Hi, this ist he command:
setenv MDRUN mdrun_mpi g_tune_pme_mpi -np 48 -s ../eq_nvt/1ZG4_nvt.tpr -launch Here the output of perf.out ------------------------------------------------------------ P E R F O R M A N C E R E S U L T S ------------------------------------------------------------ g_tune_pme_mpi for Gromacs VERSION 5.0.1 Number of ranks : 48 The mpirun command is : mpirun Passing # of ranks via : -np The mdrun command is : mdrun_mpi mdrun args benchmarks : -resetstep 100 -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e bench.edr -g bench.log Benchmark steps : 1000 dlb equilibration steps : 100 mdrun args at launchtime: Repeats for each test : 2 Input file : ../eq_nvt/1ZG4_nvt.tpr PME/PP load estimate : 0.151964 Number of particles : 39489 Coulomb type : PME Grid spacing x y z : 0.114561 0.114561 0.114561 Van der Waals type : Cut-off Will try these real/reciprocal workload settings: No. scaling rcoulomb nkx nky nkz spacing rvdw tpr file 0 1.000000 1.200000 72 72 72 0.120000 1.200000 ../eq_nvt/1ZG4_nvt_bench00.tpr 1 1.100000 1.320000 64 64 64 0.132000 1.320000 ../eq_nvt/1ZG4_nvt_bench01.tpr 2 1.200000 1.440000 60 60 60 0.144000 1.440000 ../eq_nvt/1ZG4_nvt_bench02.tpr Note that in addition to the Coulomb radius and the Fourier grid other input settings were also changed (see table above). Please check if the modified settings are appropriate. Individual timings for input file 0 (../eq_nvt/1ZG4_nvt_bench00.tpr): PME ranks Gcycles ns/day PME/f Remark ------------------------------------------------------------ Cannot run the benchmark simulations! Please check the error message of mdrun for the source of the problem. Did you provide a command line argument that neither g_tune_pme nor mdrun understands? Offending command: mpirun -np 48 mdrun_mpi -npme 11 -s ../eq_nvt/1ZG4_nvt_bench00.tpr -resetstep 100 -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e bench.edr -g bench.log -nsteps 1 -quiet and here are parts of the bench.log: Log file opened on Mon Sep 29 08:56:38 2014 Host: node-e1-67 pid: 24470 rank ID: 0 number of ranks: 48 GROMACS: gmx mdrun, VERSION 5.0.1 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Peter Kasson 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 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) 2001-2014, 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 5.0.1 Executable: /home/apps/Logiciels/gromacs/gromacs-5.0.1/bin/gmx_mpi Library dir: /home/apps/Logiciels/gromacs/gromacs-5.0.1/share/gromacs/top Command line: mdrun_mpi -npme 11 -s ../eq_nvt/1ZG4_nvt_bench00.tpr -resetstep 100 -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e bench.edr -g bench.log -nsteps 1 -quiet Gromacs version: VERSION 5.0.1 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled GPU support: disabled invsqrt routine: gmx_software_invsqrt(x) SIMD instructions: SSE4.1 FFT library: fftw-3.3.3-sse2 RDTSCP usage: enabled C++11 compilation: enabled TNG support: enabled Tracing support: disabled Built on: Tue Sep 23 09:58:07 EDT 2014 Built by: rqchpbib@briaree1 [CMAKE] Build OS/arch: Linux 2.6.32-71.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /RQusagers/apps/Logiciels/gcc/4.8.1/bin/gcc GNU 4.8.1 C compiler flags: -msse4.1 -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /RQusagers/apps/Logiciels/gcc/4.8.1/bin/g++ GNU 4.8.1 C++ compiler flags: -msse4.1 -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG Boost version: 1.55.0 (internal) .... n = 0 E-zt: n = 0 swapcoords = no adress = FALSE userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 10175.6 70836.4 ref-t: 304.65 304.65 tau-t: 0.5 0.5 annealing: Single Single annealing-npoints: 4 4 annealing-time [0]: 0.0 200.0 300.0 750.0 annealing-temp [0]: 10.0 100.0 100.0 304.6 annealing-time [1]: 0.0 200.0 300.0 750.0 annealing-temp [1]: 10.0 100.0 100.0 304.6 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Overriding nsteps with value passed on the command line: 1 steps, 0.002 ps Initializing Domain Decomposition on 48 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.422 nm, LJ-14, atoms 1444 1452 multi-body bonded interactions: 0.422 nm, Proper Dih., atoms 1444 1452 Minimum cell size due to bonded interactions: 0.464 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm Estimated maximum distance required for P-LINCS: 0.218 nm ------------------------------------------------------- Program mdrun_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/mdlib/domdec_setup.c, line: 728 Fatal error: The number of ranks you selected (37) contains a large prime factor 37. In most cases this will lead to bad performance. Choose a number with smaller prime factors or set the decomposition (option -dd) manually. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Carsten Kutzner Sent: Montag, 29. September 2014 15:23 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi Hi, is this the only output? Don't you get a perf.out file that lists which settings are optimal? What exactly was the command line you used? Carsten On 29 Sep 2014, at 15:01, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > Hi, > > I just tried that and I got the following error message (bench.log). Any idea > what could be wrong? > > Thank you very much, > > Max > > Initializing Domain Decomposition on 48 ranks Dynamic load balancing: > auto Will sort the charge groups at every domain (re)decomposition > Initial maximum inter charge-group distances: > two-body bonded interactions: 0.422 nm, LJ-14, atoms 1444 1452 > multi-body bonded interactions: 0.422 nm, Proper Dih., atoms 1444 1452 > Minimum cell size due to bonded interactions: 0.464 nm Maximum > distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm > Estimated maximum distance required for P-LINCS: 0.218 nm > > ------------------------------------------------------- > Program mdrun_mpi, VERSION 5.0.1 > Source code file: > /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/mdlib/domdec_se > tup.c, line: 728 > > Fatal error: > The number of ranks you selected (37) contains a large prime factor 37. In > most cases this will lead to bad performance. Choose a number with smaller > prime factors or set the decomposition (option -dd) manually. > For more information and tips for troubleshooting, please check the > GROMACS website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf > Of Carsten Kutzner > Sent: Donnerstag, 25. September 2014 19:29 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi > > Hi, > > don't invoke g_tune_pme with 'mpirun', because it is a serial executable that > itself invokes parallel MD runs for testing. > > use > export MDRUN=mdrun_mpi > > g_tune_pme -np 24 -s 1ZG4_nvt.tpr -launch > > see also > > g_tune_pme -h > > You may need to recompile g_tune_pme without MPI enabled (depends on > your queueing system) > > Best, > Carsten > > > On 25 Sep 2014, at 15:10, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > >> Dear list, >> >> I tried using g_tune_pme_mpi with the command: >> >> mpirun -np 24 g_tune_pme_mpi -np 24 -s 1ZG4_nvt.tpr -launch >> >> on GROMACS 5.0.1 but I get the following error message: >> --------------------------------------------------------------------- >> - >> ---- mpirun was unable to launch the specified application as it >> could not find an executable: >> >> Executable: mdrun >> Node: xxxx >> >> while attempting to start process rank 0. >> --------------------------------------------------------------------- >> - >> ---- >> 24 total processes failed to start >> >> >> Any idea why this is? Shouldn't g_tune_pme_mpi call mdrun_mpi instead? >> >> Thank you very much, >> >> Max >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > > > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry Theoretical and > Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www.mpibpc.mpg.de/grubmueller/kutzner > http://www.mpibpc.mpg.de/grubmueller/sppexa > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.