GROMACS

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BGQ Install

An install is available through a module:

ssh q # or q2
module load gromacs
which mdrun_md_d
which gmx_d

Building mdrun_mpi_d on the BGQ

The following instructions were tested with version 5.1.2 and assume that the working directory is the gromacs top level dir; e.g. gromacs-5.1.2 .

Setup the environment

 module load cmake xl fftw/xl

Create configure script

Create a 'doConfigureXl' script with the following contents:

 
#!/bin/bash -ex 
cmake .. -DCMAKE_C_COMPILER=`which mpicc` \
         -DCMAKE_CXX_COMPILER=`which mpicxx` \
         -DCMAKE_TOOLCHAIN_FILE=$CMAKE_XL_TOOLCHAIN \
         -DCMAKE_PREFIX_PATH=$FFTW_INSTALL_DIR \
         -DGMX_LAPACK_USER=/bgsys/ibm_essl/prod/opt/ibmmath/lib64/libesslbg.a \
         -DGMX_BLAS_USER=/bgsys/ibm_essl/prod/opt/ibmmath/lib64/libesslbg.a \
         -DGMX_MPI=ON \
         -DGMX_GPU=OFF \
         -DGMX_BUILD_MDRUN_ONLY=ON \
         -DGMX_DOUBLE=ON 

Configure

 mkdir build
 cd build
 ../doConfigureXl

Build

 make -j16

Building gmx on the BGQ for execution on the front ends (q and q2)

The following instructions were tested with version 5.1.2 and assume that the working directory is the gromacs top level dir; e.g. gromacs-5.1.2 .

Setup the environment

 module load cmake

Create configure script

Create a 'doConfigureXlFen' script with the following contents:

 
#!/bin/bash -ex 
cmake .. -DCMAKE_C_COMPILER=/usr/bin/bgxlc \
         -DCMAKE_CXX_COMPILER=/usr/bin/bgxlc++ \
         -DGMX_FFT_LIBRARY=fftpack \
         -DBUILD_SHARED_LIBS=OFF \
         -DCMAKE_SKIP_RPATH=TRUE \
         -DGMX_DOUBLE=ON \
         -DGMX_MPI=OFF \
         -DGMX_GPU=OFF 

Configure

 mkdir build
 cd build
 ../doConfigureXlFen

Build

 make -j16