output4" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_property_output4" end time: Jun 07 13:12 UTC "integration_Compare_csg_property_output4" time elapsed: 00:00:00 ---------------------------------------------------------- 125/157 Testing: Compare_csg_boltzmann_output_ppy 125/157 Test: Compare_csg_boltzmann_output_ppy Command: "/usr/bin/cmake" "-E" "compare_files" "excl.txt" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/ppy//excl.txt" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_ppy "Compare_csg_boltzmann_output_ppy" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "Compare_csg_boltzmann_output_ppy" end time: Jun 07 13:12 UTC "Compare_csg_boltzmann_output_ppy" time elapsed: 00:00:00 ---------------------------------------------------------- 128/157 Testing: Compare_csg_boltzmann_output_mma 128/157 Test: Compare_csg_boltzmann_output_mma Command: "/usr/bin/cmake" "-E" "compare_files" "excl.txt" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/mma//excl.txt" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_mma "Compare_csg_boltzmann_output_mma" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "Compare_csg_boltzmann_output_mma" end time: Jun 07 13:12 UTC "Compare_csg_boltzmann_output_mma" time elapsed: 00:00:00 ---------------------------------------------------------- 90/157 Testing: integration_Compare_csg_resample_akima_output 90/157 Test: integration_Compare_csg_resample_akima_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "table_akima" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_akima" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample "integration_Compare_csg_resample_akima_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing table_akima and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_akima to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_resample_akima_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_resample_akima_output" time elapsed: 00:00:00 ---------------------------------------------------------- 92/157 Testing: integration_Compare_csg_resample_cubic_output 92/157 Test: integration_Compare_csg_resample_cubic_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "table_cubic" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_cubic" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample "integration_Compare_csg_resample_cubic_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing table_cubic and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_cubic to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_resample_cubic_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_resample_cubic_output" time elapsed: 00:00:00 ---------------------------------------------------------- 94/157 Testing: integration_Compare_csg_resample_linear_output 94/157 Test: integration_Compare_csg_resample_linear_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "table_linear" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_linear" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample "integration_Compare_csg_resample_linear_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing table_linear and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_linear to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_resample_linear_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_resample_linear_output" time elapsed: 00:00:00 ---------------------------------------------------------- 96/157 Testing: integration_Compare_csg_resample_cubicfit_output 96/157 Test: integration_Compare_csg_resample_cubicfit_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "table_cubicfit" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_cubicfit" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample "integration_Compare_csg_resample_cubicfit_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing table_cubicfit and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_cubicfit to a tolerance of 5e-05 Test time = 0.06 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_resample_cubicfit_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_resample_cubicfit_output" time elapsed: 00:00:00 ---------------------------------------------------------- 129/157 Testing: fluctuationsHelp 129/157 Test: fluctuationsHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/fluctuations/csg_fluctuations" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps "fluctuationsHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues fluctuations, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) calculate density fluctuations in subvolumes of the simulation box.Subolumes can be either cubic slabs in dimensions (x|y|z) or sphericalslabs with respect to either the center of box or a reference molecule Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file Fluctuation options: --filter arg (=*) filter molecule names --rmax arg maximal distance to be considered --rmin arg (=0) minimal distance to be considered --refmol arg Reference molecule --nbin arg (=100) Number of bins --geometry arg (sphere|x|y|z) Take radial or x, y, z slabs from rmin to rmax --outfile arg (=fluctuations.dat) Output file Mapping options: --cg arg coarse graining mapping and bond definitions (xml-file) --map-ignore arg list of molecules to ignore separated by ; --no-map disable mapping and act on original trajectory Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "fluctuationsHelp" end time: Jun 07 13:12 UTC "fluctuationsHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 130/157 Testing: orientcorrHelp 130/157 Test: orientcorrHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/orientcorr/csg_orientcorr" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps "orientcorrHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues orientcorr, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Calculates the orientational correlation function <3/2*u(0)*u(r) - 1/2> for a polymer melt, where u is the vector pointing along a bond and r the distance between bond segments (centered on middle of bond). The output is correlation.dat (with intra-molecular contributions) and correlation_excl.dat, where inter-molecular contributions are excluded. Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file Neighbor search options: -c [ --cutoff ] arg (=1) cutoff for the neighbor search --nbins arg (=40) number of bins for the grid --nbmethod arg (=grid) neighbor search algorithm (simple or grid) Threading options: --nt arg (=1) number of threads Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "orientcorrHelp" end time: Jun 07 13:12 UTC "orientcorrHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 131/157 Testing: part_distHelp 131/157 Test: part_distHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/part_dist/csg_part_dist" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps "part_distHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_part_dist, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) This program reads a topology and (set of) trajectory(ies). For every binned value of a chosen coordinate, it outputs the time-averaged number of particles, listed by particle types. Allowed options: --top arg topology file --trj arg trajectory file --grid arg output grid spacing (min:step:max) --out arg output particle distribution table --ptypes arg particle types to include in the analysis arg: file - particle types separated by space default: all particle types --first_frame arg first frame considered for analysis --last_frame arg last frame considered for analysis --coord arg coordinate analyzed ('x', 'y', or 'z' (default)) --shift_com shift center of mass to zero --comment arg store a comment in the output table --help produce this help message Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "part_distHelp" end time: Jun 07 13:12 UTC "part_distHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 132/157 Testing: partial_rdfHelp 132/157 Test: partial_rdfHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/partial_rdf/csg_partial_rdf" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps "partial_rdfHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues csg_partial_rdf, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Calculate spatially confined rdfs Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file Mapping options: --cg arg [OPTIONAL] coarse graining mapping and bond definitions (xml-file). If no file is given, program acts on original trajectory --map-ignore arg list of molecules to ignore if mapping is done separated by ; Specific options: --options arg options file defining the rdfs --subvolume_radius arg Rdf calc. in spherical subvolume of this radius (from center of box) --do-vol-corr Correct for subvolume truncation in rdf --write-every arg (UNIMPLEMENTED) write after every block of this length, if --blocking is set, the averages are cleared after every output --do-blocks write output for blocking analysis Threading options: --nt arg (=1) number of threads Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "partial_rdfHelp" end time: Jun 07 13:12 UTC "partial_rdfHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 133/157 Testing: radiiHelp 133/157 Test: radiiHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/radii/csg_radii" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps "radiiHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues radii, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) calculate gyration- and hydrodynamic radius for a specific molecule or molecule type Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file Molecule filter options: --mol arg molecule number --molname arg (=*) pattern for molecule name Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "radiiHelp" end time: Jun 07 13:12 UTC "radiiHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 134/157 Testing: sphericalorderHelp 134/157 Test: sphericalorderHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/sphericalorder/csg_sphericalorder" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps "sphericalorderHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues sphericalorder, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) !! EXPERIMENTAL !! Calculate spherical order parameter. Needs non-spherical beads in mapping. Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file --filter arg (=*) filter molecule names --radialcut arg (=0) radial cutoff: distance from center where bead is considered --minrad arg (=0) minimal distance a parcle has to be apart from center to be considerd --refmol arg Reference molecule --rbinw arg (=0) Do multiple r_bins multiple histograms Mapping options: --cg arg coarse graining mapping and bond definitions (xml-file) --map-ignore arg list of molecules to ignore separated by ; --no-map disable mapping and act on original trajectory Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "sphericalorderHelp" end time: Jun 07 13:12 UTC "sphericalorderHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 135/157 Testing: traj_forceHelp 135/157 Test: traj_forceHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/traj_force/csg_traj_force" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps "traj_forceHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues traj_force, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) Adds/subtracts forces from given atomistic trajectories Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file --scale arg (=-1) scaling factor for trajectory forces --trj-force arg atomistic reference trajectory containing forces to add/subtract --out arg output trajectory file with resultant forces Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "traj_forceHelp" end time: Jun 07 13:12 UTC "traj_forceHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 136/157 Testing: unit_test_bead 136/157 Test: unit_test_bead Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_bead" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_bead" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_bead" end time: Jun 07 13:12 UTC "unit_test_bead" time elapsed: 00:00:00 ---------------------------------------------------------- 137/157 Testing: unit_test_beadtriple 137/157 Test: unit_test_beadtriple Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadtriple" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_beadtriple" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_beadtriple" end time: Jun 07 13:12 UTC "unit_test_beadtriple" time elapsed: 00:00:00 ---------------------------------------------------------- 138/157 Testing: unit_test_basebead 138/157 Test: unit_test_basebead Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_basebead" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_basebead" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_basebead" end time: Jun 07 13:12 UTC "unit_test_basebead" time elapsed: 00:00:00 ---------------------------------------------------------- 61/157 Testing: integration_Run_csg_fmatch_3body 61/157 Test: integration_Run_csg_fmatch_3body Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_fmatch" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_fmatch_3body.xml" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch_3body "integration_Run_csg_fmatch_3body" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- I have 648 beads in 216 molecules I have 216 beads in 216 molecules for the coarsegraining Reading frame, timestep 0 a: 0.37 ,sigma: 1 ,gamma: 0.12 Number of spline functions for the interaction CG-CG:48 a: 0.37 ,sigma: 1 ,gamma: 0.08 Number of spline functions for the interaction CG-CG-CG:36 You are using VOTCA! hey, somebody wants to forcematch! Using constrained Least Squares! Test time = 0.43 sec ---------------------------------------------------------- Test Failed. "integration_Run_csg_fmatch_3body" end time: Jun 07 13:12 UTC "integration_Run_csg_fmatch_3body" time elapsed: 00:00:00 ---------------------------------------------------------- 139/157 Testing: unit_test_beadmotif_algorithms 139/157 Test: unit_test_beadmotif_algorithms Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadmotif_algorithms" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_beadmotif_algorithms" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 4 test cases... *** No errors detected  Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "unit_test_beadmotif_algorithms" end time: Jun 07 13:12 UTC "unit_test_beadmotif_algorithms" time elapsed: 00:00:00 ---------------------------------------------------------- 140/157 Testing: unit_test_beadmotif_base 140/157 Test: unit_test_beadmotif_base Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadmotif_base" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_beadmotif_base" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 4 test cases... *** No errors detected  Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "unit_test_beadmotif_base" end time: Jun 07 13:12 UTC "unit_test_beadmotif_base" time elapsed: 00:00:00 ---------------------------------------------------------- 141/157 Testing: unit_test_beadmotif_connector 141/157 Test: unit_test_beadmotif_connector Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadmotif_connector" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_beadmotif_connector" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... *** No errors detected  Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "unit_test_beadmotif_connector" end time: Jun 07 13:12 UTC "unit_test_beadmotif_connector" time elapsed: 00:00:00 ---------------------------------------------------------- 143/157 Testing: unit_test_beadstructure_algorithms 143/157 Test: unit_test_beadstructure_algorithms Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadstructure_algorithms" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_beadstructure_algorithms" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... Calling break into structures Bead Count 1 3 Bead Count 2 5 *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_beadstructure_algorithms" end time: Jun 07 13:12 UTC "unit_test_beadstructure_algorithms" time elapsed: 00:00:00 ---------------------------------------------------------- 144/157 Testing: unit_test_bondedstatistics 144/157 Test: unit_test_bondedstatistics Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_bondedstatistics" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_bondedstatistics" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_bondedstatistics" end time: Jun 07 13:12 UTC "unit_test_bondedstatistics" time elapsed: 00:00:00 ---------------------------------------------------------- 142/157 Testing: unit_test_beadstructure_base 142/157 Test: unit_test_beadstructure_base Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadstructure_base" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_beadstructure_base" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 10 test cases... *** No errors detected  Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "unit_test_beadstructure_base" end time: Jun 07 13:12 UTC "unit_test_beadstructure_base" time elapsed: 00:00:00 ---------------------------------------------------------- 145/157 Testing: unit_test_csg_topology 145/157 Test: unit_test_csg_topology Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_csg_topology" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_csg_topology" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 6 test cases... interaction name :bond interaction name :bond *** No errors detected  Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "unit_test_csg_topology" end time: Jun 07 13:12 UTC "unit_test_csg_topology" time elapsed: 00:00:00 ---------------------------------------------------------- 146/157 Testing: unit_test_interaction 146/157 Test: unit_test_interaction Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_interaction" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_interaction" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 5 test cases... molecule 1:large 1:index 1 molecule 1:medium 1:index 1 molecule 1:small 1:index 1 *** No errors detected  Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "unit_test_interaction" end time: Jun 07 13:12 UTC "unit_test_interaction" time elapsed: 00:00:00 ---------------------------------------------------------- 148/157 Testing: unit_test_lammpsdumpreaderwriter 148/157 Test: unit_test_lammpsdumpreaderwriter Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_lammpsdumpreaderwriter" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_lammpsdumpreaderwriter" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... Reading frame, timestep 1 Reading frame, timestep 1 *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_lammpsdumpreaderwriter" end time: Jun 07 13:12 UTC "unit_test_lammpsdumpreaderwriter" time elapsed: 00:00:00 ---------------------------------------------------------- 149/157 Testing: unit_test_nblist_3body 149/157 Test: unit_test_nblist_3body Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_nblist_3body" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_nblist_3body" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_nblist_3body" end time: Jun 07 13:12 UTC "unit_test_nblist_3body" time elapsed: 00:00:00 ---------------------------------------------------------- 150/157 Testing: unit_test_nblistgrid_3body 150/157 Test: unit_test_nblistgrid_3body Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_nblistgrid_3body" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_nblistgrid_3body" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_nblistgrid_3body" end time: Jun 07 13:12 UTC "unit_test_nblistgrid_3body" time elapsed: 00:00:00 ---------------------------------------------------------- 147/157 Testing: unit_test_lammpsdatareader 147/157 Test: unit_test_lammpsdatareader Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_lammpsdatareader" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_lammpsdatareader" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles: angle atom bond full molecule These styles use the following formats in the atom block: atom-ID molecule-ID atom-type charge x y z atom-ID molecule-ID atom-type charge x y z nx ny nz atom-ID molecule-ID atom-type x y z atom-ID molecule-ID atom-type x y z nx ny nz atom-ID atom-type x y z atom-ID atom-type x y z nx ny nz WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles: angle atom bond full molecule These styles use the following formats in the atom block: atom-ID molecule-ID atom-type charge x y z atom-ID molecule-ID atom-type charge x y z nx ny nz atom-ID molecule-ID atom-type x y z atom-ID molecule-ID atom-type x y z nx ny nz atom-ID atom-type x y z atom-ID atom-type x y z nx ny nz 6.57991 5.10424 5.84802 6.57991 5.10424 5.84802 10.8431 8.3947 6.85254 10.8431 8.3947 6.85254 WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles: angle atom bond full molecule These styles use the following formats in the atom block: atom-ID molecule-ID atom-type charge x y z atom-ID molecule-ID atom-type charge x y z nx ny nz atom-ID molecule-ID atom-type x y z atom-ID molecule-ID atom-type x y z nx ny nz atom-ID atom-type x y z atom-ID atom-type x y z nx ny nz WARNING: Lammps Atoms 1 and 6 belong to different molecules (1:2) WARNING: Lammps Atoms 0 and 5 belong to different molecules (1:2) WARNING: Lammps Atoms -1 and 4 belong to different molecules (1:2) WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles: angle atom bond full molecule These styles use the following formats in the atom block: atom-ID molecule-ID atom-type charge x y z atom-ID molecule-ID atom-type charge x y z nx ny nz atom-ID molecule-ID atom-type x y z atom-ID molecule-ID atom-type x y z nx ny nz atom-ID atom-type x y z atom-ID atom-type x y z nx ny nz *** No errors detected  Test time = 0.04 sec ---------------------------------------------------------- Test Passed. "unit_test_lammpsdatareader" end time: Jun 07 13:12 UTC "unit_test_lammpsdatareader" time elapsed: 00:00:00 ---------------------------------------------------------- 151/157 Testing: unit_test_boundarycondition 151/157 Test: unit_test_boundarycondition Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_boundarycondition" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_boundarycondition" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... *** No errors detected  Test time = 0.03 sec ---------------------------------------------------------- Test Passed. "unit_test_boundarycondition" end time: Jun 07 13:12 UTC "unit_test_boundarycondition" time elapsed: 00:00:00 ---------------------------------------------------------- 152/157 Testing: unit_test_pdbreader 152/157 Test: unit_test_pdbreader Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_pdbreader" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_pdbreader" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 1 test case... The VOTCA pdb reader attempts to follow the official format: http://www.wwpdb.org/documentation/file-format NOTE the element symbol is important for associating a mass with each atom, if no element symbol is specified the atom name will be used and assumed to be an element symbol. The pdb file format does not support pseudo atoms such as a CH3 and thus VOTCA cannot read such atoms in when using a .pdb file. If you need to use pseudo atoms consider using a different file format such as the lammps data format. WARNING no charge was specified for HETATM 1 C UNL 1 -5.249 1.055 -0.000 1.00 0.00 C Assuming a charge of 0 WARNING no charge was specified for HETATM 2 H UNL 1 -6.202 1.521 -0.141 1.00 0.00 H Assuming a charge of 0 WARNING no charge was specified for HETATM 3 H UNL 1 -5.390 0.026 0.255 1.00 0.00 H Assuming a charge of 0 WARNING no charge was specified for HETATM 4 H UNL 1 -4.682 1.124 -0.904 1.00 0.00 H Assuming a charge of 0 WARNING no charge was specified for HETATM 5 H UNL 1 -4.724 1.550 0.790 1.00 0.00 H Assuming a charge of 0 WARNING no charge was specified for HETATM 6 C UNL 2 -2.248 1.671 -0.000 1.00 0.00 C Assuming a charge of 0 WARNING no charge was specified for HETATM 7 H UNL 2 -1.518 2.451 0.051 1.00 0.00 H Assuming a charge of 0 WARNING no charge was specified for HETATM 8 H UNL 2 -3.153 1.999 0.467 1.00 0.00 H Assuming a charge of 0 WARNING no charge was specified for HETATM 9 H UNL 2 -2.442 1.430 -1.024 1.00 0.00 H Assuming a charge of 0 WARNING no charge was specified for HETATM 10 H UNL 2 -1.880 0.804 0.507 1.00 0.00 H Assuming a charge of 0 Consistency check for pdbreader Molecule 0 Atoms: 6 7 8 9 10 Molecule 1 Atoms: 1 2 3 4 5 *** No errors detected  Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "unit_test_pdbreader" end time: Jun 07 13:12 UTC "unit_test_pdbreader" time elapsed: 00:00:00 ---------------------------------------------------------- 155/157 Testing: template_serialHelp 155/157 Test: template_serialHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/share/template/template_serial" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/share/template "template_serialHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues template_nblist, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) rough template for rdf calculations Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file RDF options: --c arg (=1) the cutoff Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.01 sec ---------------------------------------------------------- Test Passed. "template_serialHelp" end time: Jun 07 13:12 UTC "template_serialHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 157/157 Testing: regression_UninstallExists 157/157 Test: regression_UninstallExists Command: "/usr/bin/cmake" "-DFileToCheck=/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg-tutorials/cmake_uninstall.cmake" "-P" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg-tutorials/CMakeModules/FileExists.cmake" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg-tutorials "regression_UninstallExists" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg-tutorials/cmake_uninstall.cmake exists. Test time = 0.01 sec ---------------------------------------------------------- Test Passed. "regression_UninstallExists" end time: Jun 07 13:12 UTC "regression_UninstallExists" time elapsed: 00:00:00 ---------------------------------------------------------- 156/157 Testing: template_threadedHelp 156/157 Test: template_threadedHelp Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/share/template/template_threaded" "--help" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/share/template "template_threadedHelp" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== please submit bugs to https://github.com/votca/csg/issues template_threaded_rdf, version 2022.1 (compiled Jun 7 2023, 13:11:39) votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) gromacs, 2023.1 (single precision) template for threaded rdf calculations Allowed options: -h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file RDF options: --c arg (=1) the cutoff Threading options: --nt arg (=1) number of threads Trajectory options: --trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames Test time = 0.01 sec ---------------------------------------------------------- Test Passed. "template_threadedHelp" end time: Jun 07 13:12 UTC "template_threadedHelp" time elapsed: 00:00:00 ---------------------------------------------------------- 154/157 Testing: unit_test_triplelist 154/157 Test: unit_test_triplelist Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_triplelist" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_triplelist" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 2 test cases... *** No errors detected  Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "unit_test_triplelist" end time: Jun 07 13:12 UTC "unit_test_triplelist" time elapsed: 00:00:00 ---------------------------------------------------------- 87/157 Testing: integration_Compare_csg_stat-imc_multi_output_2 87/157 Test: integration_Compare_csg_stat-imc_multi_output_2 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "all.gmc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/all.gmc" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_imc_multi "integration_Compare_csg_stat-imc_multi_output_2" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing all.gmc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/all.gmc to a tolerance of 5e-05 Test time = 0.14 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_stat-imc_multi_output_2" end time: Jun 07 13:12 UTC "integration_Compare_csg_stat-imc_multi_output_2" time elapsed: 00:00:00 ---------------------------------------------------------- 62/157 Testing: integration_Compare_csg_fmatch_3body_output1 62/157 Test: integration_Compare_csg_fmatch_3body_output1 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.force" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.force.fmatch_3body" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch_3body "integration_Compare_csg_fmatch_3body_output1" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== THE VOTCA::TOOLS FILE COMPARISON please submit bugs to bugs@votca.org votca_compare, version 2022.1 votca_compare: error: argument -f1/--file1: can't open 'CG-CG.force': [Errno 2] No such file or directory: 'CG-CG.force' Test time = 0.05 sec ---------------------------------------------------------- Test Failed. "integration_Compare_csg_fmatch_3body_output1" end time: Jun 07 13:12 UTC "integration_Compare_csg_fmatch_3body_output1" time elapsed: 00:00:00 ---------------------------------------------------------- 63/157 Testing: integration_Compare_csg_fmatch_3body_output2 63/157 Test: integration_Compare_csg_fmatch_3body_output2 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG-CG.force" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG-CG.force.fmatch_3body" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch_3body "integration_Compare_csg_fmatch_3body_output2" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== THE VOTCA::TOOLS FILE COMPARISON please submit bugs to bugs@votca.org votca_compare, version 2022.1 votca_compare: error: argument -f1/--file1: can't open 'CG-CG-CG.force': [Errno 2] No such file or directory: 'CG-CG-CG.force' Test time = 0.05 sec ---------------------------------------------------------- Test Failed. "integration_Compare_csg_fmatch_3body_output2" end time: Jun 07 13:12 UTC "integration_Compare_csg_fmatch_3body_output2" time elapsed: 00:00:00 ---------------------------------------------------------- 64/157 Testing: integration_Compare_csg_fmatch_3body_output3 64/157 Test: integration_Compare_csg_fmatch_3body_output3 Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG-CG.pot" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG-CG.pot.fmatch_3body" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch_3body "integration_Compare_csg_fmatch_3body_output3" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== THE VOTCA::TOOLS FILE COMPARISON please submit bugs to bugs@votca.org votca_compare, version 2022.1 votca_compare: error: argument -f1/--file1: can't open 'CG-CG-CG.pot': [Errno 2] No such file or directory: 'CG-CG-CG.pot' Test time = 0.05 sec ---------------------------------------------------------- Test Failed. "integration_Compare_csg_fmatch_3body_output3" end time: Jun 07 13:12 UTC "integration_Compare_csg_fmatch_3body_output3" time elapsed: 00:00:00 ---------------------------------------------------------- 110/157 Testing: integration_Run_gmx_mdrun 110/157 Test: integration_Run_gmx_mdrun Command: "/usr/bin/gmx" "mdrun" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Run_gmx_mdrun" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- :-) GROMACS - gmx mdrun, 2023.1 (-: Executable: /usr/bin/gmx Data prefix: /usr Working dir: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols Command line: gmx mdrun hwloc verbose debug enabled, may be disabled with HWLOC_DEBUG_VERBOSE=0 in the environment. CPU phase discovery... CPU phase discovery in component linux... hwloc verbose debug enabled, may be disabled with HWLOC_DEBUG_VERBOSE=0 in the environment. Found sysfs cpu files under /sys/devices/system/cpu with new topology filenames * Topology extraction from /proc/cpuinfo * processor 0 processor 1 processor 2 processor 3 processor 4 processor 5 processor 6 processor 7 processor 8 processor 9 processor 10 processor 11 processor 12 processor 13 processor 14 processor 15 processor 16 processor 17 processor 18 processor 19 processor 20 processor 21 processor 22 processor 23 processor 24 processor 25 processor 26 processor 27 processor 28 processor 29 processor 30 processor 31 processor 32 processor 33 processor 34 processor 35 processor 36 processor 37 processor 38 processor 39 processor 40 processor 41 processor 42 processor 43 processor 44 processor 45 processor 46 processor 47 processor 48 processor 49 processor 50 processor 51 processor 52 processor 53 processor 54 processor 55 processor 56 processor 57 processor 58 processor 59 processor 60 processor 61 processor 62 processor 63 Found cgroup2 mount point on /sys/fs/cgroup/unified Failed to read cgroup2 controllers from `/sys/fs/cgroup/unified/cgroup.controllers' Found cgroup1/cpuset mount point on /sys/fs/cgroup/cpuset Found cgroup name `/' Trying to read cgroup1 file cpuset includes 0xffffffff,0xffffffff Trying to read cgroup1 file cpuset includes 0x00000001 * Topology extraction from /sys/devices/system/cpu/ * online CPUs 0xffffffff,0xffffffff found 64 cpu topologies, cpuset 0xffffffff,0xffffffff os core 0 has cpuset 0x00000001,0x00000001 os package 0 has cpuset 0xffffffff,0xffffffff os cluster 65535 has cpuset 0x00000001,0x00000001 thread 0 has cpuset 0x00000001 cache depth 1 has cpuset 0x00000001,0x00000001 cache depth 2 has cpuset 0x00000001,0x00000001 cache depth 3 has cpuset 0x000000ff,0x000000ff os core 1 has cpuset 0x00000002,0x00000002 os cluster 65535 has cpuset 0x00000002,0x00000002 thread 1 has cpuset 0x00000002 cache depth 1 has cpuset 0x00000002,0x00000002 cache depth 2 has cpuset 0x00000002,0x00000002 os core 2 has cpuset 0x00000004,0x00000004 os cluster 65535 has cpuset 0x00000004,0x00000004 thread 2 has cpuset 0x00000004 cache depth 1 has cpuset 0x00000004,0x00000004 cache depth 2 has cpuset 0x00000004,0x00000004 os core 3 has cpuset 0x00000008,0x00000008 os cluster 65535 has cpuset 0x00000008,0x00000008 thread 3 has cpuset 0x00000008 cache depth 1 has cpuset 0x00000008,0x00000008 cache depth 2 has cpuset 0x00000008,0x00000008 os core 4 has cpuset 0x00000010,0x00000010 os cluster 65535 has cpuset 0x00000010,0x00000010 thread 4 has cpuset 0x00000010 cache depth 1 has cpuset 0x00000010,0x00000010 cache depth 2 has cpuset 0x00000010,0x00000010 os core 5 has cpuset 0x00000020,0x00000020 os cluster 65535 has cpuset 0x00000020,0x00000020 thread 5 has cpuset 0x00000020 cache depth 1 has cpuset 0x00000020,0x00000020 cache depth 2 has cpuset 0x00000020,0x00000020 os core 6 has cpuset 0x00000040,0x00000040 os cluster 65535 has cpuset 0x00000040,0x00000040 thread 6 has cpuset 0x00000040 cache depth 1 has cpuset 0x00000040,0x00000040 cache depth 2 has cpuset 0x00000040,0x00000040 os core 7 has cpuset 0x00000080,0x00000080 os cluster 65535 has cpuset 0x00000080,0x00000080 thread 7 has cpuset 0x00000080 cache depth 1 has cpuset 0x00000080,0x00000080 cache depth 2 has cpuset 0x00000080,0x00000080 os core 8 has cpuset 0x00000100,0x00000100 os cluster 65535 has cpuset 0x00000100,0x00000100 thread 8 has cpuset 0x00000100 cache depth 1 has cpuset 0x00000100,0x00000100 cache depth 2 has cpuset 0x00000100,0x00000100 cache depth 3 has cpuset 0x0000ff00,0x0000ff00 os core 9 has cpuset 0x00000200,0x00000200 os cluster 65535 has cpuset 0x00000200,0x00000200 thread 9 has cpuset 0x00000200 cache depth 1 has cpuset 0x00000200,0x00000200 cache depth 2 has cpuset 0x00000200,0x00000200 os core 10 has cpuset 0x00000400,0x00000400 os cluster 65535 has cpuset 0x00000400,0x00000400 thread 10 has cpuset 0x00000400 cache depth 1 has cpuset 0x00000400,0x00000400 cache depth 2 has cpuset 0x00000400,0x00000400 os core 11 has cpuset 0x00000800,0x00000800 os cluster 65535 has cpuset 0x00000800,0x00000800 thread 11 has cpuset 0x00000800 cache depth 1 has cpuset 0x00000800,0x00000800 cache depth 2 has cpuset 0x00000800,0x00000800 os core 12 has cpuset 0x00001000,0x00001000 os cluster 65535 has cpuset 0x00001000,0x00001000 thread 12 has cpuset 0x00001000 cache depth 1 has cpuset 0x00001000,0x00001000 cache depth 2 has cpuset 0x00001000,0x00001000 os core 13 has cpuset 0x00002000,0x00002000 os cluster 65535 has cpuset 0x00002000,0x00002000 thread 13 has cpuset 0x00002000 cache depth 1 has cpuset 0x00002000,0x00002000 cache depth 2 has cpuset 0x00002000,0x00002000 os core 14 has cpuset 0x00004000,0x00004000 os cluster 65535 has cpuset 0x00004000,0x00004000 thread 14 has cpuset 0x00004000 cache depth 1 has cpuset 0x00004000,0x00004000 cache depth 2 has cpuset 0x00004000,0x00004000 os core 15 has cpuset 0x00008000,0x00008000 os cluster 65535 has cpuset 0x00008000,0x00008000 thread 15 has cpuset 0x00008000 cache depth 1 has cpuset 0x00008000,0x00008000 cache depth 2 has cpuset 0x00008000,0x00008000 os core 16 has cpuset 0x00010000,0x00010000 os cluster 65535 has cpuset 0x00010000,0x00010000 thread 16 has cpuset 0x00010000 cache depth 1 has cpuset 0x00010000,0x00010000 cache depth 2 has cpuset 0x00010000,0x00010000 cache depth 3 has cpuset 0x00ff0000,0x00ff0000 os core 17 has cpuset 0x00020000,0x00020000 os cluster 65535 has cpuset 0x00020000,0x00020000 thread 17 has cpuset 0x00020000 cache depth 1 has cpuset 0x00020000,0x00020000 cache depth 2 has cpuset 0x00020000,0x00020000 os core 18 has cpuset 0x00040000,0x00040000 os cluster 65535 has cpuset 0x00040000,0x00040000 thread 18 has cpuset 0x00040000 cache depth 1 has cpuset 0x00040000,0x00040000 cache depth 2 has cpuset 0x00040000,0x00040000 os core 19 has cpuset 0x00080000,0x00080000 os cluster 65535 has cpuset 0x00080000,0x00080000 thread 19 has cpuset 0x00080000 cache depth 1 has cpuset 0x00080000,0x00080000 cache depth 2 has cpuset 0x00080000,0x00080000 os core 20 has cpuset 0x00100000,0x00100000 os cluster 65535 has cpuset 0x00100000,0x00100000 thread 20 has cpuset 0x00100000 cache depth 1 has cpuset 0x00100000,0x00100000 cache depth 2 has cpuset 0x00100000,0x00100000 os core 21 has cpuset 0x00200000,0x00200000 os cluster 65535 has cpuset 0x00200000,0x00200000 thread 21 has cpuset 0x00200000 cache depth 1 has cpuset 0x00200000,0x00200000 cache depth 2 has cpuset 0x00200000,0x00200000 os core 22 has cpuset 0x00400000,0x00400000 os cluster 65535 has cpuset 0x00400000,0x00400000 thread 22 has cpuset 0x00400000 cache depth 1 has cpuset 0x00400000,0x00400000 cache depth 2 has cpuset 0x00400000,0x00400000 os core 23 has cpuset 0x00800000,0x00800000 os cluster 65535 has cpuset 0x00800000,0x00800000 thread 23 has cpuset 0x00800000 cache depth 1 has cpuset 0x00800000,0x00800000 cache depth 2 has cpuset 0x00800000,0x00800000 os core 24 has cpuset 0x01000000,0x01000000 os cluster 65535 has cpuset 0x01000000,0x01000000 thread 24 has cpuset 0x01000000 cache depth 1 has cpuset 0x01000000,0x01000000 cache depth 2 has cpuset 0x01000000,0x01000000 cache depth 3 has cpuset 0xff000000,0xff000000 os core 25 has cpuset 0x02000000,0x02000000 os cluster 65535 has cpuset 0x02000000,0x02000000 thread 25 has cpuset 0x02000000 cache depth 1 has cpuset 0x02000000,0x02000000 cache depth 2 has cpuset 0x02000000,0x02000000 os core 26 has cpuset 0x04000000,0x04000000 os cluster 65535 has cpuset 0x04000000,0x04000000 thread 26 has cpuset 0x04000000 cache depth 1 has cpuset 0x04000000,0x04000000 cache depth 2 has cpuset 0x04000000,0x04000000 os core 27 has cpuset 0x08000000,0x08000000 os cluster 65535 has cpuset 0x08000000,0x08000000 thread 27 has cpuset 0x08000000 cache depth 1 has cpuset 0x08000000,0x08000000 cache depth 2 has cpuset 0x08000000,0x08000000 os core 28 has cpuset 0x10000000,0x10000000 os cluster 65535 has cpuset 0x10000000,0x10000000 thread 28 has cpuset 0x10000000 cache depth 1 has cpuset 0x10000000,0x10000000 cache depth 2 has cpuset 0x10000000,0x10000000 os core 29 has cpuset 0x20000000,0x20000000 os cluster 65535 has cpuset 0x20000000,0x20000000 thread 29 has cpuset 0x20000000 cache depth 1 has cpuset 0x20000000,0x20000000 cache depth 2 has cpuset 0x20000000,0x20000000 os core 30 has cpuset 0x40000000,0x40000000 os cluster 65535 has cpuset 0x40000000,0x40000000 thread 30 has cpuset 0x40000000 cache depth 1 has cpuset 0x40000000,0x40000000 cache depth 2 has cpuset 0x40000000,0x40000000 os core 31 has cpuset 0x80000000,0x80000000 os cluster 65535 has cpuset 0x80000000,0x80000000 thread 31 has cpuset 0x80000000 cache depth 1 has cpuset 0x80000000,0x80000000 cache depth 2 has cpuset 0x80000000,0x80000000 thread 32 has cpuset 0x00000001,0x0 thread 33 has cpuset 0x00000002,0x0 thread 34 has cpuset 0x00000004,0x0 thread 35 has cpuset 0x00000008,0x0 thread 36 has cpuset 0x00000010,0x0 thread 37 has cpuset 0x00000020,0x0 thread 38 has cpuset 0x00000040,0x0 thread 39 has cpuset 0x00000080,0x0 thread 40 has cpuset 0x00000100,0x0 thread 41 has cpuset 0x00000200,0x0 thread 42 has cpuset 0x00000400,0x0 thread 43 has cpuset 0x00000800,0x0 thread 44 has cpuset 0x00001000,0x0 thread 45 has cpuset 0x00002000,0x0 thread 46 has cpuset 0x00004000,0x0 thread 47 has cpuset 0x00008000,0x0 thread 48 has cpuset 0x00010000,0x0 thread 49 has cpuset 0x00020000,0x0 thread 50 has cpuset 0x00040000,0x0 thread 51 has cpuset 0x00080000,0x0 thread 52 has cpuset 0x00100000,0x0 thread 53 has cpuset 0x00200000,0x0 thread 54 has cpuset 0x00400000,0x0 thread 55 has cpuset 0x00800000,0x0 thread 56 has cpuset 0x01000000,0x0 thread 57 has cpuset 0x02000000,0x0 thread 58 has cpuset 0x04000000,0x0 thread 59 has cpuset 0x08000000,0x0 thread 60 has cpuset 0x10000000,0x0 thread 61 has cpuset 0x20000000,0x0 thread 62 has cpuset 0x40000000,0x0 thread 63 has cpuset 0x80000000,0x0 linux/cpufreq: max frequency values will be adjusted by up to 10% * Topology extraction from /sys/devices/system/node * possible NUMA nodes 0x00000001 NUMA indexes: 0 os node 0 has cpuset 0xffffffff,0xffffffff found DMIProductName 'PowerEdge R6515' found DMIProductVersion '' found DMIBoardVendor 'Dell Inc.' found DMIBoardName '035YY8' found DMIBoardVersion 'A03' found DMIChassisVendor 'Dell Inc.' found DMIChassisType '23' found DMIChassisVersion '' found DMIChassisAssetTag '' found DMIBIOSVendor 'Dell Inc.' found DMIBIOSVersion '2.6.6' found DMIBIOSDate '01/13/2022' found DMISysVendor 'Dell Inc.' CPU phase discovery in component x86... --- Package level has number 1 --- L3Cache level has number 2 --- L2Cache level has number 3 --- L1Cache level has number 4 --- Core level has number 5 --- PU level has number 6 hwloc verbose debug enabled, may be disabled with HWLOC_DEBUG_VERBOSE=0 in the environment. highest cpuid 10, cpuid type 1 highest extended cpuid 80000023 possible CPUs are 0xffffffff,0xffffffff binding to CPU0 APIC ID 0x00 legacy_max_log_proc 64 phys 0 legacy thread 0 topoext 00000000, 0 nodes, node 4294967295, 2 threads in core 0 x2APIC 00000000 0: nextshift 1 num 2 type 1 id 0 x2APIC 00000000 1: nextshift 6 num 64 type 2 id 0 x2APIC remainder: 0 this is thread 0 of core 0 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU1 APIC ID 0x02 legacy_max_log_proc 64 phys 0 legacy thread 2 topoext 00000002, 0 nodes, node 4294967295, 2 threads in core 1 x2APIC 00000002 0: nextshift 1 num 2 type 1 id 2 x2APIC 00000002 1: nextshift 6 num 64 type 2 id 1 x2APIC remainder: 0 this is thread 2 of core 1 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU2 APIC ID 0x04 legacy_max_log_proc 64 phys 0 legacy thread 4 topoext 00000004, 0 nodes, node 4294967295, 2 threads in core 2 x2APIC 00000004 0: nextshift 1 num 2 type 1 id 4 x2APIC 00000004 1: nextshift 6 num 64 type 2 id 2 x2APIC remainder: 0 this is thread 4 of core 2 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU3 APIC ID 0x06 legacy_max_log_proc 64 phys 0 legacy thread 6 topoext 00000006, 0 nodes, node 4294967295, 2 threads in core 3 x2APIC 00000006 0: nextshift 1 num 2 type 1 id 6 x2APIC 00000006 1: nextshift 6 num 64 type 2 id 3 x2APIC remainder: 0 this is thread 6 of core 3 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU4 APIC ID 0x08 legacy_max_log_proc 64 phys 0 legacy thread 8 topoext 00000008, 0 nodes, node 4294967295, 2 threads in core 4 x2APIC 00000008 0: nextshift 1 num 2 type 1 id 8 x2APIC 00000008 1: nextshift 6 num 64 type 2 id 4 x2APIC remainder: 0 this is thread 8 of core 4 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU5 APIC ID 0x0a legacy_max_log_proc 64 phys 0 legacy thread 10 topoext 0000000a, 0 nodes, node 4294967295, 2 threads in core 5 x2APIC 0000000a 0: nextshift 1 num 2 type 1 id 10 x2APIC 0000000a 1: nextshift 6 num 64 type 2 id 5 x2APIC remainder: 0 this is thread 10 of core 5 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU6 APIC ID 0x0c legacy_max_log_proc 64 phys 0 legacy thread 12 topoext 0000000c, 0 nodes, node 4294967295, 2 threads in core 6 x2APIC 0000000c 0: nextshift 1 num 2 type 1 id 12 x2APIC 0000000c 1: nextshift 6 num 64 type 2 id 6 x2APIC remainder: 0 this is thread 12 of core 6 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU7 APIC ID 0x0e legacy_max_log_proc 64 phys 0 legacy thread 14 topoext 0000000e, 0 nodes, node 4294967295, 2 threads in core 7 x2APIC 0000000e 0: nextshift 1 num 2 type 1 id 14 x2APIC 0000000e 1: nextshift 6 num 64 type 2 id 7 x2APIC remainder: 0 this is thread 14 of core 7 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU8 APIC ID 0x10 legacy_max_log_proc 64 phys 0 legacy thread 16 topoext 00000010, 0 nodes, node 4294967295, 2 threads in core 8 x2APIC 00000010 0: nextshift 1 num 2 type 1 id 16 x2APIC 00000010 1: nextshift 6 num 64 type 2 id 8 x2APIC remainder: 0 this is thread 16 of core 8 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU9 APIC ID 0x12 legacy_max_log_proc 64 phys 0 legacy thread 18 topoext 00000012, 0 nodes, node 4294967295, 2 threads in core 9 x2APIC 00000012 0: nextshift 1 num 2 type 1 id 18 x2APIC 00000012 1: nextshift 6 num 64 type 2 id 9 x2APIC remainder: 0 this is thread 18 of core 9 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU10 APIC ID 0x14 legacy_max_log_proc 64 phys 0 legacy thread 20 topoext 00000014, 0 nodes, node 4294967295, 2 threads in core 10 x2APIC 00000014 0: nextshift 1 num 2 type 1 id 20 x2APIC 00000014 1: nextshift 6 num 64 type 2 id 10 x2APIC remainder: 0 this is thread 20 of core 10 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU11 APIC ID 0x16 legacy_max_log_proc 64 phys 0 legacy thread 22 topoext 00000016, 0 nodes, node 4294967295, 2 threads in core 11 x2APIC 00000016 0: nextshift 1 num 2 type 1 id 22 x2APIC 00000016 1: nextshift 6 num 64 type 2 id 11 x2APIC remainder: 0 this is thread 22 of core 11 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU12 APIC ID 0x18 legacy_max_log_proc 64 phys 0 legacy thread 24 topoext 00000018, 0 nodes, node 4294967295, 2 threads in core 12 x2APIC 00000018 0: nextshift 1 num 2 type 1 id 24 x2APIC 00000018 1: nextshift 6 num 64 type 2 id 12 x2APIC remainder: 0 this is thread 24 of core 12 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU13 APIC ID 0x1a legacy_max_log_proc 64 phys 0 legacy thread 26 topoext 0000001a, 0 nodes, node 4294967295, 2 threads in core 13 x2APIC 0000001a 0: nextshift 1 num 2 type 1 id 26 x2APIC 0000001a 1: nextshift 6 num 64 type 2 id 13 x2APIC remainder: 0 this is thread 26 of core 13 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU14 APIC ID 0x1c legacy_max_log_proc 64 phys 0 legacy thread 28 topoext 0000001c, 0 nodes, node 4294967295, 2 threads in core 14 x2APIC 0000001c 0: nextshift 1 num 2 type 1 id 28 x2APIC 0000001c 1: nextshift 6 num 64 type 2 id 14 x2APIC remainder: 0 this is thread 28 of core 14 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU15 APIC ID 0x1e legacy_max_log_proc 64 phys 0 legacy thread 30 topoext 0000001e, 0 nodes, node 4294967295, 2 threads in core 15 x2APIC 0000001e 0: nextshift 1 num 2 type 1 id 30 x2APIC 0000001e 1: nextshift 6 num 64 type 2 id 15 x2APIC remainder: 0 this is thread 30 of core 15 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU16 APIC ID 0x20 legacy_max_log_proc 64 phys 0 legacy thread 32 topoext 00000020, 0 nodes, node 4294967295, 2 threads in core 16 x2APIC 00000020 0: nextshift 1 num 2 type 1 id 32 x2APIC 00000020 1: nextshift 6 num 64 type 2 id 16 x2APIC remainder: 0 this is thread 32 of core 16 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU17 APIC ID 0x22 legacy_max_log_proc 64 phys 0 legacy thread 34 topoext 00000022, 0 nodes, node 4294967295, 2 threads in core 17 x2APIC 00000022 0: nextshift 1 num 2 type 1 id 34 x2APIC 00000022 1: nextshift 6 num 64 type 2 id 17 x2APIC remainder: 0 this is thread 34 of core 17 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU18 APIC ID 0x24 legacy_max_log_proc 64 phys 0 legacy thread 36 topoext 00000024, 0 nodes, node 4294967295, 2 threads in core 18 x2APIC 00000024 0: nextshift 1 num 2 type 1 id 36 x2APIC 00000024 1: nextshift 6 num 64 type 2 id 18 x2APIC remainder: 0 this is thread 36 of core 18 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU19 APIC ID 0x26 legacy_max_log_proc 64 phys 0 legacy thread 38 topoext 00000026, 0 nodes, node 4294967295, 2 threads in core 19 x2APIC 00000026 0: nextshift 1 num 2 type 1 id 38 x2APIC 00000026 1: nextshift 6 num 64 type 2 id 19 x2APIC remainder: 0 this is thread 38 of core 19 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU20 APIC ID 0x28 legacy_max_log_proc 64 phys 0 legacy thread 40 topoext 00000028, 0 nodes, node 4294967295, 2 threads in core 20 x2APIC 00000028 0: nextshift 1 num 2 type 1 id 40 x2APIC 00000028 1: nextshift 6 num 64 type 2 id 20 x2APIC remainder: 0 this is thread 40 of core 20 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU21 APIC ID 0x2a legacy_max_log_proc 64 phys 0 legacy thread 42 topoext 0000002a, 0 nodes, node 4294967295, 2 threads in core 21 x2APIC 0000002a 0: nextshift 1 num 2 type 1 id 42 x2APIC 0000002a 1: nextshift 6 num 64 type 2 id 21 x2APIC remainder: 0 this is thread 42 of core 21 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU22 APIC ID 0x2c legacy_max_log_proc 64 phys 0 legacy thread 44 topoext 0000002c, 0 nodes, node 4294967295, 2 threads in core 22 x2APIC 0000002c 0: nextshift 1 num 2 type 1 id 44 x2APIC 0000002c 1: nextshift 6 num 64 type 2 id 22 x2APIC remainder: 0 this is thread 44 of core 22 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU23 APIC ID 0x2e legacy_max_log_proc 64 phys 0 legacy thread 46 topoext 0000002e, 0 nodes, node 4294967295, 2 threads in core 23 x2APIC 0000002e 0: nextshift 1 num 2 type 1 id 46 x2APIC 0000002e 1: nextshift 6 num 64 type 2 id 23 x2APIC remainder: 0 this is thread 46 of core 23 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU24 APIC ID 0x30 legacy_max_log_proc 64 phys 0 legacy thread 48 topoext 00000030, 0 nodes, node 4294967295, 2 threads in core 24 x2APIC 00000030 0: nextshift 1 num 2 type 1 id 48 x2APIC 00000030 1: nextshift 6 num 64 type 2 id 24 x2APIC remainder: 0 this is thread 48 of core 24 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU25 APIC ID 0x32 legacy_max_log_proc 64 phys 0 legacy thread 50 topoext 00000032, 0 nodes, node 4294967295, 2 threads in core 25 x2APIC 00000032 0: nextshift 1 num 2 type 1 id 50 x2APIC 00000032 1: nextshift 6 num 64 type 2 id 25 x2APIC remainder: 0 this is thread 50 of core 25 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU26 APIC ID 0x34 legacy_max_log_proc 64 phys 0 legacy thread 52 topoext 00000034, 0 nodes, node 4294967295, 2 threads in core 26 x2APIC 00000034 0: nextshift 1 num 2 type 1 id 52 x2APIC 00000034 1: nextshift 6 num 64 type 2 id 26 x2APIC remainder: 0 this is thread 52 of core 26 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU27 APIC ID 0x36 legacy_max_log_proc 64 phys 0 legacy thread 54 topoext 00000036, 0 nodes, node 4294967295, 2 threads in core 27 x2APIC 00000036 0: nextshift 1 num 2 type 1 id 54 x2APIC 00000036 1: nextshift 6 num 64 type 2 id 27 x2APIC remainder: 0 this is thread 54 of core 27 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU28 APIC ID 0x38 legacy_max_log_proc 64 phys 0 legacy thread 56 topoext 00000038, 0 nodes, node 4294967295, 2 threads in core 28 x2APIC 00000038 0: nextshift 1 num 2 type 1 id 56 x2APIC 00000038 1: nextshift 6 num 64 type 2 id 28 x2APIC remainder: 0 this is thread 56 of core 28 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU29 APIC ID 0x3a legacy_max_log_proc 64 phys 0 legacy thread 58 topoext 0000003a, 0 nodes, node 4294967295, 2 threads in core 29 x2APIC 0000003a 0: nextshift 1 num 2 type 1 id 58 x2APIC 0000003a 1: nextshift 6 num 64 type 2 id 29 x2APIC remainder: 0 this is thread 58 of core 29 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU30 APIC ID 0x3c legacy_max_log_proc 64 phys 0 legacy thread 60 topoext 0000003c, 0 nodes, node 4294967295, 2 threads in core 30 x2APIC 0000003c 0: nextshift 1 num 2 type 1 id 60 x2APIC 0000003c 1: nextshift 6 num 64 type 2 id 30 x2APIC remainder: 0 this is thread 60 of core 30 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU31 APIC ID 0x3e legacy_max_log_proc 64 phys 0 legacy thread 62 topoext 0000003e, 0 nodes, node 4294967295, 2 threads in core 31 x2APIC 0000003e 0: nextshift 1 num 2 type 1 id 62 x2APIC 0000003e 1: nextshift 6 num 64 type 2 id 31 x2APIC remainder: 0 this is thread 62 of core 31 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU32 APIC ID 0x01 legacy_max_log_proc 64 phys 0 legacy thread 1 topoext 00000001, 0 nodes, node 4294967295, 2 threads in core 0 x2APIC 00000001 0: nextshift 1 num 2 type 1 id 1 x2APIC 00000001 1: nextshift 6 num 64 type 2 id 0 x2APIC remainder: 0 this is thread 1 of core 0 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU33 APIC ID 0x03 legacy_max_log_proc 64 phys 0 legacy thread 3 topoext 00000003, 0 nodes, node 4294967295, 2 threads in core 1 x2APIC 00000003 0: nextshift 1 num 2 type 1 id 3 x2APIC 00000003 1: nextshift 6 num 64 type 2 id 1 x2APIC remainder: 0 this is thread 3 of core 1 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU34 APIC ID 0x05 legacy_max_log_proc 64 phys 0 legacy thread 5 topoext 00000005, 0 nodes, node 4294967295, 2 threads in core 2 x2APIC 00000005 0: nextshift 1 num 2 type 1 id 5 x2APIC 00000005 1: nextshift 6 num 64 type 2 id 2 x2APIC remainder: 0 this is thread 5 of core 2 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU35 APIC ID 0x07 legacy_max_log_proc 64 phys 0 legacy thread 7 topoext 00000007, 0 nodes, node 4294967295, 2 threads in core 3 x2APIC 00000007 0: nextshift 1 num 2 type 1 id 7 x2APIC 00000007 1: nextshift 6 num 64 type 2 id 3 x2APIC remainder: 0 this is thread 7 of core 3 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU36 APIC ID 0x09 legacy_max_log_proc 64 phys 0 legacy thread 9 topoext 00000009, 0 nodes, node 4294967295, 2 threads in core 4 x2APIC 00000009 0: nextshift 1 num 2 type 1 id 9 x2APIC 00000009 1: nextshift 6 num 64 type 2 id 4 x2APIC remainder: 0 this is thread 9 of core 4 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU37 APIC ID 0x0b legacy_max_log_proc 64 phys 0 legacy thread 11 topoext 0000000b, 0 nodes, node 4294967295, 2 threads in core 5 x2APIC 0000000b 0: nextshift 1 num 2 type 1 id 11 x2APIC 0000000b 1: nextshift 6 num 64 type 2 id 5 x2APIC remainder: 0 this is thread 11 of core 5 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU38 APIC ID 0x0d legacy_max_log_proc 64 phys 0 legacy thread 13 topoext 0000000d, 0 nodes, node 4294967295, 2 threads in core 6 x2APIC 0000000d 0: nextshift 1 num 2 type 1 id 13 x2APIC 0000000d 1: nextshift 6 num 64 type 2 id 6 x2APIC remainder: 0 this is thread 13 of core 6 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU39 APIC ID 0x0f legacy_max_log_proc 64 phys 0 legacy thread 15 topoext 0000000f, 0 nodes, node 4294967295, 2 threads in core 7 x2APIC 0000000f 0: nextshift 1 num 2 type 1 id 15 x2APIC 0000000f 1: nextshift 6 num 64 type 2 id 7 x2APIC remainder: 0 this is thread 15 of core 7 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU40 APIC ID 0x11 legacy_max_log_proc 64 phys 0 legacy thread 17 topoext 00000011, 0 nodes, node 4294967295, 2 threads in core 8 x2APIC 00000011 0: nextshift 1 num 2 type 1 id 17 x2APIC 00000011 1: nextshift 6 num 64 type 2 id 8 x2APIC remainder: 0 this is thread 17 of core 8 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU41 APIC ID 0x13 legacy_max_log_proc 64 phys 0 legacy thread 19 topoext 00000013, 0 nodes, node 4294967295, 2 threads in core 9 x2APIC 00000013 0: nextshift 1 num 2 type 1 id 19 x2APIC 00000013 1: nextshift 6 num 64 type 2 id 9 x2APIC remainder: 0 this is thread 19 of core 9 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU42 APIC ID 0x15 legacy_max_log_proc 64 phys 0 legacy thread 21 topoext 00000015, 0 nodes, node 4294967295, 2 threads in core 10 x2APIC 00000015 0: nextshift 1 num 2 type 1 id 21 x2APIC 00000015 1: nextshift 6 num 64 type 2 id 10 x2APIC remainder: 0 this is thread 21 of core 10 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU43 APIC ID 0x17 legacy_max_log_proc 64 phys 0 legacy thread 23 topoext 00000017, 0 nodes, node 4294967295, 2 threads in core 11 x2APIC 00000017 0: nextshift 1 num 2 type 1 id 23 x2APIC 00000017 1: nextshift 6 num 64 type 2 id 11 x2APIC remainder: 0 this is thread 23 of core 11 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU44 APIC ID 0x19 legacy_max_log_proc 64 phys 0 legacy thread 25 topoext 00000019, 0 nodes, node 4294967295, 2 threads in core 12 x2APIC 00000019 0: nextshift 1 num 2 type 1 id 25 x2APIC 00000019 1: nextshift 6 num 64 type 2 id 12 x2APIC remainder: 0 this is thread 25 of core 12 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU45 APIC ID 0x1b legacy_max_log_proc 64 phys 0 legacy thread 27 topoext 0000001b, 0 nodes, node 4294967295, 2 threads in core 13 x2APIC 0000001b 0: nextshift 1 num 2 type 1 id 27 x2APIC 0000001b 1: nextshift 6 num 64 type 2 id 13 x2APIC remainder: 0 this is thread 27 of core 13 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU46 APIC ID 0x1d legacy_max_log_proc 64 phys 0 legacy thread 29 topoext 0000001d, 0 nodes, node 4294967295, 2 threads in core 14 x2APIC 0000001d 0: nextshift 1 num 2 type 1 id 29 x2APIC 0000001d 1: nextshift 6 num 64 type 2 id 14 x2APIC remainder: 0 this is thread 29 of core 14 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU47 APIC ID 0x1f legacy_max_log_proc 64 phys 0 legacy thread 31 topoext 0000001f, 0 nodes, node 4294967295, 2 threads in core 15 x2APIC 0000001f 0: nextshift 1 num 2 type 1 id 31 x2APIC 0000001f 1: nextshift 6 num 64 type 2 id 15 x2APIC remainder: 0 this is thread 31 of core 15 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU48 APIC ID 0x21 legacy_max_log_proc 64 phys 0 legacy thread 33 topoext 00000021, 0 nodes, node 4294967295, 2 threads in core 16 x2APIC 00000021 0: nextshift 1 num 2 type 1 id 33 x2APIC 00000021 1: nextshift 6 num 64 type 2 id 16 x2APIC remainder: 0 this is thread 33 of core 16 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU49 APIC ID 0x23 legacy_max_log_proc 64 phys 0 legacy thread 35 topoext 00000023, 0 nodes, node 4294967295, 2 threads in core 17 x2APIC 00000023 0: nextshift 1 num 2 type 1 id 35 x2APIC 00000023 1: nextshift 6 num 64 type 2 id 17 x2APIC remainder: 0 this is thread 35 of core 17 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU50 APIC ID 0x25 legacy_max_log_proc 64 phys 0 legacy thread 37 topoext 00000025, 0 nodes, node 4294967295, 2 threads in core 18 x2APIC 00000025 0: nextshift 1 num 2 type 1 id 37 x2APIC 00000025 1: nextshift 6 num 64 type 2 id 18 x2APIC remainder: 0 this is thread 37 of core 18 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU51 APIC ID 0x27 legacy_max_log_proc 64 phys 0 legacy thread 39 topoext 00000027, 0 nodes, node 4294967295, 2 threads in core 19 x2APIC 00000027 0: nextshift 1 num 2 type 1 id 39 x2APIC 00000027 1: nextshift 6 num 64 type 2 id 19 x2APIC remainder: 0 this is thread 39 of core 19 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU52 APIC ID 0x29 legacy_max_log_proc 64 phys 0 legacy thread 41 topoext 00000029, 0 nodes, node 4294967295, 2 threads in core 20 x2APIC 00000029 0: nextshift 1 num 2 type 1 id 41 x2APIC 00000029 1: nextshift 6 num 64 type 2 id 20 x2APIC remainder: 0 this is thread 41 of core 20 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU53 APIC ID 0x2b legacy_max_log_proc 64 phys 0 legacy thread 43 topoext 0000002b, 0 nodes, node 4294967295, 2 threads in core 21 x2APIC 0000002b 0: nextshift 1 num 2 type 1 id 43 x2APIC 0000002b 1: nextshift 6 num 64 type 2 id 21 x2APIC remainder: 0 this is thread 43 of core 21 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU54 APIC ID 0x2d legacy_max_log_proc 64 phys 0 legacy thread 45 topoext 0000002d, 0 nodes, node 4294967295, 2 threads in core 22 x2APIC 0000002d 0: nextshift 1 num 2 type 1 id 45 x2APIC 0000002d 1: nextshift 6 num 64 type 2 id 22 x2APIC remainder: 0 this is thread 45 of core 22 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU55 APIC ID 0x2f legacy_max_log_proc 64 phys 0 legacy thread 47 topoext 0000002f, 0 nodes, node 4294967295, 2 threads in core 23 x2APIC 0000002f 0: nextshift 1 num 2 type 1 id 47 x2APIC 0000002f 1: nextshift 6 num 64 type 2 id 23 x2APIC remainder: 0 this is thread 47 of core 23 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU56 APIC ID 0x31 legacy_max_log_proc 64 phys 0 legacy thread 49 topoext 00000031, 0 nodes, node 4294967295, 2 threads in core 24 x2APIC 00000031 0: nextshift 1 num 2 type 1 id 49 x2APIC 00000031 1: nextshift 6 num 64 type 2 id 24 x2APIC remainder: 0 this is thread 49 of core 24 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU57 APIC ID 0x33 legacy_max_log_proc 64 phys 0 legacy thread 51 topoext 00000033, 0 nodes, node 4294967295, 2 threads in core 25 x2APIC 00000033 0: nextshift 1 num 2 type 1 id 51 x2APIC 00000033 1: nextshift 6 num 64 type 2 id 25 x2APIC remainder: 0 this is thread 51 of core 25 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU58 APIC ID 0x35 legacy_max_log_proc 64 phys 0 legacy thread 53 topoext 00000035, 0 nodes, node 4294967295, 2 threads in core 26 x2APIC 00000035 0: nextshift 1 num 2 type 1 id 53 x2APIC 00000035 1: nextshift 6 num 64 type 2 id 26 x2APIC remainder: 0 this is thread 53 of core 26 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU59 APIC ID 0x37 legacy_max_log_proc 64 phys 0 legacy thread 55 topoext 00000037, 0 nodes, node 4294967295, 2 threads in core 27 x2APIC 00000037 0: nextshift 1 num 2 type 1 id 55 x2APIC 00000037 1: nextshift 6 num 64 type 2 id 27 x2APIC remainder: 0 this is thread 55 of core 27 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU60 APIC ID 0x39 legacy_max_log_proc 64 phys 0 legacy thread 57 topoext 00000039, 0 nodes, node 4294967295, 2 threads in core 28 x2APIC 00000039 0: nextshift 1 num 2 type 1 id 57 x2APIC 00000039 1: nextshift 6 num 64 type 2 id 28 x2APIC remainder: 0 this is thread 57 of core 28 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU61 APIC ID 0x3b legacy_max_log_proc 64 phys 0 legacy thread 59 topoext 0000003b, 0 nodes, node 4294967295, 2 threads in core 29 x2APIC 0000003b 0: nextshift 1 num 2 type 1 id 59 x2APIC 0000003b 1: nextshift 6 num 64 type 2 id 29 x2APIC remainder: 0 this is thread 59 of core 29 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU62 APIC ID 0x3d legacy_max_log_proc 64 phys 0 legacy thread 61 topoext 0000003d, 0 nodes, node 4294967295, 2 threads in core 30 x2APIC 0000003d 0: nextshift 1 num 2 type 1 id 61 x2APIC 0000003d 1: nextshift 6 num 64 type 2 id 30 x2APIC remainder: 0 this is thread 61 of core 30 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB binding to CPU63 APIC ID 0x3f legacy_max_log_proc 64 phys 0 legacy thread 63 topoext 0000003f, 0 nodes, node 4294967295, 2 threads in core 31 x2APIC 0000003f 0: nextshift 1 num 2 type 1 id 63 x2APIC 0000003f 1: nextshift 6 num 64 type 2 id 31 x2APIC remainder: 0 this is thread 63 of core 31 cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB Summary of x86 CPUID topology: PU 0 present=1 apicid=0 on PKG 0 CORE 0 DIE -1 NODE -1 PU 1 present=1 apicid=2 on PKG 0 CORE 1 DIE -1 NODE -1 PU 2 present=1 apicid=4 on PKG 0 CORE 2 DIE -1 NODE -1 PU 3 present=1 apicid=6 on PKG 0 CORE 3 DIE -1 NODE -1 PU 4 present=1 apicid=8 on PKG 0 CORE 4 DIE -1 NODE -1 PU 5 present=1 apicid=10 on PKG 0 CORE 5 DIE -1 NODE -1 PU 6 present=1 apicid=12 on PKG 0 CORE 6 DIE -1 NODE -1 PU 7 present=1 apicid=14 on PKG 0 CORE 7 DIE -1 NODE -1 PU 8 present=1 apicid=16 on PKG 0 CORE 8 DIE -1 NODE -1 PU 9 present=1 apicid=18 on PKG 0 CORE 9 DIE -1 NODE -1 PU 10 present=1 apicid=20 on PKG 0 CORE 10 DIE -1 NODE -1 PU 11 present=1 apicid=22 on PKG 0 CORE 11 DIE -1 NODE -1 PU 12 present=1 apicid=24 on PKG 0 CORE 12 DIE -1 NODE -1 PU 13 present=1 apicid=26 on PKG 0 CORE 13 DIE -1 NODE -1 PU 14 present=1 apicid=28 on PKG 0 CORE 14 DIE -1 NODE -1 PU 15 present=1 apicid=30 on PKG 0 CORE 15 DIE -1 NODE -1 PU 16 present=1 apicid=32 on PKG 0 CORE 16 DIE -1 NODE -1 PU 17 present=1 apicid=34 on PKG 0 CORE 17 DIE -1 NODE -1 PU 18 present=1 apicid=36 on PKG 0 CORE 18 DIE -1 NODE -1 PU 19 present=1 apicid=38 on PKG 0 CORE 19 DIE -1 NODE -1 PU 20 present=1 apicid=40 on PKG 0 CORE 20 DIE -1 NODE -1 PU 21 present=1 apicid=42 on PKG 0 CORE 21 DIE -1 NODE -1 PU 22 present=1 apicid=44 on PKG 0 CORE 22 DIE -1 NODE -1 PU 23 present=1 apicid=46 on PKG 0 CORE 23 DIE -1 NODE -1 PU 24 present=1 apicid=48 on PKG 0 CORE 24 DIE -1 NODE -1 PU 25 present=1 apicid=50 on PKG 0 CORE 25 DIE -1 NODE -1 PU 26 present=1 apicid=52 on PKG 0 CORE 26 DIE -1 NODE -1 PU 27 present=1 apicid=54 on PKG 0 CORE 27 DIE -1 NODE -1 PU 28 present=1 apicid=56 on PKG 0 CORE 28 DIE -1 NODE -1 PU 29 present=1 apicid=58 on PKG 0 CORE 29 DIE -1 NODE -1 PU 30 present=1 apicid=60 on PKG 0 CORE 30 DIE -1 NODE -1 PU 31 present=1 apicid=62 on PKG 0 CORE 31 DIE -1 NODE -1 PU 32 present=1 apicid=1 on PKG 0 CORE 0 DIE -1 NODE -1 PU 33 present=1 apicid=3 on PKG 0 CORE 1 DIE -1 NODE -1 PU 34 present=1 apicid=5 on PKG 0 CORE 2 DIE -1 NODE -1 PU 35 present=1 apicid=7 on PKG 0 CORE 3 DIE -1 NODE -1 PU 36 present=1 apicid=9 on PKG 0 CORE 4 DIE -1 NODE -1 PU 37 present=1 apicid=11 on PKG 0 CORE 5 DIE -1 NODE -1 PU 38 present=1 apicid=13 on PKG 0 CORE 6 DIE -1 NODE -1 PU 39 present=1 apicid=15 on PKG 0 CORE 7 DIE -1 NODE -1 PU 40 present=1 apicid=17 on PKG 0 CORE 8 DIE -1 NODE -1 PU 41 present=1 apicid=19 on PKG 0 CORE 9 DIE -1 NODE -1 PU 42 present=1 apicid=21 on PKG 0 CORE 10 DIE -1 NODE -1 PU 43 present=1 apicid=23 on PKG 0 CORE 11 DIE -1 NODE -1 PU 44 present=1 apicid=25 on PKG 0 CORE 12 DIE -1 NODE -1 PU 45 present=1 apicid=27 on PKG 0 CORE 13 DIE -1 NODE -1 PU 46 present=1 apicid=29 on PKG 0 CORE 14 DIE -1 NODE -1 PU 47 present=1 apicid=31 on PKG 0 CORE 15 DIE -1 NODE -1 PU 48 present=1 apicid=33 on PKG 0 CORE 16 DIE -1 NODE -1 PU 49 present=1 apicid=35 on PKG 0 CORE 17 DIE -1 NODE -1 PU 50 present=1 apicid=37 on PKG 0 CORE 18 DIE -1 NODE -1 PU 51 present=1 apicid=39 on PKG 0 CORE 19 DIE -1 NODE -1 PU 52 present=1 apicid=41 on PKG 0 CORE 20 DIE -1 NODE -1 PU 53 present=1 apicid=43 on PKG 0 CORE 21 DIE -1 NODE -1 PU 54 present=1 apicid=45 on PKG 0 CORE 22 DIE -1 NODE -1 PU 55 present=1 apicid=47 on PKG 0 CORE 23 DIE -1 NODE -1 PU 56 present=1 apicid=49 on PKG 0 CORE 24 DIE -1 NODE -1 PU 57 present=1 apicid=51 on PKG 0 CORE 25 DIE -1 NODE -1 PU 58 present=1 apicid=53 on PKG 0 CORE 26 DIE -1 NODE -1 PU 59 present=1 apicid=55 on PKG 0 CORE 27 DIE -1 NODE -1 PU 60 present=1 apicid=57 on PKG 0 CORE 28 DIE -1 NODE -1 PU 61 present=1 apicid=59 on PKG 0 CORE 29 DIE -1 NODE -1 PU 62 present=1 apicid=61 on PKG 0 CORE 30 DIE -1 NODE -1 PU 63 present=1 apicid=63 on PKG 0 CORE 31 DIE -1 NODE -1 CPU phase discovery in component no_os... Fixup root sets Propagate sets Removing unauthorized sets from all sets Ok, finished tweaking, now connect PCI phase discovery... PCI phase discovery in component linux... hwloc verbose debug enabled, may be disabled with HWLOC_DEBUG_VERBOSE=0 in the environment. PCI hierarchy: 0000:00:00.0 Device [1022:1480 (1028:08fc) rev=00 class=0600] Adding new PCI hostbridge 0000:00 new PCI hostbridge covers 0000:[00-02] Adding new PCI hostbridge 0000:40 new PCI hostbridge covers 0000:[40-47] Adding new PCI hostbridge 0000:80 new PCI hostbridge covers 0000:[80-84] Adding new PCI hostbridge 0000:c0 new PCI hostbridge covers 0000:[c0-c9] Looking for parent of PCI busid 0000:00:00.0 will attach PCI bus to cpuset 0xffffffff,0xffffffff Adding PCI locality Machine P#0 for bus 0000:[00:02] Looking for parent of PCI busid 0000:40:00.0 will attach PCI bus to cpuset 0xffffffff,0xffffffff Adding PCI locality Machine P#0 for bus 0000:[40:47] Looking for parent of PCI busid 0000:80:00.0 will attach PCI bus to cpuset 0xffffffff,0xffffffff Adding PCI locality Machine P#0 for bus 0000:[80:84] Looking for parent of PCI busid 0000:c0:00.0 will attach PCI bus to cpuset 0xffffffff,0xffffffff Adding PCI locality Machine P#0 for bus 0000:[c0:c9] IO phase discovery... IO phase discovery in component linux... pcidisc looking for bus id 0000:81:00.0 found pci locality for 0000:[80:84] looking for bus 0000:81:00.0 below Machine P#0 found busid 0000:81:00.0 pcidisc looking for bus id 0000:c3:00.0 found pci locality for 0000:[c0:c9] looking for bus 0000:c3:00.0 below Machine P#0 found busid 0000:c3:00.0 pcidisc looking for bus id 0000:82:00.0 found pci locality for 0000:[80:84] looking for bus 0000:82:00.0 below Machine P#0 found busid 0000:82:00.0 pcidisc looking for bus id 0000:c3:00.0 found pci locality for 0000:[c0:c9] looking for bus 0000:c3:00.0 below Machine P#0 found busid 0000:c3:00.0 pcidisc looking for bus id 0000:41:00.0 found pci locality for 0000:[40:47] looking for bus 0000:41:00.0 below Machine P#0 found busid 0000:41:00.0 pcidisc looking for bus id 0000:41:00.1 found pci locality for 0000:[40:47] looking for bus 0000:41:00.1 below Machine P#0 found busid 0000:41:00.1 pcidisc looking for bus id 0000:41:00.0 found pci locality for 0000:[40:47] looking for bus 0000:41:00.0 below Machine P#0 found busid 0000:41:00.0 pcidisc looking for bus id 0000:41:00.1 found pci locality for 0000:[40:47] looking for bus 0000:41:00.1 below Machine P#0 found busid 0000:41:00.1 MISC phase discovery... MISC phase discovery in component linux... ANNOTATE phase discovery... ANNOTATE phase discovery in component linux... pcidisc looking for bus id 0000:c7:00.0 found pci locality for 0000:[c0:c9] looking for bus 0000:c7:00.0 below Machine P#0 found busid 0000:c0:03.4 pcidisc looking for bus id 0000:c5:00.0 found pci locality for 0000:[c0:c9] looking for bus 0000:c5:00.0 below Machine P#0 found busid 0000:c0:03.2 pcidisc looking for bus id 0000:81:00.0 found pci locality for 0000:[80:84] looking for bus 0000:81:00.0 below Machine P#0 found busid 0000:81:00.0 pcidisc looking for bus id 0000:40:01.0 found pci locality for 0000:[40:47] looking for bus 0000:40:01.0 below Machine P#0 found busid 0000:40:01.0 pcidisc looking for bus id 0000:44:00.0 found pci locality for 0000:[40:47] looking for bus 0000:44:00.0 below Machine P#0 found busid 0000:40:03.3 pcidisc looking for bus id 0000:00:03.0 found pci locality for 0000:[00:02] looking for bus 0000:00:03.0 below Machine P#0 found busid 0000:00:03.0 pcidisc looking for bus id 0000:42:00.0 found pci locality for 0000:[40:47] looking for bus 0000:42:00.0 below Machine P#0 found busid 0000:40:03.1 pcidisc looking for bus id 0000:c6:00.0 found pci locality for 0000:[c0:c9] looking for bus 0000:c6:00.0 below Machine P#0 found busid 0000:c0:03.3 pcidisc looking for bus id 0000:c4:00.0 found pci locality for 0000:[c0:c9] looking for bus 0000:c4:00.0 below Machine P#0 found busid 0000:c0:03.1 pcidisc looking for bus id 0000:82:00.0 found pci locality for 0000:[80:84] looking for bus 0000:82:00.0 below Machine P#0 found busid 0000:82:00.0 pcidisc looking for bus id 0000:c0:01.0 found pci locality for 0000:[c0:c9] looking for bus 0000:c0:01.0 below Machine P#0 found busid 0000:c0:01.0 pcidisc looking for bus id 0000:45:00.0 found pci locality for 0000:[40:47] looking for bus 0000:45:00.0 below Machine P#0 found busid 0000:40:03.4 pcidisc looking for bus id 0000:43:00.0 found pci locality for 0000:[40:47] looking for bus 0000:43:00.0 below Machine P#0 found busid 0000:40:03.2 ANNOTATE phase discovery in component pci... --- Package level has number 1 --- L3Cache level has number 2 --- L2Cache level has number 3 --- L1Cache level has number 4 --- Core level has number 5 --- PU level has number 6 Removing bridge objects if needed Removing empty objects Removing levels with HWLOC_TYPE_FILTER_KEEP_STRUCTURE --- Package level has number 1 --- L3Cache level has number 2 --- L2Cache level has number 3 --- L1Cache level has number 4 --- Core level has number 5 --- PU level has number 6 Propagate total memory up hwloc verbose debug enabled, may be disabled with HWLOC_DEBUG_VERBOSE=0 in the environment. Sorting memory tiers... tier 0 = node L#0 P#0 with tier type 0 and local BW #0 UNKNOWN-memory-tier max bandwidth 0 SPM-memory-tier min bandwidth 0 cannot assume SPM means HBM Reading file topol.tpr, VERSION 2023.1 (single precision) NOTE: Parallelization is limited by the small number of atoms, only starting 1 thread-MPI ranks. You can use the -nt and/or -ntmpi option to optimize the number of threads. Using 1 MPI thread Using 16 OpenMP threads starting mdrun 'Flex water' 1 steps, 0.0 ps. Writing final coordinates. NOTE: 27 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 3.202 3.543 90.4 (ns/day) (hour/ns) Performance: 0.098 246.073 GROMACS reminds you: "I Used To Care, But Things Have Changed" (Bob Dylan) Test time = 4.97 sec ---------------------------------------------------------- Test Passed. "integration_Run_gmx_mdrun" end time: Jun 07 13:12 UTC "integration_Run_gmx_mdrun" time elapsed: 00:00:04 ---------------------------------------------------------- 111/157 Testing: integration_Run_csg_map_gmx 111/157 Test: integration_Run_csg_map_gmx Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_map" "--top" "topol.tpr" "--trj" "traj.trr" "--out" "traj.gro" "--no-map" "--nframes" "1" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Run_csg_map_gmx" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Reading file topol.tpr, VERSION 2023.1 (single precision) I have 9 beads in 3 molecules trr version: GMX_trn_file (single precision) Reading frame 0 time 0.000 writing coarse-grained trajectory to traj.gro Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_map_gmx" end time: Jun 07 13:12 UTC "integration_Run_csg_map_gmx" time elapsed: 00:00:00 ---------------------------------------------------------- 113/157 Testing: integration_Run_csg_map_gmx_xtc 113/157 Test: integration_Run_csg_map_gmx_xtc Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_map" "--top" "topol.tpr" "--trj" "traj_comp.xtc" "--out" "traj_comp.gro" "--no-map" "--nframes" "1" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Run_csg_map_gmx_xtc" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Reading file topol.tpr, VERSION 2023.1 (single precision) I have 9 beads in 3 molecules Reading frame 0 time 0.000 writing coarse-grained trajectory to traj_comp.gro Test time = 0.02 sec ---------------------------------------------------------- Test Passed. "integration_Run_csg_map_gmx_xtc" end time: Jun 07 13:12 UTC "integration_Run_csg_map_gmx_xtc" time elapsed: 00:00:00 ---------------------------------------------------------- 112/157 Testing: integration_Compare_csg_map_gmx_output 112/157 Test: integration_Compare_csg_map_gmx_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "traj.gro" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/conf.gro" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Compare_csg_map_gmx_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing traj.gro and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/conf.gro to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_map_gmx_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_map_gmx_output" time elapsed: 00:00:00 ---------------------------------------------------------- 114/157 Testing: integration_Compare_csg_map_gmx_xtc_output 114/157 Test: integration_Compare_csg_map_gmx_xtc_output Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "traj_comp.gro" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/conf.gro" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols "integration_Compare_csg_map_gmx_xtc_output" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Comparing traj_comp.gro and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/conf.gro to a tolerance of 5e-05 Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "integration_Compare_csg_map_gmx_xtc_output" end time: Jun 07 13:12 UTC "integration_Compare_csg_map_gmx_xtc_output" time elapsed: 00:00:00 ---------------------------------------------------------- 153/157 Testing: unit_test_tabulatedpotential 153/157 Test: unit_test_tabulatedpotential Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_tabulatedpotential" Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests "unit_test_tabulatedpotential" start time: Jun 07 13:12 UTC Output: ---------------------------------------------------------- Running 3 test cases... Number of H2 96 bonded_values after pulling out of statistics 4560 histogram created using 4560 data-rows, written to file_interactions.txt histogram created using 4560 data-rows, written to file_interactions.txt histogram created using 4560 data-rows, written to file_interactions.txt histogram created using 4560 data-rows, written to file_interactions.txt histogram created using 4560 data-rows, written to file_interactions.txt histogram created using 4560 data-rows, written to file_interactions.txt histogram created using 4560 data-rows, written to file_interactions.txt histogram created using 4560 data-rows, written to file_interactions.txt *** No errors detected  Test time = 5.86 sec ---------------------------------------------------------- Test Passed. "unit_test_tabulatedpotential" end time: Jun 07 13:12 UTC "unit_test_tabulatedpotential" time elapsed: 00:00:05 ---------------------------------------------------------- End testing: Jun 07 13:12 UTC csg = 16.39 sec*proc csg-tutorials = 0.01 sec*proc csgapps = 0.22 sec*proc integration = 9.19 sec*proc tools = 11.71 sec*proc unit = 8.15 sec*proc votca = 18.16 sec*proc