From 2eb4a6e69e8ba36dbb5e69dc94d26fba0621167c Mon Sep 17 00:00:00 2001 From: Camilla Harris Date: Mon, 23 Sep 2024 15:14:52 +0100 Subject: [PATCH 1/3] Update login and compute node --- _includes/snippets_library/UCL_Myriad_sge/_config_options.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/_includes/snippets_library/UCL_Myriad_sge/_config_options.yml b/_includes/snippets_library/UCL_Myriad_sge/_config_options.yml index 79650711..41b1ffe1 100644 --- a/_includes/snippets_library/UCL_Myriad_sge/_config_options.yml +++ b/_includes/snippets_library/UCL_Myriad_sge/_config_options.yml @@ -7,7 +7,8 @@ local: remote: name: "Myriad" login: "myriad.rc.ucl.ac.uk" - node: node-d00a-001 + host: "login12.myriad.ucl.ac.uk" + node: node-d00a-005 location: "University College London" homedir: "/home" user: "yourUsername" From a209d453e3df8ef482571ecdf50531796165416b Mon Sep 17 00:00:00 2001 From: Camilla Harris Date: Mon, 23 Sep 2024 17:05:37 +0100 Subject: [PATCH 2/3] Update new python scripts with Myriad env setup --- .../UCL_Myriad_sge/parallel/eight-tasks-jobscript.snip | 10 +++++++--- .../UCL_Myriad_sge/parallel/four-tasks-jobscript.snip | 10 +++++++--- .../UCL_Myriad_sge/parallel/one-task-jobscript.snip | 8 ++++++-- 3 files changed, 20 insertions(+), 8 deletions(-) diff --git a/_includes/snippets_library/UCL_Myriad_sge/parallel/eight-tasks-jobscript.snip b/_includes/snippets_library/UCL_Myriad_sge/parallel/eight-tasks-jobscript.snip index f0e8716f..5f564db8 100644 --- a/_includes/snippets_library/UCL_Myriad_sge/parallel/eight-tasks-jobscript.snip +++ b/_includes/snippets_library/UCL_Myriad_sge/parallel/eight-tasks-jobscript.snip @@ -1,13 +1,17 @@ ``` {{ site.remote.bash_shebang }} {{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job -{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }} -{{ site.sched.comment }} -l nodes=1:ppn=8 +{{ site.sched.comment }} -l mem=3G +{{ site.sched.comment }} -l h_rt=00:30:00 +{{ site.sched.comment }} -pe mpi 8 +{{ site.sched.comment }} -cwd # Load the computing environment we need module load python3 +module unload compilers mpi +module load mpi4py # Execute the task -mpiexec amdahl +gerun amdahl ``` {: .language-bash} diff --git a/_includes/snippets_library/UCL_Myriad_sge/parallel/four-tasks-jobscript.snip b/_includes/snippets_library/UCL_Myriad_sge/parallel/four-tasks-jobscript.snip index e1ba5c5c..ac523d57 100644 --- a/_includes/snippets_library/UCL_Myriad_sge/parallel/four-tasks-jobscript.snip +++ b/_includes/snippets_library/UCL_Myriad_sge/parallel/four-tasks-jobscript.snip @@ -1,13 +1,17 @@ ``` {{ site.remote.bash_shebang }} {{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job -{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }} -{{ site.sched.comment }} -l nodes=1:ppn=4 +{{ site.sched.comment }} -l mem=3G +{{ site.sched.comment }} -l h_rt=00:30:00 +{{ site.sched.comment }} -pe mpi 4 +{{ site.sched.comment }} -cwd # Load the computing environment we need module load python3 +module unload compilers mpi +module load mpi4py # Execute the task -mpiexec amdahl +gerun amdahl ``` {: .language-bash} diff --git a/_includes/snippets_library/UCL_Myriad_sge/parallel/one-task-jobscript.snip b/_includes/snippets_library/UCL_Myriad_sge/parallel/one-task-jobscript.snip index 42fdd337..4836b3e3 100644 --- a/_includes/snippets_library/UCL_Myriad_sge/parallel/one-task-jobscript.snip +++ b/_includes/snippets_library/UCL_Myriad_sge/parallel/one-task-jobscript.snip @@ -1,11 +1,15 @@ ``` {{ site.remote.bash_shebang }} {{ site.sched.comment }} {{ site.sched.flag.name }} solo-job -{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }} -{{ site.sched.comment }} -l nodes=1:ppn=1 +{{ site.sched.comment }} -l mem=3G +{{ site.sched.comment }} -l h_rt=00:30:00 +{{ site.sched.comment }} -pe mpi 1 +{{ site.sched.comment }} -cwd # Load the computing environment we need module load python3 +module unload compilers mpi +module load mpi4py # Execute the task amdahl From c7b43fc0a0acf5f82c9a44a17750eb2028d8a5c3 Mon Sep 17 00:00:00 2001 From: Camilla Harris Date: Mon, 23 Sep 2024 17:06:06 +0100 Subject: [PATCH 3/3] Update option flags for Myriad SGE --- .../UCL_Myriad_sge/scheduler/option-flags-list.snip | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_includes/snippets_library/UCL_Myriad_sge/scheduler/option-flags-list.snip b/_includes/snippets_library/UCL_Myriad_sge/scheduler/option-flags-list.snip index f6961da7..e7f9010c 100644 --- a/_includes/snippets_library/UCL_Myriad_sge/scheduler/option-flags-list.snip +++ b/_includes/snippets_library/UCL_Myriad_sge/scheduler/option-flags-list.snip @@ -4,8 +4,8 @@ * `-pe mpi ` — How many CPUs does your job need? If you only need one CPU you can leave this out. -* `mem=` — How much memory per process does your job need? Must be +* `-l mem=` — How much memory per process does your job need? Must be an integer followed by M, G, or T to specify Mega, Giga or Terabytes. -* `wd /home//Scratch/` — Set the working +* `-wd /home//Scratch/` — Set the working directory to somewhere in your scratch space.