diff --git a/docs/e1000-migration/index.md b/docs/e1000-migration/index.md index 94f0bcc4..8c35ffa8 100644 --- a/docs/e1000-migration/index.md +++ b/docs/e1000-migration/index.md @@ -37,22 +37,18 @@ The old `/work` file system will be available as read-only and we ask you to cop The old read-only file system will be removed on **1st May** so please retrieve all required data by then. For username in project x01, to copy data from
-`/mnt/lustre/indy2lfs/work/username/directory_to_copy ` -to
-`/work/x01/x01/username/destination_directory`
+`/mnt/lustre/indy2lfs/work/x01/x01/username/directory_to_copy ` +
to
+`/work/x01/x01/username/destination_directory`
you would do this by running: -```cp -r /mnt/lustre/indy2lfs/work/username/directory_to_copy \ ``` +```cp -r /mnt/lustre/indy2lfs/work/x01/x01/username/directory_to_copy \ ```
-```/work/x01/x01/username/destination_directory -``` +```/work/x01/x01/username/destination_directory ``` -Note that the project code appears once in the path for the old `/work` file system and twice in the path on the new `/work` file system. Further details of [Data Management and Transfer on Cirrus](https://docs.cirrus.ac.uk/user-guide/data/ ) - - !!! note **Slurm Pending Jobs**
@@ -66,99 +62,83 @@ Our Computational Science and Engineering (CSE) Team have taken the opportunity Please [contact the service desk](mailto:support@cirrus.ac.uk) if you have concerns about the removal of any of the older modules. +### TO BE REMOVED -### TO BE REMOVED (Alphabetical order!) - - +
- - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - -
Package/module Advice for usersDocumentation?Comments
altair-hwsolvers/13.0.213 Please contact the service desk if you wish to use Altair Hyperworks.

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

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

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

autoconf/2.69

 Please use autoconf/2.71n/a

bison/3.6.4

 Please use bison/3.8.2

boost/1.67.0

 Please use boost/1.84.0n/a

boost/1.73.0

 Please use boost/1.84.0

cmake/3.17.3

cmake/3.22.1

 Please use cmake/3.25.2

CUnit/2.1.3

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

dolfin/2019.1.0-intel-mpi

dolfin/2019.1.0-mpt

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

eclipse/2020-09

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

expat/2.2.9

 Please use expat/2.6.0n/a

fenics/2019.1.0-intel-mpi

fenics/2019.1.0-mpt

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

fftw/3.3.8-gcc8-ompi4

@@ -175,8 +155,7 @@ Please [contact the service desk](mailto:support@cirrus.ac.uk) if you have conce

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

@@ -187,188 +166,158 @@ Please [contact the service desk](mailto:support@cirrus.ac.uk) if you have conce

flacs-cfd/22.1


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

forge/22.1.3

 Please use forge/23.1.1UPDATE REQUIREDPENDING

gcc/6.2.0

 Please use gcc/8.2.0 or later

gcc/6.3.0

 Please use gcc/8.2.0 or later

gcc/12.2.0-offload

 Please use gcc/12.3.0-offload

gdal/2.1.2-gcc

gdal/2.1.2-intel 

gdal/2.4.4-gcc

 Please 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

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

gnu-parallel/20200522-gcc6

 Please use gnu-parallel/20240122-gcc10TODO

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

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



hdf5parallel/1.10.4-intel18-impi18

 Please use hdf5parallel/1.14.3-intel20-impi20

hdf5parallel/1.10.6-gcc6-mpt225

 Please use hdf5parallel/1.14.3-gcc10-mpt225

hdf5parallel/1.10.6-intel18-mpt225

 Please use hdf5parallel/1.14.3-intel20-mpt225

hdf5parallel/1.10.6-intel19-mpt225

 Please use hdf5parallel/1.14.3-intel20-mpt225

hdf5serial/1.10.6-intel18

 Please use hdf5serial/1.14.3-intel20

horovod/0.25.0

horovod/0.25.0-gpu

horovod/0.26.1-gpu

 Please use one of the pytorch or tensorflow modulesTODO

htop/3.1.2 

 Please use htop/3.2.1 

intel 18.0 compilers etc

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

intel 19.0 compilers etc

 Please 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

Please use one of:

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



libxkbcommon/1.0.1

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

libnsl/1.3.0 

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

libpng/1.6.30

 This is no longer supported as the central module.

libtirpc/1.2.6

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

libtool/2.4.6

 Please use libtool/2.4.7

nco/4.9.3 Please use nco/5.1.9

nco/4.9.7 Please use nco/5.1.9

ncview/2.1.7 Please use ncview/2.1.10

netcdf-parallel/4.6.2-intel18-impi18

 Please use netcdf-parallel/4.9.2-intel20-impi20

netcdf-parallel/4.6.2-intel19-mpt225

 Please use netcdf-parallel/4.9.2-intel20-mpt225

nvidia/cudnn/8.2.1-cuda-11.6

@@ -379,38 +328,32 @@ Please [contact the service desk](mailto:support@cirrus.ac.uk) if you have conce

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

 Use nvidia/nvhpc/22.11

nvidia/tensorrt/7.2.3.4

 Please use nvidia/tensorrt/8.4.3.1-u2TODO

openfoam/v8.0

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

openfoam/v9.0

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

openfoam/v2006

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

openmpi/4.1.2-cuda-11.6

@@ -430,21 +373,18 @@ Please [contact the service desk](mailto:support@cirrus.ac.uk) if you have conce

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

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

pyfr/1.14.0-gpu

 Please use pyfr/1.15.0-gpuTODO

pytorch/1.12.1

@@ -453,22 +393,17 @@ Please [contact the service desk](mailto:support@cirrus.ac.uk) if you have conce

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

 Please use QE/6.5-intel-20.4

specfem3d

 Please contact the helpdesk if you wish to use SPECFEM3D

starccm+/14.04.013-R8

@@ -478,8 +413,7 @@ Please [contact the service desk](mailto:support@cirrus.ac.uk) if you have conce

starccm+/15.06.008-R8 → 2020.3.1-R8

starccm+/16.02.009 → 2021.1.1

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

tensorflow/2.9.1-gpu

@@ -489,9 +423,7 @@ Please [contact the service desk](mailto:support@cirrus.ac.uk) if you have conce

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

@@ -502,18 +434,15 @@ Please [contact the service desk](mailto:support@cirrus.ac.uk) if you have conce

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

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