[gmx-users] mdrun don't write a checkpoint file
Menig, Simon
simon.menig at tum.de
Thu Oct 6 14:23:17 CEST 2016
Thank you for your fast answer Justin
I looked up the log files but I found no error and my disc space is sufficient and the simulation seem to end normal. Could the Problem be that my Simulation time is shorter than 15 min (max 5000 steps) ? (Shouldn't it write a cpt file after the End of the simulation)
Parts of my log file:
Log file opened on Thu Oct 6 14:09:27 2016
Host: linux-286u pid: 4384 rank ID: 0 number of ranks: 1
:-) GROMACS - gmx mdrun, 2016 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
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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: gmx mdrun, version 2016
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/simon/simu_test_cg/build_cg_membrane_test1
Command line:
gmx mdrun -s input/ab26_wt_POPE_POPG_cg_eqi_1.tpr -o out_trr/ab26_wt_POPE_POPG_cg_eqi_1.trr -c output/ab26_wt_POPE_POPG_cg_eqi_1.gro -e output/ab26_wt_POPE_POPG_cg_eqi_1.edr -g output/ab26_wt_POPE_POPG_cg_eqi_1.log -cpo output/ab26_wt_POPE_POPG_cg_eqi_1 -v -cpt 1
GROMACS version: 2016
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support: disabled
SIMD instructions: AVX_256
FFT library: fftw-3.3.4-sse2-avx
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
Built on: Do 1. Sep 09:46:51 CEST 2016
Built by: simon at linux-286u [CMAKE]
Build OS/arch: Linux 4.1.12-1-default x86_64
Build CPU vendor: Intel
Build CPU brand: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz
Build CPU family: 6 Model: 45 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 4.8.5
C compiler flags: -mavx -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler: /usr/bin/c++ GNU 4.8.5
C++ compiler flags: -mavx -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
Running on 1 node with total 4 cores, 8 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz
Family: 6 Model: 45 Stepping: 7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256
Hardware topology: Basic
Sockets, cores, and logical processors:
Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7]
-----------------------------------------
Energies (kJ/mol)
Bond G96Angle Proper Dih. LJ (SR) Coulomb (SR)
1.36475e+04 2.16816e+04 1.59230e+03 -2.94378e+06 -2.60982e+04
Potential Pressure (bar) Constr. rmsd
-2.93295e+06 -8.86450e+01 5.54635e-06
Steepest Descents converged to Fmax < 100 in 3325 steps
Potential Energy = -2.9329548e+06
Maximum force = 9.9675224e+01 on atom 3030
Norm of force = 3.0542336e+00
M E G A - F L O P S A C C O U N T I N G
NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
W3=SPC/TIP3p W4=TIP4p (single or pairs)
V&F=Potential and force V=Potential only F=Force only
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------------
Pair Search distance check 38504.672646 346542.054 16.3
NxN RF Elec. + LJ [V&F] 5384.910400 290785.162 13.7
NxN LJ [V&F] 33611.193952 1445281.340 68.2
NxN RF Electrostatics [V&F] 11.133472 400.805 0.0
Shift-X 360.001075 2160.006 0.1
Bonds 114.715825 6768.234 0.3
Angles 98.420000 16534.560 0.8
Propers 8.309175 1902.801 0.1
Virial 360.150700 6482.713 0.3
Lincs 27.923350 1675.401 0.1
Lincs-Mat 430.840200 1723.361 0.1
Constraint-Vir 13.961675 335.080 0.0
-----------------------------------------------------------------------------
Total 2120591.516 100.0
-----------------------------------------------------------------------------
R E A L C Y C L E A N D T I M E A C C O U N T I N G
On 1 MPI rank, each using 8 OpenMP threads
Computing: Num Num Call Wall time Giga-Cycles
Ranks Threads Count (s) total sum %
-----------------------------------------------------------------------------
Neighbor search 1 8 3325 25.303 1453.945 29.1
Force 1 8 3325 14.350 824.541 16.5
NB X/F buffer ops. 1 8 3325 1.208 69.396 1.4
Constraints 1 8 6649 0.464 26.688 0.5
Rest 45.522 2615.757 52.4
-----------------------------------------------------------------------------
Total 86.847 4990.327 100.0
-----------------------------------------------------------------------------
NOTE: 29 % 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: 694.774 86.847 800.0
(steps/hour)
Performance: 137829.1
Finished mdrun on rank 0 Thu Oct 6 14:10:54 2016
________________________________________
Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> im Auftrag von Justin Lemkul <jalemkul at vt.edu>
Gesendet: Donnerstag, 6. Oktober 2016 13:55
An: gmx-users at gromacs.org
Betreff: Re: [gmx-users] mdrun don't write a checkpoint file
On 10/6/16 7:41 AM, Menig, Simon wrote:
> Hi,
>
>
> I am new to GROMACS and I wanted to run a Coars-Grain simulation but gmx mdrun doesn't write a checkpoint file and I found no solution for my Problem in the Docs or Internet. I hope someone can help me with this problem, I need this files for extending my Simulation (similar to Lysozyme tutorial) . I use GROMACS 5.1, the mdrun command I used is:
>
>
>
> gmx mdrun -s input/name.tpr -o out_trr/name.trr -c output/name.gro -e output/name.edr -g output/name.log -cpo output/name.cpt
>
>
> I also tried the -deffnm option
>
>
> Could this be a bug or is another parameter needed (tried -cpt option) ?
>
That command should produce a checkpoint file every 15 minutes, which is the
default behavior. The only reasons that it wouldn't be written are if the run
terminated abnormally or if you ran out of disk space. Either way, the .log
file or stderr/stdout should have informative information.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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