As part of the May 2024 CSF4 upgrade the Operating System was upgraded from CentOS 7.9 to Red Hat Enterprise Linux 9.3. As a result, there’s a possibility certain pieces of software will require re-installing, or perhaps additional modulefiles will need to be loaded in your jobscript.<\/p>\n
We list below known problems and work-arounds discovered so far.<\/p>\n
Your own testing of your jobs will help us. If you discover any such things in your own jobs, please do let us know!<\/p>\n
If you would like to report a problem with a piece of software following the May 2024 upgrade, please do ONE<\/strong> of the following (no need to do both).<\/p>\n OR<\/strong><\/li>\n If you submit a multinode job using:<\/p>\n When you submit the job you will see an error:<\/p>\n The solution<\/strong> is to ALSO specify the number of nodes:<\/p>\n We are looking in to this behaviour change in SLURM.<\/p>\n Known applications affected: GROMACS<\/strong><\/p>\n Solution<\/strong>: Please load the following module file in any job scripts that report the above error.<\/p>\n When adding lines such as the following to your jobscript, you won’t actually receive any email:<\/p>\n There is no workaround – we will address this issue next week.<\/p>\n gview.exe: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory<\/p>\n Solution<\/strong>: Solution<\/strong>: The Known applications affected:MATLBAB,StarCCM, other applications that contact on-campus license servers will more than likely be affected.<\/strong> Known applications affected:StarCCM<\/strong><\/p>\n Solution<\/strong>: Missing dependency has been installed<\/strong><\/p>\n Solution<\/strong>: Please add the following to your jobscript, after loading your usual modulefiles:<\/p>\n Solution<\/strong>: Please add the following additional modules in your jobscript, after loading your LAMMPS module, in the given order<\/strong>:<\/p>\n CSF4 wiki on LAMMPS<\/a> updated with this info.<\/p>\n","protected":false},"excerpt":{"rendered":" As part of the May 2024 CSF4 upgrade the Operating System was upgraded from CentOS 7.9 to Red Hat Enterprise Linux 9.3. As a result, there’s a possibility certain pieces of software will require re-installing, or perhaps additional modulefiles will need to be loaded in your jobscript. We list below known problems and work-arounds discovered so far. Your own testing of your jobs will help us. If you discover any such things in your own.. Read more »<\/a><\/p>\n","protected":false},"author":8,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1213","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/pages\/1213","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/users\/8"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/comments?post=1213"}],"version-history":[{"count":20,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/pages\/1213\/revisions"}],"predecessor-version":[{"id":1288,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/pages\/1213\/revisions\/1288"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/media?parent=1213"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}\n
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Known Issues and Workarounds<\/h2>\n
sbatch: error: Batch job submission failed: Node count specification invalid<\/h3>\n
#!\/bin\/bash --login\r\n#SBATCH -p multinode\r\n#SBATCH -n 80 # 80 cores in total = 2 x 40-core compute nodes\r\nmodule load ......\r\nmpirun -n $SLURM_NTASKS someapp.exe<\/em>\r\n\r\n######## THIS JOB WILL BE REJECTED<\/strong> #########\r\n<\/pre>\n
sbatch myjobscript\r\nsbatch: error: Batch job submission failed: Node count specification invalid\r\n<\/pre>\n
#!\/bin\/bash --login\r\n#SBATCH -p multinode\r\n#SBATCH -N 2 # 2 nodes<\/strong> \r\n#SBATCH -n 80 # 80 cores in total = 2 x 40-core compute nodes\r\nmodule load ......\r\nmpirun -n $SLURM_NTASKS someapp.exe<\/em>\r\n\r\n######## THIS JOB WILL BE ACCEPTED<\/strong> #########\r\n<\/pre>\n
version `XZ_5.2′ not found<\/h3>\n
\r\nflatpak: \/opt\/software\/RI\/apps\/XZ\/5.2.5-GCCcore-10.3.0\/lib\/liblzma.so.5: version `XZ_5.2' not found (required by \/lib64\/libarchive.so.13)\r\nflatpak: \/opt\/software\/RI\/apps\/XZ\/5.2.5-GCCcore-10.3.0\/lib\/liblzma.so.5: version `XZ_5.2' not found (required by \/lib64\/librpmio.so.9)\r\n<\/pre>\n
module load xz\/5.2.5-gcccore-10.3.0\r\n<\/pre>\n
Job email notifications not working<\/h3>\n
#SBATCH --mail-type=ALL\r\n#SBATCH --mail-user=firstname.lastname<\/em>@manchester.ac.uk\r\n<\/pre>\n
Gaussview gview.exe: libGLU.so.1: cannot open shared object file<\/h3>\n
Please load the following module to prevent this error:<\/del>
\n14\/06\/2024: The libglu libraries are now installed on the login and compute nodes, so there is no need to load this modulefile.<\/p>\nmodule load libglu\/9.0.1-gcccore-10.3.0<\/pre>\n
-bash: nano: command not found<\/h3>\n
nano<\/code> editor has now been installed on the login nodes.<\/p>\nLicensing errors<\/h3>\n
\nExample of errors<\/p>\n\r\nMATLAB\r\nLicense checkout failed.\r\nLicense Manager Error -15\r\nUnable to connect to the license server. \r\nCheck that the network license manager has been started, and that the client machine can communicate\r\nwith the license server.\r\n<\/pre>\n
Currently under investigation<\/del>
\n11\/06\/24 – root cause has been identified and a solution is being worked on.<\/del>
\n16\/06\/24 – this issue has now been resolved – applications that use the campus license servers will now run.
\nSolution<\/strong>: Please just submit your jobs as usual – no changes are required to youor jobscripts.<\/p>\nError Running Paraview Macro<\/h3>\n
\r\nHYDU_create_process (utils\/launch\/launch.c:73): execvp error on file srun (No such file or directory)\r\n<\/pre>\n
currently under investigation<\/del>
\nSolution<\/strong>: Please just submit your jobs as usual – no changes are required to your jobscripts.<\/p>\nlibnsl.so.1: cannot open shared object file<\/h3>\n
\r\nerror while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory\r\n<\/pre>\n
libssl.so.10: cannot open shared object file<\/h3>\n
\r\nflatpak: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory\r\n<\/pre>\n
\r\nmodule load openssl\/1.0.2k\r\n<\/pre>\n
LAMMPS libssl.so.10, libcrypto.so.10, libz.so.1 : not found \/ cannot open shared object file<\/h3>\n
\r\nmodule load openssl\/1.0.2k\r\nmodule load zlib\/1.2.11-gcccore-9.3.0\r\n<\/pre>\n