Cleaning scripts

2024-09-27 03:51:01 +02:00 · 2018-12-21 17:50:24 +01:00 · 2018-12-21 17:50:24 +01:00 · e9e768877d
commit e9e768877d
parent 7409eefcc6
4 changed files with 89 additions and 76 deletions
--- a/62
+++ b/62
@ -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."

@ -81,7 +82,7 @@ function error() {
 }

 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() {
@ -149,8 +150,9 @@ for PACKAGE in ${PACKAGES} ; do
            download \
              "https://github.com/scemama/irpf90/archive/v1.7.2.tar.gz" \
              "${QP_ROOT}"/external/irpf90.tar.gz
+            (
              cd "${QP_ROOT}"/external
-            tar -zxf irpf90.tar.gz
+              tar --gunzip --extract --file irpf90.tar.gz
              rm irpf90.tar.gz
              cd irpf90-*
              make
@ -163,7 +165,7 @@ EOF

                      chmod +x "${QP_ROOT}"/bin/$i
              done
-            cd "${QP_ROOT}"
+            )
    

    elif [[ ${PACKAGE} = zeromq ]] ; then
@ -171,14 +173,15 @@ EOF
            download \
              "https://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz" \
              "${QP_ROOT}"/external/zeromq.tar.gz
+            (
              cd "${QP_ROOT}"/external
-            tar -zxf zeromq.tar.gz
+              tar --gunzip --extract --file zeromq.tar.gz
              rm zeromq.tar.gz
              cd zeromq-*
              ./configure --prefix="$QP_ROOT" --without-libsodium --enable-libunwind=no
              make
              make install
-            cd "${QP_ROOT}"
+            )


    elif [[ ${PACKAGE} = f77zmq ]] ; then
@ -186,8 +189,9 @@ EOF
            download \
              "https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz" \
              "${QP_ROOT}"/external/f77_zmq.tar.gz
+            (
              cd "${QP_ROOT}"/external
-            tar -zxf f77_zmq.tar.gz
+              tar --gunzip --extract --file f77_zmq.tar.gz
              rm f77_zmq.tar.gz
              cd f77_zmq-*
              export ZMQ_H="$QP_ROOT"/include/zmq.h
@ -195,7 +199,7 @@ EOF
              cp libf77zmq.a "${QP_ROOT}"/lib
              cp libf77zmq.so "${QP_ROOT}"/lib
              cp f77_zmq_free.h "${QP_ROOT}"/include
-            cd "${QP_ROOT}"
+            )

    
    elif [[ ${PACKAGE} = ocaml ]] ; then
@ -204,7 +208,7 @@ EOF
              "https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh" \
              "${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
                # Special commands for Travis CI
@ -224,10 +228,12 @@ EOF
            source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
            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)
-            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 [[ ${PACKAGE} = ezfio ]] ; then
@ -235,10 +241,11 @@ EOF
            download \
              "https://gitlab.com/scemama/EZFIO/-/archive/master/EZFIO-master.tar.gz" \
              "${QP_ROOT}"/external/ezfio.tar.gz
+            (
              cd "${QP_ROOT}"/external
-            tar -zxf ezfio.tar.gz
+              tar --gunzip --extract --file ezfio.tar.gz
              mv EZFIO-* ezfio
-            cd "${QP_ROOT}"
+            )

            
    elif [[ ${PACKAGE} = emsl ]] ; then
@ -246,10 +253,11 @@ EOF
            download \
              "https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local/archive/v1.0.tar.gz" \
              "${QP_ROOT}"/external/EMSL.tar.gz
+            (
              cd "${QP_ROOT}"/external
-            tar -zxf EMSL.tar.gz
+              tar --gunzip --extract --file EMSL.tar.gz
              mv EMSL_Basis* emsl
-            cd "${QP_ROOT}"
+            )


    elif [[ ${PACKAGE} = docopt ]] ; then
@ -257,11 +265,12 @@ EOF
            download \
              "https://github.com/docopt/docopt/archive/0.6.2.tar.gz" \
              "${QP_ROOT}"/external/docopt.tar.gz
+            (
              cd "${QP_ROOT}"/external
-            tar -zxf docopt.tar.gz 
+              tar --gunzip --extract --file docopt.tar.gz 
              mv docopt-*/docopt.py "${QP_ROOT}/external/Python"
-            rm -rf docopt-*/ docopt.tar.gz
-            cd "${QP_ROOT}"
+              rm --recursive --force -- docopt-*/ docopt.tar.gz
+            )


    elif [[ ${PACKAGE} = resultsFile ]] ; then
@ -269,24 +278,27 @@ EOF
            download \
              "https://gitlab.com/scemama/resultsFile/-/archive/master/resultsFile-master.tar.gz" \
              "${QP_ROOT}"/external/resultsFile.tar.gz
+            (
              cd "${QP_ROOT}"/external
-            tar -zxf resultsFile.tar.gz 
+              tar --gunzip --extract --file resultsFile.tar.gz 
              mv resultsFile-master/resultsFile "${QP_ROOT}/external/Python"
-            rm -rf resultsFile-master resultsFile.tar.gz
-            cd "${QP_ROOT}"
+              rm --recursive --force resultsFile-master resultsFile.tar.gz
+            )

    elif [[ ${PACKAGE} = bats ]] ; then

            download \
              "https://github.com/bats-core/bats-core/archive/v1.1.0.tar.gz" \
              "${QP_ROOT}"/external/bats.tar.gz
-            cd "${QP_ROOT}"/external
+            (
              tar -zxf bats.tar.gz 
+              (
              cd bats-core-1.1.0/
              ./install.sh $QP_ROOT
-            cd ..
-            rm -rf bats-core-1.1.0 "${QP_ROOT}"/external/bats.tar.gz
-            cd "${QP_ROOT}"
+              )
+              rm --recursive --force -- bats-core-1.1.0 \
+                  "${QP_ROOT}"/external/bats.tar.gz
+            )

    fi

--- a/scripts/qp_export_as_tgz
+++ b/scripts/qp_export_as_tgz
@ -46,7 +46,7 @@ function find_libs ()
  for i in $@
  do
      ldd $i
-  done | sort | grep '/' | cut -d ' ' -f 3 | uniq
+  done | sort | grep '/' | cut --delimiter=' ' --fields=3 | uniq
 }

 function find_exec ()
@ -60,8 +60,8 @@ function find_exec ()
 echo "Creating root of static directory"
 #     ---------------------------------

-rm -rf -- ${QPACKAGE_STATIC}
-mkdir -p -- ${QPACKAGE_STATIC}/{bin,lib,extra_lib,external}
+rm --recursive --force -- "${QPACKAGE_STATIC}"
+mkdir --parents -- ${QPACKAGE_STATIC}/{bin,lib,extra_lib,external}
 if [[ $? -ne 0 ]] ;
 then
  echo "Error creating ${QPACKAGE_STATIC}/{bin,lib,extra_lib,external}"
@ -94,21 +94,22 @@ then
  exit 1
 fi

+(
 cd ${QPACKAGE_STATIC}/bin
  for i in *.native
  do
    mv "$i" $(basename "$i" .native)
  done
-cd -
+)

-cp -r ${QP_ROOT}/data ${QPACKAGE_STATIC}/data
+cp --recursive -- ${QP_ROOT}/data ${QPACKAGE_STATIC}/data
 for i in ${FORTRAN_EXEC}
 do
  i=$(basename $i)
  echo $i \$QP_ROOT/bin/$i
 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

 #
@ -140,10 +141,10 @@ cp -- ${QPACKAGE_STATIC}/extra_lib/lib{[gi]omp*,mkl*,lapack*,blas*,z*} ${QPACKAG
 echo "Copying scripts directory"
 #     ------------------------- 

-cp -r -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/
+cp --recursive -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/
 if [[ $? -ne 0 ]] ;
 then
-  echo 'cp -r -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/'
+  echo 'cp --recursive -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/'
  exit 1
 fi
 #
@ -151,17 +152,17 @@ fi
 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 ]] ;
 then
-  echo 'cp -r -- ${QP_ROOT}/external/emsl ${QPACKAGE_STATIC}/'
+  echo 'cp --recursive -- ${QP_ROOT}/external/emsl ${QPACKAGE_STATIC}/'
  exit 1
 fi

-cp -r ${QP_ROOT}/external/Python ${QPACKAGE_STATIC}/external/
+cp --recursive -- ${QP_ROOT}/external/Python ${QPACKAGE_STATIC}/external/
 mkdir ${QPACKAGE_STATIC}/external/ezfio
-cp -r ${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/Python ${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"
 #     --------------------

-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 [[ $? -ne 0 ]] ;
 then
-  echo 'tar -zcf "${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
 fi

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

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