The Biowulf cluster compute nodes, the Biowulf login node and Helix will transition from RHEL7/CentOS7 to the RHEL8/Rocky8 operating system in June 2023.
As of 8 May 2023, application installs on the existing RHEL/CentOS 7 system are frozen. New versions of applications will only be installed on the RHEL/Rocky 8 cluster.
Please log in to the RHEL8 login node by connecting to biowulf8.nih.gov. (Note: When the entire cluster switches to Rhel8, the login node will be accessed as biowulf.nih.gov)
Note that only a subset of node types is available on the Rhel8/Rocky8 system. These can be seen with freen. If you wish to test your application on a node type that is not listed, let us know.
You can use ssh, NX or X11 to connect to biowulf8. As on Biowulf, to submit an interactive job, use 'sinteractive'.
[user@biowulf8 ~]$ sinteractive salloc: Pending job allocation 61681262 salloc: job 61681262 queued and waiting for resources salloc: job 61681262 has been allocated resources salloc: Granted job allocation 61681262 salloc: Waiting for resource configuration salloc: Nodes cn4338 are ready for job [user@cn4338 ~]$
To allocate an interactive session on a GPU node:
[user@biowulf8 ~]$ sinteractive --gres=gpu:v100:1
As on Biowulf, use 'sbatch' to submit batch jobs. Use 'freen' to see the nodes available on the Rhel8 cluster.
# simple batch job with default parameters sbatch jobscript # job requesting 8 cpus and 10 GB memory sbatch --cpus-per-task=8 --mem=10g jobscript # job requesting 4 MPI ntasks sbatch --ntasks=4 --ntasks-per-core=1 jobscript # job requesting 1 k80 GPU and 4 MPI tasks sbatch --gres=gpu:k80:1 --ntasks=7 --ntasks-per-core=1 jobscript
The HPC staff has rebuilt and transitioned the majority of scientific applications onto the Centos 8 system, prioritizing applications by usage.
As of 8 May 2023, application installs on the existing RHEL/CentOS 7 system are frozen. New versions of applications will only be installed on the RHEL/Rocky 8 cluster.
Only the most recent versions of each application have been migrated to RHEL8. You can see what versions are available by typing, as usual:
module avail module avail appnameIf your scripts specify loading an older version than is available, you may need to update your scripts. If you absolutely require an older version of an application, let us know.
If you have compiled your own versions of an application which link older libraries, you may need to recompile them on CentOS8. Performance-sensitive applications (e.g. parallel molecular simulations) should be recompiled.
The Biowulf utilities are available on the Rhel8 system. The 'freen' command will show only the nodes in the RHEL/Rocky 8 cluster.
biowulf8% freen
.......Per-Node Resources......
Part. FreeNds FreeCPUs FreeGPUs Cores CPUs GPUs Mem Disk Features
-------------------------------------------------------------------------------------------
rhel8 0 / 1 56 / 64 0 / 4 32 64 4 247g 3200g cpu64,core32,g256,ssd3200,e7543p,ibhdr200,gpua100
rhel8 0 / 1 98 / 128 64 128 499g 3200g cpu128,core64,g512,ssd3200,e7543,ibhdr200,rhel8
rhel8 5 / 6 80 / 336 28 56 247g 400g cpu56,core28,g256,ssd400,x2695,ibfdr,rhel8
rhel8 1 / 1 72 / 72 4 / 4 36 72 4 373g 1600g cpu72,core36,g384,ssd1600,x6140,ibhdr,gpuv100x,rhel8
rhel8 1 / 1 72 / 72 36 72 373g 3200g cpu72,core36,g384,ssd3200,x6140,ibhdr100,rhel8
rhel8 1 / 1 56 / 56 4 / 4 28 56 4 121g 650g cpu56,core28,g128,ssd650,x2680,ibfdr,gpup100,rhel8
rhel8 1 / 1 56 / 56 4 / 4 28 56 4 247g 400g cpu56,core28,g256,ssd400,x2695,ibfdr,gpuk80,rhel8
rhel8 1 / 1 56 / 56 4 / 4 28 56 4 247g 800g cpu56,core28,g256,ssd800,x2680,ibfdr,gpuk80,rhel8
rhel8 1 / 1 56 / 56 4 / 4 28 56 4 121g 800g cpu56,core28,g128,ssd800,x2680,ibfdr,gpuv100,rhel8
Nodes may be added to the RHEL/Rocky 8 cluster as more beta users get on the system.
The usual Biowulf partitions (norm, multinode, gpu etc) do not exist on the test RHEL/Rocky 8 cluster. After the transition of the entire cluster, the usual partitions will all be present. During this test phase, if you want to submit to a particular type of node, use --constraint. e.g. if you normally submit to the multinode partition, you can use
sbatch --constraint=x2695 --ntasks=56 --ntasks-per-core=1 --nodes=2 jobscriptTo submit to a GPU node
sbatch --gres=gpu:v100x:1 --cpus-per-task=8 jobscript
Batch system limits may be different (and changing during the beta phase!) on the RHEL/Rocky 8 cluster.
python/2.7 environment on rhel8.
Some users have cron jobs running on the Biowulf login node and on Helix. All cron jobs will be copied to the RHEL8 systems during the migration, but they will all be initially commented out. Each user will need to test their cron job on the RHEL8 system before enabling it.