Merge pull request #11 from rse-ops/add/spack-intel-mpi-libfabric

add variant with intel mpi and libfabric

spack-intel-mpi-libfabric/Dockerfile

@@ -0,0 +1,187 @@
+ARG tag="8"
+FROM rockylinux:${tag} as builder
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV SPACK_ROOT=/opt/spack-environment/spack
+ARG spack_cpu_arch=x86_64
+
+#  Enable PowerTools for development packages
+RUN yum -y update \
+ && dnf -y install 'dnf-command(config-manager)' \
+ && yum config-manager --set-enabled powertools \
+ && yum -y update \
+#  Enable EPEL
+ && yum -y install epel-release \
+#  Utilities
+ && yum -y install \
+	wget \
+	man-db \
+	less \
+	xz \
+	lbzip2 \
+        fftw-devel \
+        fftw \
+	git \
+	curl \
+	bind-utils \
+	sudo \
+	munge \
+	ccache \
+	lua \
+	valgrind \
+	jq \
+	which \
+	file \
+	unzip \
+	vim \
+	patch \
+	diffutils \
+#  Compilers, autotools
+	pkgconfig \
+	libtool \
+	autoconf \
+	automake \
+	gcc-gfortran \
+	gcc \
+	gcc-c++ \
+	make \
+	cmake \
+	bison \	
+	flex \
+#  Python
+	python36 \
+	python3-devel \
+	python3-cffi \
+	python3-six \
+	python3-yaml \
+	python3-jsonschema \
+	python3-sphinx \
+#  Development dependencies
+	libsodium-devel \
+        libyaml-devel \
+        libgomp \
+	zeromq-devel \
+	czmq-devel \
+	jansson-devel \
+	munge-devel \
+	ncurses-devel \
+	lz4-devel \
+	sqlite-devel \
+        boost-devel \
+	libuuid-devel \
+	hwloc-devel \
+	lua-devel \
+        libedit-devel \
+	valgrind-devel \
+	libs3-devel \
+	systemd-devel \
+	libarchive-devel \
+	pam-devel \
+#  Other deps
+        openssh-server \
+        openssh-clients \
+	perl-Time-HiRes \
+	lua-posix \
+	libfaketime \
+	cppcheck \
+	enchant \
+	aspell \
+	aspell-en \
+	sudo \
+	glibc-langpack-en \
+	hwloc \
+ && yum clean all
+
+#  Set default /usr/bin/python to python3
+RUN alternatives --set python /usr/bin/python3
+
+ENV LANG=C.UTF-8
+RUN printf "LANG=C.UTF-8" > /etc/locale.conf
+
+# What we want to install and how we want to install it
+# is specified in a manifest file (spack.yaml)
+RUN mkdir /opt/spack-environment \
+    &&  (echo "spack:" \
+    &&   echo "  specs:" \
+    &&   echo "  - intel-mpi@2021.8.0 target=${spack_cpu_arch}" \
+    &&   echo "  - flux-sched target=${spack_cpu_arch}" \
+    &&   echo "  - flux-core+mpi target=${spack_cpu_arch}" \
+    &&   echo "  concretizer:" \
+    &&   echo "    unify: true" \
+    &&   echo "  packages:" \
+    &&   echo "    intel-mpi:" \
+    &&   echo "      externals:" \
+    &&   echo "       - spec: intel-mpi@2021.8.0" \
+    &&   echo "         prefix: /opt/intel/mpi/2021.8.0" \
+    &&   echo "         buildable: false" \
+    &&   echo "    all:" \
+    &&   echo "      providers:"\
+    &&   echo "        mpi:" \
+    &&   echo "         - intel-mpi" \
+    &&   echo "  config:" \
+    &&   echo "    install_tree: /opt/software" \
+    &&   echo "  view: /opt/view") > /opt/spack-environment/spack.yaml
+
+WORKDIR /opt/spack-environment
+RUN git clone https://github.com/spack/spack.git && \
+    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
+
+# And then
+# FI_PROVIDER_PATH=<install_dir> to invoke the provider
+# FI_PROVIDER=<net|psm3>.
+
+# Install the software, remove unnecessary deps
+RUN cd /opt/spack-environment && \
+    cd spack && \
+    # When flux-core 0.49.0 added, but flux-pmix 0.3.0 not added yet
+    git checkout b32edd3a72e8c39d69dea4ab0dd2066d460913d5 && \
+    mkdir -p /opt/spack-environment/spack/var/spack/repos/builtin/packages/flux-security 
+
+# This has openmpi replaced with virtual package mpi
+# Enable Intel(R) MPI 2021 Libraries with:
+# source /opt/intel/mpi/latest/env/vars.sh 
+COPY ./package.py /opt/spack-environment/spack/var/spack/repos/builtin/packages/flux-core/package.py 
+COPY ./flux-security/package.py /opt/spack-environment/spack/var/spack/repos/builtin/packages/flux-security/package.py 
+RUN . /opt/intel/mpi/latest/env/vars.sh && \
+    cd /opt/spack-environment \
+    && . spack/share/spack/setup-env.sh \
+    && spack env activate . \
+    && spack external find intel-mpi \
+    && spack external find openssh \
+    && spack external find cmake \
+    && spack external find python \
+    && spack install --reuse --fail-fast \
+    && spack gc -y
+
+# Strip all the binaries
+RUN find -L /opt/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 -s
+
+# Modifications to the environment that are necessary to run
+RUN cd /opt/spack-environment \
+    && . spack/share/spack/setup-env.sh \
+    && echo ". /opt/intel/mpi/latest/env/vars.sh" >> /etc/profile.d/z10_spack_environment.sh \
+    && spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
+
+# Important! The versions of flux with pmix won't work without this flag
+# the flux-restful api added support via version 0.0.15 of the python client
+ENV FLUX_OPTION_FLAGS="-ompi=openmpi@5"
+
+# Make sure that flux owns the spack install (so we see it)
+RUN sudo adduser --password flux --uid 1000 flux && \
+    chown -R flux /opt && \
+    sudo chmod -R +r /opt
+
+COPY ./etc.sudoers /etc/sudoers
+COPY ./entrypoint.sh /entrypoint.sh
+ENTRYPOINT ["/bin/bash", "/entrypoint.sh"]

spack-intel-mpi-libfabric/entrypoint.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+. /etc/profile.d/z10_spack_environment.sh 
+
+exec "$@"

spack-intel-mpi-libfabric/etc.sudoers

@@ -0,0 +1,31 @@
+#
+# This file MUST be edited with the 'visudo' command as root.
+#
+# Please consider adding local content in /etc/sudoers.d/ instead of
+# directly modifying this file.
+#
+# See the man page for details on how to write a sudoers file.
+#
+Defaults	env_reset
+Defaults	mail_badpass
+Defaults	secure_path="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/opt/view/bin"
+
+# Host alias specification
+
+# User alias specification
+
+# Cmnd alias specification
+
+# User privilege specification
+root	ALL=(ALL:ALL) ALL
+flux  ALL=(ALL) NOPASSWD:ALL
+
+# Members of the admin group may gain root privileges
+%admin ALL=(ALL) ALL
+
+# Allow members of group sudo to execute any command
+%sudo	ALL=(ALL:ALL) ALL
+
+# See sudoers(5) for more information on "#include" directives:
+
+#includedir /etc/sudoers.d

spack-intel-mpi-libfabric/flux-security/package.py

@@ -0,0 +1,62 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
+import spack.util.executable
+from spack.package import *
+
+
+class FluxSecurity(AutotoolsPackage):
+    """Independent project for Flux security code and APIs."""
+
+    homepage = "https://github.com/flux-framework/flux-security"
+    url = "https://github.com/flux-framework/flux-security/releases/download/v0.8.0/flux-security-0.8.0.tar.gz"
+    git = "https://github.com/flux-framework/flux-security.git"
+    tags = ["radiuss", "e4s"]
+
+    maintainers("grondo")
+
+    version("master", branch="master")
+    version("0.9.0", sha256="2258120c6f32ca0b5b13b166bae56d9bd82a44c6eeaa6bc6187e4a4419bdbcc0")
+    version("0.8.0", sha256="9963628063b4abdff6bece03208444c8f23fbfda33c20544c48b21e9f4819ce2")
+
+    # Need autotools when building on master:
+    depends_on("autoconf", type="build", when="@master")
+    depends_on("automake", type="build", when="@master")
+    depends_on("libtool", type="build", when="@master")
+
+    depends_on("pkgconfig")
+    depends_on("libsodium@1.0.14:")
+    depends_on("jansson")
+    depends_on("libuuid")
+    depends_on("munge")
+    depends_on("libpam")
+
+    def setup(self):
+        pass
+
+    @when("@master")
+    def setup(self):
+        with working_dir(self.stage.source_path):
+            # Allow git-describe to get last tag so flux-version works:
+            git = which("git")
+            # When using spack develop, this will already be unshallow
+            try:
+                git("fetch", "--unshallow")
+                git("config", "remote.origin.fetch", "+refs/heads/*:refs/remotes/origin/*")
+                git("fetch", "origin")
+            except spack.util.executable.ProcessError:
+                git("fetch")
+
+    def autoreconf(self, spec, prefix):
+        self.setup()
+        if os.path.exists(self.configure_abs_path):
+            return
+        # make sure configure doesn't get confused by the staging symlink
+        with working_dir(self.configure_directory):
+            # Bootstrap with autotools
+            bash = which("bash")
+            bash("./autogen.sh")