add documentation and singularity container definition files

.gitignore

+*.sif

Makefile

+
+pism.sif:	petsc.sif
+petsc.sif:	openmpi.sif
+
+
+%.sif:	%.def
+	sudo singularity build $@ $<

README.md

 # singularity-pism
 
-Singularity containers for the parallel ice sheet model (PISM)
\ No newline at end of file
+Using [singularity](https://sylabs.io/docs/) to build the [parallel ice sheet model (PISM)](https://pism-docs.org/wiki/doku.php) on Scientific Linux 7.
+
+PISM is modern ice sheet model written C++ using [PETSc](https://www.mcs.anl.gov/petsc/). The cmake build system doesn't find the system provided openmpi implementation. 
+
+This repository provides three singularity container definition files. One for basic OpenMPI, one for PETSc and one for PISM.
+
+You can run the container using
+```
+mpirun -n 4 singularity exec --bind /scratch pism.sif /opt/pism/bin/pismv -test G -y 200
+```
+
+This runs PSIM using 4 MPI processes. The `--bind /scratch` option exposes the `/scratch` directory to the container. Other directories can be exposed using the same approach.
\ No newline at end of file

openmpi.def

+Bootstrap: docker
+From: ubuntu:20.04
+
+%environment
+    export OMPI_DIR=/opt/ompi
+    export SINGULARITY_OMPI_DIR=$OMPI_DIR
+    export SINGULARITYENV_APPEND_PATH=$OMPI_DIR/bin
+    export SINGULARITYENV_APPEND_LD_LIBRARY_PATH=$OMPI_DIR/lib
+
+%post
+    echo "Installing required packages..."
+    export DEBIAN_FRONTEND="noninteractive"
+    apt-get -y update
+    apt install -y bash gcc gfortran g++ make file wget libxml2-dev  zlib1g-dev libpapi-dev
+
+    echo "Installing Open MPI"
+    export OMPI_DIR=/opt/ompi
+    export OMPI_VERSION=1.10.7
+    export HWLOC_VERS=1.11.8
+    export OMPI_URL="https://download.open-mpi.org/release/open-mpi/v1.10/openmpi-${OMPI_VERSION}.tar.bz2"
+    mkdir -p /tmp/ompi
+    mkdir -p /opt
+
+    # install hwloc
+    cd /tmp/ompi
+    wget -O hwloc-${HWLOC_VERS}.tar.bz2 https://download.open-mpi.org/release/hwloc/v1.11/hwloc-${HWLOC_VERS}.tar.bz2 && tar -xjf hwloc-${HWLOC_VERS}.tar.bz2
+    wget -O openmpi-$OMPI_VERSION.tar.bz2 $OMPI_URL && tar -xjf openmpi-$OMPI_VERSION.tar.bz2
+
+    # Compile and install
+    cd /tmp/ompi/hwloc-${HWLOC_VERS}
+    ./configure --prefix=$OMPI_DIR
+    make install
+
+    cd /tmp/ompi/openmpi-$OMPI_VERSION 
+    ./configure --prefix=$OMPI_DIR \
+       --disable-silent-rules \
+       --enable-mpi-thread-multiple \
+       --with-hwloc=$OMPI_DIR
+    make install
+    # Set env variables so we can compile our application
+    export PATH=$OMPI_DIR/bin:$PATH
+    export LD_LIBRARY_PATH=$OMPI_DIR/lib:$LD_LIBRARY_PATH
+    export MANPATH=$OMPI_DIR/share/man:$MANPATH
+

petsc.def

+Bootstrap: localimage
+From: /scratch/local/mhagdorn/pism/singularity/openmpi.sif
+
+%environment
+    export PETSC_DIR=/opt/petsc
+    export SINGULARITY_PETSC_DIR=$PETSC_DIR
+    export SINGULARITYENV_APPEND_PATH=$PETSC_DIR/bin
+    export SINGULARITYENV_APPEND_LD_LIBRARY_PATH=$PETSC_DIR/lib
+
+
+%post
+    apt install -y libblas-dev liblapack-dev python
+
+    export OMPI_DIR=/opt/ompi
+    export PATH=$OMPI_DIR/bin:$PATH
+    export LD_LIBRARY_PATH=$OMPI_DIR/lib:$LD_LIBRARY_PATH
+    export MANPATH=$OMPI_DIR/share/man:$MANPATH
+
+    export PATH=$PETSC_DIR/bin:$PATH
+    export LD_LIBRARY_PATH=$PETSC_DIR/lib:$LD_LIBRARY_PATH
+    export MANPATH=$PETSC_DIR/share/man:$MANPATH
+
+    echo "Installing PETSc"
+    export PETSC_ARCH=opt
+    export PETSC_VERSION=3.13.4
+    export PETSC_DIR=/opt/petsc-${PETSC_VERSION}
+    export PETSC_URL=http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${PETSC_VERSION}.tar.gz
+
+    mkdir -p /tmp/petsc
+
+    cd /tmp/petsc
+    wget -O petsc-lite-${PETSC_VERSION}.tar.gz ${PETSC_URL}
+    cd /opt
+    tar xzf /tmp/petsc/petsc-lite-${PETSC_VERSION}.tar.gz
+    
+    # Compile and install
+    cd ${PETSC_DIR}
+    CC=mpicc CXX=mpicxx ./config/configure.py --with-shared-libraries \
+                                          --with-debugging=0 \
+                                          --with-fc=0
+    make all

pism.def

+Bootstrap: localimage
+From: /scratch/local/mhagdorn/pism/singularity/petsc.sif
+
+%environment
+    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=3.13.4
+    export PETSC_DIR=/opt/petsc-${PETSC_VERSION}
+
+%post
+    apt install -y cmake libgsl-dev libfftw3-dev libudunits2-dev libproj-dev git libnetcdf-dev netcdf-bin
+
+    export OMPI_DIR=/opt/ompi
+    export PATH=$OMPI_DIR/bin:$PATH
+    export LD_LIBRARY_PATH=$OMPI_DIR/lib:$LD_LIBRARY_PATH
+    export MANPATH=$OMPI_DIR/share/man:$MANPATH
+
+    export PETSC_ARCH=opt
+    export PETSC_VERSION=3.13.4
+    export PETSC_DIR=/opt/petsc-${PETSC_VERSION}
+
+    export PISM_VERSION=v1.2.1
+
+    mkdir -p /opt/pism
+    cd /opt/pism
+    git clone https://github.com/pism/pism.git
+    cd pism
+    git checkout ${PISM_VERSION}
+
+    mkdir build
+    cd build
+    PISM_INSTALL_PREFIX=/opt/pism CC=mpicc CXX=mpicxx cmake ..
+    make install