Ubuntu HPC Install Openmpi from master node

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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

   The above export PATH and export LD_LIBRARY_PATH approach is used only for testing mpi. We will ideally setup modules Ubuntu HPC Install and Configure Modules to configure above settings for each user before they run/compile a program that depends on particular version of mpi.

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.

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