Originally posted by uncle_fungus
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New test-set (md-gromacs) & suite (molecular-dynamics)
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Michael Larabel
https://www.michaellarabel.com/
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Ok v0.3 with fixed flop counting, verbosity and result parsing.
Patch:
Code:diff --git a/pts/test-profiles/md-gromacs.xml b/pts/test-profiles/md-gromacs.xml index 548a63d..20da79f 100644 --- a/pts/test-profiles/md-gromacs.xml +++ b/pts/test-profiles/md-gromacs.xml @@ -1,6 +1,6 @@ <PhoronixTestSuite> <TestProfile> - <Version>0.2</Version> + <Version>0.3</Version> <TestType>Processor</TestType> <SoftwareType>Scientific</SoftwareType> <License>FREE</License> @@ -13,7 +13,7 @@ <Version>3.3.3</Version> <TimesToRun>3</TimesToRun> <Executable>gromacs</Executable> - <ResultScale>Gflops</ResultScale> + <ResultScale>GFLOPS</ResultScale> <Proportion>HIB</Proportion> <Description>This test runs a series of molecular dynamics simulations using the GROMACS MD package. This test is capable of running on multiple cores by using the MPICH2 library, and is similar in configuration to the SMP GROMACS cores (FahCore_a1) used by the Folding@HOME distributed computing project.</Description> <ExternalDependencies>build-utilities, fortran-compiler</ExternalDependencies> diff --git a/pts/test-resources/md-gromacs/install.sh b/pts/test-resources/md-gromacs/install.sh index 2e0e375..21ff98f 100644 --- a/pts/test-resources/md-gromacs/install.sh +++ b/pts/test-resources/md-gromacs/install.sh @@ -44,8 +44,12 @@ if [ -d $THIS_DIR/gmxbench ] then rm -rf $THIS_DIR/gmxbench/ fi +if [ -f $THIS_DIR/flopcount ] + then + rm -f $THIS_DIR/flopcount +fi mkdir $THIS_DIR/gmxbench -tar -xvf gmxbench-3.0.tar.gz -C $THIS_DIR/gmxbench/ +tar -xvf gmxbench-3.0.tar.gz -C $THIS_DIR/gmxbench/ &>/dev/null case "\$1" in \"villin\") @@ -71,18 +75,20 @@ esac case "\$2" in \"mpi\") - $THIS_DIR/gromacs333_/bin/grompp -np \$NUM_CPU_CORES - $THIS_DIR/mpich2_/bin/mpiexec -np \$NUM_CPU_CORES $THIS_DIR/gromacs333_/bin/mdrun 2>&1 + $THIS_DIR/gromacs333_/bin/grompp -np \$NUM_CPU_CORES -nov &>/dev/null + $THIS_DIR/mpich2_/bin/mpiexec -np \$NUM_CPU_CORES $THIS_DIR/gromacs333_/bin/mdrun &> $THIS_DIR/flopcount ;; \"single-node\") - $THIS_DIR/gromacs333_/bin/grompp - $THIS_DIR/gromacs333_/bin/mdrun_single 2>&1 + $THIS_DIR/gromacs333_/bin/grompp -nov &>/dev/null + $THIS_DIR/gromacs333_/bin/mdrun_single &> $THIS_DIR/flopcount ;; *) exit ;; esac +grep -C 1 'Performance:' $THIS_DIR/flopcount + cd $THIS_DIR/ sleep 3" > gromacs chmod +x gromacs diff --git a/pts/test-resources/md-gromacs/parse-results.php b/pts/test-resources/md-gromacs/parse-results.php index c9b3c9f..74f622a 100644 --- a/pts/test-resources/md-gromacs/parse-results.php +++ b/pts/test-resources/md-gromacs/parse-results.php @@ -1,5 +1,29 @@ <?php +preg_match("/\((.{0,1})Flops\)/", $argv[1], $match); + +switch($match[1]) +{ + case 'K': + $factor = 0.000001; + break; + case 'M': + $factor = 0.001; + break; + case 'G': + $factor = 1; + break; + case 'T': + $factor = 1000; + break; + case 'P': + $factor = 1000000; + break; + default: + $factor = 0.000000001; //nothing detected, therefore flops + break; +} + $BENCHMARK_RESULTS = substr($argv[1], strpos($argv[1], "Performance:")); $BENCHMARK_RESULTS = substr($BENCHMARK_RESULTS, 0, strpos($BENCHMARK_RESULTS, "\n")); $array = explode(" ", $BENCHMARK_RESULTS); @@ -10,5 +34,5 @@ foreach($array as $value) array_push($array2, $value); if(!empty($array2[2])) - echo $array2[2]; + echo $array2[2] * $factor; ?>
Comment
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Pushed it into git, but it seems broken for at least the test I tried:
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: futil.c, line: 345
File input/output error:
grompp.mdp
-------------------------------------------------------
"Got Coffee, Got Donuts, Got Wasted" (F. Black)
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 3.3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /home/michael/pts-benchmark-env/md-gromacs/gromacs333_/bin/mdrun_single (-:
Option Filename Type Description
------------------------------------------------------------
-s topol.tpr Input Generic run input: tpr tpb tpa xml
-o traj.trr Output Full precision trajectory: trr trj
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
-c confout.gro Output Generic structure: gro g96 pdb xml
-e ener.edr Output Generic energy: edr ene
-g md.log Output Log file
-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-pi pull.ppa Input, Opt. Pull parameters
-po pullout.ppa Output, Opt. Pull parameters
-pd pull.pdo Output, Opt. Pull data output
-pn pull.ndx Input, Opt. Index file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-deffnm string Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-np int 1 Number of nodes, must be the same as used for
grompp
-nt int 1 Number of threads to start on each node
-[no]v bool no Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]sepdvdl bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-[no]multi bool no Do multiple simulations in parallel (only with
-np > 1)
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Back Off! I just backed up md.log to ./#md.log.1#
-------------------------------------------------------
Program mdrun_single, VERSION 3.3.3
Source code file: gmxfio.c, line: 706
Can not open file:
topol.tpr
-------------------------------------------------------
"Got Coffee, Got Donuts, Got Wasted" (F. Black)
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 3.3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /home/michael/pts-benchmark-env/md-gromacs/gromacs333_/bin/grompp (-:
creating statusfile for 1 node...
d.dppc/
d.dppc/conf.gro
d.dppc/grompp.mdp
d.dppc/topol.top
d.lzm/
d.lzm/conf.gro
d.lzm/cutoff.mdp
d.lzm/topol.top
d.lzm/pme.mdp
d.poly-ch2/
d.poly-ch2/grompp.mdp
d.poly-ch2/conf.gro
d.poly-ch2/topol.top
d.villin/
d.villin/conf.gro
d.villin/topol.top
d.villin/grompp.mdp
====================================
GROMACS MD Benchmark (Run 3 of 3)
====================================
cd: 30: can't cd to /home/michael/pts-benchmark-env/md-gromacs/gmxbench/d.poly-ch2/
Option Filename Type Description
------------------------------------------------------------
-f grompp.mdp Input, Opt. grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c conf.gro Input Generic structure: gro g96 pdb tpr tpb tpa
xml
-r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-n index.ndx Input, Opt. Index file
-deshuf deshuf.ndx Output, Opt. Index file
-p topol.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o topol.tpr Output Generic run input: tpr tpb tpa xml
-t traj.trr Input, Opt. Full precision trajectory: trr trj
-e ener.edr Input, Opt. Generic energy: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-np int 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-load string Releative load capacity of each node on a
parallel machine. Be sure to use quotes around
the string, which should contain a number for
each node
-maxwarn int 10 Number of warnings after which input processing
stops
-[no]check14 bool no Remove 1-4 interactions without Van der Waals
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: futil.c, line: 345
File input/output error:
grompp.mdp
-------------------------------------------------------Michael Larabel
https://www.michaellarabel.com/
Comment
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Poly-CH2 single threaded
and it also occurs with the villin.Michael Larabel
https://www.michaellarabel.com/
Comment
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-------------------------------------------------------
Program mdrun_single, VERSION 3.3.3
Source code file: gmxfio.c, line: 706
Can not open file:
topol.tpr
-------------------------------------------------------
Err I've now tried it with all four and they all fail.Michael Larabel
https://www.michaellarabel.com/
Comment
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The tests all work for me.
This is the problem:
cd: 30: can't cd to /home/michael/pts-benchmark-env/md-gromacs/gmxbench/d.poly-ch2/
Edit: I've tried it on another machine which is using the latest git code and it works fine too.
Comment
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Hmmm I still can't get it working for me. I've wiped out everything and did a fresh install, etc.Michael Larabel
https://www.michaellarabel.com/
Comment
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