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Update UCL site snippets #458

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merged 3 commits into from
Sep 23, 2024
Merged

Update UCL site snippets #458

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2eb4a6e
Update login and compute node
cdkharris Sep 23, 2024
a209d45
Update new python scripts with Myriad env setup
cdkharris Sep 23, 2024
c7b43fc
Update option flags for Myriad SGE
cdkharris Sep 23, 2024
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3 changes: 2 additions & 1 deletion _includes/snippets_library/UCL_Myriad_sge/_config_options.yml
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Expand Up @@ -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"
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10 changes: 7 additions & 3 deletions _includes/snippets_library/UCL_Myriad_sge/parallel/eight-tasks-jobscript.snip
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@@ -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}
10 changes: 7 additions & 3 deletions _includes/snippets_library/UCL_Myriad_sge/parallel/four-tasks-jobscript.snip
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@@ -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}
8 changes: 6 additions & 2 deletions _includes/snippets_library/UCL_Myriad_sge/parallel/one-task-jobscript.snip
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@@ -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
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4 changes: 2 additions & 2 deletions _includes/snippets_library/UCL_Myriad_sge/scheduler/option-flags-list.snip
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Expand Up @@ -4,8 +4,8 @@
* `-pe mpi <ncpus>` &mdash; How many CPUs does your job need? If you only need
one CPU you can leave this out.

* `mem=<bytes>` &mdash; How much memory per process does your job need? Must be
* `-l mem=<bytes>` &mdash; 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/<your_UCL_id>/Scratch/<your_run_directory>` &mdash; Set the working
* `-wd /home/<your_UCL_id>/Scratch/<your_run_directory>` &mdash; Set the working
directory to somewhere in your scratch space.
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