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Operating system migration from CentOS to Rocky Linux
Preface
The operating system “CentOS 7” has reached its end of life. For this reason Lise’s CPU partition will be updated to “Rocky Linux 9”. This affects all login and compute nodes equipped with Intel Xeon Cascade Lake processors ("clx" for short). Lise's GPU-A100 partition and GPU-PVC partition are not affected.
It is important for users to follow the action items specified below. Rocky Linux 9 introduces new versions of various system tools and libraries. Some codes compiled earlier under CentOS 7 might not be working under Rocky Linux 9 anymore. Thus, legacy versions of environment modules offered under CentOS 7 were not transferred to the new OS environment or have been replaced by more recent versions.
The migration to the new OS is organised in three consecutive phases. It is expected to be complete by the end of July September.
The first phase starts with 2 login nodes and 112 compute nodes already migrated to Rocky Linux 9 for testing. The other nodes remain available under CentOS 7 for continued production.
After the test phase, a major fraction of nodes will be switched to Rocky Linux 9 to allow for general job production under the new OS.
During the last phase, only a few nodes still remain under CentOS 7. At the very end, they will be migrated to Rocky Linux 9, too.
During the migration phase the use of Rocky Linux 9 "clx" compute nodes will be was free of charge.
Current migration state: complete
nodes | CentOS 7 | Rocky Linux 9 |
|---|---|---|
login | - | blogin[1-8] |
compute (384 GB RAM) | - | 948 |
compute (768 GB RAM) | - | 32 |
compute (1536 GB RAM) | - | 2 |
Latest news
date | subject |
|---|---|
2024-09-30 | migration of remaining nodes from CentOS 7 to Rocky Linux 9 |
2024-09-16 | generic login name “blogin” resolves to blogin[3-6] |
2024-08-14 | migration of blogin[3-6] |
2024-07-30 | migration of another 576 standard compute nodes to Rocky Linux 9 |
2024-07-03 | official start of the migration phase with 2 login and 112 compute nodes running Rocky Linux 9 |
What has changed
SLURM partitions
CentOS 7 | Rocky Linux 9 | |
|---|---|---|
old partition name | new partition name | current job limits |
● | ● | 512 nodes, 12 h wall time |
● | ● | 16 nodes, 1 h wall time |
● | ● | 50 nodes, 12 h wall time |
● | ● | 32 nodes, 48 h wall time |
● |
|
|
● |
|
|
● | ● | 1 node, 48 h wall time |
( ● available ● closed/not available yet )
Jobs submitted without a partition name are placed in the default partition. The old default was standard96, the new default is cpu-clx.
Software and environment modules
| CentOS 7 | Rocky Linux 9 |
|---|---|---|
OS components | glibc 2.17 | glibc 2.34 |
Python 3.6 | Python 3.9 | |
GCC 4.8 | GCC 11.4 | |
bash 4.2 | bash 5.1 | |
check disk quota |
|
|
Environment modules version | 4.8 (Tmod) | 5.4 (Tmod) |
Modules loaded initially |
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| |
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| |
compiler modules |
|
|
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| |
MPI modules |
|
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| |
… | … | … |
Shell environment variables
CentOS 7 | Rocky Linux 9 |
|---|---|
| (undefined, local |
|
|
(undefined) |
|
(undefined) |
|
| |
|
What remains unchanged
node hardware and node names
communication network (Intel Omnipath)
file systems (HOME, WORK, PERM) and disk quotas
environment modules system (still based on Tcl, a.k.a. “Tmod”)
access credentials (user IDs, SSH keys) and project IDs
charge rates and CPU time accounting (early migrators' jobs are were free of charge)
Lise’s Nvidia-A100 and Intel-PVC partitions
Special remarks
For users of SLURM’s
srunjob launcher:
Open MPI 5.x has dropped support for the PMI-2 API, it solely depends on PMIx to bootstrap MPI processes. For this reason the environment setting was changed fromSLURM_MPI_TYPE=pmi2toSLURM_MPI_TYPE=pmix, so binaries linked against Open MPI can be started as usual “out of the box” usingsrun mybinary. For the case of a binary linked against Intel-MPI, this works too when a recent version (≥2021.11) of Intel-MPI has been used. If an older version of Intel-MPI has been used, and relinking/recompiling is not possible, one can follow the workaround for PMI-2 withsrunas described in the Q&A section below. Switching fromsruntompiruninstead should also be considered.Using more processes per node than available physical cores (PPN > 96; hyperthreads) when defining
FI_PROVIDER=opx:
The OPX provider currently does not support using hyperthreads/PPN > 96 on the clx partitions. Doing so may result in segmentation faults in libfabric during process startup. If a high number of PPN is really required, the libfabric provider has to be changed back to PSM2 by re-definingFI_PROVIDER=psm2(which is the default setting). Note that the usage of hyperthreads may not be advisable. We encourage users to test performance before using more threads than available physical cores.
Note that Open MPI’smpirun/execdefaults to use all hyperthreads if a Slurm job/allocation is used that does not explicitly set--ntasks-per-node(or similar options).
Action items for users
All users of Lise are recommended to
log in to an already migrated login node (see the current state table), for example to
blogin7.nhr.zib.de(fully qualified domain name for external ssh connections to Lise) or simplyblogin7(from within Lise)get familiar with the new environment (check
module avail)check self-compiled software for continued operability
relink/recompile software as needed
adapt and test job scripts and workflows
submit test jobs to the new "cpu-clx:test" SLURM partition
read the Q&A section and ask for support in case of further questions, problems, or software requests (support@nhr.zib.de)