CREDO FAQ

CREDO’s capabilities

Can I get CREDO to submit PBS jobs, or run it via PBS?

The answer to the first of these is: no, not currently. The ability to get CREDO to create and submit PBS scripts is a possible future feature.

You can however submit a Python CREDO script in parallel on a HPC system running PBS by writing the appropriate PBS script.

See Different ways to launch CREDO scripts for an example.

Problems running tests

When I try to run a CREDO system test script get an “ImportError” message

This problem is usually because you haven’t add the directory containing the CREDO Python source to your PYTHONPATH. See Setting up your environment to use CREDO for the various ways to do this.

Problem with parallel system tests, a CVGReadError occurs trying to read CVGs

Q: I have a problem running parallel CREDO system tests, along the lines of being unable to parse Field convergence results, where it brings up an exception message along the lines of: “credo.io.stgcvg.CVGReadError: Error, couldn’t read expected error” ...

A: This problem is often caused by using an “mpirun” or “mpiexec” not corresponding to the MPI library you compiled the code with. Not doing this (eg running the code with OpenMPI that you compiled with MPICH2) can result in annoying parallel bugs e.g. corruptions when writing output files, which among other things throw off the CREDO system testing now included with the code.

What are the ways of dealing with this?

1. On clusters using the “module” system, just make sure you load the same modules when running the code (eg in PBS scripts) as when you compiled it.
2. Make sure your PATH system environment variable is set up correctly so that “mpirun” will launch the correct version you compiled with. (You can test this by running ‘which mpirun’). It’s a good idea to set this up in your login scripts, e.g. .bashrc.
3. For CREDO specifically, you can set the environment variable MPI_RUN_COMMAND to tell it to use a custom mpirun/mpiexec rather than the default one in your PATH. (E.g. setting MPI_RUN_COMMAND=”/usr/local/packages/mpich2-1.2.1p1-debug/bin/”.)