Ubuntu HPC Install Openmpi from master node

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Revision as of 04:35, 27 February 2023 by Saurabh (talk | contribs) (Created page with "Home > Ubuntu > HPC setup with openpbs and openmpi > Install Openmpi from master node We can install OpenMPI using source code by using: #Create temporary directory for compilation of sources. Download openmpi tar ball and extract sources in temporary compilation folder. #:<pre> #:: mkdir -p /export/apps/temp #:: cd /export/apps/temp #:: wget https://www.open...")
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Home > Ubuntu > HPC setup with openpbs and openmpi > Install Openmpi from master node

We can install OpenMPI using source code by using:

  1. Create temporary directory for compilation of sources. Download openmpi tar ball and extract sources in temporary compilation folder.
    mkdir -p /export/apps/temp
    cd /export/apps/temp
    wget https://www.open-mpi.org/software/ompi/v4.1/downloads/openmpi-4.1.1.tar.gz
    tar xzf openmpi-4.1.1.tar.gz
  2. Create directory for openmpi installation
    mkdir -p /export/apps/mpi/openmpi-4.1.1
  3. Install openmpi
    cd /export/apps/temp/openmpi-4.1.1
    ./configure --enable-orterun-prefix-by-default --prefix=/export/apps/mpi/openmpi-4.1.1
    make -j 10
    make install
    In place of 'make -j 10' we can run 'nproc' and give higher value as parameter to '-j'. The higher value indicates we can do more parallel compilation, if there are multiple concurrent compilation options within the sources.
  4. Disable StrictHostKeyChecking by editing '/etc/ssh/ssh_config' file and under 'Host *' set:
    StrictHostKeyChecking no
  5. Set Passwordless authentication for HPC users. (Eg user1 in below example)
    ssh user1@<master> #Or su - user1, if already on master node
    ssh-keygen #Leave all prompts blank, just press enter-enter-enter
    cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys; chmod 600 ~/.ssh/authorized_keys #OR ssh-copy-id user@<compute1>
    Due to home folder sharing between nodes the above should result into user1 password-less SSH to all nodes in the cluster.
  6. Set mpi path for user1 account
    su - user1
    export PATH=/export/apps/mpi/openmpi-4.1.1/bin:$PATH
    export LD_LIBRARY_PATH=/export/apps/mpi/openmpi-4.1.1/lib:$LD_LIBRARY_PATH
  7. Check mpi version and path from user1
    mpirun --version
    which mpirun
    echo $PATH
    echo $LD_LIBRARY_PATH
  8. Run parallel job
    mpirun -host master,<node-1>,<node-2> -n 3 /usr/bin/stress --cpu 4 --vm 2 --vm-bytes 300M --timeout 60s
  9. While above command is executing, in parallel on each node open a terminal / shell and run
    htop #or top
    and validate that at least 4CPU on each node are utilized up to 100% for 60 seconds during the above mpirun.


Home > Ubuntu > HPC setup with openpbs and openmpi > Install Openmpi from master node