For jobs that require 2-168 CPU cores – running on one AMD Genoa compute node. A jobscript template is shown below. Please also consult the Partitions<\/a> page for details on available compute resources.<\/p>\n Please also consult the software page<\/a> for the code \/ application you want to use, for advice on running that application<\/strong><\/em>.<\/p>\n A parallel job script will run in the directory (folder) from which you submit the job.<\/p>\n The jobscript takes the form:<\/p>\n Here we request 1 “task” (process, or copy of your executable running) and multiple CPUs per task. <\/p>\n On the CSF, this is functionally equivalent to the above jobscript, which simply uses If you use the Slurm Here we run a small number of MPI processes, and each one of those will run OpenMP threads to do multi-core processing. This type of job is mostly run in the HPC Pool<\/a> because it is more suited to multi-node jobs. Remember that the Please see the Partitions<\/a> page for details on available compute resources.<\/p>\n","protected":false},"excerpt":{"rendered":" Parallel batch job submission (Slurm) For jobs that require 2-168 CPU cores – running on one AMD Genoa compute node. A jobscript template is shown below. Please also consult the Partitions page for details on available compute resources. Please also consult the software page for the code \/ application you want to use, for advice on running that application. A parallel job script will run in the directory (folder) from which you submit the job… Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":9105,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-9233","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/9233","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=9233"}],"version-history":[{"count":18,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/9233\/revisions"}],"predecessor-version":[{"id":11924,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/9233\/revisions\/11924"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/9105"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=9233"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}MPI parallel apps<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#SBATCH -p multicore # Partition is required<\/strong>. Runs on an AMD Genoa<\/strong> hardware.\r\n#SBATCH -n numcores<\/em> # (or --ntasks=) where numcores<\/em> is between 2 and 168.\r\n#SBATCH -t 4-0 # Wallclock limit (days-hours). Required!<\/strong>\r\n # Max permitted is 7 days (7-0).\r\n\r\n# Load any required modulefiles. A purge is used to start with a clean environment.\r\nmodule purge\r\nmodule load apps\/some\/example\/1.2.3<\/em>\r\n\r\n### MPI jobs ###<\/strong>\r\n# mpirun will run $SLURM_NTASKS (-n above) MPI processes\r\nmpirun mpi-app.exe<\/em>\r\n<\/pre>\n
OpenMP parallel apps<\/h3>\n
-n numcores<\/em><\/code>, so you can use either. In fact, many of our jobscript examples in the software pages<\/a> use only -n<\/code> to specify the number of cores. But this is because jobs in the multicore<\/code> partition are single-node jobs. Slurm can distribute the -n<\/code> cores across all of the compute nodes in a job, but in this case there is only ever one compute node.<\/p>\nsrun<\/code> starter to run your executable inside the batch job (optional, and in most cases we don’t use this) then the distinction between -n<\/code> and -c<\/code> is important.<\/p>\n\r\n#!\/bin\/bash --login\r\n#SBATCH -p multicore # Partition is required<\/strong>. Runs on an AMD Genoa<\/strong> hardware.\r\n#SBATCH -n 1 # (or --ntasks=) The default is 1 so this line can be omitted.\r\n#SBATCH -c numcores<\/em> # (or --cpus-per-task) where numcores<\/em> is between 2 and 168\r\n#SBATCH -t 4-0 # Wallclock limit (days-hours). Required!<\/strong>\r\n # Max permitted is 7 days (7-0).\r\n\r\n# Load any required modulefiles. A purge is used to start with a clean environment.\r\nmodule purge\r\nmodule load apps\/some\/example\/1.2.3<\/em>\r\n\r\n### OpenMP jobs ###<\/strong>\r\n# OpenMP code will use $SLURM_CPUS_PER_TASK cores (-c above)\r\nexport OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK\r\nomp-app.exe\r\n<\/pre>\n
MPI+OpenMP mixed-mode apps<\/h3>\n
multicore<\/code> partition can only run single-node jobs.<\/p>\n\r\n#!\/bin\/bash --login\r\n#SBATCH -p multicore # Partition is required<\/strong>. Runs on an AMD Genoa<\/strong> hardware.\r\n#SBATCH -n numtasks<\/em> # (or --ntasks=) Number of MPI processes (e.g., 4)\r\n#SBATCH -c numcores<\/em> # (or --cpus-per-task) Number of OpenMP threads per MPI process (e.g., 42)\r\n # This will use numtasks<\/em> x numcores<\/em> cores in total (e.g., 168)\r\n#SBATCH -t 4-0 # Wallclock limit (days-hours). Required!<\/strong>\r\n # Max permitted is 7 days (7-0).\r\n\r\n# Load any required modulefiles. A purge is used to start with a clean environment.\r\nmodule purge\r\nmodule load apps\/some\/example\/1.2.3<\/em>\r\n\r\n### OpenMP ###<\/strong>\r\n# Each MPI process uses OpenMP to run on $SLURM_CPUS_PER_TASK cores (-c above)\r\nexport OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK\r\n\r\n### MPI ###<\/strong>\r\n# The MPI application is then started with $SLURM_NTASKS processes (copies of the app)\r\n# We inform MPI how many cores each MPI process should bind to so that OpenMP can use them.\r\nmpirun --map-by ppr:${SLURM_NTASKS}:node:pe=$OMP_NUM_THREADS mix-mode-app.exe\r\n<\/pre>\nAvailable Hardware and Resources<\/h2>\n