Compiling Gromacs

Available Compilations

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

Compiling your own GROMACS executables

Below you will find 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

-- 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. 1. 1. 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

TODO list

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.