[gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi
Ebert Maximilian
m.ebert at umontreal.ca
Mon Sep 29 15:37:06 CEST 2014
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 at 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-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Carsten Kutzner
Sent: Montag, 29. September 2014 15:23
To: gmx-users at 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.ebert at 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-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf
> Of Carsten Kutzner
> Sent: Donnerstag, 25. September 2014 19:29
> To: gmx-users at 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.ebert at 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
>> --
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>
>
> --
> 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
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>
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--
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
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