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Code Issues Releases Wiki Activity

Cleaning scripts

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This commit is contained in:
Anthony Scemama 2018-12-21 17:50:24 +01:00
parent 7409eefcc6
commit e9e768877d
4 changed files with 89 additions and 76 deletions
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130
configure vendored
View File

@ -53,7 +53,8 @@ PACKAGES=$(echo $PACKAGES | xargs)
sed "s!^export QP_ROOT=.*\$!export QP_ROOT=\"$PWD\"!" quantum_package.rc.default > quantum_package.rc sed "s!^export QP_ROOT=.*\$!export QP_ROOT=\"$PWD\"!" \
quantum_package.rc.default > quantum_package.rc
echo "quantum_package.rc created." echo "quantum_package.rc created."
@ -81,7 +82,7 @@ function error() {
} }
function download() { function download() {
wget --no-check-certificate $1 -O $2 || error "Unable to download $1" wget --no-check-certificate $1 --output-document=$2 || error "Unable to download $1"
} }
function find_exe() { function find_exe() {
@ -149,21 +150,22 @@ for PACKAGE in ${PACKAGES} ; do
download \ download \
"https://github.com/scemama/irpf90/archive/v1.7.2.tar.gz" \ "https://github.com/scemama/irpf90/archive/v1.7.2.tar.gz" \
"${QP_ROOT}"/external/irpf90.tar.gz "${QP_ROOT}"/external/irpf90.tar.gz
cd "${QP_ROOT}"/external (
tar -zxf irpf90.tar.gz cd "${QP_ROOT}"/external
rm irpf90.tar.gz tar --gunzip --extract --file irpf90.tar.gz
cd irpf90-* rm irpf90.tar.gz
make cd irpf90-*
for i in irpf90 irpman irpf90_indent make
do for i in irpf90 irpman irpf90_indent
cat << EOF > "${QP_ROOT}"/bin/$i do
cat << EOF > "${QP_ROOT}"/bin/$i
#!/bin/sh #!/bin/sh
exec $PWD/bin/$i \$@ exec $PWD/bin/$i \$@
EOF EOF
chmod +x "${QP_ROOT}"/bin/$i chmod +x "${QP_ROOT}"/bin/$i
done done
cd "${QP_ROOT}" )
elif [[ ${PACKAGE} = zeromq ]] ; then elif [[ ${PACKAGE} = zeromq ]] ; then
@ -171,14 +173,15 @@ EOF
download \ download \
"https://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz" \ "https://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz" \
"${QP_ROOT}"/external/zeromq.tar.gz "${QP_ROOT}"/external/zeromq.tar.gz
cd "${QP_ROOT}"/external (
tar -zxf zeromq.tar.gz cd "${QP_ROOT}"/external
rm zeromq.tar.gz tar --gunzip --extract --file zeromq.tar.gz
cd zeromq-* rm zeromq.tar.gz
./configure --prefix="$QP_ROOT" --without-libsodium --enable-libunwind=no cd zeromq-*
make ./configure --prefix="$QP_ROOT" --without-libsodium --enable-libunwind=no
make install make
cd "${QP_ROOT}" make install
)
elif [[ ${PACKAGE} = f77zmq ]] ; then elif [[ ${PACKAGE} = f77zmq ]] ; then
@ -186,16 +189,17 @@ EOF
download \ download \
"https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz" \ "https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz" \
"${QP_ROOT}"/external/f77_zmq.tar.gz "${QP_ROOT}"/external/f77_zmq.tar.gz
cd "${QP_ROOT}"/external (
tar -zxf f77_zmq.tar.gz cd "${QP_ROOT}"/external
rm f77_zmq.tar.gz tar --gunzip --extract --file f77_zmq.tar.gz
cd f77_zmq-* rm f77_zmq.tar.gz
export ZMQ_H="$QP_ROOT"/include/zmq.h cd f77_zmq-*
make export ZMQ_H="$QP_ROOT"/include/zmq.h
cp libf77zmq.a "${QP_ROOT}"/lib make
cp libf77zmq.so "${QP_ROOT}"/lib cp libf77zmq.a "${QP_ROOT}"/lib
cp f77_zmq_free.h "${QP_ROOT}"/include cp libf77zmq.so "${QP_ROOT}"/lib
cd "${QP_ROOT}" cp f77_zmq_free.h "${QP_ROOT}"/include
)
elif [[ ${PACKAGE} = ocaml ]] ; then elif [[ ${PACKAGE} = ocaml ]] ; then
@ -204,7 +208,7 @@ EOF
"https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh" \ "https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh" \
"${QP_ROOT}"/external/opam_installer.sh "${QP_ROOT}"/external/opam_installer.sh
chmod +x "${QP_ROOT}"/external/opam_installer.sh chmod +x "${QP_ROOT}"/external/opam_installer.sh
rm -f ${QP_ROOT}/bin/opam rm --force ${QP_ROOT}/bin/opam
if [[ -n ${TRAVIS} ]] ; then if [[ -n ${TRAVIS} ]] ; then
# Special commands for Travis CI # Special commands for Travis CI
@ -224,10 +228,12 @@ EOF
source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
rm ${QP_ROOT}/external/opam_installer.sh rm ${QP_ROOT}/external/opam_installer.sh
${QP_ROOT}/bin/opam init --disable-sandboxing --verbose --yes --comp=4.07.0 ${QP_ROOT}/bin/opam init --disable-sandboxing --verbose \
--yes --comp=4.07.0
eval $(${QP_ROOT}/bin/opam env) eval $(${QP_ROOT}/bin/opam env)
opam install -y ocamlbuild cryptokit zmq core sexplib ppx_sexp_conv ppx_deriving opam install -y ocamlbuild cryptokit zmq core sexplib \
ppx_sexp_conv ppx_deriving
elif [[ ${PACKAGE} = ezfio ]] ; then elif [[ ${PACKAGE} = ezfio ]] ; then
@ -235,10 +241,11 @@ EOF
download \ download \
"https://gitlab.com/scemama/EZFIO/-/archive/master/EZFIO-master.tar.gz" \ "https://gitlab.com/scemama/EZFIO/-/archive/master/EZFIO-master.tar.gz" \
"${QP_ROOT}"/external/ezfio.tar.gz "${QP_ROOT}"/external/ezfio.tar.gz
cd "${QP_ROOT}"/external (
tar -zxf ezfio.tar.gz cd "${QP_ROOT}"/external
mv EZFIO-* ezfio tar --gunzip --extract --file ezfio.tar.gz
cd "${QP_ROOT}" mv EZFIO-* ezfio
)
elif [[ ${PACKAGE} = emsl ]] ; then elif [[ ${PACKAGE} = emsl ]] ; then
@ -246,10 +253,11 @@ EOF
download \ download \
"https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local/archive/v1.0.tar.gz" \ "https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local/archive/v1.0.tar.gz" \
"${QP_ROOT}"/external/EMSL.tar.gz "${QP_ROOT}"/external/EMSL.tar.gz
cd "${QP_ROOT}"/external (
tar -zxf EMSL.tar.gz cd "${QP_ROOT}"/external
mv EMSL_Basis* emsl tar --gunzip --extract --file EMSL.tar.gz
cd "${QP_ROOT}" mv EMSL_Basis* emsl
)
elif [[ ${PACKAGE} = docopt ]] ; then elif [[ ${PACKAGE} = docopt ]] ; then
@ -257,11 +265,12 @@ EOF
download \ download \
"https://github.com/docopt/docopt/archive/0.6.2.tar.gz" \ "https://github.com/docopt/docopt/archive/0.6.2.tar.gz" \
"${QP_ROOT}"/external/docopt.tar.gz "${QP_ROOT}"/external/docopt.tar.gz
cd "${QP_ROOT}"/external (
tar -zxf docopt.tar.gz cd "${QP_ROOT}"/external
mv docopt-*/docopt.py "${QP_ROOT}/external/Python" tar --gunzip --extract --file docopt.tar.gz
rm -rf docopt-*/ docopt.tar.gz mv docopt-*/docopt.py "${QP_ROOT}/external/Python"
cd "${QP_ROOT}" rm --recursive --force -- docopt-*/ docopt.tar.gz
)
elif [[ ${PACKAGE} = resultsFile ]] ; then elif [[ ${PACKAGE} = resultsFile ]] ; then
@ -269,24 +278,27 @@ EOF
download \ download \
"https://gitlab.com/scemama/resultsFile/-/archive/master/resultsFile-master.tar.gz" \ "https://gitlab.com/scemama/resultsFile/-/archive/master/resultsFile-master.tar.gz" \
"${QP_ROOT}"/external/resultsFile.tar.gz "${QP_ROOT}"/external/resultsFile.tar.gz
cd "${QP_ROOT}"/external (
tar -zxf resultsFile.tar.gz cd "${QP_ROOT}"/external
mv resultsFile-master/resultsFile "${QP_ROOT}/external/Python" tar --gunzip --extract --file resultsFile.tar.gz
rm -rf resultsFile-master resultsFile.tar.gz mv resultsFile-master/resultsFile "${QP_ROOT}/external/Python"
cd "${QP_ROOT}" rm --recursive --force resultsFile-master resultsFile.tar.gz
)
elif [[ ${PACKAGE} = bats ]] ; then elif [[ ${PACKAGE} = bats ]] ; then
download \ download \
"https://github.com/bats-core/bats-core/archive/v1.1.0.tar.gz" \ "https://github.com/bats-core/bats-core/archive/v1.1.0.tar.gz" \
"${QP_ROOT}"/external/bats.tar.gz "${QP_ROOT}"/external/bats.tar.gz
cd "${QP_ROOT}"/external (
tar -zxf bats.tar.gz tar -zxf bats.tar.gz
cd bats-core-1.1.0/ (
./install.sh $QP_ROOT cd bats-core-1.1.0/
cd .. ./install.sh $QP_ROOT
rm -rf bats-core-1.1.0 "${QP_ROOT}"/external/bats.tar.gz )
cd "${QP_ROOT}" rm --recursive --force -- bats-core-1.1.0 \
"${QP_ROOT}"/external/bats.tar.gz
)
fi fi

31
scripts/qp_export_as_tgz
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@ -46,7 +46,7 @@ function find_libs ()
for i in $@ for i in $@
do do
ldd $i ldd $i
done | sort | grep '/' | cut -d ' ' -f 3 | uniq done | sort | grep '/' | cut --delimiter=' ' --fields=3 | uniq
} }
function find_exec () function find_exec ()
@ -60,8 +60,8 @@ function find_exec ()
echo "Creating root of static directory" echo "Creating root of static directory"
# --------------------------------- # ---------------------------------
rm -rf -- ${QPACKAGE_STATIC} rm --recursive --force -- "${QPACKAGE_STATIC}"
mkdir -p -- ${QPACKAGE_STATIC}/{bin,lib,extra_lib,external} mkdir --parents -- ${QPACKAGE_STATIC}/{bin,lib,extra_lib,external}
if [[ $? -ne 0 ]] ; if [[ $? -ne 0 ]] ;
then then
echo "Error creating ${QPACKAGE_STATIC}/{bin,lib,extra_lib,external}" echo "Error creating ${QPACKAGE_STATIC}/{bin,lib,extra_lib,external}"
@ -94,21 +94,22 @@ then
exit 1 exit 1
fi fi
(
cd ${QPACKAGE_STATIC}/bin cd ${QPACKAGE_STATIC}/bin
for i in *.native for i in *.native
do do
mv "$i" $(basename "$i" .native) mv "$i" $(basename "$i" .native)
done done
cd - )
cp -r ${QP_ROOT}/data ${QPACKAGE_STATIC}/data cp --recursive -- ${QP_ROOT}/data ${QPACKAGE_STATIC}/data
for i in ${FORTRAN_EXEC} for i in ${FORTRAN_EXEC}
do do
i=$(basename $i) i=$(basename $i)
echo $i \$QP_ROOT/bin/$i echo $i \$QP_ROOT/bin/$i
done > ${QPACKAGE_STATIC}/data/executables done > ${QPACKAGE_STATIC}/data/executables
mkdir -p ${QPACKAGE_STATIC}/src/Bitmask mkdir --parents -- ${QPACKAGE_STATIC}/src/Bitmask
cp ${QP_ROOT}/src/Bitmask/bitmasks_module.f90 ${QPACKAGE_STATIC}/src/Bitmask cp ${QP_ROOT}/src/Bitmask/bitmasks_module.f90 ${QPACKAGE_STATIC}/src/Bitmask
# #
@ -140,10 +141,10 @@ cp -- ${QPACKAGE_STATIC}/extra_lib/lib{[gi]omp*,mkl*,lapack*,blas*,z*} ${QPACKAG
echo "Copying scripts directory" echo "Copying scripts directory"
# ------------------------- # -------------------------
cp -r -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/ cp --recursive -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/
if [[ $? -ne 0 ]] ; if [[ $? -ne 0 ]] ;
then then
echo 'cp -r -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/' echo 'cp --recursive -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/'
exit 1 exit 1
fi fi
# #
@ -151,17 +152,17 @@ fi
echo "Copying external libraries" echo "Copying external libraries"
# -------------------------- # --------------------------
cp -r -- ${QP_ROOT}/external/emsl ${QPACKAGE_STATIC}/external cp --recursive -- ${QP_ROOT}/external/emsl ${QPACKAGE_STATIC}/external
if [[ $? -ne 0 ]] ; if [[ $? -ne 0 ]] ;
then then
echo 'cp -r -- ${QP_ROOT}/external/emsl ${QPACKAGE_STATIC}/' echo 'cp --recursive -- ${QP_ROOT}/external/emsl ${QPACKAGE_STATIC}/'
exit 1 exit 1
fi fi
cp -r ${QP_ROOT}/external/Python ${QPACKAGE_STATIC}/external/ cp --recursive -- ${QP_ROOT}/external/Python ${QPACKAGE_STATIC}/external/
mkdir ${QPACKAGE_STATIC}/external/ezfio mkdir ${QPACKAGE_STATIC}/external/ezfio
cp -r ${QP_ROOT}/external/ezfio/Python ${QPACKAGE_STATIC}/external/ezfio/ cp --recursive -- ${QP_ROOT}/external/ezfio/Python ${QPACKAGE_STATIC}/external/ezfio/
cp -r ${QP_ROOT}/external/ezfio/Bash ${QPACKAGE_STATIC}/external/ezfio/ cp --recursive -- ${QP_ROOT}/external/ezfio/Bash ${QPACKAGE_STATIC}/external/ezfio/
# #
@ -175,10 +176,10 @@ sed "s!^export QP_ROOT=.*\$!export QP_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}")
echo "Creating the archive" echo "Creating the archive"
# -------------------- # --------------------
tar -zcf "${QPACKAGE_STATIC}".tar.gz quantum_package_static && rm -rf -- "${QPACKAGE_STATIC}" tar --gzip --compress --file "${QPACKAGE_STATIC}".tar.gz quantum_package_static && rm --recursive --force -- "${QPACKAGE_STATIC}"
if [[ $? -ne 0 ]] ; if [[ $? -ne 0 ]] ;
then then
echo 'tar -zcf "${QPACKAGE_STATIC}".tar.gz "${QPACKAGE_STATIC}" && rm -rf -- "${QPACKAGE_STATIC}"' echo 'tar --gzip --compress --file "${QPACKAGE_STATIC}".tar.gz "${QPACKAGE_STATIC}" && rm --recursive --force -- "${QPACKAGE_STATIC}"'
exit 1 exit 1
fi fi

2
scripts/qp_mpirun
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@ -67,7 +67,7 @@ as a single-node job before re-submitting the current job.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
" "
fi fi
rm -f $INPUT/work/qp_run_address rm --force "${INPUT}"/work/qp_run_address
set -x set -x
mpiexec.hydra -n 1 -hosts "$MASTER_NODE" qp_run $PROG $INPUT & mpiexec.hydra -n 1 -hosts "$MASTER_NODE" qp_run $PROG $INPUT &

2
scripts/qp_srun
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@ -67,7 +67,7 @@ as a single-node job before re-submitting the current job.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
" "
fi fi
rm -f $INPUT/work/qp_run_address rm --force -- "${INPUT}"/work/qp_run_address
set -x set -x
srun -N 1 -n 1 qp_run $PROG $INPUT & srun -N 1 -n 1 qp_run $PROG $INPUT &