base: manually compile OpenMPI

Problem: the OpenMPI packaged with centos 7 does not include the PMI
plugin, which is required to boot under Flux. The OpenMPI version
packaged with centos 8 (4.0.5) has a bug that causes a segfault on
finalization, which is fixed in the next patch version.
PR that fixes the bug: (open-mpi/ompi#8380)

Solution: for centos 7, hand compile the same version of OpenMPI (1.10),
but with the `--with-pmi` flag.  For centos 8, hand compile the version
of OpenMPI with the patch (4.0.6).  Since this is an involved process,
add a helper script that will also make adding other MPIs much easier.

Author: SteVwonder

docker/base/centos7/Dockerfile

@@ -70,8 +70,6 @@ RUN yum -y update \
     # Radical Pilot Deps
     python3-pip \
     mongodb-org \
-    # MPI Dep
-    ${MPI} \
  && yum clean all \
  && python3 -m venv ${VIRTUAL_ENV} \
  && pip install --upgrade pip setuptools pytest \
@@ -86,3 +84,5 @@ RUN wget https://archive.apache.org/dist/ant/binaries/apache-ant-1.9.15-bin.tar.
     && ln -s /opt/apache-ant-1.9.15 /opt/ant \
     && sudo ln -s /opt/ant/bin/ant /usr/bin/ant
 
+COPY ./install-mpi.sh /install-mpi.sh
+RUN bash install-mpi.sh ${MPI}

docker/base/centos7/install-mpi.sh

@@ -0,0 +1,42 @@
+#!/bin/bash
+
+if [[ -z $1 ]]; then
+    echo "Must provide MPI that you want to install"
+    exit 1
+fi
+
+# Install only the dependencies for a given package
+# Source: https://serverfault.com/questions/429123/howto-get-yum-to-install-only-dependencies-for-a-given-pakage
+yum_install_only_deps () {
+    if [[ -z "$1" ]]; then
+        echo "Package required for installing deps"
+        exit 1
+    fi
+    yum deplist $1 | grep provider | awk '{print $2}' | sort | uniq | grep -v $PACKAGE | sed ':a;N;$!ba;s/\n/ /g' | xargs yum -y install
+}
+
+if [[ "$1" == "openmpi-devel" ]]; then
+    yum install -y slurm-pmi-devel
+
+    MAJOR_MINOR=1.10
+    PATCH=7
+    OPENMPI=openmpi-${MAJOR_MINOR}.${PATCH}
+    
+    wget https://download.open-mpi.org/release/open-mpi/v${MAJOR_MINOR}/${OPENMPI}.tar.gz
+    tar -xf ./${OPENMPI}.tar.gz
+    rm ./${OPENMPI}.tar.gz
+    
+    cd ${OPENMPI}
+    ./configure
+    make -j 4
+    make install
+    cd ..
+    rm -rf ${OPENMPI}
+
+    yum remove -y slurm-pmi-devel
+    yum autoremove -y
+    yum clean all
+else 
+    echo "Unknown/unsupported MPI. Existing without installing."
+    exit 1
+fi

docker/base/centos8/Dockerfile

@@ -71,8 +71,6 @@ RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.n
     # RADICAL-Pilot Dependencies
     python3-pip \
     mongodb-org \
-    # MPI Dep
-    ${MPI} \
  && dnf clean all \
  && python3 -m venv ${VIRTUAL_ENV} \
  && pip install --upgrade pip setuptools pytest \
@@ -87,3 +85,5 @@ RUN wget https://archive.apache.org/dist/ant/binaries/apache-ant-1.9.15-bin.tar.
     && ln -s /opt/apache-ant-1.9.15 /opt/ant \
     && sudo ln -s /opt/ant/bin/ant /usr/bin/ant
 
+COPY ./install-mpi.sh /install-mpi.sh
+RUN bash install-mpi.sh ${MPI}

docker/base/centos8/install-mpi.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+if [[ -z $1 ]]; then
+    echo "Must provide MPI that you want to install"
+    exit 1
+fi
+
+# Install only the dependencies for a given package
+# Source: https://serverfault.com/questions/429123/howto-get-yum-to-install-only-dependencies-for-a-given-pakage
+yum_install_only_deps () {
+    if [[ -z "$1" ]]; then
+        echo "Package required for installing deps"
+        exit 1
+    fi
+    yum deplist $1 | grep provider | awk '{print $2}' | sort | uniq | grep -v $PACKAGE | sed ':a;N;$!ba;s/\n/ /g' | xargs yum -y install
+}
+
+if [[ "$1" == "openmpi-devel" ]]; then
+    yum_install_only_deps $1
+    
+    MAJOR_MINOR=4.0
+    PATCH=6
+    OPENMPI=openmpi-${MAJOR_MINOR}.${PATCH}
+    
+    wget https://download.open-mpi.org/release/open-mpi/v${MAJOR_MINOR}/${OPENMPI}.tar.gz
+    tar -xf ./${OPENMPI}.tar.gz
+    rm ./${OPENMPI}.tar.gz
+    
+    cd ${OPENMPI}
+    ./configure
+    make -j 4
+    make install
+    cd ..
+    rm -rf ${OPENMPI}
+else 
+    echo "Unknown/unsupported MPI. Existing without installing."
+    exit 1
+fi