Gromacs

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Download and general information: http://www.gromacs.org

Search the mailing list archives: http://oldwww.gromacs.org/swish-e/search/search2.php

Peculiarities of running single node GROMACS jobs on SCINET

This is VERY IMPORTANT !!! Please read the [relevant user tips section] for information that is essential for your single node (up to 8 core) MPI GROMACS jobs.

-- cneale 14 September 2009

Compiling and Running GROMACS on Scinet (general information)

Chris Neale has compiled gromacs on GPC, with assistance from Scott Northrup, and on the power6 cluster with assistance from Ching-Hsing Yu. Users are welcome to utilize these binary executables, but only at their own peril since compiling and testing your own executable is safer and more stable.

Gromacs executables:

GPC: /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin

TCS: /scratch/cneale/exe/gromacs-4.0.4_aix/exec/bin

Below you will find, in order, scripts for the different compilations that you can follow to make your own binaries.

NOTE: the steps are not listed in order! You must compile fftw before compiling gromacs, and if you are going to use mvapich2-1.4rc1 then you must compile it also before compiling parallel gromacs.

  1. Compiling serial single precision gromacs on GPC
  2. Compiling openmpi parallel gromacs on GPC
  3. Compiling serial gromacs on the power6 (submitted to the queue):
  4. Compiling parallel gromacs on the power6 (submitted to the queue):
  5. fftw single precision compilation
  6. Change to get mvapich2-1.4rc1 to compile gromacs
  7. Compiling mvapich2-1.4rc1
  8. Compiling gromacs on GPC using mvapich2-1.4rc1
  9. Submitting an IB GPC job using openmpi
  10. Submitting an IB GPC job using mvapich2-1.4rc1
  11. Submitting a non-IB GPC job using openmpi

-- cneale 18 August 2009

Compiling serial single precision gromacs on GPC

<source lang="sh"> cd /scratch/cneale/exe/intel/gromacs-4.0.5 mkdir exec module purge module load intel export FFTW_LOCATION=/scratch/cneale/exe/intel/fftw-3.1.2/exec export GROMACS_LOCATION=/scratch/cneale/exe/intel/gromacs-4.0.5/exec export CPPFLAGS=-I$FFTW_LOCATION/include export LDFLAGS=-L$FFTW_LOCATION/lib ./configure --prefix=$GROMACS_LOCATION --without-motif-includes --without-motif-libraries --without-x --without-xml >output.configure 2>&1 make >output.make 2>&1 make install >output.make_install 2>&1 make distclean </source>

-- cneale 18 August 2009

Compiling openmpi parallel gromacs on GPC:

<source lang="sh"> cd /scratch/cneale/exe/intel/gromacs-4.0.5 mkdir exec module purge module load openmpi intel export FFTW_LOCATION=/scratch/cneale/exe/intel/fftw-3.1.2/exec export GROMACS_LOCATION=/scratch/cneale/exe/intel/gromacs-4.0.5/exec export CPPFLAGS="-I$FFTW_LOCATION/include -I/scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/include -I/scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/lib" export LDFLAGS=-L$FFTW_LOCATION/lib /gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/lib/openmpi -I/scinet/gpc/x1/intel/Compiler/11.0/081/lib/intel64 -I/scinet/gpc/x1/intel/Compiler/11.0/081/mkl/lib/em64t/" ./configure --prefix=$GROMACS_LOCATION --without-motif-includes --without-motif-libraries --without-x --without-xml --enable-mpi --program-suffix="_openmpi" >output.configure.mpi 2>&1 make >output.make.mpi 2>&1 make install-mdrun >output.make_install.mpi 2>&1 make distclean </source>

-- cneale 18 August 2009

Compiling serial gromacs on the power6 (submitted to the queue)

Note that the -O5 flag for the power6 compilation makes it take about 20 hours to compile. You can drop that if you want, but it does give you a few more percent performance.

<source lang="sh">

  1. ======================================================================
  2. Specifies the name of the shell to use for the job
  3. @ shell = /usr/bin/ksh
  4. @ job_type = serial
  5. @ class = verylong
    1. # @ node = 1
    2. # @ tasks_per_node = 1
  6. @ output = $(jobid).out
  7. @ error = $(jobid).err
  8. @ wall_clock_limit = 40:00:00
  9. =====================================
    1. this is necessary in order to avoid core dumps for batch files
    2. which can cause the system to be overloaded
  10. ulimits
  11. @ core_limit = 0
  12. =====================================
    1. necessary to force use of infiniband network for MPI traffic
      1. TURN IT OFF # @ network.MPI = csss,not_shared,US,HIGH
  13. =====================================
  14. @ environment=COPY_ALL
  15. @ queue

export PATH=/usr/lpp/ppe.hpct/bin:/usr/vacpp/bin:.:/usr/bin:/etc:/usr/sbin:/usr/ucb:/usr/bin/X11:/sbin:/usr/java14/jre/bin:/usr/java14/bin:/usr/lpp/LoadL/full/bin:/usr/local/bin export F77=xlf_r export CC=xlc_r export CXX=xlc++_r export FFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export CFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export CXXFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export FFTW_LOCATION=/scratch/cneale/exe/fftw-3.1.2_aix/exec export GROMACS_LOCATION=/scratch/cneale/exe/gromacs-4.0.4_aix/exec export CPPFLAGS=-I$FFTW_LOCATION/include export LDFLAGS=-L$FFTW_LOCATION/lib cd /scratch/cneale/exe/gromacs-4.0.4_aix mkdir exec ./configure --prefix=$GROMACS_LOCATION --without-motif-includes --without-motif-libraries --without-x --without-xml >output.configure 2>&1 make >output.make 2>&1 make install >output.make_install 2>&1 make distclean </source>

-- cneale 18 August 2009

Compiling parallel gromacs on the power6 (submitted to the queue)

<source lang="sh">

  1. ===============================================================================
  2. Specifies the name of the shell to use for the job
  3. @ shell = /usr/bin/ksh
          1. @ job_type = serial
  4. @ job_type = parallel
  5. @ class = verylong
  6. @ node = 1
  7. @ tasks_per_node = 1
  8. @ output = $(jobid).out
  9. @ error = $(jobid).err
  10. @ wall_clock_limit = 40:00:00
  11. =====================================
    1. this is necessary in order to avoid core dumps for batch files
    2. which can cause the system to be overloaded
  12. ulimits
  13. @ core_limit = 0
  14. =====================================
    1. necessary to force use of infiniband network for MPI traffic
      1. TURN IT OFF # @ network.MPI = csss,not_shared,US,HIGH
  15. =====================================
  16. @ environment=COPY_ALL
  17. @ queue

export F77=xlf_r export CC=xlc_r export CXX=xlc++_r export FFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export CFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export CXXFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export FFTW_LOCATION=/scratch/cneale/exe/fftw-3.1.2_aix/exec export GROMACS_LOCATION=/scratch/cneale/exe/gromacs-4.0.4_aix/exec export CPPFLAGS=-I$FFTW_LOCATION/include export LDFLAGS=-L$FFTW_LOCATION/lib cd /scratch/cneale/exe/gromacs-4.0.4_aix echo "cn-r0-10" > ~/.rhosts echo localhost > ~/host.list for((i=2;i<=16;i++)); do 

 echo localhost >> ~/host.list

done export MP_HOSTFILE=~/host.list ./configure --prefix=$GROMACS_LOCATION --without-motif-includes --without-motif-libraries --without-x --without-xml --enable-mpi --disable-nice --program-suffix="_mpi" CC=mpcc_r F77=mpxlf_r > output.configure_mpi 2>&1 make mdrun > output.make_mpi 2>&1 make install-mdrun > output.make_install_mpi 2>&1 make distclean </source>

-- cneale 18 August 2009

fftw single precision compilation

FFTW is required by GROMACS. This compilation must be completed before compiling GROMACS.

<source lang="sh"> mkdir exec export FFTW_LOCATION=/scratch/cneale/exe/intel/fftw-3.1.2/exec module purge module load openmpi intel ./configure --enable-float --enable-threads --prefix=${FFTW_LOCATION} make make install make distclean </source>

-- cneale 18 August 2009

Change to get mvapich2-1.4rc1 to compile gromacs

This change is required to the mvapich2-1.4rc1 source code in order to compile GROMACS with it.

<source lang="sh"> src/mpid/ch3/channels/mrail/src/gen2/ibv_channel_manager.c line 503 unsigned long debug = 0; to static unsigned long debug = 0; </source>

-- cneale 18 August 2009

Compiling mvapich2-1.4rc1

<source lang="sh"> cd /scratch/cneale/exe/mvapich2-1.4rc1 mkdir exec module purge module load intel ./configure --prefix=/scratch/cneale/exe/mvapich2-1.4rc1/exec CC=icc CXX=icpc F90=ifort F77=ifort >output.configure 2>&1 make >output.make 2>&1 make install >output.make_install 2>&1 make distclean </source>

-- cneale 18 August 2009

Compiling gromacs on GPC using mvapich2-1.4rc1

<source lang="sh">

  1. !/bin/bash

cd /scratch/cneale/exe/intel/gromacs-4.0.5 mkdir exec PATH=/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/xcat/bin:/opt/xcat/sbin:/root/bin:/opt/torque/bin:/opt/xcat/bin:/opt/xcat/sbin:/usr/lpp/mmfs/bin:/scratch/cneale/exe/mvapich2-1.4rc1/exec/bin/:/scinet/gpc/x1/intel/Compiler/11.0/081/bin/intel64 LD_LIBRARY_PATH=/scratch/cneale/exe/mvapich2-1.4rc1/exec/lib/:/scinet/gpc/x1/intel/Compiler/11.0/081/lib/intel64:/scinet/gpc/x1/intel/Compiler/11.0/081/mkl/lib/em64t/ export FFTW_LOCATION=/scratch/cneale/exe/intel/fftw-3.1.2/exec export GROMACS_LOCATION=/scratch/cneale/exe/intel/gromacs-4.0.5/exec export CPPFLAGS="-I$FFTW_LOCATION/include -I/scratch/cneale/exe/mvapich2-1.4rc1/exec/include -I/scratch/cneale/exe/mvapich2-1.4rc1/exec/lib" export LDFLAGS=-L$FFTW_LOCATION/lib ./configure --prefix=$GROMACS_LOCATION --without-motif-includes --without-motif-libraries --without-x --without-xml --enable-mpi --program-suffix="_mvapich2" >output.configure.mpi.mvapich2 2>&1 make >output.make.mpi.mvapich2 2>&1 make install-mdrun >output.make_install.mpi.mvapich2 2>&1 make distclean </source>

-- cneale 18 August 2009

Submitting an IB GPC job using openmpi

<source lang="sh">

  1. !/bin/bash
  2. PBS -l nodes=10:ib:ppn=8,walltime=40:00:00,os=centos53computeA
  3. PBS -N 1

if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then 

 if [ -n "$PBS_O_WORKDIR" ]; then
   cd $PBS_O_WORKDIR
 fi

fi /scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/bin/mpirun -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -machinefile $PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_openmpi -deffnm pagp -nosum -dlb yes -npme 24 -cpt 120

    1. To submit type: qsub this.sh

</source>

-- cneale 18 August 2009

Submitting an IB GPC job using mvapich2-1.4rc1

Note that mvapich2-1.4rc1 is not configured to fall back to ethernet so this will not work on the non-IB nodes, even for 8 cores.

<source lang="sh">

  1. !/bin/bash
  2. PBS -l nodes=4:ib:ppn=8,walltime=30:00:00,os=centos53computeA
  3. PBS -N 1

if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then 

 if [ -n "$PBS_O_WORKDIR" ]; then
   cd $PBS_O_WORKDIR
 fi

fi module purge module load mvapich2 intel /scratch/cneale/exe/mvapich2-1.4rc1/bin/mpirun_rsh -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -hostfile $PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_mvapich2 -deffnm pagp -nosum -dlb yes -npme 12 -cpt 120

    1. To submit type: qsub this.sh

</source>

-- cneale 18 August 2009

Submitting a non-IB GPC job using openmpi

<source lang="sh">

  1. !/bin/bash
  2. PBS -l nodes=1:compute-eth:ppn=8,walltime=40:00:00,os=centos53computeA
  3. PBS -N 1

if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then 

 if [ -n "$PBS_O_WORKDIR" ]; then
   cd $PBS_O_WORKDIR
 fi

fi /scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/bin/mpirun -mca btl_sm_num_fifos 7 -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -mca btl self,sm -machinefile $PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_openmpi -deffnm pagp -nosum -dlb yes -npme 24 -cpt 120

    1. To submit type: qsub this.sh

</source>

This is VERY IMPORTANT !!! Please read the [relevant user tips section] for information that is essential for your single node (up to 8 core) MPI GROMACS jobs.

-- cneale 14 September 2009

Things still left to do for GROMACS

Intel has it's own fast fourier transform library, which we expect to yield improved performance over fftw. We have not yet attempted such a compilation.

-- cneale 18 August 2009

GROMACS benchmarks on Scinet

This is a rudimentary list of scaling information.

I have a 50K atom system running performance on GPC right now. On 56 cores connected with IB I am getting 55 ns/day. I set up 50 such simulations, each with 2 proteins in a bilayer and I'm getting a total of 5.5 us per day. I am using gromacs 4.0.5 and a 5 fs timestep by fixing the bond lengths and all angles involving hydrogen.

I can get about 12 ns/day on 8 cores of the non-IB part of GPC -- also excellent.

As for larger systems, My speedup over saw.sharcnet.ca for a 1e6 atom system is only 1.2x running on 128 cores in single precision. Although saw.sharcnet.ca is composed of xeons, they are running at 2.83 GHz (https://www.sharcnet.ca/my/systems/show/41), which is a faster clock speed than the Scinet 2.5 GHz for Intel's next-generation X86-CPU architecture. While GROMACS is generally not excellent for scaling up to or beyond 128 cores (even for large systems), our benchmarking of this system on saw.sharcnet.ca indicated that it was running at about 65% efficiency. Benchmarking was also done on Scinet for this system, but was not recorded as we were mostly tinkering with the -npme option to mdrun in an attempt to optimize it. My recollection, though, is that the scaling was similar on scinet.

-- cneale 19 August 2009

Strong scaling for GROMACS on GPC

Requested, and on our list to complete, but not yet available in a complete chart form.

-- cneale 19 August 2009

Scientific studies being carried out using GROMACS on GPC

Requested, but not yet available

-- cneale 19 August 2009

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