Run test without submitting to CDash.

This reverts commit a968cfb1d4.

.gitlab-ci.yml

@@ -0,0 +1,79 @@
+variables:
+  SCHEDULER_PARAMETERS: "-P CSC419 -nnodes 1 -W 30"
+  GIT_STRATEGY: clone
+
+stages:
+  # The 'build-nobatch-standard' stage uses the default build space (/root/* on the login node - not accessible on compute nodes)
+  - build-nobatch-standard
+  # The 'test' stage copies the binary created from "build-nobatch-standard" to /ccsopen/home/<uid>.
+  # Otherwise the binary is not found on compute nodes during a batch run.
+  - test
+
+
+
+#### Standard Build and Test Stages ####
+build-nobatch-standard:
+  stage: build-nobatch-standard
+  before_script:
+    - module avail mpi
+    - module avail cmake
+    - module load cmake
+    - echo "-- modules used for this GitLab run are"
+    - module list
+    - echo "------------------------------------------------"
+
+  script:
+    - echo "This is the building with nobatch"
+    - ls
+    
+    - echo "this is a test"
+    - whoami
+    - echo "HOSTNAME=$HOSTNAME"
+
+    - echo "Check type of available disk drives\n"
+    - df -T
+
+    - export CC=mpicc
+    - export FC=mpif90        
+    - export CXX=mpicxx
+    - uname -a
+
+    - CI_PROJ_DIR=${PWD}
+    - echo "CI_PROJ_DIR="${CI_PROJ_DIR}
+# running 1 ctest process to build HDF5 without tools or examples and skip running tests.
+    - HDF5_VER=`bin/h5vers`
+    - ln -s . hdf5-$HDF5_VER
+    - ln -s config/cmake/scripts/CTestScript.cmake .
+    - ln -s config/cmake/scripts/HDF5config.cmake .
+    - ln -s config/cmake/scripts/HDF5options.cmake .
+    - echo 'set (LOCAL_SKIP_TEST "TRUE")' >> config/cmake/scripts/HDF5options.cmake
+    - echo 'set (MAX_PROC_COUNT 8)' >> config/cmake/scripts/HDF5options.cmake
+    - echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_TOOLS:BOOL=OFF")' >> config/cmake/scripts/HDF5options.cmake
+    - echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_EXAMPLES:BOOL=OFF")' >> config/cmake/scripts/HDF5options.cmake
+    - echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_NUMPROC_FLAG:STRING=-n")' >> config/cmake/scripts/HDF5options.cmake
+    - echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_MAX_NUMPROCS:STRING=6")' >> config/cmake/scripts/HDF5options.cmake
+    - SKIP_TESTS="-E '"
+    - SKIP_TESTS=$SKIP_TESTS"H5TEST-btree2"
+    - SKIP_TESTS=$SKIP_TESTS"|H5TEST-cache"
+    - SKIP_TESTS=$SKIP_TESTS"|H5TEST-fheap"
+    - SKIP_TESTS=$SKIP_TESTS"|H5TEST-objcopy"
+    - SKIP_TESTS=$SKIP_TESTS"'"
+    - SKIP_TESTS2="-E '"
+    - SKIP_TESTS2=$SKIP_TESTS2"H5TEST-earray"
+    - SKIP_TESTS2=$SKIP_TESTS2"|H5TEST-set_extent"
+    - SKIP_TESTS2=$SKIP_TESTS2"|H5TEST-testhdf5-base"
+    - SKIP_TESTS2=$SKIP_TESTS2"'"
+    - ctest -S HDF5config.cmake,SITE_BUILDNAME_SUFFIX="1.13.0-ascent",BUILD_GENERATOR=Unix,LOCAL_SUBMIT=false ${SKIP_TESTS} ${SKIP_TESTS2} -C Release -VV --timeout 1800
+#      look at the dirs to see how the build worked
+    - echo $PWD
+#   - cd ..
+#   - echo $PWD
+
+
+  artifacts:
+    paths:
+#     - zlib-1.2.11/
+#     - hdf5-1.10.5/
+
+  tags:
+    - nobatch

.gitlab/nnsa.sh

@@ -0,0 +1,346 @@
+#!/bin/bash -l
+
+IN_DIR=`pwd`
+
+#Defaults
+
+HDF5_VER=""
+KNL="false"
+HDF5_BRANCH=""
+SKIP_TESTS=""
+
+# READ COMMAND LINE FOR THE TEST TO RUN
+CTEST_OPTS=""
+POSITIONAL=()
+while [[ $# -gt 0 ]]
+do
+key="$1"
+case $key in
+    -v|--version)
+    HDF5_VER="$2"
+    shift # past argument
+    shift # past value
+    BRANCH_VERSTR=`echo $HDF5_VER | sed -e s/\\\./_/g`
+    HDF5_BRANCH=hdf5_$BRANCH_VERSTR
+    ;;
+    -a|--account)
+    CTEST_OPTS="LOCAL_BATCH_SCRIPT_ARGS=$2,$CTEST_OPTS"
+    shift # past argument
+    shift # past value
+    ;;
+    -knl)
+    CTEST_OPTS="KNL=true,$CTEST_OPTS"
+    shift # past argument
+    ;;
+    -h|--help)
+    echo "USAGE: nnsa.sh [-v,--version x.x.x] [-knl] [-h,--help]
+
+    where:
+
+       -v,--version x.x.x    hdf5 version to test 
+                             [default is develop; do not specify version]
+       -knl                  compile for KNL [default: no]
+       -a,--acount id        batch job account
+       -h,--help             show this help text"
+    exit 0
+    ;;
+    *)    # unknown option
+    POSITIONAL+=("$1") # save it in an array for later
+    shift # past argument
+    ;;
+esac
+done
+set -- "${POSITIONAL[@]}" # restore positional parameters
+
+# Get the host name
+UNAME="unknown"
+if [ -x /usr/bin/uname ]
+then
+  UNAME=`/usr/bin/uname -n`
+  PROC=`/usr/bin/uname -p`
+  OSTYPE=`/usr/bin/uname -s`
+fi
+if [ -x /usr/local/bin/uname ]
+then
+  UNAME=`/usr/local/bin/uname -n`
+  PROC=`/usr/local/bin/uname -p`
+  OSTYPE=`/usr/local/bin/uname -s`
+fi
+if [ -x /bin/uname ]
+then
+  UNAME=`/bin/uname -n`
+  PROC=`/bin/uname -p`
+  OSTYPE=`/bin/uname -s`
+fi
+
+# Remove the domain name if present
+UNAME=`echo $UNAME | sed 's;\..*;;'`
+
+#mkdir -p CI; cd CI
+#rm -rf hdf5-* HDF5-* build hdf5.log* Failed* slurm-*.out
+#sleep 1
+
+#if [[ $HDF5_BRANCH == "" ]]; then
+#  git clone https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5.git hdf5
+#else
+#  git clone https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5.git -b $HDF5_BRANCH hdf5
+#fi
+#cd hdf5
+#HDF5_VER=`bin/h5vers`
+#cd ..
+#mv hdf5 hdf5-$HDF5_VER
+
+HDF5_VER=`bin/h5vers`
+ln -s . hdf5-$HDF5_VER
+
+# Summary of command line inputs
+echo "HDF5_VER: $HDF5_VER"
+echo "MISC OPTIONS: $CTEST_OPTS"
+echo "HDF5_BRANCH: $HDF5_BRANCH"
+echo "Current Directory:"
+pwd
+
+#sleep 1
+#rm -f CTestScript.cmake HDF5config.cmake HDF5options.cmake
+sleep 1
+ln -s config/cmake/scripts/CTestScript.cmake .
+ln -s config/cmake/scripts/HDF5config.cmake .
+ln -s config/cmake/scripts/HDF5options.cmake .
+echo "Contents of current directory"
+ls -l
+
+if [[ $UNAME == cori* ]];then
+# Get the curent PrgEnv module setting
+    module list &> out
+    PRGENV_TYPE=`grep -i PrgEnv out | sed -e 's/.*PrgEnv-\(.*\)\/.*/\1/'`
+    module unload cke
+
+    module load cmake/3.14.0
+#    module load cmake
+# unload the current PrgEnv and compiler associated with PrgEnv
+    module unload PrgEnv-$PRGENV_TYPE
+    module unload $PRGENV_TYPE
+# the modules to test
+#   the PrgEnv to test
+    MASTER_MOD="PrgEnv-gnu/6.0.4"
+    module load gcc/8.2.0
+#   the Compiler to switch to:
+#    Format: <number of compiler versions to check> <compiler type> <list of compiler versions (modules) ... repeat)
+    CC_VER=(2 intel intel/17.0.4 intel/18.0.2 2 gcc gcc/7.3.0 gcc/8.2.0)
+    CTEST_OPTS="HPC=sbatch -C haswell,$CTEST_OPTS"
+
+    _CC=cc
+    _FC=ftn
+    _CXX=CC
+
+elif [[ $UNAME == serrano* ]]; then
+
+    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_EXECUTABLE:STRING=mpirun")' >> hdf5-$HDF5_VER/config/cmake/scripts/HPC/sbatch-HDF5options.cmake
+    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_PREFLAGS:STRING=--mca;io;ompio")' >> hdf5-$HDF5_VER/config/cmake/scripts/HPC/sbatch-HDF5options.cmake
+
+    perl -i -pe "s/^CMD=\"ctest.*/CMD=\"ctest . -R MPI_TEST_ -E MPI_TEST_testphdf5|MPI_TEST_t_shapesame -C Release -T test\"/" hdf5-$HDF5_VER/bin/batch/ctestP.sl.in.cmake
+
+    module purge
+    module load cmake
+
+    MASTER_MOD="openmpi-intel/3.0"
+    CC_VER=(2 intel intel/17.0 intel/18.0)
+    CTEST_OPTS="HPC=sbatch,$CTEST_OPTS"
+
+    _CC=mpicc
+    _FC=mpif90
+    _CXX=mpicxx
+
+elif [[ $UNAME == p90* ]]; then
+
+    if [[ $ALL_TESTS == 'false' ]];then
+      SKIP_TESTS="-E '"
+      SKIP_TESTS=$SKIP_TESTS"H5TEST_vds"
+      SKIP_TESTS=$SKIP_TESTS"|H5TEST_objcopy"
+      SKIP_TESTS=$SKIP_TESTS"|H5TEST_btree2"
+      SKIP_TESTS=$SKIP_TESTS"|H5TEST_fheap"
+      SKIP_TESTS=$SKIP_TESTS"|H5TEST_links"
+      SKIP_TESTS=$SKIP_TESTS"|H5TEST_cache"
+      SKIP_TESTS=$SKIP_TESTS"'"
+    fi
+    perl -i -pe "s/^CMD=.*/CMD=\"ctest . -R H5TEST_links -C Release -T test\"/" hdf5-$HDF5_VER/bin/batch/ctestS.sl.in.cmake
+    perl -i -pe "s/.*CMD .*/ctest . -R H5TEST_links -C Release -T test >& ctestS.out/" hdf5-$HDF5_VER/bin/batch/ctestS.sl.in.cmake
+#    perl -i -pe "s/^CMD=.*/CMD=\"ctest . -E MPI_TEST_ ${SKIP_TESTS} -C Release -j 16 -T test\"/" hdf5-$HDF5_VER/bin/batch/ctestS.sl.in.cmake
+#    perl -i -pe "s/.*CMD .*/ctest . -E MPI_TEST_ ${SKIP_TESTS} -C Release -j 16 -T test >& ctestS.out/" hdf5-$HDF5_VER/bin/batch/ctestS.sl.in.cmake
+
+#    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_EXECUTABLE:STRING=mpirun")' >> hdf5-$HDF5_VER/config/cmake/scripts/HPC/sbatch-HDF5options.cmake
+#    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_PREFLAGS:STRING=--mca;io;ompio")' >> hdf5-$HDF5_VER/config/cmake/scripts/HPC/sbatch-HDF5options.cmake
+
+    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_TOOLS:BOOL=OFF")' >> hdf5-$HDF5_VER/config/cmake/scripts/HDF5options.cmake
+    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_EXAMPLES:BOOL=OFF")' >> hdf5-$HDF5_VER/config/cmake/scripts/HDF5options.cmake
+    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_NUMPROC_FLAG:STRING=-n")' >> hdf5-$HDF5_VER/config/cmake/scripts/HDF5options.cmake
+    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_MAX_NUMPROCS:STRING=6")' >> hdf5-$HDF5_VER/config/cmake/scripts/HDF5options.cmake
+
+#    perl -i -pe "s/^CMD=\"ctest.*/CMD=\"ctest . -R MPI_TEST_ -E MPI_TEST_testphdf5|MPI_TEST_t_filters_parallel|MPI_TEST_t_shapesame -C Release -T test\"/" hdf5-$HDF5_VER/bin/batch/ctestP.sl.in.cmake
+
+#    module purge
+#    module load cmake/3.13.4
+#    module load mpi/openmpi3-ppc64le
+
+    MASTER_MOD="openmpi"
+    CC_VER=(1 gcc/8.3.0)
+    CTEST_OPTS="$CTEST_OPTS"
+
+    _CC=mpicc
+    _FC=mpif90
+    _CXX=mpicxx 
+
+elif [[ $UNAME == eclipse* ]]; then
+
+    module purge
+    module load cmake
+
+    MASTER_MOD="intel-mpi/2018"
+    CC_VER=(2 intel intel/16.0 intel/18.0)
+    CTEST_OPTS="HPC=sbatch,$CTEST_OPTS"
+
+    _CC=mpicc
+    _FC=mpif90
+    _CXX=mpicxx
+
+elif [[ $UNAME == quartz* ]]; then
+
+    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_EXECUTABLE:STRING=mpirun")' >> hdf5-$HDF5_VER/config/cmake/scripts/HPC/sbatch-HDF5options.cmake
+    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_PREFLAGS:STRING=--mca;io;ompio")' >> hdf5-$HDF5_VER/config/cmake/scripts/HPC/sbatch-HDF5options.cmake
+
+    perl -i -pe "s/^CMD=\"ctest.*/CMD=\"ctest . -R MPI_TEST_ -E MPI_TEST_t_bigio -C Release -T test\"/" hdf5-$HDF5_VER/bin/batch/ctestP.sl.in.cmake
+
+    module purge
+    module load cmake/3.12.1
+    module load intel/16.0.4
+
+    MASTER_MOD="openmpi/4.0.0 openmpi/4.0.0 openmpi/4.0.0"
+    CC_VER=(1 intel intel/16.0.4 2 gcc gcc/7.1.0 gcc/8.1.0 1 clang clang/3.9.0)
+    CTEST_OPTS="HPC=sbatch,$CTEST_OPTS"
+
+    _CC=mpicc
+    _FC=mpif90
+    _CXX=mpicxx
+
+elif [[ $UNAME == ray* ]]; then
+
+    perl -i -pe "s/^ctest.*/ctest . -R 'MPI_TEST_' -E 'MPI_TEST_t_filters_parallel|MPI_TEST_testphdf5|MPI_TEST_t_shapesame|MPI_TEST_H5DIFF-h5diff_80' -C Release -T test > & ctestP.out;/" hdf5-$HDF5_VER/bin/batch/ray_ctestP.lsf.in.cmake
+    
+    module purge
+    module load cmake/3.12.1
+    module load xl/2016.12.02
+
+    MASTER_MOD="spectrum-mpi spectrum-mpi spectrum-mpi"
+    CC_VER=(1 xl xl/2016.12.02 1 gcc gcc/7.3.1 1 clang clang/coral-2018.08.08)
+    CTEST_OPTS="HPC=raybsub,$CTEST_OPTS"
+
+    _CC=mpicc
+    _FC=mpif90
+    _CXX=mpicxx
+
+elif [[ $UNAME == lassen* ]]; then
+
+    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_EXECUTABLE:STRING=mpirun")' >> hdf5-$HDF5_VER/config/cmake/scripts/HPC/bsub-HDF5options.cmake
+
+    perl -i -pe "s/^ctest.*/ctest . -E MPI_TEST_ -C Release -j 32 -T test >& ctestS.out/" hdf5-$HDF5_VER/bin/batch/ctestS.lsf.in.cmake
+    perl -i -pe "s/^ctest.*/ctest . -R MPI_TEST_ -E 'MPI_TEST_testphdf5|MPI_TEST_t_shapesame' -C Release -T test >& ctestP.out/" hdf5-$HDF5_VER/bin/batch/ctestP.lsf.in.cmake
+    
+    module purge
+    module load cmake/3.12.1
+    module load xl/2016.12.02
+
+    MASTER_MOD="spectrum-mpi"
+    CC_VER=(1 xl xl/2019.02.07)
+    #MASTER_MOD="spectrum-mpi spectrum-mpi spectrum-mpi"
+    #CC_VER=(1 xl xl/2019.02.07 1 gcc gcc/7.3.1 1 clang clang/coral-2018.08.08)
+    CTEST_OPTS="HPC=bsub,$CTEST_OPTS"
+
+    _CC=mpicc
+    _FC=mpif90
+    _CXX=mpicxx
+
+fi
+module list
+
+icnt=0
+for master_mod in $MASTER_MOD; do
+
+  #icnt=$(($icnt+1))
+  num_CC=${CC_VER[$icnt]} # number of compilers for the  master_mod
+
+  module load $master_mod # Load the master module
+
+  icnt=$(($icnt+1))
+  COMPILER_TYPE=`echo ${CC_VER[icnt]} | sed 's/\/.*//'`
+  module unload ${COMPILER_TYPE} # unload the general compiler type
+
+  for i in `seq 1 $num_CC`; do # loop over compiler versions
+    cc_ver=${CC_VER[$icnt]} # compiler version
+    rm -fr build
+
+    module load $cc_ver # load the compiler with version
+    module load $master_mod
+
+    export CC=$_CC
+    export FC=$_FC
+    export CXX=$_CXX
+
+    module list
+
+    echo "timeout 3h ctest . -S HDF5config.cmake,SITE_BUILDNAME_SUFFIX=\"$HDF5_VER-$master_mod-$cc_ver\",${CTEST_OPTS}MPI=true,BUILD_GENERATOR=Unix,LOCAL_SUBMIT=true,MODEL=HPC -C Release -V -O hdf5.log"
+    timeout 3h ctest . -S HDF5config.cmake,SITE_BUILDNAME_SUFFIX="$HDF5_VER-$master_mod-$cc_ver",${CTEST_OPTS}MPI=true,BUILD_GENERATOR=Unix,LOCAL_SUBMIT=true,MODEL=HPC -C Release -V -O hdf5.log
+
+    module unload $cc_ver  # unload the compiler with version
+
+    icnt=$(($icnt+1))
+
+    #rm -fr build
+  done
+  module unload $master_mod #unload master module
+done
+
+#Serial only tests
+# Turn off parallel options for serial-only tests.  (Just be sure not to include
+#  MPI=true in the ctest line.)
+
+if [[ $UNAME == chama* ]]; then
+
+# These are temporary workarounds that should be fixed in *-HDF5options.cmake by moving the 'set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "ctestP.sl")' (or equivalent ) into the if (DEFINED MPI) block, and otherwise either setting it to "" or maybe moving both of these to that block. 
+    echo 'set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "")' >> hdf5-$HDF5_VER/config/cmake/scripts/HPC/sbatch-HDF5options.cmake
+    echo 'set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_PARALLEL_NAME:STRING=${LOCAL_BATCH_SCRIPT_PARALLEL_NAME}")' >> hdf5-$HDF5_VER/config/cmake/scripts/HPC/sbatch-HDF5options.cmake
+
+    module purge
+    module load cmake
+
+    CC_VER=(2 clang clang/5.0 clang/4.0)
+    CTEST_OPTS="HPC=sbatch,$CTEST_OPTS"
+
+    _CC=clang
+    _FC=gfortran
+    _CXX=clang++
+
+fi
+
+for i in `seq 1 $num_CC`; do # loop over compiler versions
+  icnt=$(($icnt+1))
+  cc_ver=${CC_VER[$icnt]} # compiler version
+  rm -fr build
+
+  module load $cc_ver # load the compiler with version
+
+  export CC=$_CC
+  export FC=$_FC
+  export CXX=$_CXX
+
+  module list
+
+  echo "cest . -S HDF5config.cmake,SITE_BUILDNAME_SUFFIX=\"$HDF5_VER-$cc_ver\",${CTEST_OPTS}MPI=true,BUILD_GENERATOR=Unix,LOCAL_SUBMIT=true,MODEL=HPC -C Release -VV -O hdf5.log"
+  ctest . -S HDF5config.cmake,SITE_BUILDNAME_SUFFIX="$HDF5_VER-$cc_ver",${CTEST_OPTS}MPI=true,BUILD_GENERATOR=Unix,LOCAL_SUBMIT=true,MODEL=HPC -C Release -VV -O hdf5.log
+
+  module unload $cc_ver  # unload the compiler with version
+
+  #rm -fr build
+done
+pwd
+cd $IN_DIR
+