ARCHER » Compiling Gromacs 5.0.x on ARCHER Phase 2

Compiling Gromacs 5.0.x on ARCHER Phase 2

Gromacs compilation consists of two steps:

Compiling the serial tools (for the postprocessing nodes).
Compiling the parallel MD simulation program (for the compute nodes).

Note: Gromacs ust be built on the /work file system as it is a dynamic executable and has library files that will be required at runtime.

Build the serial tools for the PP nodes

Log into a PP node

You must build on the PP nodes to ensure the correct versions of executables are built:

ssh espp2

Set up your environment for the serial build

Switch to the GNU programming environment:

module swap PrgEnv-cray PrgEnv-gnu

and load the FFTW 3 and CMake modules:

module add fftw
module add cmake

Module list for centrally installed executables:

Currently Loaded Modulefiles:
  1) modules/3.2.10.2
  2) eswrap/1.1.0-1.010400.915.0
  3) switch/1.0-1.0501.47124.1.93.ari
  4) craype-network-aries
  5) craype/2.2.1
  6) pbs/12.2.401.141761
  7) craype-xeon
  8) cray-mpich/7.1.1
  9) packages-archer
 10) budgets/1.1
 11) checkScript/1.1
 12) checkQueue/1.0
 13) checkDisk/1.0
 14) bolt/0.6
 15) serialJobs/1.0
 16) python/2.7.6
 17) tkdiff/4.2
 18) nano/2.2.6
 19) imagemagick/6.8.8-2
 20) leave_time/1.0.0
 21) quickstart/1.0
 22) epcc-tools/1.4
 23) gcc/4.9.2
 24) cray-libsci/13.0.1
 25) udreg/2.3.2-1.0501.7914.1.13.ari
 26) ugni/5.0-1.0501.8253.10.22.ari
 27) pmi/5.0.6-1.0000.10439.140.2.ari
 28) dmapp/7.0.1-1.0501.8315.8.4.ari
 29) gni-headers/3.0-1.0501.8317.12.1.ari
 30) xpmem/0.1-2.0501.48424.3.3.ari
 31) job/1.5.5-0.1_2.0501.48066.2.43.ari
 32) csa/3.0.0-1_2.0501.47112.1.91.ari
 33) dvs/2.4_0.9.0-1.0501.1672.2.122.ari
 34) alps/5.1.1-2.0501.8507.1.1.ari
 35) rca/1.0.0-2.0501.48090.7.46.ari
 36) atp/1.7.5
 37) PrgEnv-gnu/5.1.29
 38) fftw/3.3.4.1
 39) cmake/2.8.12

Configure the single-precision build

Create a build directory in the source tree

cd gromacs-5.0.5
mkdir build
cd build

Set the environment variables for the CMake build. (Note, for at least 4.6.3 and 4.6.5, FLAGS=-ffast-math results in errors and test failures.)

export CXX=g++
export CC=gcc
export CMAKE_PREFIX_PATH=/opt/cray/fftw/3.3.4.1/x86_64/lib
export FLAGS="-dynamic -O3 -ftree-vectorize -funroll-loops"

Use CMake to configure the build:

cmake ../ -DGMX_MPI=OFF -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF -DGMX_DOUBLE=OFF \
          -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" \
          -DFFTWF_INCLUDE_DIR=/opt/cray/fftw/3.3.4.1/x86_64/include \
          -DGMX_SIMD=SSE2 \
          -DCMAKE_INSTALL_PREFIX=/work/y07/y07/gmx/5.0.5-phase2

Build the serial, single-precision code

make install

Configure and build the serial, double-precision code

Create a build directory in the source tree

cd gromacs-5.0.0
mkdir build_d
cd build_d

Set the environment variables for the CMake build. (Note, for at least 4.6.3 and 4.6.5, FLAGS=-ffast-math results in errors and test failures.)

export CXX=g++
export CC=gcc
export CMAKE_PREFIX_PATH=/opt/cray/fftw/3.3.4.1/x86_64/lib
export FLAGS="-dynamic -O3 -ftree-vectorize -funroll-loops"

Use CMake to configure the build:

cmake ../ -DGMX_MPI=OFF -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF -DGMX_DOUBLE=ON \
          -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" \
          -DFFTWF_INCLUDE_DIR=/opt/cray/fftw/3.3.4.1/x86_64/include \
          -DGMX_SIMD=SSE2 \
          -DCMAKE_INSTALL_PREFIX=/work/y07/y07/gmx/5.0.5-phase2

Build the serial, double-precision code

make install

Build the parallel simulation code for the compute nodes

Set up your environment for the parallel build

Switch to the GNU programming environment:

module swap PrgEnv-cray PrgEnv-gnu

and load the FFTW 3 and CMake modules:

module add fftw
module add cmake

Module list for centrally installed parallel executables:

Currently Loaded Modulefiles:
  1) modules/3.2.10.2
  2) eswrap/1.1.0-1.010400.915.0
  3) switch/1.0-1.0501.47124.1.93.ari
  4) craype-network-aries
  5) craype/2.2.1
  6) pbs/12.2.401.141761
  7) craype-ivybridge
  8) cray-mpich/7.1.1
  9) packages-archer
 10) budgets/1.1
 11) checkScript/1.1
 12) checkQueue/1.0
 13) checkDisk/1.0
 14) bolt/0.6
 15) serialJobs/1.0
 16) python/2.7.6
 17) tkdiff/4.2
 18) nano/2.2.6
 19) imagemagick/6.8.8-2
 20) leave_time/1.0.0
 21) quickstart/1.0
 22) epcc-tools/1.4
 23) gcc/4.9.2
 24) cray-libsci/13.0.1
 25) udreg/2.3.2-1.0501.7914.1.13.ari
 26) ugni/5.0-1.0501.8253.10.22.ari
 27) pmi/5.0.6-1.0000.10439.140.2.ari
 28) dmapp/7.0.1-1.0501.8315.8.4.ari
 29) gni-headers/3.0-1.0501.8317.12.1.ari
 30) xpmem/0.1-2.0501.48424.3.3.ari
 31) job/1.5.5-0.1_2.0501.48066.2.43.ari
 32) csa/3.0.0-1_2.0501.47112.1.91.ari
 33) dvs/2.4_0.9.0-1.0501.1672.2.122.ari
 34) alps/5.1.1-2.0501.8507.1.1.ari
 35) rca/1.0.0-2.0501.48090.7.46.ari
 36) atp/1.7.5
 37) PrgEnv-gnu/5.1.29
 38) fftw/3.3.4.1
 39) cmake/2.8.12

Configure and build the parallel, single-precision build

Create a build directory in the source tree

cd gromacs-5.0.0
mkdir build_mpi
cd build_mpi

Set the environment variables for the CMake build. (Note, for at least 4.6.3 and 4.6.5, FLAGS=-ffast-math results in errors and test failures.)

export CXX=CC
export CC=cc
export CMAKE_PREFIX_PATH=/opt/cray/fftw/3.3.4.1/sandybridge/lib
export FLAGS="-dynamic -O3 -ftree-vectorize -funroll-loops"

Use CMake to configure the build and then build and install:

cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF -DGMX_DOUBLE=OFF \
          -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" -DGMX_BUILD_MDRUN_ONLY=ON  \
          -DFFTWF_INCLUDE_DIR=/opt/cray/fftw/3.3.4.1/sandybridge/include \
          -DCMAKE_INSTALL_PREFIX=/work/y07/y07/gmx/5.0.5-phase2

make install

Configure and build the parallel, double-precision build

Create a build directory in the source tree

cd gromacs-5.0.0
mkdir build_mpi_d
cd build_mpi_d

Set the environment variables for the CMake build. (Note, for at least 4.6.3 and 4.6.5, FLAGS=-ffast-math results in errors and test failures.)

export CXX=CC
export CC=cc
export CMAKE_PREFIX_PATH=/opt/cray/fftw/3.3.4.1/sandybridge/lib
export FLAGS="-dynamic -O3 -ftree-vectorize -funroll-loops"

Use CMake to configure the build and then build and install:

cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF -DGMX_DOUBLE=ON \
          -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" -DGMX_BUILD_MDRUN_ONLY=ON  \
          -DFFTWF_INCLUDE_DIR=/opt/cray/fftw/3.3.4.1/sandybridge/include \
          -DCMAKE_INSTALL_PREFIX=/work/y07/y07/gmx/5.0.5-phase2

make install

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Compiling Gromacs 5.0.x on ARCHER Phase 2

Build the serial tools for the PP nodes

Log into a PP node

Set up your environment for the serial build

Configure the single-precision build

Build the serial, single-precision code

Configure and build the serial, double-precision code

Build the serial, double-precision code

Build the parallel simulation code for the compute nodes

Set up your environment for the parallel build

Configure and build the parallel, single-precision build

Configure and build the parallel, double-precision build