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Changelog and Known Issues for OS Upgrade

Module changes

As part of the operating system upgrade, the module naming scheme has been revised so it is no longer necessary to load a "gateway" set of modules before accessing other software. However, this means that nearly every module name has changed to show the dependencies it uses.

To handle this transition, search the Available Software page or use the module spider command to find the new name of modules you are currently using, e.g.,

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module spider Python

However, there are some specific module changes that are not clear from the output of module spider:

  • For Python and R, consider using bundles instead of the plain module names. These include many helpful pre-installed packages (use the module spider <insert-bundle-name> command for specifics):
    • For Python, we recommend either Scipy-Bundle and/or Python-bundle-PyPI
    • For R, we recommend either R-bundle-CRAN and/or R-bundle-Bioconductor
  • The PGI module has been replaced by NVHPC (installation still in progress). This is due to NVIDIA's rebranding of PGI.
  • The LiftOver software is provided by the Kent_tools module.

Changelog

Known issues

Below are issues that ICER is aware of and is taking steps to resolve. If you find an issue that is not on this page, please contact us with the subject line "OS Upgrade 2024"

  • When starting up RStudio Server, you may only see a gray blank screen. To fix, this open a command line and run

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    mv .local/share/rstudio .local/share/rstudio.backup

    This will move your RStudio configuration files to a backup. Note that this will likely reset your RStudio session, so you may need to reopen previous projects and files, and could lose any unsaved work.

  • Job scripts that start with #!/bin/sh will result in errors like /var/lib/slurmd/jobXXXXXXXX/slurm_script: XX: module: not found. Please change this line to #!/bin/bash.

  • When logging in to upgraded nodes using SSH keys and proxy jumps, you may receive a message like:

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    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@    WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!     @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that a host key has just been changed.
The fingerprint for the RSA key sent by the remote host is
SHA256:rydhZ58BeXsXgWQisWlbH6E0IFG+2+LSxC9a7OfZBro.
Please contact your system administrator.
Add correct host key in <location>/.ssh/known_hosts to get rid of this message.
Offending RSA key in <location>/.ssh/known_hosts:6
You can use following command to remove the offending key:
ssh-keygen -R dev-amd20 -f <location>/.ssh/known_hosts
Host key for dev-amd20 has changed and you have requested strict checking.
Host key verification failed.

    or:

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    The authenticity of host 'dev-amd20 (<no hostip for proxy command>)' can't be established.
RSA key fingerprint is SHA256:rydhZ58BeXsXgWQisWlbH6E0IFG+2+LSxC9a7OfZBro.
This key is not known by any other names.
Are you sure you want to continue connecting (yes/no/[fingerprint])?

    These messages are expected as the keys used to verify the "identity" of the development nodes have changed from what your computer has used before. To fix the first error, run the command

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    ssh-keygen -R <dev-node-name> -f ~/.ssh/known_hosts

    on your local computer, not the HPCC. Alternatively, you can also delete the file ~/.ssh/known_hosts to reset all host keys. This will result in receiving the second message anytime you SSH to any other computer (even ones outside of ICER, like GitHub) until you've accepted the connection again.

    To accept the new connection and fix the second error, enter "yes" and hit enter.

  • The module load command is case sensitive, e.g., module load Python works, but module load python does not. Please use module spider to find the correct name, including capitalization, of the modules you would like to load. We are working on bringing case insensitivity back to the module system.

  • When using the OnDemand Desktop, you may receive an error dialog stating "The panel encountered a problem while loading 'IndicatorAppletCompleteFactory::IndicatorAppletComplete'. Do you want to delete the applet from your configuration?" Click the "Delete" option, and this error will not return in the future.
  • Please note that all jobs need to be submitted from a node running on the same operating system as the target node (i.e., only submit a job that can run on Ubuntu using a development node running Ubuntu).
  • We are noticing problems with the GROMACS MPI tests on older nodes. For this reason, GROMACS is currently available on every cluster except for intel14 and intel16.

  • The R package Matrix (which is a dependency for many other packages including ggplot2) is incompatible with versions of R earlier than 4.4.0 (i.e., all of the versions installed on the new operating system. We recommend using the R-bundle-CRAN module instead of R which includes a pre-installed version of Matrix. If you need to install it yourself using install.packages, use the command

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    install.packages(https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz, repos=NULL, type="source")

  • The powertools module is available, but some tools still require modification to work on the new system. If one of the tools you need is not working, please request that we update it using the contact form to help us prioritize our updates.

  • Firefox can't open from an Interactive Desktop on OnDemand. The fix is to run mv ~/.mozilla ~/.mozilla_backup.

  • The OnDemand Job Composer cannot submit jobs until the OnDemand server is moved to Ubuntu, which is expected to occur mid July.