Hi Max, On 30 Sep 2014, at 09:40, Ebert Maximilian <m.eb...@umontreal.ca> wrote:
> Hi, > > This all sounds super interesting. However, is there anything I can do for > now or do I need to just find the best combination by hand? For now you can add the “-npme all -min 0.25 -max 0.33” options to g_tune_pme to make it work. Note that the values are just examples (further explanation in g_tune_pme -h). The idea here is that by choosing a -max value other than 0.5 (the default) you make the initial check work, then the rest will also run through. Maybe you have to play around a bit with the exact value (slightly) until you end up with something else than 37 PP ranks at the beginning. Carsten > > Thank you very much, > > Max > > -----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 19:23 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi > > On 29 Sep 2014, at 18:40, Mark Abraham <mark.j.abra...@gmail.com> wrote: > >> Hi, >> >> That seems suitable. >> > Oh, it just occurred to me that on systems that use the Load Leveler, we have > no means of specifying the number of MPI ranks on the command line, since > 'poe' has no switch for that. > So at least for this case I guess we also need to make the test optional. > > Carsten > >> >> Mark >> >> On Mon, Sep 29, 2014 at 6:32 PM, Carsten Kutzner <ckut...@gwdg.de> wrote: >> >>> Hi, >>> >>> On 29 Sep 2014, at 18:17, Mark Abraham <mark.j.abra...@gmail.com> wrote: >>> >>>> 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. >>> What about making this check on two ranks always, regardless of what >>> was specified on the g_tune_pme command line? On two ranks, we will >>> never have separate PME ranks, so it should always work, since we end >>> up with two ranks, doing PP and then PME. >>> If the system is so small that you can not decompose it in two DD >>> domains, there is no use to do tuning anyway. >>> >>> So even if you say >>> g_tune_pme -np 48 -s input.tpr >>> >>> we first check with >>> mpirun -np 2 mdrun -s input.tpr >>> >>> and only after that continue with -np 48. >>> >>> Carsten >>> >>>> 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_s >>> etup.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/domd >>>>>>> ec_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? 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Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-user >>>>>>> s 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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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? 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