Merge branch 'master' into CBM-47-singularity-not-linking-oiio-and-dcmtk

insigneo-pfire · Jan 2, 2023 · b5b0d4e · b5b0d4e
2 parents e397147 + 54b4556
commit b5b0d4e
Show file tree

Hide file tree

Showing 7 changed files with 154 additions and 358 deletions.
diff --git a/singularity/base_centos8_for_pfire.def b/singularity/base_centos8_for_pfire.def
@@ -1,44 +1,59 @@
-# base_centos8_for_pfire.sif
-# Generate using:
-# sudo singularity build -F base_centos8_for_pfire.sif base_centos8_for_pfire.def
-
 Bootstrap: docker
 From: centos:8
 
-
+#
 # Bind system folders into container folders with writing permissions
 # 1) run, exec, shell, and instance start will accept the --bind/-B command-line option to specify bind paths [:dest_in_container[:ro|rw]]
 #    -B can be repeated or the paths can be comma separated
 # 2) $SINGULARITY_BIND or $SINGULARITY_BINDPATH
+#
+#
+
+
 
-
-%post
 
+%post
+
+    # Setup directory structure
+    export SANDBOX=/singularity_sandbox
+    mkdir -p $SANDBOX 
+    cd ${SANDBOX}
+
     #### System-wide installations
 
     # change repository stream    
     dnf -y --disablerepo '*' --enablerepo=extras swap centos-linux-repos centos-stream-repos
 	dnf -y distro-sync
 
 	yum install -y wget https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm
-
-    dnf install -y https://download1.rpmfusion.org/free/el/rpmfusion-free-release-8.noarch.rpm
-	dnf install -y https://download1.rpmfusion.org/nonfree/el/rpmfusion-nonfree-release-8.noarch.rpm
-
+
     yum update -y
     dnf install -y 'dnf-command(config-manager)'
     dnf config-manager --set-enabled powertools
-    dnf groupinstall -y "Development Tools"
-
-    yum install -y  git cmake make automake python3.9 vim yum-utils gcc-toolset-9-gcc-gfortran
-
-    alternatives --set python /usr/bin/python3.9
-
-    # yum install -y  gcc-toolset-9    tzdata 
-    # yum install -y   boost-program-options boost-test boost-filesystem boost-iostreams boost-serialization boost-timer boost-program-options boost-test boost-filesystem boost-iostreams boost-serialization boost-devel 
 
+    yum update -y 
 
+    yum install -y  git cmake make automake python2 python3 vim
+    yum install -y  gcc-toolset-9     vim    #tzdata 
+    yum install -y   boost-program-options boost-test boost-filesystem boost-iostreams boost-serialization boost-timer boost-program-options boost-test boost-filesystem boost-iostreams boost-serialization boost-devel 
+
+    #OpenImageIO-devel dcmtk-devel \
+    #hdf5-openmpi-devel petsc
+
+
+
     dnf groupinstall -y "Development Tools"
+
+    ##############################################################
+
+
 
-
+
+####################################################################################
+
+# Build time not runtime but not build time
+
+
+
 %runscript    
+    alias ll='ls -lrath'
diff --git a/singularity/base_centos8_openmpi_for_pfire.def b/singularity/base_centos8_openmpi_for_pfire.def
@@ -1,8 +1,5 @@
-# base_centos8_openmpi_for_pfire.def
-# sudo singularity build -F  base_centos8_openmpi_for_pfire.sif base_centos8_openmpi_for_pfire.def
-
-Bootstrap: localimage
-From: base_centos8_for_pfire.sif
+Bootstrap: docker
+From: centos:8
 
 #
 # Bind system folders into container folders with writing permissions
@@ -13,41 +10,48 @@ From: base_centos8_for_pfire.sif
 #
 
 
+
 
 %post
 
-
+    # Setup directory structure
+    export SANDBOX=/singularity_sandbox
+    mkdir -p $SANDBOX 
+    cd ${SANDBOX}
 
-    #########################################################################
-    # System-wide installations
-    #########################################################################
-
+    #### System-wide installations
+    dnf -y --disablerepo '*' --enablerepo=extras swap centos-linux-repos centos-stream-repos   
+    yum install -y wget https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm    
+    yum update -y
+    dnf install -y 'dnf-command(config-manager)'
+    dnf config-manager --set-enabled powertools
+
     yum update -y 
 
-
-
-    yum install -y     boost-program-options boost-test boost-filesystem boost-iostreams boost-serialization boost-timer boost-program-options boost-test boost-filesystem boost-iostreams boost-serialization boost-devel 
+    yum install -y  git cmake make automake python2 python3 vim
+    yum install -y  gcc-toolset-9-gcc-gfortran  
+    # yum install -y  gcc-toolset-9    
+    yum install -y     boost-program-options boost-test boost-filesystem boost-iostreams boost-serialization boost-timer boost-program-options boost-test boost-filesystem boost-iostreams boost-serialization boost-devel \
 
-    # yum install -y   openmpi-devel openmpi
-    # OpenImageIO-devel dcmtk-devel hdf5-openmpi-devel petsc openmpi-devel openmpi\  tzdata 
-
+    #OpenImageIO-devel dcmtk-devel \
+    #hdf5-openmpi-devel petsc
+    #openmpi-devel openmpi\  tzdata 
 
+    dnf groupinstall -y "Development Tools"
 
     ##############################################################
-    # Installing OpenMPI
-    ##############################################################
-
+    # yum install -y   openmpi-devel openmpi
+
+
+
     echo "Installing OpenMPI..."
 
-	export OMPI_VERSION=4.0.1
-    export OMPI_DIR=/opt/ompi
-    export OMPI_ROOT=${OMPI_DIR}
-    export OMPI_URL="https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-$OMPI_VERSION.tar.bz2"
-
     # Install support of omnipath
     yum install -y rdma-core-devel libibmad-devel libpsm2 opa-basic-tools libfabric libfabric-devel libpsm2-compat libpsm2-devel
 
-
+    export OMPI_VERSION=4.0.1
+    export OMPI_DIR=/opt/ompi
+    export OMPI_URL="https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-$OMPI_VERSION.tar.bz2"
     mkdir -p /tmp/ompi
     mkdir -p /opt
 
@@ -61,22 +65,19 @@ From: base_centos8_for_pfire.sif
     export PATH=$OMPI_DIR/bin:$PATH
     export LD_LIBRARY_PATH=$OMPI_DIR/lib:$LD_LIBRARY_PATH
 
-    echo "export MPI_ROOT=${OMPI_ROOT}" 	 		   >> $SINGULARITY_ENVIRONMENT
-    echo "export MPI_DIR=${OMPI_ROOT}" 				      >> $SINGULARITY_ENVIRONMENT
-    echo "export CPATH=\"\${CPATH}:${MPI_ROOT}/include\"" >> $SINGULARITY_ENVIRONMENT
-    echo "export PATH=\"\${PATH}:$PATH}\""  		      >> $SINGULARITY_ENVIRONMENT  
+
+
 ####################################################################################
 
-# environemnt variables. may be overwritten by SINGULARITY_ENVIRONMENT
+# Build time not runtime but not build time
 %environment
     # Point to OMPI binaries, libraries, man pages
-	export OMPI_VERSION=4.0.1
     export OMPI_DIR=/opt/ompi
+    export MPI_ROOT=${OMPI_DIR}
+    export PATH="$OMPI_DIR/bin:$PATH"
     export LD_LIBRARY_PATH="$OMPI_DIR/lib:$LD_LIBRARY_PATH"
     export MANPATH="$OMPI_DIR/share/man:$MANPATH"
-
 
 
-
 %runscript    
-
+    alias ll='ls -lrath'
diff --git a/singularity/base_openmpi_petsc_for_pfire.def b/singularity/base_openmpi_petsc_for_pfire.def
@@ -1,8 +1,7 @@
-#base_openmpi_petsc_for_pfire.sif
-Bootstrap: localimage
-From: base_centos8_openmpi_for_pfire.sif
-# Generate with:
-# sudo singularity build -F base_openmpi_petsc_for_pfire.sif base_openmpi_petsc_for_pfire.def
+	Bootstrap: localimage
+	From: base_centos8_openmpi_for_pfire.sif
+
+#
 # Bind system folders into container folders with writing permissions
 # 1) run, exec, shell, and instance start will accept the --bind/-B command-line option to specify bind paths [:dest_in_container[:ro|rw]]
 #    -B can be repeated or the paths can be comma separated
@@ -13,21 +12,23 @@ From: base_centos8_openmpi_for_pfire.sif
 
 %post
 
-
-    yum install -y python39 python39-lxml python39-numpy-doc python39-pip python39-devel  python2
-
-    yum install -y swig libxml2 libxml2-devel python3-libxml2 openssl openssl-devel doxygen
+    # Install system wide packages and updates
+    dnf -y --disablerepo '*' --enablerepo=extras swap centos-linux-repos centos-stream-repos
+	dnf -y distro-sync
+
+    yum install -y wget https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm
 
-    # danielta yum install -y OpenImageIO  python3-openimageio OpenImageIO-utils OpenImageIO-iv OpenImageIO-devel
+    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
 
     pip3 install --upgrade pip
-    python3 -m pip install  PyQt5==5.15.4 
-    python3 -m pip install  PyQt5-Qt5==5.15.2 
-    python3 -m pip install  PyQt5-sip==12.9.0
-    python3 -m pip install  cached-property configobj cycler decorator docutils  dpath h5py 
-    python3 -m pip install  kiwisolver
-    python3 -m pip install matplotlib networkx numpy Pillow pyparsing   
-    python3 -m pip install python-dateutil PyWavelets PyYAML scikit-image scipy six tabulate tifffile 
+    pip3 install PyQt5==5.15.4 
+    pip3 install PyQt5-Qt5==5.15.2 
+    pip3 install PyQt5-sip==12.9.0
+    pip3 install cached-property configobj cycler decorator docutils  dpath h5py 
+    pip3 install imageio kiwisolver
+    pip3 install matplotlib networkx numpy Pillow pyparsing   
+    pip3 install python-dateutil PyWavelets PyYAML scikit-image scipy six tabulate tifffile 
 
     # Setup directory structure
     export SANDBOX=/singularity_sandbox
@@ -51,27 +52,25 @@ From: base_centos8_openmpi_for_pfire.sif
 
 	cd hdf5-${HDF5_VERSION}
 
-	export HDF5_ROOT="/opt/HDF5/${HDF5_VERSION}"
-
-	echo "export HDF5_ROOT=\"${HDF5_ROOT}\""   >> $SINGULARITY_ENVIRONMENT
-	export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HDF5_ROOT}
-	echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH"   >> $SINGULARITY_ENVIRONMENT
-
+	HDF5_ROOT="/opt/HDF5/${HDF5_VERSION}"
+
     CC=/opt/ompi/bin/mpicc ./configure --enable-parallel --prefix=${HDF5_ROOT}
     make -j 4
     make install
 
     ###################################################################
     echo "Installing PETSc"
 
+    #export OMPI_DIR=/opt/ompi
+    #export PATH=$OMPI_DIR/bin:$PATH
+    #export LD_LIBRARY_PATH=$OMPI_DIR/lib:$LD_LIBRARY_PATH
+    #export MANPATH=$OMPI_DIR/share/man:$MANPATH
+
     export PETSC_ARCH=opt
     export PETSC_VERSION=3.10.5
     export PETSC_DIR=/opt/petsc-${PETSC_VERSION}
     export PETSC_URL=http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${PETSC_VERSION}.tar.gz
 
-	echo "export PETSC_DIR=\"${PETSC_DIR}\""   >> $SINGULARITY_ENVIRONMENT
-	echo "export PETSC_ARCH=\"${PETSC_ARCH}\"" >> $SINGULARITY_ENVIRONMENT
-
     mkdir -p /tmp/petsc
 
     cd /tmp/petsc
@@ -83,9 +82,6 @@ From: base_centos8_openmpi_for_pfire.sif
     #yum install -y hdf5-openmpi-devel hdf5-devel vim 
     #yum install -y mpich-devel hdf5-mpich-devel hdf5-mpich vim mpich
 
-    ls -lrat $PETSC_DIR
-    #ls -lrat $PETSC_DIR/$PETSC_ARCH/
-
     # Compile and install
     cd ${PETSC_DIR}
     CC=mpicc CXX=mpicxx python2 config/configure.py --with-make-np=10  --download-f2cblaslapack  --with-hdf5-dir=${HDF5_ROOT} 
@@ -104,22 +100,14 @@ From: base_centos8_openmpi_for_pfire.sif
 
     export MPI_ROOT=${OMPI_DIR}
 
-	echo "MPI_ROOT=/opt/ompi/" 				              >> $SINGULARITY_ENVIRONMENT
-    echo "MPI_DIR=/opt/ompi/" 				              >> $SINGULARITY_ENVIRONMENT
-    echo "export CPATH=\"\${CPATH}:${MPI_ROOT}/include\"" >> $SINGULARITY_ENVIRONMENT
-	echo "export CPATH=\"\${CPATH}:$PETSC_DIR/$PETSC_ARCH/include\"" >> $SINGULARITY_ENVIRONMENT
-
-    #echo "export PATH=$PETSC_DIR/bin:\"${PATH}\""               >> $SINGULARITY_ENVIRONMENT
-    echo "export PATH=$PETSC_DIR/$PETSC_ARCH/bin:\"${PATH}\""    >> $SINGULARITY_ENVIRONMENT
-    echo "export LD_LIBRARY_PATH=$PETSC_DIR/$PETSC_ARCH/lib:\"${LD_LIBRARY_PATH}\""  >> $SINGULARITY_ENVIRONMENT
-    #echo "export LD_LIBRARY_PATH=$PETSC_DIR/lib:\"${LD_LIBRARY_PATH}\""              >> $SINGULARITY_ENVIRONMENT
-
+    export PATH=$PETSC_DIR/bin:$PATH
+    export LD_LIBRARY_PATH=$PETSC_DIR/lib:$LD_LIBRARY_PATH
     export MANPATH=$PETSC_DIR/share/man:$MANPATH
 
 
     ##############################################################
 	# Configure mpich environment 
-	# Information about the version of MPICH to use
+	    # Information about the version of MPICH to use
     #export MPICH_VERSION=3.3.2
     #export MPICH_URL="http://www.mpich.org/static/downloads/$MPICH_VERSION/mpich-$MPICH_VERSION.tar.gz"
     #export MPICH_DIR=/opt/mpich
@@ -130,3 +118,4 @@ From: base_centos8_openmpi_for_pfire.sif
 
 
 %runscript    
+    alias ll='ls -lrath'
diff --git a/singularity/base_petsc_for_pfire.def b/singularity/base_petsc_for_pfire.def
@@ -19,7 +19,7 @@ From: base_centos8_for_pfire.sif
     mkdir -p $SANDBOX 
     cd ${SANDBOX}
 
-
+    837144
     /etc/.profile
     echo "alias ll='ls -lrath'" >> /etc/.bashrc
 ###################################################################
@@ -63,9 +63,8 @@ From: base_centos8_for_pfire.sif
 
     export MPI_ROOT=/opt/petsc-3.10.5/opt/
     export HDF5_ROOT=/opt/petsc-3.10.5/opt/
-
-
-    echo "export HDF5_ROOT=\"${HDF5_ROOT}\""   >> $SINGULARITY_ENVIRONMENT
+    export PETSC_ARCH=opt
+    export PETSC_DIR=/opt/petsc-3.10.5/
 
     ##############################################################
 	# Configure mpich environment 
@@ -86,7 +85,7 @@ From: base_centos8_for_pfire.sif
 # disable python
 # /home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/pfire_ext_libs
 
-# TODO separate build dir in oiio from its dependencies
+# TODO separate build dire in oiio from its dependencies
 export ILMBASE_ROOT=/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist
 export OPENEXR_ROOT=/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist
 export ILMBASE_LIBRARY_DIR=/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist/lib
@@ -116,6 +115,6 @@ export LD_LIBRARY_PATH=/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singul
 
 export pybind11_ROOT=/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist
 
-export pugixml_ROOT=/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist
++ export pugixml_ROOT=/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist
 
-export LD_LIBRARY_PATH=/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist/lib:/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist/lib64:/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist/lib:/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/pFIRE/build/openexr/build/src/:/.singularity.d/libs:/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist/lib
++ export LD_LIBRARY_PATH=/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist/lib:/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist/lib64:/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist/lib:/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/pFIRE/build/openexr/build/src/:/.singularity.d/libs:/home/sa_ac1dt/DEVELOP/INSIGNEO/PFIRE/docker-pfire/singularity/singularity_sandbox/oiio_git/build/ext/dist/lib
diff --git a/singularity/build_pfire_singularity.bash b/singularity/build_pfire_singularity.bash
@@ -3,7 +3,5 @@
 singularity build -F base_centos8_for_pfire.sif  base_centos8_for_pfire.def  
 singularity build -F base_centos8_openmpi_for_pfire.sif  base_centos8_openmpi_for_pfire.def 
 singularity build -F base_openmpi_petsc_for_pfire.sif base_openmpi_petsc_for_pfire.def  
-#singularity build -F base_petsc_for_pfire.sif  base_petsc_for_pfire.def
-
-singularity build -F base_openmpi_petsc_dcmtk_oiio_for_pfire.sif base_openmpi_petsc_dcmtk_oiio_for_pfire.def
+singularity build -F base_petsc_for_pfire.sif  base_petsc_for_pfire.def  
 singularity build -F pfire_openmpi.sif pfire_openmpi.def