4. News & Events

  • General information about the Maintenance is applicable to all scheduled downtime periods.

  • Any additional information is outlined in notification emails to hpc-users@uci.edu (all current users) and is described in the details below.

  • When the maintenance is completed all users are notified via emails to hpc-users@uci.edu.

4.1. July, 2025

HPC3 Downtime July XX, 2025
2025-05-13 by Nadya Williams
The next outage will be July (date to be determined), 2025, beginning at 8am.
The cluster will be unavailable all day.
Maintenance Items:

  1. OS version update from Rocky 8.10 to Rocky 9.

  2. Top-to-bottom re-installation of all compute and login nodes.

  3. Full rebuild of all applications software, see table below for software changes.

  4. Full rebuild of Slurm software.

Impacts:

This is a full outage.

  1. All existing logins will be terminated.

  2. You will NOT have access to HPC3 during the planned downtime.

  3. You will have access to CRSP using Web based File browser or CRSP Desktop App.

  4. No Slurm jobs can run or can be pending in the queue.

  5. All jobs remaining in the queue on the maintenance day will be terminated.

  6. Slurm jobs that are not guaranteed (via TimeLimit) to complete before 8am on the day of maintenance will need to be resubmitted after the maintenance. Please see requesting time limits on queues.

Software changes:

The operating system update involves many changes across the software stack. While we try to build all the previous software versions for the new OS, some builds are impossible. As a result, some modules will be removed because they cannot be built on a new system or because the underlying requirements are no longer satisfied.

Note, the table below will be periodically updated till the maintenance date.

Table 4.1 Software changes

Module name

Comments

Removed modules

bcftools/1.10.2

Cannot build, use newer version

bustools/0.40.0

Unused, use newer version

canu/2.0

Unused

charm/6.10.1/gcc.11.2.0

Unused

charm/6.10.1/gcc.11.2.0-openmpi.5.0.1

Unused

charm/7.0.0/gcc.11.2.0

Unused

cuda/10.1.243

Not supported on Rocky 9, use newer version

gatk/4.1.9.0

Security vulnerability, use newer version

gromacs/2021.2/gcc.8.4.0-cuda.10.1.243.openmpi.4.0.3

Unused

gromacs/2022.1/gcc.8.4.0-openmpi.4.1.2

Unused

intel/2020u1

Intel compiler deoends upon a shared library that is unavailable on Rocky 9.

Removed affected modules:

  • mpich/3.4/intel.2020u1

  • openmpi/4.0.3/intel.2020u1

  • hdf5/1.10.5/intel.2020u1

  • ioapi/3.2/intel.2020u1

  • netcdf-c/4.7.0/intel.2020u1 (including dependent netcdf-f version 4.5.2)

Use modules with newer intel compier where available

ioapi/3.2/gcc.11.2.0

Unused

petsc/3.20.1/gcc.11.2.0

petsc/3.20.1/gcc.11.2.0-cuda.11.7.1

Unused

Unused

protobuf/3.11.4

protobuf/3.19.4

Unused

Unused

R/4.1.2

Seurat and leiden libraries cannot be built. Use newer R if you need these specific packages.

R/4.2.2

Seurat and leiden libraries cannot be built. Use newer R if you need these specific packages.

salmon/1.2.1

Cannot build, use newer version

tensorflow/2.0.0

Cannot build, use newer version

tensorRT/6.0.1.5

Cannot build, use newer version

tk/8.6.12

Unused. Functionality is provided by tcl/8.6.12

Updated modules

CUDA 10 compiled modules:

  • gromacs/2020.4/gcc.8.4.0-cuda.10.1.243

  • gromacs/2021.2/gcc.8.4.0-cuda.10.1.243

  • gromacs/2021.2/gcc.8.4.0-cuda.10.1.243.openmpi.4.0.3

  • namd/2.14b2/gcc.8.4.0-cuda.10.1.243

Replaced by CUDA 11 compiled modules:

  • gromacs/2020.4/gcc.8.4.0-cuda.11.7.1

  • gromacs/2021.2/gcc.8.4.0-cuda.11.7.1

  • gromacs/2021.2/gcc.8.4.0-cuda.11.7.1.openmpi.4.0.3

  • namd/2.14b2/gcc.8.4.0-cuda.11.7.1

gcc/<any version>

No longer provides go. To use go please load module go/1.22.3

gcc/system

System compiler is updated to version 11.5.0.

Modules compiled with system compiler:

  • openmpi/4.1.1/gcc.system

  • ucx/1.8.0/gcc.system

  • ucx/1.12.0/gcc.system

  • ucx/1.15.0/gcc.system

  • fftw/3.3.8/gcc.system

  • hdf5/1.10.5/gcc.system

  • hdf5/1.13.1/gcc.system

  • hdf5/1.13.1/gcc.system-openmpi.4.1.1

gdal/3.1.0

gdal/3.4.1

gdal/3.6.2

Replaced by gdal/3.1.0/gcc.8.4.0

Replaced by gdal/3.4.1/gcc.11.2.0

Replaced by gdal/3.6.2/gcc.11.2.0

geos/3.8.1

geos/3.10.2

geos/3.11.1

Replaced by geos/3.8.1/gcc.8.4.0

Replaced by geos/3.10.2/gcc.11.2.0

Replaced by geos/3.11.1/gcc.11.2.0

intel-tbb/2021.5.0

Replaced by intel-tbb/2021.11

mpich/4.0/gcc.11.2.0

Replaced by mpich/4.0/gcc.system

proj/6.3.2

proj/9.0.0

proj/9.1.1

Replaced by proj/6.3.2/gcc.8.4.0

Replaced by proj/9.0.0/gcc.11.2.0

Replaced by proj/9.1.1/gcc.11.2.0

sqlite3/3.32.3

sqlite3/3.38.2

sqlite3/3.41.0

Replaced by sqlite3/3.32.3/gcc.8.4.0

Replaced by sqlite3/3.38.2/gcc.11.2.0

Replaced by sqlite3/3.41.0/gcc.11.2.0

R/4.3.3

Updated packages:

  • Seurat to version 5.3.0

  • SeuratObject to version 5.0.2

  • replace leiden by leidenbase

R/4.4.2

Updated packages:

  • Seurat to version 5.3.0

  • SeuratObject to version 5.0.2

  • replace leiden by leidenbase

New modules

gatk/4.6.2.0

Added

hdf5/1.14.1/gcc.11.2.0-openmpi.5.0.1

Added

intel-tbb/2022.1

Added (part of intel 2025 compiler)

intel/2025.1.0

Added
After the maintenance:

  • User compiled and installed software will need to be reinstalled.

  • User installed conda environments will VERY LIKELY need to be reinstalled.

  • If you previously used a module that has been removed, try to use a newer version of it where available.