Content Comparison

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Accessing the HPC Cluster

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Shell and Data Access

Shell Access

• Use SSH to access the command shell use SSH; to upload files use SFTP or SCP:

  • Host: login.hpc.lab

  • Port: 22

  • Credentials : your Florida Poly username and password

Submitting a job to LSF

• Submitting jobs to the LSF (use bsub)

  1. Compile the hello_world example code provided by default

     1. /opt/ibm/platform_mpi/bin/mpicc -o hello_world.exe /opt/ibm/platform_mpi/help/hello_world.c

  2. Submit a job through LSF to test the message passing

     1. bsub -n 10 -R "span[ptile=1]" -o %J.out "/opt/ibm/platform_mpi/bin/mpirun -lsf -vapi /home/(Username)/hello_world.exe; wait"

  3. Check the output of the %J.out file to verify results

Applications

Spack

File Upload

• Use SFTP or SCP to upload files with the access parameters shown above.

Applications and Packages

Libraries

MPI

The Message Passing Interface (MPI) is a library specification that allows the HPC to pass information between its various nodes and clusters.

Compiling Source

The following compilers are installed:

• IBM PE Runtime (mpicc, et. al) v09.01.02.00u including C, C++, and Fortran.

• GNU Compiler Collection v4.4.7 including C, C++, Objective-C, Fortran, Ada, Go, and D.

Packaged Binaries

You can install applications on our HPC using Spack: a Linux package manager that makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.

• To list all available packages:

  • spack find

• To load a package into your environment:

  • spack load

  • You can specify a software version as part of the load:

  • spack load python@3.7.3 loads Python 3.7.3

Python and PIP

If you load install Python using Spack (above) you can use PIP to install other modules:

• spack load python

• python3 -mpip install matplotlib

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If you need an application that’s not available through Spack please contact the Helpdesk: helpdesk@floridapoly.edu or 863.874.8888.

Submitting a Job

Linux binaries

You'll submit jobs through bsub, part of IBM’s LSF workload management platform. IBM provides documentation for bsub.

You may wish to use IBM’s mpirun script to abstract the job from underlying hardware. IBM provides documentation for mpirun.

Some examples:
bsub -n 10 -R "span[ptile=1]"-o ~/hello_world.out "mpirun -lsf -vapi ~/hello_world”

bsub -n 20 -R "span[ptile=6]"-o ~/hello_world.out "python3 ~/hello_world.py”

Python

• Install Python
  spack load python

• Install Python bsub
  python3 -mpip install bsub

• Run your code with bsub
  bsub -n 10 -o my_job.out "python3 my_job.py"

Other

For help with other jobs please contact the Helpdesk: helpdesk@floridapoly.edu or 863.874.8888.

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