diff --git a/docs/e1000-migration/index.md b/docs/e1000-migration/index.md new file mode 100644 index 00000000..6cec834d --- /dev/null +++ b/docs/e1000-migration/index.md @@ -0,0 +1,559 @@ +# Cirrus migration to E1000 system migration + +This section of the documentation is a guide for users migrating to the E1000 taking place in March 2024 + +It covers: + +- [Change of authentication from ldap to free-ipa](#change-of-authentication-from-ldap-to-free-ipa) +- [New storage -> Data migration](#new-storage-data-migration) +- [CSE Module Updates](#cse-module-updates) + + + +!!! tip + If you need help or have questions on the Cirrus E1000 migration + please [contact the Cirrus service desk](https://www.cirrus.ac.uk/support/) + + +## Change of authentication from ldap to free-ipa: + +This change should be transparent to users and the TOTP and ssh keys should work as previously +If users do experience issues then please reset your TOTP and ssh keys and try to reconnect. +If issues persist, then please contact the service desk + +## New storage -> Data migration + +The old data will be made available from the Cirrus login nodes and will be read-ony. +Users will be asked to migrate any data they require from the old data disks to the new disks on the E1000 + +Old data is mounted as:
+`/mnt/lustre/indy2lfs` with user files being at `/mnt/lustre/indy2lfs/work/` + +Need Example command to do this: + +- Do we just use `mv` or suggest `rsync`? + + + +!!! note + Due to the change of location of the data, all pending jobs within slurm will be removed and users will need to resubmit any required jobs to ensure they are submitted with the correct pathname and data destination + + +## CSE Module Updates + +We are taking the opportunity to update modules and remove outdated modules. + + +### TO BE REMOVED (Alphabetical order!) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Package/moduleOwnerAdvice for usersDocumentation?Comments
altair-hwsolvers/13.0.213WilliamPlease contact the service desk if you wish to use Altair Hyperworks.

altair-hwsolvers/14.0.210WilliamPlease contact the service desk if you wish to use Altair Hyperworks.

ansys/18.0WilliamPlease contact the service desk if you wish to use ANSYS Fluent.

ansys/19.0WilliamPlease contact the service desk if you wish to use ANSYS Fluent.

+

autoconf/2.69

MichaelBPlease use autoconf/2.71n/a
+

bison/3.6.4

SebastienPlease use bison/3.8.2

+

boost/1.67.0

XuPlease use boost/1.84.0n/a
+

boost/1.73.0

XuPlease use boost/1.84.0

+

cmake/3.17.3

+

cmake/3.22.1

KevinPlease use cmake/3.25.2

+

CUnit/2.1.3

WilliamPlease contact the service desk if you wish to use CUnit.

+

dolfin/2019.1.0-intel-mpi

+

dolfin/2019.1.0-mpt

SebastienDolfin is no longer supported and will not be replaced.
See also RFC 158
+

eclipse/2020-09

WilliamPlease contact the service desk if you wish to use Eclipse.

+

expat/2.2.9

MichaelBPlease use expat/2.6.0n/a
+

fenics/2019.1.0-intel-mpi

+

fenics/2019.1.0-mpt

SebastienFenics is no longer supported and will not be replaced.
See also RFC158
+

fftw/3.3.8-gcc8-ompi4

+

fftw/3.3.8-intel19

+

fftw/3.3.9-ompi4-cuda11-gcc8 

+

fftw/3.3.8-intel18   

+

fftw/3.3.9-impi19-gcc8  

+

fftw/3.3.10-intel19-mpt225   

+

fftw/3.3.10-ompi4-cuda116-gcc8

Xu +

Please use one of the following

+

fftw/3.3.10-gcc10.2-mpt2.25

+

fftw/3.3.10-gcc10.2-impi20.4

+

fftw/3.3.10-gcc10.2-ompi4-cuda11.8

+

fftw/3.3.10-gcc12.3-impi20.4

+

fftw/3.3.10-intel20.4-impi20.4



+

flacs/10.9.1

+

flacs-cfd/20.1

+

flacs-cfd/20.2

+

flacs-cfd/21.1

+

flacs-cfd/21.2

+

flacs-cfd/22.1

+


KevinPlease contact the helpdesk if you wish to use FLACS.REMOVE documentation (but not yet)
+

forge/22.1.3

KevinPlease use forge/23.1.1UPDATE REQUIREDPENDING
+

gcc/6.2.0

WilliamPlease use gcc/8.2.0 or later

+

gcc/6.3.0

WilliamPlease use gcc/8.2.0 or later

+

gcc/12.2.0-offload

WilliamPlease use gcc/12.3.0-offload

+

gdal/2.1.2-gcc

+

gdal/2.1.2-intel 

+

gdal/2.4.4-gcc

MichaelBPlease use gcc/3.6.2-gccn/a
+

git/2.21.0


Please use git/2.37.3
No change: automatically loads git/2.37.3 via epcc/utils
+

gmp/6.2.0-intel 

+

gmp/6.2.1-mpt

+

gmp/6.3.0-mpt

EleanorPlease use gmp/6.3.0-gcc or gmp/6.3.0-intel 

+

gnu-parallel/20200522-gcc6

MichaelBPlease use gnu-parallel/20240122-gcc10TODO
+

gromacs/2022.1
gromacs/2022.1-gpu
gromacs/2022.3-gpu

RuiA +

Please use one of:
gromacs/2023.4
gromacs/2023.4-gpu



+

hdf5parallel/1.10.4-intel18-impi18

WilliamPlease use hdf5parallel/1.14.3-intel20-impi20

+

hdf5parallel/1.10.6-gcc6-mpt225

WilliamPlease use hdf5parallel/1.14.3-gcc10-mpt225

+

hdf5parallel/1.10.6-intel18-mpt225

WilliamPlease use hdf5parallel/1.14.3-intel20-mpt225

+

hdf5parallel/1.10.6-intel19-mpt225

WilliamPlease use hdf5parallel/1.14.3-intel20-mpt225

+

hdf5serial/1.10.6-intel18

WilliamPlease use hdf5serial/1.14.3-intel20

+

horovod/0.25.0

+

horovod/0.25.0-gpu

+

horovod/0.26.1-gpu

MichaelBPlease use one of the pytorch or tensorflow modulesTODO
+

htop/3.1.2 

Installed by AJPlease use htop/3.2.1 

+

intel 18.0 compilers etc

KevinPlease use Intel 19.5 or later; or oneAPIADD ONEAPI informationShould be moving to oneAPI
+

intel 19.0 compilers etc

KevinPlease use Intel 19.5 or later

+

lammps/23Jun2022_intel19_mpt
lammps/8Feb2023-gcc8-impi
lammps/23Sep2023-gcc8-impi
lammps/8Feb2023-gcc8-impi-cuda118
lammps/23Sep2023-gcc8-impi-cuda118

RuiA +

Please use one of:

+

lammps/15Dec2023-gcc10.2-impi20.4
lammps-gpu/15Dec2023-gcc10.2-impi20.4-cuda11.8



+

libxkbcommon/1.0.1

WilliamPlease contact the service desk if you wish to use libxkbcommon.

+

libnsl/1.3.0 

EleanorPlease contact the helpdesk if you wish to use libnsl.
Dependancy for STARCCM+.
+

libpng/1.6.30

(Xu)This is no longer supported as the central module.

+

libtirpc/1.2.6

EleanorPlease contact the helpdesk if you wish to use libtirpc.
Dependancy for STARCCM+.
+

libtool/2.4.6

SebastienPlease use libtool/2.4.7

nco/4.9.3WilliamPlease use nco/5.1.9

nco/4.9.7WilliamPlease use nco/5.1.9

ncview/2.1.7WilliamPlease use ncview/2.1.10

+

netcdf-parallel/4.6.2-intel18-impi18

WilliamPlease use netcdf-parallel/4.9.2-intel20-impi20

+

netcdf-parallel/4.6.2-intel19-mpt225

WilliamPlease use netcdf-parallel/4.9.2-intel20-mpt225

+

nvidia/cudnn/8.2.1-cuda-11.6

+

nvidia/cudnn/8.2.1-cuda-11.6

+

nvidia/cudnn/8.9.4-cuda-11.6

+

nvidia/cudnn/8.9.7-cuda-11.6

MichaelB +

Please use one of the following

+

nvidia/cudnn/8.6.0-cuda-11.6

+

nvidia/cudnn/8.6.0-cuda-11.6

TODO
+

nvidia/nvhpc/22.11-no-gcc

KevinUse nvidia/nvhpc/22.11

+

nvidia/tensorrt/7.2.3.4

MichaelBPlease use nvidia/tensorrt/8.4.3.1-u2TODO
+

openfoam/v8.0

KevinPlease consider a later version, e.g., v10.0

+

openfoam/v9.0

KevinPlease consider a later version, e.g, v11.0

+

openfoam/v2006

KevinPlease consider a later version, e.g., v2306

+

openmpi/4.1.2-cuda-11.6

+

openmpi/4.1.4

+

openmpi/4.1.4-cuda-11.6

+

openmpi/4.1.4-cuda-11.6-nvfortran

+

openmpi/4.1.4-cuda-11.8

+

openmpi/4.1.4-cuda-11.8-nvfortran

+

openmpi/4.1.5

+

openmpi/4.1.5-cuda-11.6

+


MichaelB +

Please use one of the following

+

openmpi/4.1.6

+

openmpi/4.1.6-cuda-11.6

+

openmpi/4.1.6-cuda-11.6-nvfortran

+

openmpi/4.1.6-cuda-11.8

+

openmpi/4.1.6-cuda-11.8-nvfortran

+


TODO
+

petsc/3.13.2-intel-mpi-18

+

petsc/3.13.2-mpt

KevinPlease contact the helpdesk if you require a more recent version of PETSc.

+

pyfr/1.14.0-gpu

MichaelBPlease use pyfr/1.15.0-gpuTODO
+

pytorch/1.12.1

+

pytorch/1.12.1-gpu

MichaelB +

Please use one of the following

+

pytorch/1.13.1

+

pytorch/1.13.1-gpu

TODO +

The PyTorch Lightning packages have been removed from the environments provided by the pytorch 1.13.1 modules. This is too save space. If a user requires those packages they can build their own local environment based on the appropriate pytorch module as explained in the user docs.

+

For the same reasons, the fastai, pyspark, scikit and opencv-python packages have also been removed.

+

quantum-espresso/6.5-intel-19

EleanorPlease use QE/6.5-intel-20.4

+

specfem3d

JuanPlease contact the helpdesk if you wish to use SPECFEM3D

+

starccm+/14.04.013-R8

+

starccm+/14.06.013-R8 → 2019.3.1-R8

+

starccm+/15.02.009-R8 → 2020.1.1-R8 

+

starccm+/15.04.010-R8 → 2020.2.1-R8 

+

starccm+/15.06.008-R8 → 2020.3.1-R8

+

starccm+/16.02.009 → 2021.1.1

EleanorPlease contact the helpdesk if you wish to use STAR-CCM+

+

tensorflow/2.9.1-gpu

+

tensorflow/2.10.0

+

tensorflow/2.11.0-gpu

MichaelB +

Please use one of the following

+

tensorflow/2.15.0

+

tensorflow/2.15.0-gpu

TODO +

The fastai, pyspark, scikit and opencv-python packages have been removed from the environments provided by the tensorflow 2.15.0 modules. This is too save space. If a user requires those packages they can build their own local environment based on the appropriate tensorflow module as explained in the user docs.

+

ucx/1.9.0

+

ucx/1.9.0-cuda-11.6

+

ucx/1.9.0-cuda-11.8

MichaelB +

Please use one of the following

+

ucx/1.15.0

+

ucx/1.15.0-cuda-11.6

+

ucx/1.15.0-cuda-11.8

TODO
+

vasp-5.4.4-intel19-mpt220




NO VASP5 at all?
+

zlib/1.2.11

KevinPlease use zlib/1.3.1
nb. /usr/lib64 has 1.2.11
+