Hi, It can't be fixed, because there is no surefire way to run an arbitrary tpr on arbitrary number of ranks, regardless of how you guess -npme might succeed. We should just make the check optional, instead of being a deal breaker.
Mark On Sep 29, 2014 4:35 PM, "Carsten Kutzner" <ckut...@gwdg.de> wrote: > Hi, > > I see where the problem is. > There is an initial check in g_tune_pme to make sure that parallel > runs can be executed at all. This is being run with the automatic > number of PME-only ranks, which is 11 for your input file. > Unfortunately, this results in 37 PP ranks, for which no domain > decomposition can be found. > > At some point in the past we discussed that this could happen > and it should be fixed. Will open a bug entry. > > Thanks, > Carsten > > > On 29 Sep 2014, at 15:36, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > > > 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? 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