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Update README.md file for noaa-aws 1.8.0 installation.
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| # Provisiong ParallelWorks AWS clusters | ||
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| ## Steps to perform when provisioning a cluster for the very first time | ||
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| This section provides step by step instructions for installing the basic packages (OS packages, external packages) for spack-stack. Following these steps ensures that the site configuration files in `configs/sites/noaa-aws` work out of the box. | ||
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| ### Basic system packages | ||
| ``` | ||
| sudo su | ||
| chmod 777 /contrib | ||
| # The following three commands were necessary to fix failures accessing these repos | ||
| yum-config-manager --disable intel-clck-2019-repo | ||
| yum-config-manager --disable intel-hpc-platform | ||
| yum-config-manager --disable intelpython | ||
| yum install -y qt5-qtbase-devel | ||
| yum install -y qt5-qtsvg-devel | ||
| yum install -y xorg-x11-xauth | ||
| yum install -y xorg-x11-apps | ||
| yum install -y perl-IPC-Cmd | ||
| yum install -y gettext-devel | ||
| yum install -y m4 | ||
| exit | ||
| ``` | ||
| Create a script that can be added to the cluster resource config so that these packages get installed automatically when provisioning new clusters later: | ||
| ``` | ||
| mkdir -p /contrib/admin | ||
| cat <<EOF > /contrib/admin/basic_setup.sh | ||
| #!/bin/bash | ||
| chmod 777 /contrib | ||
| yum install -y qt5-qtbase-devel | ||
| yum install -y qt5-qtsvg-devel | ||
| yum install -y xorg-x11-xauth | ||
| yum install -y xorg-x11-apps | ||
| yum install -y perl-IPC-Cmd | ||
| yum install -y gettext-devel | ||
| yum install -y m4 | ||
| EOF | ||
| chmod a+x /contrib/admin/basic_setup.sh | ||
| ``` | ||
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| ### Create a mysql config for local R2D2 use (if applicable) | ||
| ``` | ||
| sudo su | ||
| cat <<EOF > /contrib/admin/my.cnf | ||
| [mysqld] | ||
| datadir=/mysql_local/data | ||
| socket=/mysql_local/data/mysql.sock | ||
| symbolic-links=0 | ||
| default-authentication-plugin=mysql_native_password | ||
| [mysqld_safe] | ||
| log-error=/mysql_local/log/mariadb.log | ||
| pid-file=/mysql_local/run/mariadb.pid | ||
| EOF | ||
| chmod 644 /contrib/admin/my.cnf | ||
| exit | ||
| ``` | ||
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| ### Build external packages for spack-stack | ||
| ``` | ||
| mkdir -p /contrib/spack-stack | ||
| mkdir /contrib/spack-stack/modulefiles | ||
| cd /contrib/spack-stack/ | ||
| mkdir -p git-lfs-2.4.1/src | ||
| cd git-lfs-2.4.1/src | ||
| wget http://mirror.centos.org/centos/7/sclo/x86_64/rh/Packages/r/rh-git218-git-lfs-2.4.1-3.el7.x86_64.rpm | ||
| rpm2cpio rh-git218-git-lfs-2.4.1-3.el7.x86_64.rpm | cpio -idmv | ||
| mv opt/rh/rh-git218/root/usr/* .. | ||
| rm -fr opt | ||
| cd /contrib/spack-stack/modulefiles | ||
| mkdir git-lfs | ||
| # Create the modulefile from the template in doc/modulefile_templates | ||
| cd /contrib/spack-stack/ | ||
| mkdir -p mysql-8.0.31/src | ||
| cd mysql-8.0.31/src | ||
| ldd --version | ||
| wget https://dev.mysql.com/get/Downloads/MySQL-8.0/mysql-8.0.31-linux-glibc2.17-x86_64-minimal.tar.xz | ||
| tar -xvf mysql-8.0.31-linux-glibc2.17-x86_64-minimal.tar.xz | ||
| mv mysql-8.0.31-linux-glibc2.17-x86_64-minimal/* .. | ||
| rmdir mysql-8.0.31-linux-glibc2.17-x86_64-minimal | ||
| cd /contrib/spack-stack/modulefiles | ||
| mkdir mysql | ||
| # Create the modulefile from the template in doc/modulefile_templates | ||
| cd /contrib/spack-stack/ | ||
| mkdir -p cmake-3.27.2/src | ||
| cd cmake-3.27.2/src | ||
| wget https://github.com/Kitware/CMake/releases/download/v3.27.2/cmake-3.27.2-linux-x86_64.tar.gz | ||
| tar -xvzf cmake-3.27.2-linux-x86_64.tar.gz | ||
| mv cmake-3.27.2-linux-x86_64/* .. | ||
| rmdir cmake-3.27.2-linux-x86_64 | ||
| cd /contrib/spack-stack/modulefiles | ||
| mkdir cmake | ||
| # Create the modulefile from the template in doc/modulefile_templates | ||
| # Set up basic modules for building the external ecflow package | ||
| module unuse /opt/cray/craype/default/modulefiles | ||
| module unuse /opt/cray/modulefiles | ||
| module purge | ||
| module load gnu/9.2.0 | ||
| module use /contrib/spack-stack/modulefiles | ||
| module load cmake/3.27.2 | ||
| mkdir -p /contrib/spack-stack/ecflow-5.8.4/src | ||
| cd /contrib/spack-stack/ecflow-5.8.4/src | ||
| wget https://confluence.ecmwf.int/download/attachments/8650755/ecFlow-5.8.4-Source.tar.gz?api=v2 | ||
| wget https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.tar.gz | ||
| mv ecFlow-5.8.4-Source.tar.gz\?api\=v2 ecFlow-5.8.4-Source.tar.gz | ||
| tar -xvzf boost_1_78_0.tar.gz | ||
| tar -xvzf ecFlow-5.8.4-Source.tar.gz | ||
| export WK=/contrib/spack-stack/ecflow-5.8.4/src/ecFlow-5.8.4-Source | ||
| export BOOST_ROOT=/contrib/spack-stack/ecflow-5.8.4/src/boost_1_78_0 | ||
| # Build static boost (to not interfere with spack-stack boost) | ||
| cd $BOOST_ROOT | ||
| ./bootstrap.sh 2>&1 | tee bootstrap.log | ||
| $WK/build_scripts/boost_build.sh 2>&1 | tee boost_build.log | ||
| # Build ecFlow | ||
| cd $WK | ||
| mkdir build | ||
| cd build | ||
| cmake .. -DCMAKE_INSTALL_PREFIX=/contrib/spack-stack/ecflow-5.8.4 2>&1 | tee log.cmake | ||
| make -j4 2>&1 | tee log.make | ||
| make install 2>&1 | tee log.install | ||
| cd /contrib/spack-stack/modulefiles | ||
| mkdir ecflow | ||
| # Create the modulefile from the template in doc/modulefile_templates | ||
| ``` | ||
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| ## Steps to perform when starting a new cluster | ||
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| This should be done automatically, but doesn't hurt to run again just in case: | ||
| ``` | ||
| sudo /contrib/admin/basic_setup.sh | ||
| ``` | ||
| Configure `git` and `aws` command line utilities | ||
| ``` | ||
| module unuse /opt/cray/craype/default/modulefiles | ||
| module unuse /opt/cray/modulefiles | ||
| module use /contrib/spack-stack/modulefiles | ||
| module load cmake/3.27.2 | ||
| module load ecflow/5.8.4 | ||
| module load mysql/8.0.31 | ||
| module load git-lfs/2.4.1 | ||
| git lfs install | ||
| git config --global credential.helper cache # or store | ||
| git config --global user.email "[email protected]" | ||
| git config --global user.name "Your Name" | ||
| mkdir ~/.aws | ||
| # Create ~/.aws/config | ||
| # Create ~/.aws/credentials | ||
| chmod 400 ~/.aws/credentials | ||
| ``` | ||
| ## Steps to perform to install spack-stack version 1.8.0 | ||
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| sudo su - | ||
| chmod 755 /contrib | ||
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| cd /contrib/spack-stack-rocky8/ | ||
| git clone --recursive https://github.com/JCSDA/spack-stack spack-stack-1.8.0 | ||
| cd spack-stack-1.8.0 | ||
| . setup.sh | ||
| spack stack create env --name ue-intel-2021.10.0 --template unified-dev --site noaa-aws --compiler intel | ||
| cd envs/ue-intel-2021.10.0 | ||
| spack env activate . | ||
| spack concretize 2>&1 | tee log.concretize | ||
| spack install --verbose 2>&1 | tee log.install | ||
| spack module lmod refresh -y | ||
| spack stack setup-meta-modules |