Merge pull request #2 from jithinjosepkl/master

CentOS HPC image
Azure · Oct 11, 2019 · 98fcfe0 · 98fcfe0
2 parents 9bd0431 + 0303cec
commit 98fcfe0
Show file tree

Hide file tree

Showing 16 changed files with 295 additions and 0 deletions.
diff --git a/centos/centos-7.6/hpc-tuning.sh b/centos/centos-7.6/hpc-tuning.sh
@@ -0,0 +1 @@
+../common/hpc-tuning.sh
diff --git a/centos/centos-7.6/install.sh b/centos/centos-7.6/install.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -ex
+
+# install utils
+./install_utils.sh
+
+# install compilers
+./install_gcc-8.2.sh
+
+# install mellanox ofed
+./install_mellanoxofed.sh
+
+# install mpi libraries
+./install_mpis.sh
+
+# optimizations
+./hpc-tuning.sh
+
diff --git a/centos/centos-7.6/install_gcc-8.2.sh b/centos/centos-7.6/install_gcc-8.2.sh
@@ -0,0 +1 @@
+../../common/install_gcc-8.2.sh
diff --git a/centos/centos-7.6/install_mellanoxofed.sh b/centos/centos-7.6/install_mellanoxofed.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+set -ex
+
+wget https://www.mellanox.com/downloads/ofed/MLNX_OFED-4.7-1.0.0.1/MLNX_OFED_LINUX-4.7-1.0.0.1-rhel7.6-x86_64.tgz
+tar zxvf MLNX_OFED_LINUX-4.7-1.0.0.1-rhel7.6-x86_64.tgz
+./MLNX_OFED_LINUX-4.7-1.0.0.1-rhel7.6-x86_64/mlnxofedinstall --force
+
diff --git a/centos/centos-7.6/install_mpis.sh b/centos/centos-7.6/install_mpis.sh
@@ -0,0 +1 @@
+../../common/install_mpis.sh
diff --git a/centos/centos-7.6/install_utils.sh b/centos/centos-7.6/install_utils.sh
@@ -0,0 +1 @@
+../common/install_utils.sh
diff --git a/centos/centos-7.7/hpc-tuning.sh b/centos/centos-7.7/hpc-tuning.sh
@@ -0,0 +1 @@
+../common/hpc-tuning.sh
diff --git a/centos/centos-7.7/install.sh b/centos/centos-7.7/install.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -ex
+
+# install utils
+./install_utils.sh
+
+# install compilers
+./install_gcc-8.2.sh
+
+# install mellanox ofed
+./install_mellanoxofed.sh
+
+# install mpi libraries
+./install_mpis.sh
+
+# optimizations
+./hpc-tuning.sh
+
diff --git a/centos/centos-7.7/install_gcc-8.2.sh b/centos/centos-7.7/install_gcc-8.2.sh
@@ -0,0 +1 @@
+../../common/install_gcc-8.2.sh
diff --git a/centos/centos-7.7/install_mellanoxofed.sh b/centos/centos-7.7/install_mellanoxofed.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+set -ex
+
+wget http://content.mellanox.com/ofed/MLNX_OFED-4.7-1.0.0.1/MLNX_OFED_LINUX-4.7-1.0.0.1-rhel7.7-x86_64.tgz
+tar zxvf MLNX_OFED_LINUX-4.7-1.0.0.1-rhel7.7-x86_64.tgz
+./MLNX_OFED_LINUX-4.7-1.0.0.1-rhel7.7-x86_64/mlnxofedinstall --force
+
diff --git a/centos/centos-7.7/install_mpis.sh b/centos/centos-7.7/install_mpis.sh
@@ -0,0 +1 @@
+../../common/install_mpis.sh
diff --git a/centos/centos-7.7/install_utils.sh b/centos/centos-7.7/install_utils.sh
@@ -0,0 +1 @@
+../common/install_utils.sh
diff --git a/centos/common/hpc-tuning.sh b/centos/common/hpc-tuning.sh
@@ -0,0 +1,22 @@
+# Disable some unneeded services by default (administrators can re-enable if desired)
+systemctl disable wpa_supplicant
+systemctl disable abrtd
+systemctl disable firewalld
+
+# Update memory limits
+cat << EOF >> /etc/security/limits.conf
+*               hard    memlock         unlimited
+*               soft    memlock         unlimited
+*               soft    nofile          65535
+*               hard    nofile          65535
+EOF
+
+# Enable reclaim mode
+echo "vm.zone_reclaim_mode = 1" >> /etc/sysctl.conf
+sysctl -p
+
+# Configure WALinuxAgent
+sed -i -e 's/# OS.EnableRDMA=y/OS.EnableRDMA=y/g' /etc/waagent.conf
+sed -i -e 's/CGroups.EnforceLimits=n/CGroups.EnforceLimits=y/g' /etc/waagent.conf
+systemctl enable waagent
+
diff --git a/centos/common/install_utils.sh b/centos/common/install_utils.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+set -ex
+
+# Install pre-reqs and development tools
+yum groupinstall -y "Development Tools"
+yum install -y numactl \
+    numactl-devel \
+    libxml2-devel \
+    byacc \
+    environment-modules \
+    python-devel \
+    python-setuptools \
+    gtk2 \
+    atk \
+    cairo \
+    tcl \
+    tk \
+    m4 \
+    glibc-devel \
+    glibc-static \
+    libudev-devel \
+    binutils \
+    binutils-devel \
+	selinux-policy-devel \
+	kernel-headers \
+	nfs-utils
diff --git a/common/install_gcc-8.2.sh b/common/install_gcc-8.2.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+set -x
+
+# Install gcc 8.2
+
+wget ftp://gcc.gnu.org/pub/gcc/infrastructure/gmp-6.1.0.tar.bz2
+tar -xvf gmp-6.1.0.tar.bz2
+cd ./gmp-6.1.0
+./configure && make -j &&  make install
+cd ..
+
+wget ftp://gcc.gnu.org/pub/gcc/infrastructure/mpfr-3.1.4.tar.bz2
+tar -xvf mpfr-3.1.4.tar.bz2
+cd mpfr-3.1.4
+./configure && make -j &&  make install
+cd ..
+
+wget ftp://gcc.gnu.org/pub/gcc/infrastructure/mpc-1.0.3.tar.gz
+tar -xvf mpc-1.0.3.tar.gz
+cd mpc-1.0.3
+./configure && make -j &&  make install
+cd ..
+
+# install gcc 8.2
+wget https://ftp.gnu.org/gnu/gcc/gcc-8.2.0/gcc-8.2.0.tar.gz
+tar -xvf gcc-8.2.0.tar.gz
+cd gcc-8.2.0
+./configure --disable-multilib --prefix=/opt/gcc-8.2.0 && make -j && make install
+cd ..
+
+
+# create modulefile
+cat << EOF >> /usr/share/Modules/modulefiles/gcc-8.2.0
+#%Module 1.0
+#
+#  GCC 8.2.0
+#
+
+prepend-path    PATH            /opt/gcc-8.2.0/bin
+prepend-path    LD_LIBRARY_PATH /opt/gcc-8.2.0/lib64
+setenv          CC              /opt/gcc-8.2.0/bin/gcc
+setenv          GCC             /opt/gcc-8.2.0/bin/gcc
+EOF
+
diff --git a/common/install_mpis.sh b/common/install_mpis.sh
@@ -0,0 +1,145 @@
+# Load gcc-8.2.0
+export PATH=/opt/gcc-8.2.0/bin:$PATH
+export LD_LIBRARY_PATH=/opt/gcc-8.2.0/lib64:$LD_LIBRARY_PATH
+set CC=/opt/gcc-8.2.0/bin/gcc
+set GCC=/opt/gcc-8.2.0/bin/gcc
+
+
+INSTALL_PREFIX=/opt
+
+# HPC-X v2.5.0
+HPCX_VERSION="v2.5.0"
+wget http://www.mellanox.com/downloads/hpc/hpc-x/v2.5/hpcx-v2.5.0-gcc-MLNX_OFED_LINUX-4.7-1.0.0.1-redhat7.6-x86_64.tbz
+tar -xvf hpcx-v2.5.0-gcc-MLNX_OFED_LINUX-4.7-1.0.0.1-redhat7.6-x86_64.tbz
+mv hpcx-v2.5.0-gcc-MLNX_OFED_LINUX-4.7-1.0.0.1-redhat7.6-x86_64 ${INSTALL_PREFIX}
+HPCX_PATH=${INSTALL_PREFIX}/hpcx-v2.5.0-gcc-MLNX_OFED_LINUX-4.7-1.0.0.1-redhat7.6-x86_64
+HCOLL_PATH=${HPCX_PATH}/hcoll
+UCX_PATH=${HPCX_PATH}/ucx
+
+# MVAPICH2 2.3.2
+MV2_VERSION="2.3.2"
+wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-${MV2_VERSION}.tar.gz
+tar -xvf mvapich2-${MV2_VERSION}.tar.gz
+cd mvapich2-${MV2_VERSION}
+./configure --prefix=${INSTALL_PREFIX}/mvapich2-${MV2_VERSION} --enable-g=none --enable-fast=yes && make -j && make install
+cd ..
+
+
+# OpenMPI 4.0.1
+OMPI_VERSION="4.0.1"
+wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-${OMPI_VERSION}.tar.gz
+tar -xvf openmpi-${OMPI_VERSION}.tar.gz
+cd openmpi-${OMPI_VERSION}
+./configure --prefix=${INSTALL_PREFIX}/openmpi-${OMPI_VERSION} --with-ucx=${UCX_PATH} --with-hcoll=${HCOLL_PATH} --enable-mpirun-prefix-by-default --with-platform=contrib/platform/mellanox/optimized && make -j && make install
+cd ..
+
+
+# Intel MPI 2019 (update 5)
+IMPI_2019_VERSION="2019.5.281"
+wget http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15838/l_mpi_${IMPI_2019_VERSION}.tgz
+tar -xvf l_mpi_${IMPI_2019_VERSION}.tgz
+cd l_mpi_${IMPI_2019_VERSION}
+sed -i -e 's/ACCEPT_EULA=decline/ACCEPT_EULA=accept/g' silent.cfg
+./install.sh --silent ./silent.cfg
+cd ..
+
+
+# Intel MPI 2018 (update 4)
+IMPI_VERSION="2018.4.274"
+wget http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/l_mpi_${IMPI_VERSION}.tgz
+tar -xvf l_mpi_${IMPI_VERSION}.tgz
+cd l_mpi_${IMPI_VERSION}
+sed -i -e 's/ACCEPT_EULA=decline/ACCEPT_EULA=accept/g' silent.cfg
+./install.sh --silent ./silent.cfg
+cd ..
+
+
+# Setup module files for MPIs
+mkdir -p /usr/share/Modules/modulefiles/mpi/
+
+# HPC-X
+cat << EOF >> /usr/share/Modules/modulefiles/mpi/hpcx-${HPCX_VERSION}
+#%Module 1.0
+#
+#  HPCx
+#
+conflict        mpi
+module load /opt/hpcx-v2.5.0-gcc-MLNX_OFED_LINUX-4.7-1.0.0.1-redhat7.6-x86_64/modulefiles/hpcx
+EOF
+
+
+# MVAPICH2
+cat << EOF >> /usr/share/Modules/modulefiles/mpi/mvapich2-${MV2_VERSION}
+#%Module 1.0
+#
+#  MVAPICH2
+#
+conflict        mpi
+prepend-path    PATH            /opt/mvapich2-${MV2_VERSION}/bin
+prepend-path    LD_LIBRARY_PATH /opt/mvapich2-${MV2_VERSION}/lib
+prepend-path    MANPATH         /opt/mvapich2-${MV2_VERSION}/share/man
+setenv          MPI_BIN         /opt/mvapich2-${MV2_VERSION}/bin
+setenv          MPI_INCLUDE     /opt/mvapich2-${MV2_VERSION}/include
+setenv          MPI_LIB         /opt/mvapich2-${MV2_VERSION}/lib
+setenv          MPI_MAN         /opt/mvapich2-${MV2_VERSION}/share/man
+setenv          MPI_HOME        /opt/mvapich2-${MV2_VERSION}
+EOF
+
+# OpenMPI
+cat << EOF >> /usr/share/Modules/modulefiles/mpi/openmpi-${OMPI_VERSION}
+#%Module 1.0
+#
+#  OpenMPI
+#
+conflict        mpi
+prepend-path    PATH            /opt/openmpi-${OMPI_VERSION}/bin
+prepend-path    LD_LIBRARY_PATH /opt/openmpi-${OMPI_VERSION}/lib
+prepend-path    MANPATH         /opt/openmpi-${OMPI_VERSION}/share/man
+setenv          MPI_BIN         /opt/openmpi-${OMPI_VERSION}/bin
+setenv          MPI_INCLUDE     /opt/openmpi-${OMPI_VERSION}/include
+setenv          MPI_LIB         /opt/openmpi-${OMPI_VERSION}/lib
+setenv          MPI_MAN         /opt/openmpi-${OMPI_VERSION}/share/man
+setenv          MPI_HOME        /opt/openmpi-${OMPI_VERSION}
+EOF
+
+#IntelMPI-v2018
+cat << EOF >> /usr/share/Modules/modulefiles/mpi/impi_${IMPI_VERSION}
+#%Module 1.0
+#
+#  Intel MPI
+#
+conflict        mpi
+prepend-path    PATH            /opt/intel/impi/${IMPI_VERSION}/intel64/bin
+prepend-path    LD_LIBRARY_PATH /opt/intel/impi/${IMPI_VERSION}/intel64/lib
+prepend-path    MANPATH         /opt/intel/impi/${IMPI_VERSION}/man
+setenv          MPI_BIN         /opt/intel/impi/${IMPI_VERSION}/intel64/bin
+setenv          MPI_INCLUDE     /opt/intel/impi/${IMPI_VERSION}/intel64/include
+setenv          MPI_LIB         /opt/intel/impi/${IMPI_VERSION}/intel64/lib
+setenv          MPI_MAN         /opt/intel/impi/${IMPI_VERSION}/man
+setenv          MPI_HOME        /opt/intel/impi/${IMPI_VERSION}/intel64
+EOF
+
+#IntelMPI-v2019
+cat << EOF >> /usr/share/Modules/modulefiles/mpi/impi_${IMPI_2019_VERSION}
+#%Module 1.0
+#
+#  Intel MPI
+#
+conflict        mpi
+prepend-path    PATH            /opt/intel/impi/${IMPI_2019_VERSION}/intel64/bin
+prepend-path    LD_LIBRARY_PATH /opt/intel/impi/${IMPI_2019_VERSION}/intel64/lib
+prepend-path    MANPATH         /opt/intel/impi/${IMPI_2019_VERSION}/man
+setenv          MPI_BIN         /opt/intel/impi/${IMPI_2019_VERSION}/intel64/bin
+setenv          MPI_INCLUDE     /opt/intel/impi/${IMPI_2019_VERSION}/intel64/include
+setenv          MPI_LIB         /opt/intel/impi/${IMPI_2019_VERSION}/intel64/lib
+setenv          MPI_MAN         /opt/intel/impi/${IMPI_2019_VERSION}/man
+setenv          MPI_HOME        /opt/intel/impi/${IMPI_2019_VERSION}/intel64
+EOF
+
+# Create symlinks for modulefiles
+ln -s /usr/share/Modules/modulefiles/mpi/hpcx-${HPCX_VERSION} /usr/share/Modules/modulefiles/mpi/hpcx
+ln -s /usr/share/Modules/modulefiles/mpi/mvapich2-${MV2_VERSION} /usr/share/Modules/modulefiles/mpi/mvapich2
+ln -s /usr/share/Modules/modulefiles/mpi/openmpi-${OMPI_VERSION} /usr/share/Modules/modulefiles/mpi/openmpi
+ln -s /usr/share/Modules/modulefiles/mpi/impi_${IMPI_2019_VERSION} /usr/share/Modules/modulefiles/mpi/impi-2019
+ln -s /usr/share/Modules/modulefiles/mpi/impi_${IMPI_VERSION} /usr/share/Modules/modulefiles/mpi/impi
+