[gmx-users] mdrun don't write a checkpoint file

[Justin Lemkul]

On 10/6/16 8:23 AM, Menig, Simon wrote:
> 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:
>         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2015, 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:      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
>

You're doing energy minimization.  There is no checkpointing in EM.

As an aside, you also did not provide accurate information in your previous 
message.  You said you were using 5.1 but your .log indicates you are using 
2016, and your command line was different.  While it didn't matter here, please 
*always* provide accurate information to reach a resolution as quickly as 
possible.  Had there been some problem, we would have tried to reproduce it with 
5.1, which would have been entirely unproductive.

-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

==================================================