ranger.tacc.utexas.edu

Here you find information about the system http://services.tacc.utexas.edu/index.php/ranger-user-guide.

The installation of user’s packages on ranger EL4, 64-bit described below uses modules, and assumes csh shell:

  • packages are installed under ~/CAMd:

    mkdir ~/CAMd
cd ~/CAMd

  • module files are located under ~/CAMd/modulefiles

  • download the customize_ranger_EL4.py file:

    wget https://svn.fysik.dtu.dk/projects/gpaw/trunk/doc/platforms/Linux/customize_ranger_EL4.py

    scalapack = True

extra_compile_args = ['-O3', '-std=c99', '-fpic']

compiler = 'gcc'
mpicompiler = '/opt/apps/gcc4_4/openmpi/1.3b/bin/mpicc'
mpilinker = mpicompiler

mkl_lib_path = '/opt/apps/intel/mkl/10.0.1.014/lib/em64t/'
ompi_lib_path = '/opt/apps/gcc4_4/openmpi/1.3b/lib'

libraries = []

# use static linking to avoid
# "cannot allocate memory for thread-local data: ABORT"
extra_link_args = [
mkl_lib_path+'libmkl_intel_lp64.a',
mkl_lib_path+'libmkl_sequential.a',
mkl_lib_path+'libmkl_core.a',
mkl_lib_path+'libmkl_blacs_openmpi_lp64.a',
mkl_lib_path+'libmkl_scalapack_lp64.a',
mkl_lib_path+'libmkl_blacs_openmpi_lp64.a',
mkl_lib_path+'libmkl_intel_lp64.a',
mkl_lib_path+'libmkl_sequential.a',
mkl_lib_path+'libmkl_core.a',
mkl_lib_path+'libmkl_intel_lp64.a',
mkl_lib_path+'libmkl_sequential.a',
mkl_lib_path+'libmkl_core.a',
]

extra_link_args += ['-Wl,-rpath='+ompi_lib_path]

define_macros += [('GPAW_NO_UNDERSCORE_CBLACS', '1')]
define_macros += [('GPAW_NO_UNDERSCORE_CSCALAPACK', '1')]

  • download packages with download_ranger.sh, buy running sh download_ranger.sh:

    setenv APPS "/share/home/01067/tg803307/CAMd"
setenv MODULEFILES "${APPS}/modulefiles"

# download packages
set nose_version=0.11.3
wget http://python-nose.googlecode.com/files/nose-${nose_version}.tar.gz
set numpy_version=1.5.0
wget http://downloads.sourceforge.net/numpy/numpy-${numpy_version}.tar.gz
set ase_version=3.4.1.1765
wget https://wiki.fysik.dtu.dk/ase-files/python-ase-${ase_version}.tar.gz
set gpaw_version=0.7.2.6974
wget https://wiki.fysik.dtu.dk/gpaw-files/gpaw-${gpaw_version}.tar.gz
set gpaw_setups_version=0.6.6300
wget http://wiki.fysik.dtu.dk/gpaw-files/gpaw-setups-${gpaw_setups_version}.tar.gz

  • start with the following modules loaded:

    login3% module list
Currently Loaded Modules:
  1) TACC-paths           9) srb-client/3.4.1  17) globus/4.0.8
  2) Linux                10) tg-policy/0.2    18) GLOBUS-4.0
  3) cluster-paths        11) tgproxy/0.9.1    19) TERAGRID-DEV
  4) pgi/7.2-5            12) tgresid/2.3.4    20) CTSSV4
  5) mvapich/1.0.1        13) tgusage/3.0      21) gzip/1.3.12
  6) binutils-amd/070220  14) uberftp/2.4      22) tar/1.22
  7) TERAGRID-paths       15) tginfo/1.0.1     23) cluster
  8) gx-map/0.5.3.3       16) TERAGRID-BASIC   24) TACC

  • unload/load the modules:

    module switch pgi/7.2-5 gcc/4.4.5
module swap mvapich openmpi/1.3b
module load python/2.5.2
module load mkl/10.0

  • install packages, deploy modules and test with install_ranger_EL4.sh, buy running sh install_ranger_EL4.sh:

    setenv APPS "/share/home/01067/tg803307/CAMd"
setenv MODULEFILES "${APPS}/modulefiles"

# build packages

set nose_version=0.11.3
tar zxf nose-${nose_version}.tar.gz
cd nose-${nose_version}
python setup.py install --root=${APPS}/nose-${nose_version}-1
cd ..

set numpy_version=1.5.0
tar zxf numpy-${numpy_version}.tar.gz
cd numpy-${numpy_version}
python setup.py install --root=${APPS}/numpy-${numpy_version}-1
cd ..

set ase_version=3.4.1.1765
tar zxf python-ase-${ase_version}.tar.gz

set gpaw_version=0.7.2.6974
tar zxf gpaw-${gpaw_version}.tar.gz

set gpaw_setups_version=0.6.6300
tar zxf gpaw-setups-${gpaw_setups_version}.tar.gz

mkdir -p ${MODULEFILES}/nose
cat <<EOF > ${MODULEFILES}/nose/${nose_version}-1
#%Module1.0
set apps_path ${APPS}
prereq python/2.5.2
prepend-path    PATH                \$apps_path/nose-${nose_version}-1/opt/apps/python/python-2.5.2/bin/
prepend-path    PYTHONPATH          \$apps_path/nose-${nose_version}-1/opt/apps/python/python-2.5.2/lib/python2.5/site-packages/
unset apps_path
EOF

mkdir -p ${MODULEFILES}/numpy
cat <<EOF > ${MODULEFILES}/numpy/${numpy_version}-1
#%Module1.0
set apps_path ${APPS}
prereq python/2.5.2
prereq nose/0.11.3-1
prepend-path    PATH                \$apps_path/numpy-${numpy_version}-1/opt/apps/python/python-2.5.2/bin
prepend-path    PYTHONPATH          \$apps_path/numpy-${numpy_version}-1/opt/apps/python/python-2.5.2/lib/python2.5/site-packages/
unset apps_path
EOF

mkdir -p ${MODULEFILES}/campos-ase3
cat <<EOF > ${MODULEFILES}/campos-ase3/${ase_version}-1
#%Module1.0
set apps_path ${APPS}
prereq python/2.5.2
prereq nose/0.11.3-1
prereq numpy/1.5.0-1
prepend-path    PATH                \$apps_path/python-ase-${ase_version}/tools
prepend-path    PYTHONPATH          \$apps_path/python-ase-${ase_version}/
unset apps_path
EOF

mkdir -p ${MODULEFILES}/campos-gpaw-setups
cat <<EOF > ${MODULEFILES}/campos-gpaw-setups/${gpaw_setups_version}-1
#%Module1.0
set apps_path ${APPS}
prepend-path    GPAW_SETUP_PATH     \$apps_path/gpaw-setups-${gpaw_setups_version}
unset apps_path
EOF

mkdir -p ${MODULEFILES}/campos-gpaw
cat <<EOF > ${MODULEFILES}/campos-gpaw/${gpaw_version}-1
#%Module1.0
set apps_path ${APPS}
prereq python/2.5.2
prereq nose/0.11.3-1
prereq numpy/1.5.0-1
prereq campos-ase3
prereq campos-gpaw-setups
prereq gcc/4.4.5
prereq openmpi/1.3b
prereq mkl/10.0
prepend-path    PATH                \$apps_path/gpaw-${gpaw_version}/tools
prepend-path    PATH                \$apps_path/gpaw-${gpaw_version}/build/bin.linux-x86_64-2.5/
prepend-path    PYTHONPATH          \$apps_path/gpaw-${gpaw_version}/
prepend-path    PYTHONPATH          \$apps_path/gpaw-${gpaw_version}/build/lib.linux-x86_64-2.5/
setenv OMP_NUM_THREADS 1
unset apps_path
EOF

module avail

module use --append ${MODULEFILES}
module load python/2.5.2
module load nose/0.11.3-1
module load numpy/1.5.0-1
module load campos-ase3
# test numpy
python -c "import numpy; numpy.test()"
# test ase
mkdir -p testase
cd testase
testase.py --no-display >& testase.log
cd ..
# build gpaw
cd gpaw-${gpaw_version}
python setup.py build_ext --customize=../customize_ranger_EL4.py --remove-default-flags >& build_ext.log
cd ..
module load campos-gpaw-setups
module load gcc/4.4.5
module load openmpi/1.3b
module load mkl/10.0
module load campos-gpaw
mkdir -p testgpaw
cd testgpaw
mpiexec -np 4 gpaw-python `which gpaw-test` >& tee testgpaw.log

    Note that every time you wish to install a new version of a package, and deploy new module file, better keep the old module file.

  • submit the test job:

    qsub submit.sh

    using the following submit.sh:

    #!/bin/bash

#$ -V   # Inherit the submission environment
#$ -cwd         # Start job in submission directory
##$ -N myMPI    # Job Name
##$ -j y        # Combine stderr and stdout
##$ -o $JOB_NAME.o$JOB_ID       # Name of the output file (eg. myMPI.oJobID)
#$ -pe 16way 32         # Requests 16 tasks/node, 32 cores total
#$ -q development       # OR Queue name "normal"
#$ -l h_rt=00:40:00     # Run time (hh:mm:ss) - 40 mins
##$ -M  # Use email notification address
##$ -m be       # Email at Begin and End of job
#set -x         # Echo commands, use "set echo" with csh

module use --append /share/home/01067/tg803307/CAMd/modulefiles
module load python/2.5.2
module load nose/0.11.3-1
module load numpy/1.5.0-1
module load campos-ase3
module load campos-gpaw-setups
module unload pgi
module load gcc/4.4.5
module unload mvapich
module load openmpi/1.3b
module load mkl/10.0
module load campos-gpaw

# wget http://svn.fysik.dtu.dk/projects/gpaw/trunk/doc/devel/256H2O/b256H2O.py

ibrun `which gpaw-python` b256H2O.py

  • to enable the installation permanently add the following to ~/.bashrc:

    module use --append /share/home/01067/tg803307/CAMd/modulefiles
module load python/2.5.2
module load nose/0.11.3-1
module load numpy/1.5.0-1
module load campos-ase3
module load campos-gpaw-setups
module unload pgi
module load gcc/4.4.5
module unload mvapich
module load openmpi/1.3b
module load mkl/10.0
module load campos-gpaw