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Rocky 8 Transition Guide
DRAFT
Overview
As part of our June 5-8, 2023 MGHPCC Downtime, FASRC will be upgrading the cluster operating system from CentOS 7 to Rocky 8. Details as to why the transition is taking place are provided on the downtime page. This page is intended to go over the test environment for users prior to the downtime as well as a guide for different aspects of the upgrade.
Rocky 8 Test Cluster (Not Live Yet)
To help users prepare for the transition to Rocky 8 we have put together a test cluster for users to use. This cluster is running a beta version of the cluster image we will be pushing out to the whole cluster. Once the transition is complete these partitions will be reabsorbed into the cluster.
The text based login node for the test cluster can be found at rockylogin.rc.fas.harvard.edu Your normal RC login credentials should work. With the new operating system we gained the ability to limit users usage on login nodes via cgroups rather than our old pcull script which killed offending processes. Going forward users will be limited to 1 core and 4GB of memory on the login nodes, and pcull will be deprecated. Users requiring more that 1 core and 4GB will need to run an interactive session via salloc. The login nodes are intended as a point of access to the cluster not a full compute session, as such users should keep their work light in the login space.
Open OnDemand (VDI) is not currently available, but will be in the future.
From this login node you can submit to the two test partitions rocky and rocky_gpu.
| Partition | Nodes | Cores per Node | CPU Core Types | Mem per Node (GB) | Time Limit | Max Jobs | Max Cores | MPI Suitable? | GPU Capable? |
|---|---|---|---|---|---|---|---|---|---|
| rocky | 36 | 48 | Intel "Cascade Lake" | 184 | 3 days | none | none | Yes | No |
| rocky_gpu | 2 | 64 | Intel "Ice Lake" | 499 | 3 days | none | none | Yes | Yes (28 A100 5GB MIG) |
As this is a beta cluster image we would like your feedback if you have any problems or suggestions for the new environment. Please contact rchelp@rc.fas.harvard.edu if you notice anything missing.
Warning: Do not submit jobs from the CentOS 7 login nodes to the Rocky 8 partitions or from Rocky 8 login nodes to CentOS 7 partitions. Jobs will most likely fail for strange reasons. The two operating systems are not interoperable.
FASSE Rocky 8 Test Cluster
Will be forthcoming.
Software
Warning
The change in operating system means that most users software built on CentOS 7 will not work and will need to be rebuilt. Even if the code does work with out being rebuilt the change in underlying libraries may impact code execution and results. Users should test and verify that their codes are producing the expected results on the new operating system. This is a significant change with a host of bug fixes, performance upgrades, and numerical methods changes. These can change results, so users need to be sure to test and validate their codes.
Modules
FASRC has traditionally provided modules of different software packages for users. For Rocky 8 we are significantly reducing the number of modules we will support. Only modules considered core operational codes (like compilers, MPI, or software environments) or licensed software (e.g. matlab, mathematica) will be built. You can find the list of modules we provide by doing: module avail To search the modules do: module spider <name> CentOS 7 modules will not be available in Rocky 8. For modules formerly provided in CentOS 7 we are recommending users use Spack instead.
Spack
Singularity
CentOS 7 Singularity Image
For those who cannot upgrade to Rocky 8 we are providing a CentOS 7 Singularity image which contains our full CentOS 7 environment as well as access to our old CentOS 7 modules. A guide for using that environment can be found on the FASRC Singularity page.
Python
Python 2
Python 2 has been deprecated since 2020. Users are encouraged to migrate to Python 3. For those who need Python 2 for historic codes we recommend using either a Singularity container or the python/2.7.16-fasrc01 module (which uses Anaconda2).
R
Other
FAQ
Legacy CentOS 7 Support
FASRC provides a container of our full CentOS 7 environment for those who require it for their code. Beyond that support for CentOS 7 will not be maintained for the compute environment. Slurm support for CentOS 7 will be dropped with the next major Slurm upgrade, if you have a host that connects to Slurm that is CentOS 7 contact FASRC to discuss migration. Virtual Machine’s and other systems running CentOS 7 and older will need to migrate to other hosting options or coordinate upgrades with FASRC.
I don’t see the module/software I use in modules, Spack, Singularity, or User Codes
Users are always welcome to build their own codes on the cluster or download compatible binaries. We provide guides for how to accomplish this in our documentation. If you have trouble doing this or you think a module is missing contact rchelp@rc.fas.harvard.edu
SSH key or ‘DNS spoofing’ errors when connecting to login or other nodes
WARNING: POSSIBLE DNS SPOOFING DETECTED! and/or The RSA host key for login.rc.fas.harvard.edu has changed error messages. After an update of nodes the SSH key fingerprint of a node may change. This will, in turn, cause an error when you next try to log into that node as your locally stored key will no longer match. SSH uses this as a way to spot man-in-the-middle attacks or DNS spoofing. However, when a key changes for a valid reason, this does mean you need to clear out the one on your computer in order to be able to re-connect.
See this FAQ page for further instructions: SSH key error, DNS spoofing message
Modules in your .bashrc no longer work or give errors on login
If you have edited your .bashrc file to include module loads at login, you may find that some CentOS 7 modules will not be found or may not work on Rocky 8. You will need to edit your .bashrc and comment out or remove any such lines going forward. If you can no longer log in because of something in your .bashrc, contact us and we can rename your .bashrc and copy in a default version for you.
If you’d like to start from scratch, a default .bashrc contains the following:
# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# User specific aliases and functions below
My alternate shell (csh, tcsh, etc.) doesn’t work right
Having a non-standard default shell will cause problems and does not allow us to set global environmental defaults for everyone. We will no longer change the default shell on any account or support the use of alternate shells as default login shell. Users who do not have bash as their default login shell will need to change back to bash. Users can, of course, still launch an alternate shell once logged in.
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