Important Changes for HPCC Users

6 minute read

Rollout of Rocky and DUO: Feb 18 through Mar 17, 2022

Also see email notification sent to users on 18-Feb-2022.


This is to inform users about several important system upgrades the HPCC will be implementing in the next 30 days (starting February 18th, 2022). Importantly, these changes are relevant to all users including those who are accessing the HPCC systems via JupyterHub, RStudio Server, SSH or sFTP/SCP. Thus, please read the instructions below carefully. If anything is unclear or there are questions, please email support@hpcc.ucr.edu for help.

The most important change will be the switch from the old CentOS/RHEL 7 platform to the new Rocky/RHEL 8. We anticipate to finalize this upgrade on March 17th, 2022. This gives users a 30-day transition period to log into the new Rocky/RHEL 8 platform and test whether the software and other resouces they are using for their research are properly working. It is important to understand the deployment of Rocky 8 is a major upgrade that requires the systems administrators recompiling most software from the old system onto the new system.

To avoid unnecessary extra downtimes, we are also elevating with this upgrade our security standards by adopting UCR’s DUO multi factor authentication system. This is important to prevent intrusions and comply with UC-wide IT standards.

Operating System

As mentioned above, the biggest change is that we are upgrading the OS from CentOS/RHEL 7 to Rocky/RHEL 8. Rocky Linux is the community equivalent and identical to RHEL (similar to how CentOS was). Currently, pigeon is the only head/login node that is linked to the new Rocky/RHEL 8 platform. To check which platform you are on, you can run the platform command.

The upgrade from RHEL 7 to RHEL 8 will result in the following user-facing changes.

Passwords

User passwords will be expired on the current CentOS/RHEL 7 platform and users will need to reset their password during the next login. During this login, users need to provide their old password twice. The first time is to authenticate as cluster user (login password), and the second time to authorize the password reset (kerberos password). After this users will be prompted to provide their new password .

When logging into the new Rocky/RHEL 8 platform as outlined here, users also need to configure DUO if using a password, or alternatively create an SSH key pair. If a user is new to DUO, the instructions from UCR’s ITS are here. Users accessing the cluster via SSH key pairs are strongly encouraged to also reset their password upon login by following the instructions here. Additional information about login related topics are provided on this manual page.

External Users

External users are unlikely to have a UCR NetID required for DUO. This includes users with HPCC cluster and restricted data transfer accounts. Those users want to access the cluster via SSH keys. This is both convenient (no need to type a password anymore) and secure. Please refer to our SSH keys manual for detailed instructions of configuring SSH key-based access. After creating an ssh key pair, users will need to email their public SSH key to support@hpcc.ucr.edu so that the systems admin can add their public SSH key to the corresponding user account.

Note, the following instructions are only relevant for users who perform computations on our cluster(s). Users who are using our systems exclusively for data transfers can ignore them.

Software

All software installation requests will be restricted to the new cluster. New software may be installed under a different version, or may no longer be installed as a module, or may not be installed at all. Run the following command to list currently available modules:

module avail

Or you can search for a specific software (ie. vim) like so:

module avail vim
which vim

Since the new platform is built using GCC 8.5, then all previous compiled software must be re-compiled on the new platform. If you cannot find what you are looking for send an installation request to support@hpcc.ucr.edu.

Compatibility mode (singularity) can be used to run the older CentOS 7 modules, however this may not work in all cases. Please refer to our Singularity Examples for more information.

Bash

We officially support bash, even though other shells may work they have not been tested under the new Rocky/RHEL 8 platform.

When logging in under a bash shell, some errors/warnings may be visible. The most common message being that a module cannot be loaded.

Check if the module (ie. vim) is available with the following:

module avail vim

If there is no output, then the module is not currently available. Either remove the module load vim from your ~/.bashrc and/or ~/.bash_profile files, or request that it be installed.

If the software is available, ensure a proper check is in place around loading modules within your ~/.bashrc and/or ~/.bash_profile files.

For example:

if [[ "$(type -t module)" == "function" ]]; then
    module load tmux
    module load neovim
fi

It may also help to keep ~/.bashrc free of unnecessary bloat and only add customized changes to ~/.bash_profile. Also keep in mind that when running jobs with just /bin/bash the ~/.bashrc file is loaded. However, adding the lower case L to a job’s interpreter, as in /bin/bash -l this will load the ~/.bash_profile file. This can be useful since it provides flexibility to initialize a default job shell or a customized job shell.

Slurm

A newer version of Slurm is being used on the new Rocky/RHEL 8 platform, however very little is different from the previous version. All previous job submission scripts and commands/flags should still be compatible.

During the transition period From the old CentOS/RHEL 7 platform any Slurm jobs scheduled to start after March 17th will never start. Please check your jobs and ensure that they run before this time frame. You can check your start times with the following command:

squeue --start -u $USER

Be sure to move to the newer Rocky/RHEL 8 platform as soon as possible.

User-facing Changes Implemented on 23-Aug-2019

Domain Names

The old domain names biocluster.ucr.edu and bioinfo.ucr.edu have finally been discontinued. As a result, users need to use the new hpcc.ucr.edu name for the following services:

  • ssh/scp/ftp/http: cluster.hpcc.ucr.edu instead of biocluster.ucr.edu
  • RStudio Server: rstudio.hpcc.ucr.edu instead of rstudio.bioinfo.ucr.edu
  • Jupyter: jupyter.hpcc.ucr.edu instead of jupyter.bioinfo.ucr.edu
  • Email Support: support@hpcc.ucr.edu instead of support@biocluster.ucr.edu

In addition, URLs containing biocluster.ucr.edu need to be updated to cluster.hpcc.ucr.edu.

Password Reset

After the upgrade on Aug 23, 2019, all HPCC users have been emailed a temporary password with instructions how to change it. This email was sent to the address we have on file for each user. In case you missed the corresponding email notification and/or you are not able to log into the cluster, please email us at support@hpcc.ucr.edu to receive a new password.

Updated OpenMPI

If you have compiled or use software that was compiled with OpenMPI, then it will need to be recompiled. If you are running into any issues, please email us at support@hpcc.ucr.edu.

Last modified July 12, 2022: doc updates (216f74a1)