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N8-CIR-Bede / documentation

Documentation for the N8CIR Bede Tier 2 HPC faciltiy
https://bede-documentation.readthedocs.io/en/latest/
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IBM Collaboration Modules #89

Open ptheywood opened 2 years ago

ptheywood commented 2 years ago

The IBM collaboration project provides a TCL module which mutates the MODULEPATH environment variable, to enable finding of other modules, applications such as CryoEM and EMAN2.

However, the cryoem and eman2 modules are .lua files intended for LMOD, but bede instead uses Environment Modules (3.2.10 on RHEL 8), so these module files are not usable.

This has been brought up on slack previously but not yet resolved.

For now, Eman2/Cryoem bede docs in #67 describe how they can be used without these modules, and a warning is listed on the ibm-collaboration docs page highlighting that the module is not useful.

Once the modules have been converted to TCL modules compatible with environment-modules, the documentation can be extended to use the reletvant module load commands instead.

I.e. the following could be used on ibm-collaboration.rst

Once the ``ibm-collaboration`` module has been loaded, it is possible to load versions of the provided packages.

.. code-block:: bash

    # Load the ibm-collaboration module
    module load ibm-collaboration
    # Once loaded, modules provided by ibm-collaboration are available, such as Cryo-EM
    module load CryoEM
    module load Eman2
ptheywood commented 2 years ago

It was highlighted during the Bede user-group meeting on 2022-02-08 that the provided versions of CryoEM and Eman2 might need rebuildng for use on RHEL 8.

markdturner commented 2 years ago

@ptheywood to chase IBM for an update

ptheywood commented 2 years ago

I've posted on slack in the #cryo-em channel to enquiere about this. Marion has also enquired about RHEL 8 support / rebuilds.

MarionBWeinzierl commented 2 years ago

Andrew's answer:

Hi Marion,

Here's a bit of an update for you on the Relion software situation.

As you know, Ruzhu Chen was the expert on all things CryoEM within IBM, until he moved on to take a job elsewhere. A lot of his projects and other work, including the work he was doing on Relion for the ppc64le architecture have now been passed over to the Open Source Lab at Oregon State University - to which IBM provides a lot of sponsorship and support. They also host the PowerDev development hosting environment for open source projects, as well as running a POWER Continuous Integration (POWER CI) environment to help projects automate testing and keep their environments current.

The Relion application for CryoEM is now one of their focus projects, part funded by IBM and the OpenPOWER Foundation, alongside the Open Cognitive Environment (Open-CE) project that covers machine learning and deep learning tools. They have a publicly accessible Anaconda folder with a compiled and ready to install version of the software available. More information and downloads are available here: OSU Open Source Lab | Oregon State University (osuosl.org).

I was able to speak to Chris Sullivan at OSU who is currently leading the Cryo-EM project on Friday evening, and he said that they would be happy to work with other groups around the world to ensure the best results for their project. He also said that they were working on a RHEL8 specific release for the project, which I'd like to catch up with him on in a couple of weeks to find out more for you.

I was also recently working on something else when I was reminded that the University of Birmingham BEAR cluster has a well documented software catalogue for their systems, including their POWER9 based cluster. That lists a ppc64le version of Relion 3.1.2 for RHEL8 available - including GPU acceleration. So it might be worth you reaching out to the University of Birmingham team for advice.

Kind regards,

Andrew Laidlaw

I am currently in discussion with @jhodrien and @kilicomu (Leeds and York have cryoEM/Relion users) about whether and how we can support that software on Bede.