:-) GROMACS - mdrun_mpi, 2020.4 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: mdrun_mpi, version 2020.4 Executable: /opt/apps/gromacs/2020.4/gcc/8.4.0/openmpi/4.0.3/bin/mdrun_mpi Data prefix: /opt/apps/gromacs/2020.4/gcc/8.4.0/openmpi/4.0.3 Working dir: /data/homezvol1/calmasri/WRKY/WRKY_polyAT/axial/test Command line: mdrun_mpi -ntomp 20 -deffnm pull -pf pullf.xvg -px pullx.xvg Back Off! I just backed up pull.log to ./#pull.log.1# Compiled SIMD: AVX2_128, but for this host/run AVX_512 might be better (see log). Reading file pull.tpr, VERSION 2020.4 (single precision) Changing nstlist from 20 to 100, rlist from 1.418 to 1.53 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 20 OpenMP threads per MPI process NOTE: Your choice of number of MPI ranks and amount of resources results in using 20 OpenMP threads per rank, which is most likely inefficient. The optimum is usually between 1 and 6 threads per rank. Back Off! I just backed up pullx.xvg to ./#pullx.xvg.1# Back Off! I just backed up pullf.xvg to ./#pullf.xvg.1# Back Off! I just backed up pull.xtc to ./#pull.xtc.1# Back Off! I just backed up pull.trr to ./#pull.trr.1# Back Off! I just backed up pull.edr to ./#pull.edr.1# WARNING: This run will generate roughly 8307 Mb of data starting mdrun 'Protein in water' 50000000 steps, 100000.0 ps. Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000004, max 0.000025 (between atoms 1380 and 1381) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1046 1047 35.1 0.1080 0.1080 0.1080 step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step1b_n1.pdb to ./#step1b_n1.pdb.1# Back Off! I just backed up step1b_n0.pdb to ./#step1b_n0.pdb.1# Back Off! I just backed up step1c_n0.pdb to ./#step1c_n0.pdb.1# Back Off! I just backed up step1c_n1.pdb to ./#step1c_n1.pdb.1# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000004, max 0.000022 (between atoms 1380 and 1381) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1046 1047 35.0 0.1080 0.1080 0.1080 Warning: Triclinic box is too skewed. Box (3x3): Box[ 0]={-7.72778e+01, 0.00000e+00, 0.00000e+00} Box[ 1]={-0.00000e+00, -4.07725e+01, -0.00000e+00} Box[ 2]={-0.00000e+00, -0.00000e+00, -3.28548e+01} Can not fix pbc. Warning: Triclinic box is too skewed. Box (3x3): Box[ 0]={-7.72778e+01, 0.00000e+00, 0.00000e+00} Box[ 1]={-0.00000e+00, -4.07725e+01, -0.00000e+00} Box[ 2]={-0.00000e+00, -0.00000e+00, -3.28548e+01} Can not fix pbc. Warning: Triclinic box is too skewed. Box (3x3): Box[ 0]={-7.72778e+01, 0.00000e+00, 0.00000e+00} Box[ 1]={-0.00000e+00, -4.07725e+01, -0.00000e+00} Box[ 2]={-0.00000e+00, -0.00000e+00, -3.28548e+01} Can not fix pbc. Warning: Triclinic box is too skewed. Box (3x3): Box[ 0]={-7.72778e+01, 0.00000e+00, 0.00000e+00} Box[ 1]={-0.00000e+00, -4.07725e+01, -0.00000e+00} Box[ 2]={-0.00000e+00, -0.00000e+00, -3.28548e+01} Can not fix pbc. [hpc3-14-11:39089] *** Process received signal *** [hpc3-14-11:39089] Signal: Segmentation fault (11) [hpc3-14-11:39089] Signal code: Address not mapped (1) [hpc3-14-11:39089] Failing at address: 0xfffffffe02db7c00 -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 0 on node hpc3-14-11 exited on signal 11 (Segmentation fault). --------------------------------------------------------------------------