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Merge pull request #12 from insigneo-pfire/CBM-47-singularity-not-lin…
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…king-oiio-and-dcmtk

Cbm 47 singularity not linking oiio and dcmtk
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@tartarini
tartarini authored Jan 2, 2023
2 parents 54b4556 + b5b0d4e commit 249d131
Showing 1 changed file with 44 additions and 35 deletions.
79 changes: 44 additions & 35 deletions singularity/pfire_openmpi.def
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Original file line number Diff line number Diff line change
Expand Up @@ -48,17 +48,7 @@ From: base_openmpi_petsc_for_pfire.sif

###########################################################################
# Install system wide packages via Yum

# moved in included image
# yum install -y python39 python39-lxml python39-numpy-doc python39-pip python39-devel
# yum install -y dcmtk.x86_64 dcmtk-devel.x86_64 libjpeg-turbo libjpeg-turbo-devel swig libxml2 libxml2-devel python3-libxml2 openssl openssl-devel doxygen

# yum install -y wget https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm

# yum install -y OpenImageIO-devel.x86_64 OpenImageIO-utils.x86_64 OpenImageIO.x86_64 dcmtk.x86_64 dcmtk-devel.x86_64 swig
# install dependency packages only yum repoquery --requires OpenImageIO


###########################################################################
# Create Python virtual environment and install dependencies

Expand Down Expand Up @@ -110,28 +100,23 @@ From: base_openmpi_petsc_for_pfire.sif
# Install pFIRE requirements/dependencies and configure env variables

# Define environment variables
export HDF5_ROOT="/opt/HDF5/1.8.22/"
# export HDF5_ROOT="/opt/HDF5/1.8.22/"

# PETSC_DIR="/opt/petsc-3.10.5/"
export PETSC_DIR="/opt/petsc-3.10.5/"
export PETSC_ARCH="opt"
# export PETSC_DIR="/opt/petsc-3.10.5/"
# export PETSC_ARCH="opt"

export MPI_ROOT="/opt/ompi/"
export MPI_DIR="/opt/ompi/"
export CPATH="/opt/ompi/include/:$CPATH"
# export MPI_ROOT="/opt/ompi/"
# export MPI_DIR="/opt/ompi/"
# export CPATH="/opt/ompi/include/:$CPATH"


# Make variables visible in Singularity image
echo "export HDF5_ROOT=\"${HDF5_ROOT}\"" >> $SINGULARITY_ENVIRONMENT
echo "export PETSC_DIR=\"${PETSC_DIR}\"" >> $SINGULARITY_ENVIRONMENT
echo "export PETSC_ARCH=\"${PETSC_ARCH}\"" >> $SINGULARITY_ENVIRONMENT
echo "MPI_ROOT=/opt/ompi/" >> $SINGULARITY_ENVIRONMENT
echo "MPI_DIR=/opt/ompi/" >> $SINGULARITY_ENVIRONMENT
echo "export CPATH=\"\${CPATH}:${MPI_ROOT}/include\"" >> $SINGULARITY_ENVIRONMENT


###################################################
# Install XDMF
# /home/tartarini/DEVELOP/INSIGNEO/insigneo-pfire/docker-pfire/singularity/sandbox/xdmf_git_python3/xdmf/build/tests/Python
# .. insigneo-pfire/docker-pfire/singularity/sandbox/xdmf_git_python3/xdmf/build/tests/Python

cd ${SANDBOX}
XDMF_INSTALL_DIR="${SANDBOX}/xdmf_bin"
Expand Down Expand Up @@ -162,6 +147,12 @@ From: base_openmpi_petsc_for_pfire.sif
######################################################################################
# Install pFIRE
######################################################################################

# export OPENIMAGEIO_ROOT_DIR=${OIIO_ROOT}

# PFIRE_REPOSITORY=https://github.com/INSIGNEO/pFIRE.git
PFIRE_REPOSITORY=https://github.com/insigneo-pfire/pFIRE.git

PFIRE_ROOT="/opt/pfire"

PFIRE_VERSION="v0.4.0"
Expand All @@ -174,10 +165,7 @@ From: base_openmpi_petsc_for_pfire.sif
PFIRE_PATH="${PFIRE_ROOT}/${PFIRE_VERSION}/"
echo "PFIRE_PATH=${PFIRE_PATH}"

# Enabling pFIRE v0.4.0 as default version for benchmarking tests
#echo "export PATH="${PFIRE_PATH}\"\${PATH}\"" >> $SINGULARITY_ENVIRONMENT



echo "export LD_LIBRARY_PATH=\"\${LD_LIBRARY_PATH}:${PETSC_DIR}/${PETSC_ARCH}/lib:${HDF5_ROOT}/lib\"" >> $SINGULARITY_ENVIRONMENT


Expand All @@ -189,40 +177,61 @@ From: base_openmpi_petsc_for_pfire.sif
# Making v0.4.0 the pfire default binary
cp ${PFIRE_PATH}/bin/pfire ${PFIRE_PATH}/bin/pfire_${PFIRE_VERSION}

# Enabling pFIRE v0.4.0 as default version for benchmarking tests
echo "export PATH=${PFIRE_PATH}/bin/:\${PATH}" >> $SINGULARITY_ENVIRONMENT


# Set library path
echo "export LD_LIBRARY_PATH=${PFIRE_PATH}/lib/:\${LD_LIBRARY_PATH}" >> $SINGULARITY_ENVIRONMENT

#export DCMTK_DIR=/home/tartarini/DEVELOP/INSIGNEO/insigneo-pfire/docker-pfire/singularity/fix_oiio_dcmtk/dcmtk
echo "export DCMTK_DIR=/home/tartarini/DEVELOP/INSIGNEO/insigneo-pfire/docker-pfire/singularity/fix_oiio_dcmtk/dcmtk" >> $SINGULARITY_ENVIRONMENT
######################################################################################
PFIRE_VERSION="master"

## Installing
PFIRE_VERSION="test_framework_fix"


cd ${SANDBOX}

git clone -b ${PFIRE_VERSION} https://github.com/INSIGNEO/pFIRE.git ${PFIRE_VERSION}

cd ${PFIRE_VERSION}

PFIRE_SOURCE_MASTER=`pwd`

export PFIRE_DEST_DIR=${PFIRE_ROOT}/${PFIRE_VERSION}
pwd



PFIRE_SOURCE_MASTER=${SANDBOX}/${PFIRE_VERSION}
mkdir build && cd build && cmake -DCMAKE_PREFIX_PATH=/usr/local/DCMTK/single_lib/ -DBUILD_TESTS=0 \
-DPETSC_EXECUTABLE_RUNS:BOOL=Yes -DENABLE_OpenImageIO=1 -DENABLE_DCMTK=1 \
-DCMAKE_INSTALL_PREFIX=${PFIRE_ROOT}/${PFIRE_VERSION} ../ &&

echo ${DCMTK_DIR}

pwd
mkdir build && cd build && cmake -DPETSC_EXECUTABLE_RUNS:BOOL=Yes -DCMAKE_INSTALL_PREFIX=${PFIRE_ROOT}/${PFIRE_VERSION} ../ && \
make -j && make install && \
# ctest -V -L serial

# Add pFIRE filename version suffix
mv ${PFIRE_ROOT}/${PFIRE_VERSION}/bin/pfire ${PFIRE_ROOT}/${PFIRE_VERSION}/bin/pfire_${PFIRE_VERSION}
mv ${PFIRE_DEST_DIR}/bin/pfire ${PFIRE_DEST_DIR}/bin/pfire_${PFIRE_VERSION}

PFIRE_MASTER_BIN_PATH="${PFIRE_ROOT}/${PFIRE_VERSION}/bin/"
PFIRE_MASTER_BIN_PATH="${PFIRE_DEST_DIR}/bin/"

echo "PFIRE_MASTER_BIN_PATH=${PFIRE_MASTER_BIN_PATH}"

# Add to container env
echo "export PATH=${PFIRE_MASTER_BIN_PATH}:\${PATH}" >> $SINGULARITY_ENVIRONMENT

# Set library path
echo "export LD_LIBRARY_PATH=${PFIRE_DEST_DIR}/lib/:\${LD_LIBRARY_PATH}" >> $SINGULARITY_ENVIRONMENT

#petsc-dev libboost-all-dev libhdf5-openmpi-dev\ openmpi-bin libopenmpi-dev \ #libopenimageio2.1 libopenimageio-dev libdcmtk-dev #openmpi-devel hdf5-openmpi-devel





###########################################################################
# Install regression benchmark from pFIRE Master
# PFIRE_PATH
Expand Down Expand Up @@ -269,7 +278,7 @@ From: base_openmpi_petsc_for_pfire.sif

echo "PYTHONPATH=\${PYTHONPATH}"
echo "PATH=${PATH}"

##########################################################################################
# Declare environment variables to be visible when executed
# host env is visible unless launched with -e
Expand Down

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