add build with lammps and intel mpi on rocky (#29)

* add hpctoolkit build for rocky
* add build with lammps and intel mpi on rocky

this was suggested by google. it is not clear if this will
work nicely with hpctoolkit, testing now

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

.github/workflows/docker-builds.yaml

@@ -27,12 +27,14 @@ jobs:
                ["ovis-hpc", "ghcr.io/converged-computing/metric-ovis-hpc:latest"],
                ["kripke", "ghcr.io/converged-computing/metric-kripke:latest"],
                ["hpctoolkit-viewer", "ghcr.io/converged-computing/metric-hpctoolkit-viewer:latest"],
-               ["hpctoolkit-containerize", "ghcr.io/converged-computing/metric-hpctoolkit-view:latest"],
+               ["hpctoolkit-view", "ghcr.io/converged-computing/metric-hpctoolkit-view:ubuntu"],
+               ["hpctoolkit-view-rocky", "ghcr.io/converged-computing/metric-hpctoolkit-view:rocky"],
                ["hpctoolkit-spack", "ghcr.io/converged-computing/metric-hpctoolkit-spack:latest"],
                ["hpctoolkit", "ghcr.io/converged-computing/metric-hpctoolkit:latest"],
                ["bdas", "ghcr.io/converged-computing/metric-bdas:latest"],
                ["laghos", "ghcr.io/converged-computing/metric-laghos:latest"],
                ["nekbone", "ghcr.io/converged-computing/metric-nekbone:latest"],
+               ["lammps-intel-mpi-rocky", "ghcr.io/converged-computing/metric-lammps-intel-mpi:rocky"],
                ["lammps", "ghcr.io/converged-computing/metric-lammps:latest"],
                ["perf-kit-benchmarker", "ghcr.io/converged-computing/metric-perf-kit-benchmarker:latest"]] 
 

hpctoolkit-view-rocky/Dockerfile

@@ -0,0 +1,49 @@
+FROM spack/rockylinux8:latest as builder
+
+# What we want to install and how we want to install it
+# is specified in a manifest file (spack.yaml)
+RUN mkdir /opt/spack-environment \
+&&  (echo spack: \
+&&   echo '  specs: [hpctoolkit +papi +mpi]' \
+&&   echo '  view: /opt/views/view' \
+&&   echo '  concretizer:' \
+&&   echo '    unify: true' \
+&&   echo '  packages:' \
+&&   echo '    all:' \
+&&   echo '      require: ["target=:x86_64"]' \
+&&   echo '  config:' \
+&&   echo '    install_tree: /opt/software') > /opt/spack-environment/spack.yaml
+
+# Install the software, remove unnecessary deps
+RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y
+
+# Strip all the binaries
+RUN find -L /opt/views/view/* -type f -exec readlink -f '{}' \; | \
+    xargs file -i | \
+    grep 'charset=binary' | \
+    grep 'x-executable\|x-archive\|x-sharedlib' | \
+    awk -F: '{print $1}' | xargs strip
+
+# Modifications to the environment that are necessary to run
+RUN cd /opt/spack-environment && \
+    spack env activate --sh -d . > activate.sh
+
+# Bare OS image to run the installed executables
+FROM rockylinux:8
+
+COPY --from=builder /opt/spack-environment /opt/spack-environment
+COPY --from=builder /opt/software /opt/software
+
+# paths.view is a symlink, so copy the parent to avoid dereferencing and duplicating it
+COPY --from=builder /opt/views /opt/views
+
+RUN { \
+      echo '#!/bin/sh' \
+      && echo '.' /opt/spack-environment/activate.sh \
+      && echo 'exec "$@"'; \
+    } > /entrypoint.sh \
+&& chmod a+x /entrypoint.sh \
+&& ln -s /opt/views/view /opt/view
+
+ENTRYPOINT [ "/entrypoint.sh" ]
+CMD [ "/bin/bash" ]

lammps-intel-mpi-rocky/Dockerfile

@@ -0,0 +1,91 @@
+ARG tag="8"
+FROM rockylinux:${tag} as builder
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+#  Enable PowerTools for development packages
+RUN yum -y update \
+ && dnf -y install 'dnf-command(config-manager)' \
+ && yum config-manager --set-enabled powertools \
+ && yum -y update \
+ && yum -y install epel-release \
+ && yum -y install \
+	wget \
+        fftw-devel \
+        fftw \
+	git \
+	curl \
+	bind-utils \
+	sudo \
+	jq \
+	which \
+	file \
+	unzip \
+	vim \
+	patch \
+	diffutils \
+	pkgconfig \
+	libtool \
+	autoconf \
+	automake \
+	gcc-gfortran \
+	gcc \
+	gcc-c++ \
+	make \
+	cmake \
+	bison \	
+	flex \
+	python3-devel \
+        fftw3-devel fftw3 \
+        openssh-server \
+        openssh-clients \
+ && yum clean all
+
+#  Set default /usr/bin/python to python3
+RUN alternatives --set python /usr/bin/python3
+
+ENV LANG=C.UTF-8
+RUN printf "LANG=C.UTF-8" > /etc/locale.conf
+
+RUN git clone https://github.com/GoogleCloudPlatform/hpc-tools && \
+    yum group install -y "Development tools" && \
+    cd hpc-tools/rocky_linux_8 && \
+    chmod +x google_install_intelmpi google_hpc_libfabric && \
+    # installs to /opt/intel
+    ./google_install_intelmpi --impi_2021 && \
+    # And install libfabric with net/psm3 
+    ./google_hpc_libfabric --net --psm3
+
+
+# Modifications to the environment that are necessary to run
+RUN echo ". /opt/intel/mpi/latest/env/vars.sh" >> /etc/profile.d/z10_intel_environment.sh
+WORKDIR /opt/
+
+# install laamps alongside spack
+RUN . /opt/intel/mpi/latest/env/vars.sh  && \
+    git clone --depth 1 --branch stable_29Sep2021_update2 https://github.com/lammps/lammps.git /opt/lammps && \
+    cd /opt/lammps && \
+    mkdir build && \
+    cd build && \
+    . /etc/profile && \ 
+    cmake ../cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr -DPKG_REAXFF=yes -DBUILD_MPI=yes -DPKG_OPT=yes -DFFT=FFTW3 -DCMAKE_PREFIX_PATH=/opt/intel/mpi/2021.8.0 -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu && \
+    make && \
+    make install
+
+# sshd
+RUN ssh-keygen -q -t rsa -b 2048 -f /etc/ssh/ssh_host_rsa_key -N '' && \
+    ssh-keygen -q -t ecdsa -f /etc/ssh/ssh_host_ecdsa_key -N '' && \
+    ssh-keygen -t dsa -f /etc/ssh/ssh_host_ed25519_key  -N '';
+
+WORKDIR /opt/lammps/examples/reaxff/HNS
+
+# Hack for ssh for now...
+RUN echo "        LogLevel ERROR" >> /etc/ssh/ssh_config && \
+    echo "        StrictHostKeyChecking no" >> /etc/ssh/ssh_config && \
+    echo "        UserKnownHostsFile=/dev/null" >> /etc/ssh/ssh_config && \
+    cd /root && \
+    mkdir -p /run/sshd && \
+    ssh-keygen -t rsa -N "" -f /root/.ssh/id_rsa && chmod og+rX . && \
+    cd .ssh && cat id_rsa.pub > authorized_keys && chmod 644 authorized_keys
+
+EXPOSE 22