From 8bea86d776db9bec2572fb8f5ed8256c64b5ac3a Mon Sep 17 00:00:00 2001 From: cal Date: Thu, 7 Dec 2023 22:41:19 +1300 Subject: [PATCH 01/14] correct includes dir --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index f4c9dded8..0e07ea0a2 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -31,7 +31,7 @@ plugins: enable_creation_date: true - macros: module_name: macro_hooks - include_dir: docs/assets + include_dir: overrides repo_name: GitHub repo_url: https://github.com/nesi/support-docs-concept edit_uri: edit/main/docs/ From 4b702108de2453708888638f231e1fbcd6628501 Mon Sep 17 00:00:00 2001 From: cal Date: Thu, 7 Dec 2023 22:41:35 +1300 Subject: [PATCH 02/14] template update --- overrides/app.html | 2 ++ overrides/partials/appCard.html | 4 ++-- overrides/partials/appContent.html | 2 -- overrides/partials/supportedApplicationsList.html | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/overrides/app.html b/overrides/app.html index 71049accc..0c5b69810 100644 --- a/overrides/app.html +++ b/overrides/app.html @@ -1,5 +1,7 @@ {% extends "main.html" %} {% block content %} +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} {% include "partials/appContent.html" %} {% if git_page_authors %} diff --git a/overrides/partials/appCard.html b/overrides/partials/appCard.html index 6f759d768..92a9c4982 100644 --- a/overrides/partials/appCard.html +++ b/overrides/partials/appCard.html @@ -26,8 +26,8 @@

{{ app_name }}

{{ app.description }}

- {% include "partials/appVerison.html" %} -
+ {% include "partials/appVersion.html" -%} +
Links
    {% if app.homepage or app.url -%} diff --git a/overrides/partials/appContent.html b/overrides/partials/appContent.html index 31b6fc4f2..c0eb91a94 100644 --- a/overrides/partials/appContent.html +++ b/overrides/partials/appContent.html @@ -5,8 +5,6 @@ {% if "\x3ch1" not in page.content %}

    {{ page.title | d(config.site_name, true)}}

    {% endif %} -{% set app_name = page.title %} -{% set app = applications[app_name] %} {% include "partials/appCardBig.html" %} {{ page.content }} {% if page.meta and ( diff --git a/overrides/partials/supportedApplicationsList.html b/overrides/partials/supportedApplicationsList.html index fdc892d23..487098a89 100644 --- a/overrides/partials/supportedApplicationsList.html +++ b/overrides/partials/supportedApplicationsList.html @@ -15,7 +15,7 @@ {% if applications|length > 1 %} {% for app_name in applications %} {% set app = applications[app_name] %} - {% include "partials/applicationCard.html" %} + {% include "partials/appCard.html" %} {% endfor %} {% else %}

    Whoops, something has gone wrong loading the software list. Please contact support.

    From 1120f2d3e0ba684db37dbc1f9c3e150ed4dc61eb Mon Sep 17 00:00:00 2001 From: cal Date: Thu, 7 Dec 2023 22:41:52 +1300 Subject: [PATCH 03/14] Page updates --- checks/run_meta_check.py | 5 +- checks/run_pyspelling.py | 33 +++++++ .../Supported_Applications/ABAQUS.md | 29 ++++-- .../Supported_Applications/ANSYS.md | 3 +- .../Supported_Applications/AlphaFold.md | 1 + .../Supported_Applications/BLAST.md | 1 + .../Supported_Applications/BRAKER.md | 1 + .../Supported_Applications/CESM.md | 1 + .../Supported_Applications/COMSOL.md | 9 +- .../Supported_Applications/Clair3 .md | 1 + .../Supported_Applications/Cylc.md | 1 + .../Supported_Applications/Delft3D.md | 7 +- .../Supported_Applications/Dorado.md | 1 + .../Supported_Applications/FDS.md | 1 + .../Supported_Applications/GATK.md | 1 + .../Supported_Applications/GROMACS.md | 1 + .../Supported_Applications/Gaussian.md | 1 + .../Supported_Applications/Java.md | 1 + .../Supported_Applications/Julia.md | 1 + .../Supported_Applications/JupyterLab.md | 1 + .../Supported_Applications/Keras.md | 1 + .../Supported_Applications/Lambda Stack.md | 48 ++++------ .../Supported_Applications/MAKER.md | 1 + .../Supported_Applications/MATLAB.md | 5 +- .../Supported_Applications/Miniconda3.md | 1 + .../Supported_Applications/ORCA.md | 1 + .../Supported_Applications/OpenFOAM.md | 3 +- .../Supported_Applications/OpenSees.md | 3 +- .../Supported_Applications/ParaView.md | 1 + .../Supported_Applications/Python.md | 3 +- .../Supported_Applications/R.md | 1 + .../Supported_Applications/RAxML.md | 1 + .../Supported_Applications/Relion.md | 1 + .../Supported_Applications/Singularity.md | 1 + .../Software Installation Request.md | 32 +++---- .../Supported_Applications/Supernova.md | 1 + .../Supported_Applications/Synda.md | 1 + .../TensorFlow on CPUs.md | 19 ++-- .../TensorFlow on GPUs.md | 92 +++++++++---------- .../Supported_Applications/Trinity.md | 1 + .../Supported_Applications/TurboVNC.md | 1 + .../Supported_Applications/VASP.md | 1 + ...ution hot spots with VTune.md => VTune.md} | 33 ++----- .../Supported_Applications/VirSorter.md | 1 + .../Supported_Applications/WRF.md | 1 + .../{index.html => index.md} | 0 .../Supported_Applications/ipyrad.md | 1 + .../Supported_Applications/ont-guppy-gpu.md | 1 + .../Supported_Applications/snpEff.md | 1 + 49 files changed, 205 insertions(+), 152 deletions(-) create mode 100755 checks/run_pyspelling.py rename docs/Scientific_Computing/Supported_Applications/{Find execution hot spots with VTune.md => VTune.md} (82%) rename docs/Scientific_Computing/Supported_Applications/{index.html => index.md} (100%) diff --git a/checks/run_meta_check.py b/checks/run_meta_check.py index c12b3507c..4b9195322 100755 --- a/checks/run_meta_check.py +++ b/checks/run_meta_check.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 """ -Runs checks on article meta block and outputs in github action readable format. +Runs checks on article meta block and outputs in github action readable format """ __author__ = "cal w" @@ -132,6 +132,9 @@ def check_article_titles(path, meta, contents): check_title(page_title(path, meta, contents)) +def supported(path, meta, contents): + + all_checks = [check_expected_parameters, check_article_titles] diff --git a/checks/run_pyspelling.py b/checks/run_pyspelling.py new file mode 100755 index 000000000..4268c62da --- /dev/null +++ b/checks/run_pyspelling.py @@ -0,0 +1,33 @@ +#!/usr/bin/env python + +""" +Modify proselint outputs into a format recognised by github actions. +""" + +import sys +from pyspelling import util + + +files = sys.argv[1:] + +ret_code = 0 +util.read_config(".spellcheck.yml") + +util.call(input_file=None, input_text=None, encoding=None) + +# call_spellchecker(cmd, input_text=None, encoding=None) + + +# # Load defaults from config. +# config_custom = tools.load_options(config_file_path=".proselint.json", conf_default=config.default) + +# print(config_custom) + +# for file in files: +# with open(file, "r", encoding="utf8") as f: +# for notice in proselint.tools.lint(f.read(), config=config_custom): +# if (notice[7] == "error"): +# ret_code = 1 +# print(f"::{notice[7]} file={file},line={notice[2]},col={notice[3]},endLine={notice[2]+notice[6]},title={notice[0]}::'{notice[1]}'") + +# sys.exit(ret_code) diff --git a/docs/Scientific_Computing/Supported_Applications/ABAQUS.md b/docs/Scientific_Computing/Supported_Applications/ABAQUS.md index 6638b6940..3cfe5f68b 100644 --- a/docs/Scientific_Computing/Supported_Applications/ABAQUS.md +++ b/docs/Scientific_Computing/Supported_Applications/ABAQUS.md @@ -11,12 +11,29 @@ tags: - fea title: ABAQUS vote_count: 2 +# template: app.html vote_sum: 0 zendesk_article_id: 212457807 zendesk_section_id: 360000040076 --- -A list of ABAQUS commands can be found with: +{% set app_name = page.app or page.title | trim %} +{% set app = applications[app_name] %} + +{{ app.description }} + +{% if app.homepage or app.url -%} +[{{ app_name }} Homepage]({{ app.homepage or app.url }}) +{% endif -%} + +{% if app.licence_type == "proprietary" -%} +!!! warning + {{ app_name }} is proprietary software. Make sure you meet the requirements for it's usage. +{% endif -%} + +## Available Modules + +{% include "partials/appVersion.html" -%} ``` sh abaqus help @@ -73,7 +90,7 @@ Not all solvers are compatible with all types of parallelisation. #SBATCH --time 00:05:00 # Walltime #SBATCH --cpus-per-task 1 #SBATCH --mem 1500 # total mem - module load ABAQUS/{{applications.ABAQUS.machines.mahuika.versions | last}} + module load ABAQUS/{{app.machines.mahuika.versions | last}} abaqus job="propeller_s4rs_c3d8r" verbose=2 interactive ``` @@ -92,7 +109,7 @@ Not all solvers are compatible with all types of parallelisation. #SBATCH --time 00:05:00 # Walltime #SBATCH --cpus-per-task 4 #SBATCH --mem 2G # total mem - module load ABAQUS/{{applications.ABAQUS.machines.mahuika.versions}} + module load ABAQUS/{{app.machines.mahuika.versions}} abaqus job="propeller_s4rs_c3d8r verbose=2 interactive \ cpus=${SLURM_CPUS_PER_TASK} mp_mode=threads ``` @@ -111,7 +128,7 @@ Not all solvers are compatible with all types of parallelisation. #SBATCH --mem 2G # total mem module load imkl - module load ABAQUS/{{applications.ABAQUS.machines.mahuika.versions | last}} + module load ABAQUS/{{app.machines.mahuika.versions | last}} abaqus job="propeller_s4rs_c3d8r" user=my_udf.f90 \ verbose=2 interactive cpus=${SLURM_CPUS_PER_TASK} mp_mode=threads ``` @@ -136,7 +153,7 @@ Not all solvers are compatible with all types of parallelisation. #SBATCH --mem-per-cpu 1500 # Each CPU needs it's own. #SBATCH --nodes 1 - module load ABAQUS/{{applications.ABAQUS.machines.mahuika.versions | last}} + module load ABAQUS/{{app.machines.mahuika.versions | last}} abaqus job "propeller_s4rs_c3d8r" verbose=2 interactive cpus=${SLURM_NTASKS} mp_mode=mpi ``` @@ -154,7 +171,7 @@ Not all solvers are compatible with all types of parallelisation. #SBATCH --cpus-per-task 4 #SBATCH --mem 4G # total mem #SBATCH --gpus-per-node - module load ABAQUS/{{applications.ABAQUS.machines.mahuika.versions | last}} + module load ABAQUS/{{app.machines.mahuika.versions | last}} module load CUDA abaqus job="propeller_s4rs_c3d8r" verbose=2 interactive \ cpus=${SLURM_CPUS_PER_TASK} gpus=${SLURM_GPUS_PER_NODE} mp_mode=threads diff --git a/docs/Scientific_Computing/Supported_Applications/ANSYS.md b/docs/Scientific_Computing/Supported_Applications/ANSYS.md index 216122496..01944a699 100644 --- a/docs/Scientific_Computing/Supported_Applications/ANSYS.md +++ b/docs/Scientific_Computing/Supported_Applications/ANSYS.md @@ -8,6 +8,7 @@ tags: - engineering title: ANSYS vote_count: 3 +template: app.html vote_sum: 3 zendesk_article_id: 212642617 zendesk_section_id: 360000040076 @@ -76,7 +77,7 @@ Below is an example of this from a fluent script. #SBATCH --array 1-100 #SBATCH --hint nomultithread # No hyperthreading -module load ANSYS/{{applications.ANSYS.machines.mahuika.versions | last}} +module load ANSYS/{{app.machines.mahuika.versions | last}} JOURNAL_FILE=fluent_${SLURM_JOB_ID}.in cat ${JOURNAL_FILE} diff --git a/docs/Scientific_Computing/Supported_Applications/AlphaFold.md b/docs/Scientific_Computing/Supported_Applications/AlphaFold.md index 89ac16989..e555b82d9 100644 --- a/docs/Scientific_Computing/Supported_Applications/AlphaFold.md +++ b/docs/Scientific_Computing/Supported_Applications/AlphaFold.md @@ -5,6 +5,7 @@ position: 6 tags: [] title: AlphaFold vote_count: 2 +template: app.html vote_sum: 2 zendesk_article_id: 4405170961039 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/BLAST.md b/docs/Scientific_Computing/Supported_Applications/BLAST.md index d2aca6741..b1392512f 100644 --- a/docs/Scientific_Computing/Supported_Applications/BLAST.md +++ b/docs/Scientific_Computing/Supported_Applications/BLAST.md @@ -7,6 +7,7 @@ tags: - biology title: BLAST vote_count: 1 +template: app.html vote_sum: -1 zendesk_article_id: 208619807 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/BRAKER.md b/docs/Scientific_Computing/Supported_Applications/BRAKER.md index c717965fd..437d3a5b2 100644 --- a/docs/Scientific_Computing/Supported_Applications/BRAKER.md +++ b/docs/Scientific_Computing/Supported_Applications/BRAKER.md @@ -4,6 +4,7 @@ hidden: false position: 0 tags: [] vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 6529511928207 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/CESM.md b/docs/Scientific_Computing/Supported_Applications/CESM.md index 90117aa3f..8c50db273 100644 --- a/docs/Scientific_Computing/Supported_Applications/CESM.md +++ b/docs/Scientific_Computing/Supported_Applications/CESM.md @@ -5,6 +5,7 @@ position: 10 tags: [] title: CESM vote_count: 0 +# template: app.html vote_sum: 0 zendesk_article_id: 360002105076 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/COMSOL.md b/docs/Scientific_Computing/Supported_Applications/COMSOL.md index 0ad18cce5..3248ca5db 100644 --- a/docs/Scientific_Computing/Supported_Applications/COMSOL.md +++ b/docs/Scientific_Computing/Supported_Applications/COMSOL.md @@ -11,6 +11,7 @@ tags: - fea title: COMSOL vote_count: 1 +template: app.html vote_sum: 1 zendesk_article_id: 360000871556 zendesk_section_id: 360000040076 @@ -59,7 +60,7 @@ sweeps. #SBATCH --time 00:05:00 # Walltime #SBATCH --mem 1512 # total mem - module load COMSOL/{{applications.COMSOL.machines.mahuika.versions | last}} + module load COMSOL/{{app.machines.mahuika.versions | last}} comsol batch -inputfile my_input.mph ``` @@ -72,7 +73,7 @@ sweeps. #SBATCH --time 00:05:00 # Walltime #SBATCH --cpus-per-task 8 #SBATCH --mem 4G # total mem - module load COMSOL/{{applications.COMSOL.machines.mahuika.versions | last}} + module load COMSOL/{{app.machines.mahuika.versions | last}} comsol batch -mpibootstrap slurm -inputfile my_input.mph ``` @@ -87,7 +88,7 @@ sweeps. #SBATCH --ntasks 8 #SBATCH --mem-per-cpu 1500 # mem per cpu - module load COMSOL/{{applications.COMSOL.machines.mahuika.versions | last}} + module load COMSOL/{{app.machines.mahuika.versions | last}} comsolbatcH -mpibootstrap slurm -inputfile my_input.mph ``` @@ -102,7 +103,7 @@ sweeps. #SBATCH --cpus-per-task 16 #SBATCH --mem-per-cpu 1500B # total mem - module load COMSOL/{{applications.ABAQUS.machines.mahuika.versions | last}} + module load COMSOL/{{app.machines.mahuika.versions | last}} comsol batch -mpibootstrap slurm -inputfile my_input.mph ``` diff --git a/docs/Scientific_Computing/Supported_Applications/Clair3 .md b/docs/Scientific_Computing/Supported_Applications/Clair3 .md index a78ffe438..919ee3270 100644 --- a/docs/Scientific_Computing/Supported_Applications/Clair3 .md +++ b/docs/Scientific_Computing/Supported_Applications/Clair3 .md @@ -5,6 +5,7 @@ position: 3 tags: [] title: 'Clair3 ' vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 5292628239375 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Cylc.md b/docs/Scientific_Computing/Supported_Applications/Cylc.md index 51ec44ae2..76cbf3e94 100644 --- a/docs/Scientific_Computing/Supported_Applications/Cylc.md +++ b/docs/Scientific_Computing/Supported_Applications/Cylc.md @@ -5,6 +5,7 @@ position: 4 tags: [] title: Cylc vote_count: 0 +# template: app.html vote_sum: 0 zendesk_article_id: 5254610390415 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Delft3D.md b/docs/Scientific_Computing/Supported_Applications/Delft3D.md index 77c868e8e..c251631e1 100644 --- a/docs/Scientific_Computing/Supported_Applications/Delft3D.md +++ b/docs/Scientific_Computing/Supported_Applications/Delft3D.md @@ -6,6 +6,7 @@ tags: - hydrodynamics title: Delft3D vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360001593096 zendesk_section_id: 360000040076 @@ -24,7 +25,7 @@ zendesk_section_id: 360000040076 #SBATCH --time 00:05:00 # Walltime #SBATCH --mem 512M # Total Memory #SBATCH --hint nomultithread # Hyperthreading disabled - module load Delft3D/{{applications.ABAQUS.machines.mahuika.versions | last}} + module load Delft3D/{{app.machines.mahuika.versions | last}} d_hydro test_input.xml ``` @@ -42,7 +43,7 @@ zendesk_section_id: 360000040076 #SBATCH --mem 2G # Total Memory #SBATCH --hint nomultithread # Hyperthreading disabled - module load Delft3D/{{applications.Delft3D.machines.mahuika.versions | last}} + module load Delft3D/{{app.machines.mahuika.versions | last}} srun d_hyrdo test_input.xml ``` @@ -73,7 +74,7 @@ zendesk_section_id: 360000040076 #SBATCH --time 00:05:00 # Walltime #SBATCH --mem-per-cpu 1G #SBATCH --hint nomultithread # Hyperthreading disabled - module load Delft3D/{{applications.Delft3D.machines.mahuika.versions | last}} + module load Delft3D/{{app.machines.mahuika.versions | last}} srun d_hyrdo test_input.xml ``` diff --git a/docs/Scientific_Computing/Supported_Applications/Dorado.md b/docs/Scientific_Computing/Supported_Applications/Dorado.md index 4c654bc0e..b5b715a66 100644 --- a/docs/Scientific_Computing/Supported_Applications/Dorado.md +++ b/docs/Scientific_Computing/Supported_Applications/Dorado.md @@ -5,6 +5,7 @@ position: 0 tags: [] title: Dorado vote_count: 2 +template: app.html vote_sum: 2 zendesk_article_id: 6623692647951 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/FDS.md b/docs/Scientific_Computing/Supported_Applications/FDS.md index 5741f13b3..ef358ec7b 100644 --- a/docs/Scientific_Computing/Supported_Applications/FDS.md +++ b/docs/Scientific_Computing/Supported_Applications/FDS.md @@ -7,6 +7,7 @@ tags: - engineering title: FDS vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360000759275 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/GATK.md b/docs/Scientific_Computing/Supported_Applications/GATK.md index 3f35615df..543610dc4 100644 --- a/docs/Scientific_Computing/Supported_Applications/GATK.md +++ b/docs/Scientific_Computing/Supported_Applications/GATK.md @@ -5,6 +5,7 @@ position: 1 tags: [] title: GATK vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 6443618773519 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/GROMACS.md b/docs/Scientific_Computing/Supported_Applications/GROMACS.md index fe00b7926..f161888d9 100644 --- a/docs/Scientific_Computing/Supported_Applications/GROMACS.md +++ b/docs/Scientific_Computing/Supported_Applications/GROMACS.md @@ -5,6 +5,7 @@ position: 30 tags: [] title: GROMACS vote_count: 2 +template: app.html vote_sum: 2 zendesk_article_id: 360000792856 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Gaussian.md b/docs/Scientific_Computing/Supported_Applications/Gaussian.md index d39c40f8c..362e652bb 100644 --- a/docs/Scientific_Computing/Supported_Applications/Gaussian.md +++ b/docs/Scientific_Computing/Supported_Applications/Gaussian.md @@ -7,6 +7,7 @@ tags: - chemistry title: Gaussian vote_count: 5 +template: app.html vote_sum: 1 zendesk_article_id: 207127857 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Java.md b/docs/Scientific_Computing/Supported_Applications/Java.md index 0735810d7..e999a3960 100644 --- a/docs/Scientific_Computing/Supported_Applications/Java.md +++ b/docs/Scientific_Computing/Supported_Applications/Java.md @@ -7,6 +7,7 @@ tags: - general title: Java vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 207765367 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Julia.md b/docs/Scientific_Computing/Supported_Applications/Julia.md index 9610c6ed1..99ba90949 100644 --- a/docs/Scientific_Computing/Supported_Applications/Julia.md +++ b/docs/Scientific_Computing/Supported_Applications/Julia.md @@ -5,6 +5,7 @@ position: 32 tags: [] title: Julia vote_count: 3 +template: app.html vote_sum: 3 zendesk_article_id: 360001175895 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/JupyterLab.md b/docs/Scientific_Computing/Supported_Applications/JupyterLab.md index 657a70195..6a9163ae2 100644 --- a/docs/Scientific_Computing/Supported_Applications/JupyterLab.md +++ b/docs/Scientific_Computing/Supported_Applications/JupyterLab.md @@ -5,6 +5,7 @@ position: 33 tags: [] title: JupyterLab vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360001093315 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Keras.md b/docs/Scientific_Computing/Supported_Applications/Keras.md index fe28434c6..8adc8ea2f 100644 --- a/docs/Scientific_Computing/Supported_Applications/Keras.md +++ b/docs/Scientific_Computing/Supported_Applications/Keras.md @@ -5,6 +5,7 @@ position: 34 tags: [] title: Keras vote_count: 0 +# template: app.html vote_sum: 0 zendesk_article_id: 360001075936 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md b/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md index 396b15e01..6f53dfee9 100644 --- a/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md +++ b/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md @@ -5,20 +5,12 @@ position: 8 tags: [] title: Lambda Stack vote_count: 1 +# template: app.html vote_sum: 1 zendesk_article_id: 360002558216 zendesk_section_id: 360000040076 --- - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) - ## Introduction [Lambda @@ -36,7 +28,7 @@ Lambda Stack in a Slurm job or interactively via You can list the available Lambda Stack version on NeSI by running: -``` sl +``` sh $ ls /opt/nesi/containers/lambda-stack lambda-stack-focal-20201130.sif lambda-stack-focal-20201221.sif @@ -52,7 +44,7 @@ version. ## Building the Singularity image (optional) This step is optional; if you choose to use the prebuilt Singularity -images under */opt/nesi/containers/lambda-stack/* you can skip this +images under `/opt/nesi/containers/lambda-stack/` you can skip this step. Note that Singularity images are immutable, so the versions of packages @@ -76,7 +68,7 @@ Make sure you have [Docker](https://docs.docker.com/get-docker/) and [Singularity](https://sylabs.io/guides/3.7/user-guide/quick_start.html#quick-installation-steps) installed first and then follow the steps below. -``` sl +``` sh # clone the lambda stack Dockerfiles repo git clone https://github.com/lambdal/lambda-stack-dockerfiles.git cd lambda-stack-dockerfiles @@ -95,15 +87,13 @@ you don't have enough space in */tmp* for the Singularity build you could try running the following script (updating paths first) as root (e.g. using *sudo*): -``` sl +``` sh #!/bin/bash export SINGULARITY_TMPDIR=/path/to/somewhere/with/lots/of/space export SINGULARITY_CACHEDIR=/path/to/somewhere/else/with/lots/of/space singularity build lambda-stack-focal-$(date +%Y%m%d).sif docker-daemon:lambda-stack:20.04 ``` -  - ## Lambda Stack via Slurm The following Slurm script can be used as a template for running jobs @@ -142,7 +132,7 @@ First, we need to create a kernel definition and wrapper that will launch the Singularity image. Run the following commands on the Mahuika login node: -``` sl +``` sh # load the Singularity envioronment module module load Singularity @@ -157,13 +147,13 @@ singularity exec -B $HOME $SIF python -m ipykernel install --user \ If successful this should report that a kernelspec has been installed. Change to the kernelspec directory: -``` sl +``` sh cd $HOME/.local/share/jupyter/kernels/lambdastack ``` and create a wrapper script for launching the kernel, named wrapper.sh: -``` sl +``` sh #!/usr/bin/env bash # path to the singularity image file (optionally replace with your own) @@ -189,7 +179,7 @@ ${SINGULARITY} python3 $@ Make the wrapper script executable: -``` sl +``` sh chmod +x wrapper.sh ``` @@ -197,7 +187,7 @@ Next, edit the *kernel.json* to change the first element of the argv list to point to the wrapper script we just created. The file should look like this (change <username> to your NeSI username): -``` sl +``` json { "argv": [ "/home//.local/share/jupyter/kernels/lambdastack/wrapper.sh", @@ -225,7 +215,7 @@ included in the Lambda Stack distribution, the Transformers library is not, so the first thing we do is create a virtual environment and install transformers into it: -``` sl +``` sh # load the Singularity environment module module load Singularity @@ -244,7 +234,7 @@ After executing the above command your prompt should have changed to *Singularity>*, the following commands are all executed at this prompt (i.e. within the container): -``` sl +``` sh virtualenv --system-site-packages transenv source transenv/bin/activate pip install transformers psutil py3nvml @@ -253,21 +243,21 @@ pip install transformers psutil py3nvml exit ``` -Note we used *--system-site-packages* so that we can use the Lambda +Note we used `--system-site-packages`` so that we can use the Lambda Stack installed TensorFlow, PyTorch, etc., instead of installing them separately. Now clone the transformers git repo so we can run the benchmark script (these commands run outside the container): -``` sl +``` sh git clone https://github.com/huggingface/transformers.git ``` Create the following script for running the benchmarks, named *run-benchmark-torch.sh*: -``` sl +``` sh #!/bin/bash -e # load the virtual environment with transformers installed @@ -318,12 +308,6 @@ ${SINGULARITY} bash ./run-benchmark-torch.sh Submit this job to Slurm and then wait for the benchmarks to run: -``` sl +``` sh sbatch run-benchmark-torch.sl ``` - -  - -  - -  \ No newline at end of file diff --git a/docs/Scientific_Computing/Supported_Applications/MAKER.md b/docs/Scientific_Computing/Supported_Applications/MAKER.md index 43628c636..3ea636cfa 100644 --- a/docs/Scientific_Computing/Supported_Applications/MAKER.md +++ b/docs/Scientific_Computing/Supported_Applications/MAKER.md @@ -5,6 +5,7 @@ position: 13 tags: [] title: MAKER vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360001419576 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/MATLAB.md b/docs/Scientific_Computing/Supported_Applications/MATLAB.md index 7e1269ae6..4c631d29f 100644 --- a/docs/Scientific_Computing/Supported_Applications/MATLAB.md +++ b/docs/Scientific_Computing/Supported_Applications/MATLAB.md @@ -7,6 +7,7 @@ tags: - ml title: MATLAB vote_count: 1 +template: app.html vote_sum: 1 zendesk_article_id: 212639047 zendesk_section_id: 360000040076 @@ -28,7 +29,7 @@ zendesk_section_id: 360000040076 #SBATCH --time 01:00:00 # Max walltime #SBATCH --mem 512MB # Max memory - module load MATLAB/{{applications.MATLAB.machines.mahuika.versions | last}} + module load MATLAB/{{app.machines.mahuika.versions | last}} # Run the MATLAB script MATLAB_job.m matlab -nodisplay < MATLAB_job.m @@ -45,7 +46,7 @@ zendesk_section_id: 360000040076 #SBATCH --cpus-per-task 4 # 2 physical cores. #SBATCH --output %x.log # Location of output log - module load MATLAB/{{applications.MATLAB.machines.mahuika.versions | last}} + module load MATLAB/{{app.machines.mahuika.versions | last}} matlab -batch "addpath(genpath('.'));myFunction(5,20)" # For versions older than 2019a, use '-nodisplay -r' instead of '-batch' diff --git a/docs/Scientific_Computing/Supported_Applications/Miniconda3.md b/docs/Scientific_Computing/Supported_Applications/Miniconda3.md index f59359a17..6a2e4851f 100644 --- a/docs/Scientific_Computing/Supported_Applications/Miniconda3.md +++ b/docs/Scientific_Computing/Supported_Applications/Miniconda3.md @@ -5,6 +5,7 @@ position: 12 tags: [] title: Miniconda3 vote_count: 2 +template: app.html vote_sum: 2 zendesk_article_id: 360001580415 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/ORCA.md b/docs/Scientific_Computing/Supported_Applications/ORCA.md index 60d412b56..1414a23ef 100644 --- a/docs/Scientific_Computing/Supported_Applications/ORCA.md +++ b/docs/Scientific_Computing/Supported_Applications/ORCA.md @@ -7,6 +7,7 @@ tags: - chemistry title: ORCA vote_count: 3 +template: app.html vote_sum: 3 zendesk_article_id: 213718027 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/OpenFOAM.md b/docs/Scientific_Computing/Supported_Applications/OpenFOAM.md index ecf5b9167..f44371a24 100644 --- a/docs/Scientific_Computing/Supported_Applications/OpenFOAM.md +++ b/docs/Scientific_Computing/Supported_Applications/OpenFOAM.md @@ -9,6 +9,7 @@ tags: - fea title: OpenFOAM vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360000810556 zendesk_section_id: 360000040076 @@ -44,7 +45,7 @@ source $FOAM_BASH #Working directory always needs to contain 'system', 'constant', and '0' -module load OpenFOAM/{{applications.OpenFOAM.machines.mahuika.versions | last}} +module load OpenFOAM/{{app.machines.mahuika.versions | last}} source ${FOAM_BASH} decomposePar #Break domain into pieces for parallel execution. diff --git a/docs/Scientific_Computing/Supported_Applications/OpenSees.md b/docs/Scientific_Computing/Supported_Applications/OpenSees.md index 80cfb9c2b..6b215e159 100644 --- a/docs/Scientific_Computing/Supported_Applications/OpenSees.md +++ b/docs/Scientific_Computing/Supported_Applications/OpenSees.md @@ -7,6 +7,7 @@ tags: - earthquake title: OpenSees vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360001111156 zendesk_section_id: 360000040076 @@ -37,7 +38,7 @@ sweeps. #SBATCH --mem 512MB # total mem #SBATCH --hint nomultithread # Hyperthreading disabled - module load OpenSees/{{applications.OpenSees.machines.mahuika.versions | last}} + module load OpenSees/{{app.machines.mahuika.versions | last}} OpenSees "frame.tcl" ## Input from Shell diff --git a/docs/Scientific_Computing/Supported_Applications/ParaView.md b/docs/Scientific_Computing/Supported_Applications/ParaView.md index 660958e46..60d1a20b9 100644 --- a/docs/Scientific_Computing/Supported_Applications/ParaView.md +++ b/docs/Scientific_Computing/Supported_Applications/ParaView.md @@ -6,6 +6,7 @@ tags: - visualisation title: ParaView vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360001002956 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Python.md b/docs/Scientific_Computing/Supported_Applications/Python.md index 5a2d41a84..a4b1ba8d1 100644 --- a/docs/Scientific_Computing/Supported_Applications/Python.md +++ b/docs/Scientific_Computing/Supported_Applications/Python.md @@ -7,6 +7,7 @@ tags: - language title: Python vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 207782537 zendesk_section_id: 360000040076 @@ -48,7 +49,7 @@ Our most recent Python environment modules have: #SBATCH --time 01:00:00 #SBATCH --mem 512MB - module load Python/{{applications.Python.machines.mahuika.versions | last}} + module load Python/{{app.machines.mahuika.versions | last}} python MyPythonScript.py ``` diff --git a/docs/Scientific_Computing/Supported_Applications/R.md b/docs/Scientific_Computing/Supported_Applications/R.md index a0393047e..0e8a03d7d 100644 --- a/docs/Scientific_Computing/Supported_Applications/R.md +++ b/docs/Scientific_Computing/Supported_Applications/R.md @@ -7,6 +7,7 @@ tags: - general title: R vote_count: 7 +template: app.html vote_sum: 3 zendesk_article_id: 209338087 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/RAxML.md b/docs/Scientific_Computing/Supported_Applications/RAxML.md index fa2c7284d..067fb77e0 100644 --- a/docs/Scientific_Computing/Supported_Applications/RAxML.md +++ b/docs/Scientific_Computing/Supported_Applications/RAxML.md @@ -7,6 +7,7 @@ tags: - biology title: RAxML vote_count: 1 +template: app.html vote_sum: 1 zendesk_article_id: 115001854444 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Relion.md b/docs/Scientific_Computing/Supported_Applications/Relion.md index f3d2ccbfa..ebd50fbd2 100644 --- a/docs/Scientific_Computing/Supported_Applications/Relion.md +++ b/docs/Scientific_Computing/Supported_Applications/Relion.md @@ -9,6 +9,7 @@ tags: - no_ver title: Relion vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360001174055 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Singularity.md b/docs/Scientific_Computing/Supported_Applications/Singularity.md index 4ebe45a7b..4a57ec505 100644 --- a/docs/Scientific_Computing/Supported_Applications/Singularity.md +++ b/docs/Scientific_Computing/Supported_Applications/Singularity.md @@ -8,6 +8,7 @@ tags: - docker title: Singularity vote_count: 5 +template: app.html vote_sum: 5 zendesk_article_id: 360001107916 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md b/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md index 58b7dac12..efef9650b 100644 --- a/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md +++ b/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md @@ -5,57 +5,49 @@ position: 51 tags: [] title: Software Installation Request vote_count: 0 +# template: app.html vote_sum: 0 zendesk_article_id: 360000361675 zendesk_section_id: 360000040076 --- - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) - To request that we install a scientific application (either a new application, or a new version of an already installed application), please [email our support team](mailto:support@nesi.org.nz?subject=New%20software%20request). In your message, please provide the following information: -- What is the name and version number of the software you would like +- What is the name and version number of the software you would like to be installed? If you wish to use a copy from a version control repository, what tag or release do you need? Please be aware that we usually require a stable release version of a piece of software before we will install it for all users. -- Do you have a preference about which platform (Mahuika or Māui) we +- Do you have a preference about which platform (Mahuika or Māui) we install it on? -- Why would you like us to install this software package? -- What is the web site or home web page of the package? If you don't +- Why would you like us to install this software package? +- What is the web site or home web page of the package? If you don't know this information or the package doesn't have a web site, who is the author or lead developer? In some cases, there exist two or more packages with the same or very similar names. If we know the web site we can be sure that we are installing the same package that you are requesting. -- How is the package installed? For example, compiled from source, +- How is the package installed? For example, compiled from source, precompiled binary, or installed as a Python, Perl, R, etc. library? -- What dependencies, if any, does the package require? Please be aware +- What dependencies, if any, does the package require? Please be aware that the exact dependency list may depend on the particular use cases you have in mind (like the ability to read and write a specific file format). -- Have you (or another member of your project team) tried to install +- Have you (or another member of your project team) tried to install it yourself on a NeSI system? If so, were you successful? -- If you or your institution doesn't own the copyright in the +- If you or your institution doesn't own the copyright in the software, under what licence are you permitted to use it? Does that licence allow you to install and run it on a NeSI system? (Hint: Most free, open-source software licences will allow you to do this.) -- Who else do you know of who wants to use that software on a NeSI +- Who else do you know of who wants to use that software on a NeSI system? Please provide their names, institutional affiliations, and NeSI project codes (if you know them). -- What tests do you have that will allow us to verify that the +- What tests do you have that will allow us to verify that the software is performing correctly and at an acceptable speed? Our team will review your request and will make a decision as to whether -we will install the application and make it generally available. \ No newline at end of file +we will install the application and make it generally available. diff --git a/docs/Scientific_Computing/Supported_Applications/Supernova.md b/docs/Scientific_Computing/Supported_Applications/Supernova.md index 5d9004009..d645cf662 100644 --- a/docs/Scientific_Computing/Supported_Applications/Supernova.md +++ b/docs/Scientific_Computing/Supported_Applications/Supernova.md @@ -7,6 +7,7 @@ tags: - biology title: Supernova vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360000718515 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Synda.md b/docs/Scientific_Computing/Supported_Applications/Synda.md index 2939cb122..377386829 100644 --- a/docs/Scientific_Computing/Supported_Applications/Synda.md +++ b/docs/Scientific_Computing/Supported_Applications/Synda.md @@ -5,6 +5,7 @@ position: 52 tags: [] title: Synda vote_count: 1 +# template: app.html vote_sum: 1 zendesk_article_id: 360001208256 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md b/docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md index 29d8f84d0..6b5183914 100644 --- a/docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md +++ b/docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md @@ -5,6 +5,7 @@ position: 54 tags: [] title: TensorFlow on CPUs vote_count: 2 +# template: app.html vote_sum: 2 zendesk_article_id: 360000997675 zendesk_section_id: 360000040076 @@ -27,10 +28,10 @@ of the computationally demanding training and inference steps are often shorter compared to multicore CPUs. However, running TensorFlow on CPUs can nonetheless be attractive for projects where: -- Runtime is dominated by IO, so that computational performance of +- Runtime is dominated by IO, so that computational performance of GPUs does not provide much advantage with respect to overall runtime and core-hour charges -- The workflow can benefit from parallel execution on many nodes with +- The workflow can benefit from parallel execution on many nodes with large aggregated IO bandwidth (e.g., running an inference task on a very large dataset, or training a large ensemble of models) @@ -39,8 +40,8 @@ network for image classification  using a Nvidia P100 GPU and 18 Intel Broadwell cores on Mahuika (1/2 node) resulted in the following GPU-vs-CPU speedups (based on full task runtimes including IO): -- 4x for training -- 2.6x for inference +- 4x for training +- 2.6x for inference Keep in mind that these numbers will depend strongly on the application - they are only intended as an example. @@ -59,7 +60,7 @@ you include oneDNN. All TensorFlow modules on Mahuika are GPU-optimised releases. To install a CPU-optimised TensorFlow release on Mahuika, run -``` sl +``` sh module load Miniconda3 conda create -p /nesi/project//conda_envs/tf_cpu tensorflow-mkl source activate /nesi/project//conda_envs/tf_cpu @@ -67,7 +68,7 @@ source activate /nesi/project//conda_envs/tf_cpu To install TensorFlow on Māui Ancil, run -``` sl +``` sh module load Anaconda3 conda create -p /nesi/project//conda_envs/tf_cpu tensorflow-mkl source activate /nesi/project//conda_envs/tf_cpu @@ -79,7 +80,7 @@ as well using the syntax "tensorflow-mkl==x.y.z". When the installation is complete, import TensorFlow in Python as usual, -``` sl +``` sh python -c "import tensorflow" ``` @@ -144,7 +145,7 @@ these instructions are only valid for TensorFlow 1.x. Insert the following code at the beginning of your program: -``` sl +``` py import os # Get number of threads from Slurm @@ -178,5 +179,3 @@ tf.Session(config=config) It depends on your application how beneficial each operator parallelisation strategy is, so it is worth testing different configurations. - -  \ No newline at end of file diff --git a/docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md b/docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md index f4de0a7c6..f9657c8fe 100644 --- a/docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md +++ b/docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md @@ -6,20 +6,12 @@ tags: - gpu title: TensorFlow on GPUs vote_count: 2 +# template: app.html vote_sum: 2 zendesk_article_id: 360000990436 zendesk_section_id: 360000040076 --- - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) - TensorFlow is an open source library for machine learning. TensorFlow can train and run deep neural networks. It can also serve as a backend for other techniques requiring automatic differentiation and GPU @@ -28,7 +20,8 @@ acceleration. TensorFlow is callable from Python with the numerically intensive parts of the algorithms implemented in C++ for efficiency. This page focus on running TensorFlow with GPU support. -!!! prerequisite See also + +!!! tip "See also" - To request GPU resources using `--gpus-per-node` option of Slurm, see the [GPU use on NeSI](../../Scientific_Computing/Running_Jobs_on_Maui_and_Mahuika/GPU_use_on_NeSI.md) @@ -42,9 +35,9 @@ running TensorFlow with GPU support. ## Use NeSI modules TensorFlow is available on Mahuika as an [environment -module:](../../Getting_Started/Next_Steps/The_HPC_environment.md) +module](../../Getting_Started/Next_Steps/The_HPC_environment.md) -``` sl +``` sh module load TensorFlow/2.4.1-gimkl-2020a-Python-3.8.2 ``` @@ -53,14 +46,14 @@ modules needed to run TensorFlow on GPUs. You can list the available versions of the module using: -``` sl +``` sh module spider TensorFlow ``` To install additional Python packages for your project, you can either: -1. install packages in your home folder, -2. install packages in a dedicated Python virtual environment for your +1. install packages in your home folder, +2. install packages in a dedicated Python virtual environment for your project. The first option is easy but will consume space in your home folder and @@ -68,7 +61,7 @@ can create conflicts if you have multiple projects with different versions requirements. To install packages this way, you need to use`pip install --user`. For example, to install the SciKeras package: -``` sl +``` sh pip install --user scikeras ``` @@ -78,7 +71,7 @@ virtual environments in the project or nobackup folder. The following example illustrates how to create a virtual environment, activate it and install the SciKeras package in it with `pip`: -``` sl +``` sh $ export PYTHONNOUSERSITE=1 $ python3 -m venv --system-site-packages my_venv $ source my_venv/bin/activate @@ -91,7 +84,7 @@ The `--system-site-packages` option allows the virtual environment to access the TensorFlow package provided by the environment module previously loaded: -``` sl +``` sh $ module load TensorFlow/2.4.1-gimkl-2020a-Python-3.8.2 $ source my_venv/bin/activate (my_venv) $ python -c "import tensorflow as tf; print(tf.__version__)" @@ -102,10 +95,11 @@ $ source my_venv/bin/activate Don't forget to activate the virtual environment *before* calling your Python scripts in a Slurm submission script, using: -``` sl +``` sh source /bin/activate ``` -!!! prerequisite Virtual environment isolation + +!!! warning "Virtual environment isolation" Use `export PYTHONNOUSERSITE=1` to ensure that your virtual environment is isolated from packages installed in your home folder `~/.local/lib/python3.8/site-packages/`. @@ -116,7 +110,7 @@ As an alternative, you can also create *conda* environments to install a specific version of Python, TensorFlow and any additional packages required for your project. On Mahuika, use the Miniconda3 module: -``` sl +``` sh export PYTHONNOUSERSITE=1 module load Miniconda3/4.9.2 conda create -p my_conda_venv python=3.8 @@ -129,7 +123,7 @@ nobackup folder to save space in your home folder. Then activate the conda environment and install TensorFlow using `conda install` or `pip install`, depending on your preferences: -``` sl +``` sh source $(conda info --base)/etc/profile.d/conda.sh # if you didn't use "conda init" to set your .bashrc conda activate ./my_conda_venv pip install tensorflow==2.5.0 @@ -141,20 +135,21 @@ configurations](https://www.tensorflow.org/install/source#gpu) for compatibilities. For example, Tensorflow 2.5.0 requires you to load the `cuDNN/8.1.1.33-CUDA-11.2.0` module: -``` sl +``` sh module load cuDNN/8.1.1.33-CUDA-11.2.0 # for Tensorflow 2.5 ``` You can list the available versions of cuDNN (and associated CUDA module) using: -``` sl +``` sh module spider cuDNN ``` -Please contact us at if you need a version not +Please contact us at [support@nesi.org.nz](mailto:support@nesi.org.nz) if you need a version not available on the platform. -!!! prerequisite Note about Māui Ancillary Nodes + +!!! note "Māui Ancillary Nodes" - Load the Anaconda3 module instead of Miniconda3 to manipulate conda environments: ``` sl @@ -168,24 +163,26 @@ available on the platform. Additionnally, depending your version of TensorFlow, you may need to take into consideration the following: -- install the `tensorflow-gpu` Python package if your are using +- install the `tensorflow-gpu` Python package if your are using TensorFlow 1, -- make sure to use a supported version of Python when creating the +- make sure to use a supported version of Python when creating the conda environment (e.g. TensorFlow 1.14.0 requires Python 3.3 to 3.7), -- use `conda install` (not `pip install`) if your version of +- use `conda install` (not `pip install`) if your version of TensorFlow relies on GCC 4.8 (TensorFlow < 1.15). -!!! prerequisite Conda tip + +!!! tip Make sure to use `module purge` before loading Miniconda3, to ensure that no other Python module is loaded and could interfere with your conda environment. - ``` sl - module purge - module load Miniconda3/4.9.2 - export PYTHONNOUSERSITE=1 - source $(conda info --base)/etc/profile.d/conda.sh # if you didn't use "conda init" to set your .bashrc - conda ... # any conda commands (create, activate, install...) - ``` + + ``` sh + module purge + module load Miniconda3/4.9.2 + export PYTHONNOUSERSITE=1 + source $(conda info --base)/etc/profile.d/conda.sh # if you didn't use "conda init" to set your .bashrc + conda ... # any conda commands (create, activate, install...) + ``` ## Singularity containers @@ -207,13 +204,13 @@ support page. Here are the recommended options to run TensorFlow on the A100 GPUs: -- If you use TensorFlow 1, use the TF1 [container provided by +- If you use TensorFlow 1, use the TF1 [container provided by NVIDIA](https://ngc.nvidia.com/catalog/containers/nvidia:tensorflow), which comes with a version of TensorFlow 1.15 compiled specifically to support the A100 GPUs (Ampere architecture). Other official Python packages won't support the A100, triggering various crashes and slowdowns. -- If you use TensorFlow 2, any version from 2.4 and above will provide +- If you use TensorFlow 2, any version from 2.4 and above will provide support for the A100 GPUs. ## Example Slurm script @@ -226,10 +223,10 @@ the last layers of an already trained deep neural network in order to make it classify pictures of flowers. This type of task is known as "transfer learning". -1. Create a virtual environment to install the +1. Create a virtual environment to install the `tensorflow-hub[make_image_classifier]` package: - ``` sl + ``` sh module purge # start from a clean environment module load TensorFlow/2.4.1-gimkl-2020a-Python-3.8.2 export PYTHONNOUSERSITE=1 @@ -238,7 +235,7 @@ make it classify pictures of flowers. This type of task is known as pip install tensorflow-hub[make_image_classifier]~=0.12 ``` -2. Download and uncompress the example dataset containing labelled +2. Download and uncompress the example dataset containing labelled photos of flowers (daisies, dandelions, roses, sunflowers and tulips): @@ -246,7 +243,7 @@ make it classify pictures of flowers. This type of task is known as wget http://download.tensorflow.org/example_images/flower_photos.tgz -O - | tar -xz ``` -3. Copy the following code in a job submission script named +3. Copy the following code in a job submission script named `flowers.sl`: ``` sl @@ -274,9 +271,9 @@ make it classify pictures of flowers. This type of task is known as --saved_model_dir "model-${SLURM_JOBID}" ``` -4. Submit the job: +4. Submit the job: - ``` sl + ``` sh sbatch flowers.sl ``` @@ -286,10 +283,11 @@ Once the job has finished, the trained model will be saved in a All messages printed by TensorFlow during the training, including training and validation accuracies, are captured in the Slurm output file, named `slurm-JOBID.out` by default. -!!! prerequisite Tips + +!!! tip While your job is running, you can monitor the progress of model training using `tail -f` on the Slurm output file: ``` sl tail -f slurm-JOBID.out # replace JOBID with an actual number ``` - Press CTRL+C to get the bash prompt back. \ No newline at end of file + Press CTRL+C to get the bash prompt back. diff --git a/docs/Scientific_Computing/Supported_Applications/Trinity.md b/docs/Scientific_Computing/Supported_Applications/Trinity.md index 4247e1fb1..5671c148f 100644 --- a/docs/Scientific_Computing/Supported_Applications/Trinity.md +++ b/docs/Scientific_Computing/Supported_Applications/Trinity.md @@ -5,6 +5,7 @@ position: 55 tags: [] title: Trinity vote_count: 1 +template: app.html vote_sum: 1 zendesk_article_id: 360000980375 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/TurboVNC.md b/docs/Scientific_Computing/Supported_Applications/TurboVNC.md index 3923318f6..3967486d3 100644 --- a/docs/Scientific_Computing/Supported_Applications/TurboVNC.md +++ b/docs/Scientific_Computing/Supported_Applications/TurboVNC.md @@ -5,6 +5,7 @@ position: 56 tags: [] title: TurboVNC vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360001343015 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/VASP.md b/docs/Scientific_Computing/Supported_Applications/VASP.md index 97a1de407..9cd7354b2 100644 --- a/docs/Scientific_Computing/Supported_Applications/VASP.md +++ b/docs/Scientific_Computing/Supported_Applications/VASP.md @@ -7,6 +7,7 @@ tags: - chemistry title: VASP vote_count: 1 +template: app.html vote_sum: 1 zendesk_article_id: 209379527 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/Find execution hot spots with VTune.md b/docs/Scientific_Computing/Supported_Applications/VTune.md similarity index 82% rename from docs/Scientific_Computing/Supported_Applications/Find execution hot spots with VTune.md rename to docs/Scientific_Computing/Supported_Applications/VTune.md index 5126b6637..e960a34a7 100644 --- a/docs/Scientific_Computing/Supported_Applications/Find execution hot spots with VTune.md +++ b/docs/Scientific_Computing/Supported_Applications/VTune.md @@ -3,22 +3,14 @@ created_at: '2020-01-15T21:56:01Z' hidden: false position: 14 tags: [] -title: Find execution hot spots with VTune +title: VTune vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 360001332675 zendesk_section_id: 360000040076 --- - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) - ## What is VTune? VTune is a tool that allows you to quickly identify where most of the @@ -34,13 +26,13 @@ MAP](../../Scientific_Computing/Profiling_and_Debugging/Profiler-ARM_MAP.md). We'll show how to profile a C++ code with VTune - feel free to choose your own code instead. Start with  -``` sl +``` sh git clone https://github.com/pletzer/fidibench ``` and build the code using the "gimkl" tool chain -``` sl +``` sh cd fidibench mkdir build cd build @@ -54,13 +46,13 @@ require one to apply a special compiler switch to profile. You can profile an existing executable if you like. We choose "upwindCxx" as the executable to profile. It is under upwind/cxx, so -``` sl +``` sh cd upwind/cxx ``` -Run the executable with  +Run the executable with -``` sl +``` sh module load VTune srun --ntasks=1 --cpus-per-task=2 --hint=nomultithread amplxe-cl -collect hotspots -result-dir vtune-res ./upwindCxx -numCells 256 -numSteps 10 ``` @@ -87,12 +79,12 @@ free                                        libmpi.so.12  indicating that the vast majority of time is spent in the "advect" method (26s), with significant amounts of time spent allocating (6.5s) -and deallocating (9.2s) memory.  +and deallocating (9.2s) memory. ##  Drilling further into the code Often this is enough to give you a feel for where the code can be -improved. To explore further you can fire up  +improved. To explore further you can fire up ``` sl amplxe-gui & @@ -102,9 +94,4 @@ Go to the bottom and select "Open Result...", choose the directory where the profiling results are saved and click on the .amplxe file. The summary will look similar to the above table. However, you can now dive into selected functions to get more information. Below we see that 16.5 -out of 26 seconds were spent starting the two OpenMP threads.   - - -![Screen\_Shot\_2020-01-16\_at\_11.06.53\_AM.png](../../assets/images/Find execution hot spots with VTune.png)  - -  \ No newline at end of file +out of 26 seconds were spent starting the two OpenMP threads. diff --git a/docs/Scientific_Computing/Supported_Applications/VirSorter.md b/docs/Scientific_Computing/Supported_Applications/VirSorter.md index 4558bafed..d6fa67534 100644 --- a/docs/Scientific_Computing/Supported_Applications/VirSorter.md +++ b/docs/Scientific_Computing/Supported_Applications/VirSorter.md @@ -5,6 +5,7 @@ position: 7 tags: [] title: VirSorter vote_count: 1 +template: app.html vote_sum: -1 zendesk_article_id: 360003472036 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/WRF.md b/docs/Scientific_Computing/Supported_Applications/WRF.md index aa2c2cf4d..4612b6275 100644 --- a/docs/Scientific_Computing/Supported_Applications/WRF.md +++ b/docs/Scientific_Computing/Supported_Applications/WRF.md @@ -5,6 +5,7 @@ position: 9 tags: [] title: WRF vote_count: 1 +# template: app.html vote_sum: 1 zendesk_article_id: 360002109696 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/index.html b/docs/Scientific_Computing/Supported_Applications/index.md similarity index 100% rename from docs/Scientific_Computing/Supported_Applications/index.html rename to docs/Scientific_Computing/Supported_Applications/index.md diff --git a/docs/Scientific_Computing/Supported_Applications/ipyrad.md b/docs/Scientific_Computing/Supported_Applications/ipyrad.md index 4ace7a51f..66464f50c 100644 --- a/docs/Scientific_Computing/Supported_Applications/ipyrad.md +++ b/docs/Scientific_Computing/Supported_Applications/ipyrad.md @@ -5,6 +5,7 @@ position: 2 tags: [] title: ipyrad vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 5565081844623 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/ont-guppy-gpu.md b/docs/Scientific_Computing/Supported_Applications/ont-guppy-gpu.md index 1491275cc..0b7dd7926 100644 --- a/docs/Scientific_Computing/Supported_Applications/ont-guppy-gpu.md +++ b/docs/Scientific_Computing/Supported_Applications/ont-guppy-gpu.md @@ -5,6 +5,7 @@ position: 5 tags: [] title: ont-guppy-gpu vote_count: 4 +template: app.html vote_sum: 2 zendesk_article_id: 4546820344079 zendesk_section_id: 360000040076 diff --git a/docs/Scientific_Computing/Supported_Applications/snpEff.md b/docs/Scientific_Computing/Supported_Applications/snpEff.md index 028234808..990609e12 100644 --- a/docs/Scientific_Computing/Supported_Applications/snpEff.md +++ b/docs/Scientific_Computing/Supported_Applications/snpEff.md @@ -5,6 +5,7 @@ position: 0 tags: [] title: snpEff vote_count: 0 +template: app.html vote_sum: 0 zendesk_article_id: 7403361932431 zendesk_section_id: 360000040076 From db4006d9a00aab357602cb47791398f7493ba6ff Mon Sep 17 00:00:00 2001 From: cal Date: Fri, 8 Dec 2023 16:23:16 +1300 Subject: [PATCH 04/14] replace template with header --- .../Supported_Applications/ABAQUS.md | 23 +++-------- .../Supported_Applications/ANSYS.md | 7 +++- .../Supported_Applications/AlphaFold.md | 7 +++- .../Supported_Applications/BLAST.md | 7 +++- .../Supported_Applications/BRAKER.md | 7 +++- .../Supported_Applications/CESM.md | 6 +++ .../Supported_Applications/COMSOL.md | 7 +++- .../Supported_Applications/Clair3 .md | 7 +++- .../Supported_Applications/Cylc.md | 6 +++ .../Supported_Applications/Delft3D.md | 7 +++- .../Supported_Applications/Dorado.md | 7 +++- .../Supported_Applications/FDS.md | 7 +++- .../Supported_Applications/GATK.md | 7 +++- .../Supported_Applications/GROMACS.md | 7 +++- .../Supported_Applications/Gaussian.md | 7 +++- .../Supported_Applications/Java.md | 7 +++- .../Supported_Applications/Julia.md | 7 +++- .../Supported_Applications/JupyterLab.md | 7 +++- .../Supported_Applications/Keras.md | 6 +++ .../Supported_Applications/Lambda Stack.md | 6 +++ .../Supported_Applications/MAKER.md | 7 +++- .../Supported_Applications/MATLAB.md | 7 +++- .../Supported_Applications/Miniconda3.md | 7 +++- .../Supported_Applications/ORCA.md | 7 +++- .../Supported_Applications/OpenFOAM.md | 7 +++- .../Supported_Applications/OpenSees.md | 7 +++- .../Supported_Applications/ParaView.md | 7 +++- .../Supported_Applications/Python.md | 7 +++- .../Supported_Applications/R.md | 7 +++- .../Supported_Applications/RAxML.md | 7 +++- .../Supported_Applications/Relion.md | 7 +++- .../Supported_Applications/Singularity.md | 7 +++- .../Software Installation Request.md | 6 +++ .../Supported_Applications/Supernova.md | 7 +++- .../Supported_Applications/Synda.md | 6 +++ .../TensorFlow on CPUs.md | 6 +++ .../TensorFlow on GPUs.md | 6 +++ .../Supported_Applications/Trinity.md | 7 +++- .../Supported_Applications/TurboVNC.md | 7 +++- .../Supported_Applications/VASP.md | 7 +++- .../Supported_Applications/VTune.md | 7 +++- .../Supported_Applications/VirSorter.md | 7 +++- .../Supported_Applications/WRF.md | 6 +++ .../Supported_Applications/index.md | 7 +++- .../Supported_Applications/ipyrad.md | 7 +++- .../Supported_Applications/ont-guppy-gpu.md | 7 +++- .../Supported_Applications/snpEff.md | 7 +++- overrides/partials/appCardBig.html | 13 ------- overrides/partials/appContent.html | 14 ++++++- overrides/partials/appHeader.md | 16 ++++++++ overrides/partials/appVersion.html | 39 ++++++++++++------- 51 files changed, 335 insertions(+), 83 deletions(-) delete mode 100644 overrides/partials/appCardBig.html create mode 100644 overrides/partials/appHeader.md diff --git a/docs/Scientific_Computing/Supported_Applications/ABAQUS.md b/docs/Scientific_Computing/Supported_Applications/ABAQUS.md index 3cfe5f68b..fc417e6ff 100644 --- a/docs/Scientific_Computing/Supported_Applications/ABAQUS.md +++ b/docs/Scientific_Computing/Supported_Applications/ABAQUS.md @@ -11,31 +11,18 @@ tags: - fea title: ABAQUS vote_count: 2 -# template: app.html vote_sum: 0 zendesk_article_id: 212457807 zendesk_section_id: 360000040076 --- -{% set app_name = page.app or page.title | trim %} +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} {% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) -{{ app.description }} - -{% if app.homepage or app.url -%} -[{{ app_name }} Homepage]({{ app.homepage or app.url }}) -{% endif -%} - -{% if app.licence_type == "proprietary" -%} -!!! warning - {{ app_name }} is proprietary software. Make sure you meet the requirements for it's usage. -{% endif -%} - -## Available Modules - -{% include "partials/appVersion.html" -%} - -``` sh +```sh abaqus help ``` diff --git a/docs/Scientific_Computing/Supported_Applications/ANSYS.md b/docs/Scientific_Computing/Supported_Applications/ANSYS.md index 01944a699..0c7836e16 100644 --- a/docs/Scientific_Computing/Supported_Applications/ANSYS.md +++ b/docs/Scientific_Computing/Supported_Applications/ANSYS.md @@ -8,12 +8,17 @@ tags: - engineering title: ANSYS vote_count: 3 -template: app.html vote_sum: 3 zendesk_article_id: 212642617 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) ## License Types The three main ANSYS licenses are; diff --git a/docs/Scientific_Computing/Supported_Applications/AlphaFold.md b/docs/Scientific_Computing/Supported_Applications/AlphaFold.md index e555b82d9..f0a4371ef 100644 --- a/docs/Scientific_Computing/Supported_Applications/AlphaFold.md +++ b/docs/Scientific_Computing/Supported_Applications/AlphaFold.md @@ -5,13 +5,18 @@ position: 6 tags: [] title: AlphaFold vote_count: 2 -template: app.html vote_sum: 2 zendesk_article_id: 4405170961039 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/BLAST.md b/docs/Scientific_Computing/Supported_Applications/BLAST.md index b1392512f..ea2328c49 100644 --- a/docs/Scientific_Computing/Supported_Applications/BLAST.md +++ b/docs/Scientific_Computing/Supported_Applications/BLAST.md @@ -7,13 +7,18 @@ tags: - biology title: BLAST vote_count: 1 -template: app.html vote_sum: -1 zendesk_article_id: 208619807 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/BRAKER.md b/docs/Scientific_Computing/Supported_Applications/BRAKER.md index 437d3a5b2..4f9f93ee0 100644 --- a/docs/Scientific_Computing/Supported_Applications/BRAKER.md +++ b/docs/Scientific_Computing/Supported_Applications/BRAKER.md @@ -4,12 +4,17 @@ hidden: false position: 0 tags: [] vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 6529511928207 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) ## Description The rapidly growing number of sequenced genomes requires fully automated diff --git a/docs/Scientific_Computing/Supported_Applications/CESM.md b/docs/Scientific_Computing/Supported_Applications/CESM.md index 8c50db273..e2729361d 100644 --- a/docs/Scientific_Computing/Supported_Applications/CESM.md +++ b/docs/Scientific_Computing/Supported_Applications/CESM.md @@ -12,6 +12,12 @@ zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/COMSOL.md b/docs/Scientific_Computing/Supported_Applications/COMSOL.md index 3248ca5db..7a6d63cd1 100644 --- a/docs/Scientific_Computing/Supported_Applications/COMSOL.md +++ b/docs/Scientific_Computing/Supported_Applications/COMSOL.md @@ -11,12 +11,17 @@ tags: - fea title: COMSOL vote_count: 1 -template: app.html vote_sum: 1 zendesk_article_id: 360000871556 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) ``` sl comsol --help ``` diff --git a/docs/Scientific_Computing/Supported_Applications/Clair3 .md b/docs/Scientific_Computing/Supported_Applications/Clair3 .md index 919ee3270..46405fd8b 100644 --- a/docs/Scientific_Computing/Supported_Applications/Clair3 .md +++ b/docs/Scientific_Computing/Supported_Applications/Clair3 .md @@ -5,13 +5,18 @@ position: 3 tags: [] title: 'Clair3 ' vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 5292628239375 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Cylc.md b/docs/Scientific_Computing/Supported_Applications/Cylc.md index 76cbf3e94..2dfbcc1cc 100644 --- a/docs/Scientific_Computing/Supported_Applications/Cylc.md +++ b/docs/Scientific_Computing/Supported_Applications/Cylc.md @@ -12,6 +12,12 @@ zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Delft3D.md b/docs/Scientific_Computing/Supported_Applications/Delft3D.md index c251631e1..6c4d1666f 100644 --- a/docs/Scientific_Computing/Supported_Applications/Delft3D.md +++ b/docs/Scientific_Computing/Supported_Applications/Delft3D.md @@ -6,12 +6,17 @@ tags: - hydrodynamics title: Delft3D vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360001593096 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) ## Example scripts === "Serial" diff --git a/docs/Scientific_Computing/Supported_Applications/Dorado.md b/docs/Scientific_Computing/Supported_Applications/Dorado.md index b5b715a66..384b7b537 100644 --- a/docs/Scientific_Computing/Supported_Applications/Dorado.md +++ b/docs/Scientific_Computing/Supported_Applications/Dorado.md @@ -5,13 +5,18 @@ position: 0 tags: [] title: Dorado vote_count: 2 -template: app.html vote_sum: 2 zendesk_article_id: 6623692647951 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/FDS.md b/docs/Scientific_Computing/Supported_Applications/FDS.md index ef358ec7b..e7839f7db 100644 --- a/docs/Scientific_Computing/Supported_Applications/FDS.md +++ b/docs/Scientific_Computing/Supported_Applications/FDS.md @@ -7,12 +7,17 @@ tags: - engineering title: FDS vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360000759275 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) FDS (Fire Dynamics Simulator) was developed by the National Institute of Standards and Technology (NIST) for large-eddy simulation (LES) of low-speed flows, with an emphasis on smoke and heat transport from diff --git a/docs/Scientific_Computing/Supported_Applications/GATK.md b/docs/Scientific_Computing/Supported_Applications/GATK.md index 543610dc4..15edfc798 100644 --- a/docs/Scientific_Computing/Supported_Applications/GATK.md +++ b/docs/Scientific_Computing/Supported_Applications/GATK.md @@ -5,12 +5,17 @@ position: 1 tags: [] title: GATK vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 6443618773519 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) The Genome Analysis Toolkit (GATK), developed at the [Broad Institute](http://www.broadinstitute.org/), provides a wide variety of tools focusing primarily on variant discovery and genotyping. It is diff --git a/docs/Scientific_Computing/Supported_Applications/GROMACS.md b/docs/Scientific_Computing/Supported_Applications/GROMACS.md index f161888d9..b3bd7895a 100644 --- a/docs/Scientific_Computing/Supported_Applications/GROMACS.md +++ b/docs/Scientific_Computing/Supported_Applications/GROMACS.md @@ -5,13 +5,18 @@ position: 30 tags: [] title: GROMACS vote_count: 2 -template: app.html vote_sum: 2 zendesk_article_id: 360000792856 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Gaussian.md b/docs/Scientific_Computing/Supported_Applications/Gaussian.md index 362e652bb..75deec2ba 100644 --- a/docs/Scientific_Computing/Supported_Applications/Gaussian.md +++ b/docs/Scientific_Computing/Supported_Applications/Gaussian.md @@ -7,13 +7,18 @@ tags: - chemistry title: Gaussian vote_count: 5 -template: app.html vote_sum: 1 zendesk_article_id: 207127857 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Java.md b/docs/Scientific_Computing/Supported_Applications/Java.md index e999a3960..b0f657700 100644 --- a/docs/Scientific_Computing/Supported_Applications/Java.md +++ b/docs/Scientific_Computing/Supported_Applications/Java.md @@ -7,13 +7,18 @@ tags: - general title: Java vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 207765367 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Julia.md b/docs/Scientific_Computing/Supported_Applications/Julia.md index 99ba90949..e12c4fda1 100644 --- a/docs/Scientific_Computing/Supported_Applications/Julia.md +++ b/docs/Scientific_Computing/Supported_Applications/Julia.md @@ -5,13 +5,18 @@ position: 32 tags: [] title: Julia vote_count: 3 -template: app.html vote_sum: 3 zendesk_article_id: 360001175895 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/JupyterLab.md b/docs/Scientific_Computing/Supported_Applications/JupyterLab.md index 6a9163ae2..73953dbf9 100644 --- a/docs/Scientific_Computing/Supported_Applications/JupyterLab.md +++ b/docs/Scientific_Computing/Supported_Applications/JupyterLab.md @@ -5,13 +5,18 @@ position: 33 tags: [] title: JupyterLab vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360001093315 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Keras.md b/docs/Scientific_Computing/Supported_Applications/Keras.md index 8adc8ea2f..0ed55bb5a 100644 --- a/docs/Scientific_Computing/Supported_Applications/Keras.md +++ b/docs/Scientific_Computing/Supported_Applications/Keras.md @@ -12,6 +12,12 @@ zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md b/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md index 6f53dfee9..4b2b9829c 100644 --- a/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md +++ b/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md @@ -11,6 +11,12 @@ zendesk_article_id: 360002558216 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) ## Introduction [Lambda diff --git a/docs/Scientific_Computing/Supported_Applications/MAKER.md b/docs/Scientific_Computing/Supported_Applications/MAKER.md index 3ea636cfa..828cc75a4 100644 --- a/docs/Scientific_Computing/Supported_Applications/MAKER.md +++ b/docs/Scientific_Computing/Supported_Applications/MAKER.md @@ -5,13 +5,18 @@ position: 13 tags: [] title: MAKER vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360001419576 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/MATLAB.md b/docs/Scientific_Computing/Supported_Applications/MATLAB.md index 4c631d29f..3ef4e289b 100644 --- a/docs/Scientific_Computing/Supported_Applications/MATLAB.md +++ b/docs/Scientific_Computing/Supported_Applications/MATLAB.md @@ -7,12 +7,17 @@ tags: - ml title: MATLAB vote_count: 1 -template: app.html vote_sum: 1 zendesk_article_id: 212639047 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) !!! warning "No Licence?" If you want to run MATLAB code on the cluster, but are not a member of an institution without access to floating licences, MATLAB code can still be run on the cluster using MCR. diff --git a/docs/Scientific_Computing/Supported_Applications/Miniconda3.md b/docs/Scientific_Computing/Supported_Applications/Miniconda3.md index 6a2e4851f..eeebc755d 100644 --- a/docs/Scientific_Computing/Supported_Applications/Miniconda3.md +++ b/docs/Scientific_Computing/Supported_Applications/Miniconda3.md @@ -5,13 +5,18 @@ position: 12 tags: [] title: Miniconda3 vote_count: 2 -template: app.html vote_sum: 2 zendesk_article_id: 360001580415 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/ORCA.md b/docs/Scientific_Computing/Supported_Applications/ORCA.md index 1414a23ef..3429e177f 100644 --- a/docs/Scientific_Computing/Supported_Applications/ORCA.md +++ b/docs/Scientific_Computing/Supported_Applications/ORCA.md @@ -7,13 +7,18 @@ tags: - chemistry title: ORCA vote_count: 3 -template: app.html vote_sum: 3 zendesk_article_id: 213718027 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/OpenFOAM.md b/docs/Scientific_Computing/Supported_Applications/OpenFOAM.md index f44371a24..06d993b79 100644 --- a/docs/Scientific_Computing/Supported_Applications/OpenFOAM.md +++ b/docs/Scientific_Computing/Supported_Applications/OpenFOAM.md @@ -9,12 +9,17 @@ tags: - fea title: OpenFOAM vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360000810556 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) OpenFOAM (Open Field Operation And Manipulation) is a open-source C++ toolbox maintained by the OpenFOAM foundation and ESI Group. Although primarily used for CFD (Computational Fluid Dynamics) OpenFOAM can be diff --git a/docs/Scientific_Computing/Supported_Applications/OpenSees.md b/docs/Scientific_Computing/Supported_Applications/OpenSees.md index 6b215e159..b7d9833b6 100644 --- a/docs/Scientific_Computing/Supported_Applications/OpenSees.md +++ b/docs/Scientific_Computing/Supported_Applications/OpenSees.md @@ -7,12 +7,17 @@ tags: - earthquake title: OpenSees vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360001111156 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) There are three commands with which a OpenSees job can be launched. - `OpenSees`: For running a job in serial (single CPU). diff --git a/docs/Scientific_Computing/Supported_Applications/ParaView.md b/docs/Scientific_Computing/Supported_Applications/ParaView.md index 60d1a20b9..fd1afc18c 100644 --- a/docs/Scientific_Computing/Supported_Applications/ParaView.md +++ b/docs/Scientific_Computing/Supported_Applications/ParaView.md @@ -6,12 +6,17 @@ tags: - visualisation title: ParaView vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360001002956 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) !!! warning The ParaView server loaded must be the same version as the client you have installed locally. diff --git a/docs/Scientific_Computing/Supported_Applications/Python.md b/docs/Scientific_Computing/Supported_Applications/Python.md index a4b1ba8d1..91b700eb2 100644 --- a/docs/Scientific_Computing/Supported_Applications/Python.md +++ b/docs/Scientific_Computing/Supported_Applications/Python.md @@ -7,12 +7,17 @@ tags: - language title: Python vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 207782537 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) All versions of Python available on NeSI platforms are owned and licensed by the Python Software Foundation. Each version is released under a specific open-source licence. The licences are available on [the diff --git a/docs/Scientific_Computing/Supported_Applications/R.md b/docs/Scientific_Computing/Supported_Applications/R.md index 0e8a03d7d..f0bf80098 100644 --- a/docs/Scientific_Computing/Supported_Applications/R.md +++ b/docs/Scientific_Computing/Supported_Applications/R.md @@ -7,13 +7,18 @@ tags: - general title: R vote_count: 7 -template: app.html vote_sum: 3 zendesk_article_id: 209338087 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/RAxML.md b/docs/Scientific_Computing/Supported_Applications/RAxML.md index 067fb77e0..95a42e509 100644 --- a/docs/Scientific_Computing/Supported_Applications/RAxML.md +++ b/docs/Scientific_Computing/Supported_Applications/RAxML.md @@ -7,13 +7,18 @@ tags: - biology title: RAxML vote_count: 1 -template: app.html vote_sum: 1 zendesk_article_id: 115001854444 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Relion.md b/docs/Scientific_Computing/Supported_Applications/Relion.md index ebd50fbd2..9e26b376f 100644 --- a/docs/Scientific_Computing/Supported_Applications/Relion.md +++ b/docs/Scientific_Computing/Supported_Applications/Relion.md @@ -9,13 +9,18 @@ tags: - no_ver title: Relion vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360001174055 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Singularity.md b/docs/Scientific_Computing/Supported_Applications/Singularity.md index 4a57ec505..a8f57a92e 100644 --- a/docs/Scientific_Computing/Supported_Applications/Singularity.md +++ b/docs/Scientific_Computing/Supported_Applications/Singularity.md @@ -8,13 +8,18 @@ tags: - docker title: Singularity vote_count: 5 -template: app.html vote_sum: 5 zendesk_article_id: 360001107916 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md b/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md index efef9650b..f551f0a35 100644 --- a/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md +++ b/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md @@ -11,6 +11,12 @@ zendesk_article_id: 360000361675 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) To request that we install a scientific application (either a new application, or a new version of an already installed application), please [email our support diff --git a/docs/Scientific_Computing/Supported_Applications/Supernova.md b/docs/Scientific_Computing/Supported_Applications/Supernova.md index d645cf662..9cd6573b5 100644 --- a/docs/Scientific_Computing/Supported_Applications/Supernova.md +++ b/docs/Scientific_Computing/Supported_Applications/Supernova.md @@ -7,13 +7,18 @@ tags: - biology title: Supernova vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360000718515 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/Synda.md b/docs/Scientific_Computing/Supported_Applications/Synda.md index 377386829..9b0f01299 100644 --- a/docs/Scientific_Computing/Supported_Applications/Synda.md +++ b/docs/Scientific_Computing/Supported_Applications/Synda.md @@ -12,6 +12,12 @@ zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md b/docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md index 6b5183914..3a2fb250e 100644 --- a/docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md +++ b/docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md @@ -12,6 +12,12 @@ zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md b/docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md index f9657c8fe..18f059488 100644 --- a/docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md +++ b/docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md @@ -12,6 +12,12 @@ zendesk_article_id: 360000990436 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) TensorFlow is an open source library for machine learning. TensorFlow can train and run deep neural networks. It can also serve as a backend for other techniques requiring automatic differentiation and GPU diff --git a/docs/Scientific_Computing/Supported_Applications/Trinity.md b/docs/Scientific_Computing/Supported_Applications/Trinity.md index 5671c148f..1dc156cde 100644 --- a/docs/Scientific_Computing/Supported_Applications/Trinity.md +++ b/docs/Scientific_Computing/Supported_Applications/Trinity.md @@ -5,12 +5,17 @@ position: 55 tags: [] title: Trinity vote_count: 1 -template: app.html vote_sum: 1 zendesk_article_id: 360000980375 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) Trinity, developed at the [Broad Institute](http://www.broadinstitute.org/) and the [Hebrew University of Jerusalem](http://www.cs.huji.ac.il/), performs _de novo_ reconstruction diff --git a/docs/Scientific_Computing/Supported_Applications/TurboVNC.md b/docs/Scientific_Computing/Supported_Applications/TurboVNC.md index 3967486d3..73b7f082d 100644 --- a/docs/Scientific_Computing/Supported_Applications/TurboVNC.md +++ b/docs/Scientific_Computing/Supported_Applications/TurboVNC.md @@ -5,13 +5,18 @@ position: 56 tags: [] title: TurboVNC vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360001343015 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/VASP.md b/docs/Scientific_Computing/Supported_Applications/VASP.md index 9cd7354b2..a1e9867bb 100644 --- a/docs/Scientific_Computing/Supported_Applications/VASP.md +++ b/docs/Scientific_Computing/Supported_Applications/VASP.md @@ -7,13 +7,18 @@ tags: - chemistry title: VASP vote_count: 1 -template: app.html vote_sum: 1 zendesk_article_id: 209379527 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/VTune.md b/docs/Scientific_Computing/Supported_Applications/VTune.md index e960a34a7..c7de4c136 100644 --- a/docs/Scientific_Computing/Supported_Applications/VTune.md +++ b/docs/Scientific_Computing/Supported_Applications/VTune.md @@ -5,12 +5,17 @@ position: 14 tags: [] title: VTune vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 360001332675 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) ## What is VTune? VTune is a tool that allows you to quickly identify where most of the diff --git a/docs/Scientific_Computing/Supported_Applications/VirSorter.md b/docs/Scientific_Computing/Supported_Applications/VirSorter.md index d6fa67534..bfea8f4cf 100644 --- a/docs/Scientific_Computing/Supported_Applications/VirSorter.md +++ b/docs/Scientific_Computing/Supported_Applications/VirSorter.md @@ -5,13 +5,18 @@ position: 7 tags: [] title: VirSorter vote_count: 1 -template: app.html vote_sum: -1 zendesk_article_id: 360003472036 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/WRF.md b/docs/Scientific_Computing/Supported_Applications/WRF.md index 4612b6275..7aed2d1b4 100644 --- a/docs/Scientific_Computing/Supported_Applications/WRF.md +++ b/docs/Scientific_Computing/Supported_Applications/WRF.md @@ -12,6 +12,12 @@ zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/index.md b/docs/Scientific_Computing/Supported_Applications/index.md index 336e0324d..d2d2ec03a 100644 --- a/docs/Scientific_Computing/Supported_Applications/index.md +++ b/docs/Scientific_Computing/Supported_Applications/index.md @@ -1,8 +1,13 @@ --- title: Supported Applications -template: supportedApplications.html --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) === "Mahuika" On Mahuika, and Ancillary nodes (both Mahuika and Māui) software packages are provided using 'lmod' an implementation of Environment Modules with [additional features](https://lmod.readthedocs.io/en/latest/010_user.html). diff --git a/docs/Scientific_Computing/Supported_Applications/ipyrad.md b/docs/Scientific_Computing/Supported_Applications/ipyrad.md index 66464f50c..3ea2b13b5 100644 --- a/docs/Scientific_Computing/Supported_Applications/ipyrad.md +++ b/docs/Scientific_Computing/Supported_Applications/ipyrad.md @@ -5,13 +5,18 @@ position: 2 tags: [] title: ipyrad vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 5565081844623 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/ont-guppy-gpu.md b/docs/Scientific_Computing/Supported_Applications/ont-guppy-gpu.md index 0b7dd7926..5dd54f4ae 100644 --- a/docs/Scientific_Computing/Supported_Applications/ont-guppy-gpu.md +++ b/docs/Scientific_Computing/Supported_Applications/ont-guppy-gpu.md @@ -5,13 +5,18 @@ position: 5 tags: [] title: ont-guppy-gpu vote_count: 4 -template: app.html vote_sum: 2 zendesk_article_id: 4546820344079 zendesk_section_id: 360000040076 --- +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) + [//]: <> (REMOVE ME IF PAGE VALIDATED) [//]: <> (vvvvvvvvvvvvvvvvvvvv) diff --git a/docs/Scientific_Computing/Supported_Applications/snpEff.md b/docs/Scientific_Computing/Supported_Applications/snpEff.md index 990609e12..90742743c 100644 --- a/docs/Scientific_Computing/Supported_Applications/snpEff.md +++ b/docs/Scientific_Computing/Supported_Applications/snpEff.md @@ -5,12 +5,17 @@ position: 0 tags: [] title: snpEff vote_count: 0 -template: app.html vote_sum: 0 zendesk_article_id: 7403361932431 zendesk_section_id: 360000040076 --- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/appHeader.md" %} +[//]: <> (APPS PAGE BOILERPLATE END) snpEff is a genetic variant annotation, and functional effect prediction tool. diff --git a/overrides/partials/appCardBig.html b/overrides/partials/appCardBig.html deleted file mode 100644 index 6bf04f373..000000000 --- a/overrides/partials/appCardBig.html +++ /dev/null @@ -1,13 +0,0 @@ -

    {{ app.description }}

    -{% if app.homepage or app.url -%} -

    {% include ".icons/material/home.svg" %} -{{ application }} Homepage

    -{% endif -%} -{% if app.licence_type == "proprietary" -%} -
    -

    Licence

    -

    {{ application }} is proprietary software. Make sure you meet the requirements for it's usage.

    -
    -{% endif -%} -

    Modules Available

    -{% include "partials/appVersion.html" -%} \ No newline at end of file diff --git a/overrides/partials/appContent.html b/overrides/partials/appContent.html index c0eb91a94..8aa6c60b0 100644 --- a/overrides/partials/appContent.html +++ b/overrides/partials/appContent.html @@ -5,7 +5,19 @@ {% if "\x3ch1" not in page.content %}

    {{ page.title | d(config.site_name, true)}}

    {% endif %} -{% include "partials/appCardBig.html" %} +

    {{ app.description }}

    +{% if app.homepage or app.url -%} +

    {% include ".icons/material/home.svg" %} +{{ application }} Homepage

    +{% endif -%} +{% if app.licence_type == "proprietary" -%} +
    +

    Licence

    +

    {{ application }} is proprietary software. Make sure you meet the requirements for it's usage.

    +
    +{% endif -%} +

    Modules Available

    +{% include "partials/appVersion.html" -%} {{ page.content }} {% if page.meta and ( page.meta.git_revision_date_localized or diff --git a/overrides/partials/appHeader.md b/overrides/partials/appHeader.md new file mode 100644 index 000000000..5f5d5cbf6 --- /dev/null +++ b/overrides/partials/appHeader.md @@ -0,0 +1,16 @@ +{{ app.description }} + +{% if app.homepage or app.url -%} +[{{ app_name }} Homepage]({{ app.homepage or app.url }}) +{% endif -%} + +{% if app.licence_type == "proprietary" -%} + +!!! warning + {{ app_name }} is proprietary software. Make sure you meet the [requirements for it's usage](#licences). + +{% endif -%} + +## Available Modules + +{% include "partials/appVersion.html" -%} diff --git a/overrides/partials/appVersion.html b/overrides/partials/appVersion.html index 840a00573..6878cd08d 100644 --- a/overrides/partials/appVersion.html +++ b/overrides/partials/appVersion.html @@ -1,4 +1,4 @@ -
    +
    @@ -6,16 +6,27 @@ {% endfor %}
    -
    -{% for machine_name, machine in app.machines.items() %} -
    -

    -

    -

    -
    -{% endfor -%} -
    \ No newline at end of file +
    + {% for machine_name, machine in app.machines.items() -%} + {% if machine.default != 'latest' -%} + {% set latest = machine.default -%} + {% else -%} + {% set latest = machine.versions | last -%} + {% endif -%} +
    +

    + 
    module load {{app_name}}/{{latest}}
    +
    + {% endfor -%} +
    + + +
    \ No newline at end of file From b7b31b1c500a81657973de2cc2b3fa14080cd60d Mon Sep 17 00:00:00 2001 From: cal Date: Fri, 8 Dec 2023 16:23:30 +1300 Subject: [PATCH 05/14] Update CESM --- .../Supported_Applications/CESM.md | 37 +++++-------------- 1 file changed, 9 insertions(+), 28 deletions(-) diff --git a/docs/Scientific_Computing/Supported_Applications/CESM.md b/docs/Scientific_Computing/Supported_Applications/CESM.md index e2729361d..8e42a2f88 100644 --- a/docs/Scientific_Computing/Supported_Applications/CESM.md +++ b/docs/Scientific_Computing/Supported_Applications/CESM.md @@ -11,23 +11,6 @@ zendesk_article_id: 360002105076 zendesk_section_id: 360000040076 --- - -[//]: <> (APPS PAGE BOILERPLATE START) -{% set app_name = page.title | trim %} -{% set app = applications[app_name] %} -{% include "partials/appHeader.md" %} -[//]: <> (APPS PAGE BOILERPLATE END) - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) - -## CESM - The Community Earth System Model (CESM) is a coupled climate model for simulating Earth’s climate system. Composed of separate models simultaneously simulating the Earth’s atmosphere, ocean, land, river @@ -49,7 +32,7 @@ the *bin* directory in your home, add that directory to *PATH* and run a git command to finish the Git-LFS installation. The following commands will achieve this: -``` sl +```sh mkdir git-lfs cd git-lfs wget https://github.com/git-lfs/git-lfs/releases/download/v2.12.0/git-lfs-linux-amd64-v2.12.0.tar.gz @@ -69,7 +52,7 @@ First switch to your project directory (or wherever else you would like the CESM source to live) and then run the commands to download CESM (replacing *<your\_project\_code>* with your project code): -``` sl +``` sh cd /nesi/project/ git clone -b release-cesm2.1.3 https://github.com/ESCOMP/CESM.git my_cesm_sandbox cd my_cesm_sandbox @@ -90,7 +73,7 @@ Earth system models) and copy the config files to *~/.cime*. In the following, replace *<your\_project\_code>* with your project code (this will overwrite any current configuration your have in *~/.cime*): -``` sl +``` sh cd /nesi/project/ git clone https://github.com/nesi/nesi-cesm-config.git cd nesi-cesm-config @@ -113,7 +96,7 @@ above link for more information. First, create the case: -``` sl +``` sh cd /nesi/project//my_cesm_sandbox/cime/scripts ./create_newcase --case /nesi/nobackup//$USER/cesm/output/b.e20.B1850.f19_g17.test --compset B1850 --res f19_g17 --machine maui --compiler intel cd /nesi/nobackup//$USER/cesm/output/b.e20.B1850.f19_g17.test @@ -125,7 +108,7 @@ directory in the previous step. Next, set up the case and preview the run: -``` sl +``` sh ./case.setup ./preview_run ``` @@ -133,20 +116,20 @@ Next, set up the case and preview the run: Check that everything looks correct in the preview and then build the case: -``` sl +``` sh ./case.build ``` Update any settings if necessary, for example here we turn off short term archiving: -``` sl +``` sh ./xmlchange DOUT_S=FALSE ``` Finally, run the job: -``` sl +``` sh ./case.submit ``` @@ -173,6 +156,4 @@ balancing" [here](https://esmci.github.io/cime/versions/maint-5.6/html/users_guide/pes-threads.html). It involves performing a number of short model runs to determine which components are most expensive and how the individual components scale. -That information can then be used to determine an optimal load balance. - -  \ No newline at end of file +That information can then be used to determine an optimal load balance. \ No newline at end of file From 081b1026ce5d0eac882721558facbd2fa8b29d3f Mon Sep 17 00:00:00 2001 From: cal Date: Fri, 8 Dec 2023 16:25:53 +1300 Subject: [PATCH 06/14] Update WRF --- .../Supported_Applications/WRF.md | 66 +++++-------------- 1 file changed, 15 insertions(+), 51 deletions(-) diff --git a/docs/Scientific_Computing/Supported_Applications/WRF.md b/docs/Scientific_Computing/Supported_Applications/WRF.md index 7aed2d1b4..bb5d433bb 100644 --- a/docs/Scientific_Computing/Supported_Applications/WRF.md +++ b/docs/Scientific_Computing/Supported_Applications/WRF.md @@ -5,29 +5,11 @@ position: 9 tags: [] title: WRF vote_count: 1 -# template: app.html vote_sum: 1 zendesk_article_id: 360002109696 zendesk_section_id: 360000040076 --- - -[//]: <> (APPS PAGE BOILERPLATE START) -{% set app_name = page.title | trim %} -{% set app = applications[app_name] %} -{% include "partials/appHeader.md" %} -[//]: <> (APPS PAGE BOILERPLATE END) - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) - -## WRF - The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications. It @@ -36,11 +18,9 @@ architecture supporting parallel computation and system extensibility. The model serves a wide range of meteorological applications across scales from tens of meters to thousands of kilometres. -  - Download WRF: -``` sl +``` sh cd /nesi/project/ wget https://github.com/wrf-model/WRF/archive/v4.1.1.tar.gz tar xf v4.1.1.tar.gz @@ -55,17 +35,13 @@ installed. On Māui, these are available as modules. On Mahuika, we recommend to download these packages and build them by hand (instructions are provided below). -  - ## WRF on Mahuika -  - ### Environment on Mahuika -We'll use the Intel compiler and Intel MPI library.  +We'll use the Intel compiler and Intel MPI library. -``` sl +``` sh module purge module load HDF5/1.12.2-iimpi-2022a ``` @@ -74,13 +50,11 @@ Although NeSI has NetCDF modules installed, WRF wants the C and Fortran NetCDF libraries, include files and modules all installed under the same root directory. Hence we build those by hand. -  - ### Building WRF dependencies on Mahuika Copy-paste the commands below to build WRF on Mahuika: -``` sl +``` sh # create build directory for WRF's dependencies export WRF_DEPS_DIR=$PWD/wrf-deps mkdir $WRF_DEPS_DIR @@ -133,17 +107,15 @@ cd .. cd .. ``` -  - Then proceed to configure WRF by setting -``` sl +``` sh export NETCDF=$WRF_DEPS_DIR export HDF5=$WRF_DEPS_DIR export PNETCDF=$WRF_DEPS_DIR ``` -``` sl +``` sh cd WRF-4.1.1 ./configure [select 15] @@ -151,19 +123,15 @@ cd WRF-4.1.1 and build the code with -``` sl +``` sh ./compile em_real >& log.compile ``` This may take several hours to compile. Check the log file to ensure -that the compilation was successful.  - -  +that the compilation was successful. ### Running WRF on Mahuika -  - An example Slurm script for running WRF on Mahuika extension, which can be submitted with *sbatch name\_of\_script.sl*: @@ -187,10 +155,6 @@ srun --output=real.log ./real.exe srun --output=wrf.log ./wrf.exe ``` - - -  - ## WRF on Māui ### Building WRF @@ -216,7 +180,7 @@ export PNETCDF=$PNETCDF_DIR Apply patches for Polar WRF if required and then configure WRF: -``` sl +``` sh ./configure # choose option 50 - INTEL (ftn/icc) Cray XC (dmpar) # choose an appropriate nesting option or leave it at the default @@ -233,7 +197,7 @@ variable. Next compile WRF: -``` sl +``` sh ./compile em_real >& log.compile ``` @@ -283,7 +247,7 @@ the namelist when using parallel IO. Download WPS: -``` sl +``` sh wget https://github.com/wrf-model/WPS/archive/v4.2.tar.gz tar xf v4.2.tar.gz cd WPS-4.2 @@ -315,7 +279,7 @@ export CRAYPE_LINK_TYPE=dynamic Configure WPS: -``` sl +``` sh ./configure # choose option 39 - Cray XC Intel parallel build ``` @@ -325,7 +289,7 @@ way to *configure.wrf* above, if desired. Now compile WPS: -``` sl +``` sh ./compile >& log.compile ``` @@ -339,7 +303,7 @@ Māui compute nodes. However, *ungrib* is serial and should not be run on a compute node unless it is very quick to finish. Alternatively you could run *ungrib* on an interactive/login node if it will not take up many resources, or you could compile WRF and WPS on a Māui Ancillary -node and run it there.  +node and run it there. Note that WPS does a lot of file IO and therefore probably won't scale up to as many processes as WRF. @@ -366,4 +330,4 @@ export HDF5_USE_FILE_LOCKING=FALSE # run geogrid srun --output=geogrid.log ./geogrid.exe -``` \ No newline at end of file +``` From cb6e08b7565a9a1822e8efdcaa638fe64f7990ca Mon Sep 17 00:00:00 2001 From: cal Date: Fri, 8 Dec 2023 16:29:59 +1300 Subject: [PATCH 07/14] Tensorflow page updates --- ...ensorFlow on CPUs.md => TensorFlow_on_CPUs.md} | 15 ++------------- ...ensorFlow on GPUs.md => TensorFlow_on_GPUs.md} | 8 +++----- 2 files changed, 5 insertions(+), 18 deletions(-) rename docs/Scientific_Computing/Supported_Applications/{TensorFlow on CPUs.md => TensorFlow_on_CPUs.md} (94%) rename docs/Scientific_Computing/Supported_Applications/{TensorFlow on GPUs.md => TensorFlow_on_GPUs.md} (98%) diff --git a/docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md b/docs/Scientific_Computing/Supported_Applications/TensorFlow_on_CPUs.md similarity index 94% rename from docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md rename to docs/Scientific_Computing/Supported_Applications/TensorFlow_on_CPUs.md index 3a2fb250e..18843b1e0 100644 --- a/docs/Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md +++ b/docs/Scientific_Computing/Supported_Applications/TensorFlow_on_CPUs.md @@ -11,24 +11,13 @@ zendesk_article_id: 360000997675 zendesk_section_id: 360000040076 --- - -[//]: <> (APPS PAGE BOILERPLATE START) -{% set app_name = page.title | trim %} +{% set app_name = "TensorFlow" %} {% set app = applications[app_name] %} {% include "partials/appHeader.md" %} -[//]: <> (APPS PAGE BOILERPLATE END) - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) TensorFlow is a popular software library for machine learning applications, see our -[TensorFlow](../../Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md) +[TensorFlow](../../Scientific_Computing/Supported_Applications/TensorFlow_on_GPUs.md) article for further information. It is often used with GPUs, as runtimes of the computationally demanding training and inference steps are often shorter compared to multicore CPUs. However, running TensorFlow on CPUs diff --git a/docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md b/docs/Scientific_Computing/Supported_Applications/TensorFlow_on_GPUs.md similarity index 98% rename from docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md rename to docs/Scientific_Computing/Supported_Applications/TensorFlow_on_GPUs.md index 18f059488..11483ac58 100644 --- a/docs/Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md +++ b/docs/Scientific_Computing/Supported_Applications/TensorFlow_on_GPUs.md @@ -12,12 +12,10 @@ zendesk_article_id: 360000990436 zendesk_section_id: 360000040076 --- - -[//]: <> (APPS PAGE BOILERPLATE START) -{% set app_name = page.title | trim %} +{% set app_name = "TensorFlow" %} {% set app = applications[app_name] %} {% include "partials/appHeader.md" %} -[//]: <> (APPS PAGE BOILERPLATE END) + TensorFlow is an open source library for machine learning. TensorFlow can train and run deep neural networks. It can also serve as a backend for other techniques requiring automatic differentiation and GPU @@ -34,7 +32,7 @@ running TensorFlow with GPU support. documentation page. - To run TensorFlow on CPUs instead, have a look at our article [TensorFlow on - CPUs](../../Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md) + CPUs](TensorFlow_on_CPUs.md) for tips on how to configure TensorFlow and Slurm for optimal performance. From 02b3b349937912d25cb9ff71aad91abe59424f27 Mon Sep 17 00:00:00 2001 From: cal Date: Fri, 8 Dec 2023 16:32:01 +1300 Subject: [PATCH 08/14] Synda verify --- .../Supported_Applications/Synda.md | 44 ++++++------------- 1 file changed, 14 insertions(+), 30 deletions(-) diff --git a/docs/Scientific_Computing/Supported_Applications/Synda.md b/docs/Scientific_Computing/Supported_Applications/Synda.md index 9b0f01299..19c8c07ba 100644 --- a/docs/Scientific_Computing/Supported_Applications/Synda.md +++ b/docs/Scientific_Computing/Supported_Applications/Synda.md @@ -5,27 +5,11 @@ position: 52 tags: [] title: Synda vote_count: 1 -# template: app.html vote_sum: 1 zendesk_article_id: 360001208256 zendesk_section_id: 360000040076 --- - -[//]: <> (APPS PAGE BOILERPLATE START) -{% set app_name = page.title | trim %} -{% set app = applications[app_name] %} -{% include "partials/appHeader.md" %} -[//]: <> (APPS PAGE BOILERPLATE END) - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) - ## What is synda? Synda is a command line tool to search and download files from the Earth @@ -41,26 +25,26 @@ Maui\_ancil. 1\. Load Anaconda3 -``` sl +``` sh module load Anaconda3 ``` 2\. Create a conda environment and activate the environment -``` sl +``` sh conda create --prefix= ``` where <SYNDA\_ENV> is a directory of your choice. Activate your new environment -``` sl +``` sh conda activate ``` 3\. Install synda (currently version 3.10) -``` sl +``` sh conda install -c IPSL synda ``` @@ -69,7 +53,7 @@ conda install -c IPSL synda Set the ST\_HOME environment variable and populate `$ST_HOME`, for instance -``` sl +``` sh export ST_HOME=/nesi/nobackup//synda_home ``` @@ -85,7 +69,7 @@ later. To configure and store your ESGF credentials, type -``` sl +``` sh synda -h synda check-env ``` @@ -93,7 +77,7 @@ synda check-env Paste in the openID you received when creating your ESGF account. If you created an account on esgf-node.llnl.gov then your openID will be: -``` sl +``` sh openID url: https://esgf-node.llnl.gov/esgf-idp/openid/USER_NAME ``` @@ -101,7 +85,7 @@ openID url: https://esgf-node.llnl.gov/esgf-idp/openid/USER_NAME can change your default configuration by editing $ST\_HOME/conf/sdt.conf. I have -``` sl +``` sh indexes = esgf-node.llnl.gov default_index = esgf-node.llnl.gov ``` @@ -112,13 +96,13 @@ Find all the datasets for given ocean surface temperature ("tos"), variant label ("r1i1p1f1") produced by institution "NOAA-GFDL" for historical data and table Id "Omon": -``` sl +``` sh synda search project=CMIP6 realm=ocean variable=tos variant_label=r1i1p1f1 institution_id=NOAA-GFDL table_id=Omon experiment_id=historical ``` This will return -``` sl +``` sh new  CMIP6.CMIP.NOAA-GFDL.GFDL-CM4.historical.r1i1p1f1.Omon.tos.gn.v20180701 new  CMIP6.CMIP.NOAA-GFDL.GFDL-CM4.historical.r1i1p1f1.Omon.tos.gr.v20180701 new  CMIP6.CMIP.NOAA-GFDL.GFDL-ESM4.historical.r1i1p1f1.Omon.tos.gn.v20190726 @@ -127,13 +111,13 @@ new  CMIP6.CMIP.NOAA-GFDL.GFDL-ESM4.historical.r1i1p1f1.Omon.tos.gr.v20190726 Choose one of the datasets. To find out how big the dataset is, type:  -``` sl +``` sh synda stat CMIP6.CMIP.NOAA-GFDL.GFDL-ESM4.historical.r1i1p1f1.Omon.tos.gr.v20190726 ``` which returns -``` sl +``` sh Total files count: 9 New files count: 9 Total size: 262.8 MB @@ -142,9 +126,9 @@ New files size: 262.8 MB To download the dataset, type -``` sl +``` sh synda get CMIP6.CMIP.NOAA-GFDL.GFDL-CM4.historical.r1i1p1f1.Omon.tos.gn.v2018070 ``` The datasets (NetCDF files) will be downloaded locally in your -directory. \ No newline at end of file +directory. From b7557c326d72fdcadcedb480eb25d95535a027d5 Mon Sep 17 00:00:00 2001 From: cal Date: Fri, 8 Dec 2023 17:43:36 +1300 Subject: [PATCH 09/14] Rename some pages to not have spaces. --- ...d_for_Machine_Learning_and_data_science.md | 25 +- .../OpenMP_settings.md | 2 +- .../GPU_use_on_NeSI.md | 2 +- .../Supported_Applications/Cylc.md | 85 +- .../Supported_Applications/Keras.md | 47 +- .../Supported_Applications/Lambda Stack.md | 6 - .../Software Installation Request.md | 6 - docs/redirect_map.yml | 18 +- typos.txt | 3383 +++++++++-------- 9 files changed, 1863 insertions(+), 1711 deletions(-) diff --git a/docs/General/FAQs/What_software_environments_on_NeSI_are_optimised_for_Machine_Learning_and_data_science.md b/docs/General/FAQs/What_software_environments_on_NeSI_are_optimised_for_Machine_Learning_and_data_science.md index 4e1e2adad..e106394f8 100644 --- a/docs/General/FAQs/What_software_environments_on_NeSI_are_optimised_for_Machine_Learning_and_data_science.md +++ b/docs/General/FAQs/What_software_environments_on_NeSI_are_optimised_for_Machine_Learning_and_data_science.md @@ -11,39 +11,30 @@ zendesk_article_id: 360004558895 zendesk_section_id: 360000039036 --- - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) - When using NeSI's [HPC platform](https://support.nesi.org.nz/hc/en-gb/sections/360000034335), you can bring your own code to install or you can access our extensive software library which is already built and compiled, ready for you to -use.  +use. Examples of software environments on NeSI optimised for data science include: -- [R](../../Scientific_Computing/Supported_Applications/R.md) and [Python](../../Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md) users +- [R](../../Scientific_Computing/Supported_Applications/R.md) and [Python](../../Scientific_Computing/Supported_Applications/TensorFlow_on_GPUs.md) users can get right into using and exploring the several built-in packages or create custom code. -- [Jupyter on NeSI +- [Jupyter on NeSI ](../../Scientific_Computing/Interactive_computing_using_Jupyter/Jupyter_on_NeSI.md)is particularly well suited to artificial intelligence and machine learning workloads. [R Studio](../../Scientific_Computing/Interactive_computing_using_Jupyter/RStudio_via_Jupyter_on_NeSI.md) and/or Conda can be accessed via Jupyter. -- Commonly used data science environments and libraries such as +- Commonly used data science environments and libraries such as [Keras](../../Scientific_Computing/Supported_Applications/Keras.md), [LambdaStack](../../Scientific_Computing/Supported_Applications/Lambda Stack.md), - [Tensorflow](../../Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md) + [Tensorflow](../../Scientific_Computing/Supported_Applications/TensorFlow_on_GPUs.md) and [Conda](https://docs.conda.io/en/latest/) are available to create comprehensive workflows. @@ -53,15 +44,15 @@ here](https://support.nesi.org.nz/hc/en-gb/sections/360000040076). As pictured in the screenshot below, you can type keywords into the catalogue's search field to browse by a specific software name or using -more broad terms such as "machine learning".  +more broad terms such as "machine learning". ![MachineLearningSoftwareEnvironments-May2021.png](../../assets/images/What_software_environments_on_NeSI_are_optimised_for_Machine_Learning_and_data_science.png) For more information on NeSI's model and approach to application support, refer to our [policy for the management of scientific application -software](../../General/NeSI_Policies/NeSI_Application_Support_Model.md).  +software](../../General/NeSI_Policies/NeSI_Application_Support_Model.md). If you need help installing your software or would like to discuss your software needs with us, [contact NeSI -Support](https://support.nesi.org.nz/hc/en-gb/requests/new). \ No newline at end of file +Support](https://support.nesi.org.nz/hc/en-gb/requests/new). diff --git a/docs/Scientific_Computing/HPC_Software_Environment/OpenMP_settings.md b/docs/Scientific_Computing/HPC_Software_Environment/OpenMP_settings.md index cf3bc3669..3eb885910 100644 --- a/docs/Scientific_Computing/HPC_Software_Environment/OpenMP_settings.md +++ b/docs/Scientific_Computing/HPC_Software_Environment/OpenMP_settings.md @@ -48,7 +48,7 @@ export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK in your SLURM script - although this can sometimes be more complicated, e.g., with [TensorFlow on -CPUs](../../Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md). +CPUs](../../Scientific_Computing/Supported_Applications/TensorFlow_on_CPUs.md). On Mahuika, you will be charged for the number of physical cores that you requested - the second logical core on a physical core is free, diff --git a/docs/Scientific_Computing/Running_Jobs_on_Maui_and_Mahuika/GPU_use_on_NeSI.md b/docs/Scientific_Computing/Running_Jobs_on_Maui_and_Mahuika/GPU_use_on_NeSI.md index c64bd602b..4c82894de 100644 --- a/docs/Scientific_Computing/Running_Jobs_on_Maui_and_Mahuika/GPU_use_on_NeSI.md +++ b/docs/Scientific_Computing/Running_Jobs_on_Maui_and_Mahuika/GPU_use_on_NeSI.md @@ -342,7 +342,7 @@ applications: Stack](../../Scientific_Computing/Supported_Applications/Lambda Stack.md) - [Matlab](../../Scientific_Computing/Supported_Applications/MATLAB.md#GPU) - [TensorFlow on - GPUs](../../Scientific_Computing/Supported_Applications/TensorFlow on GPUs.md) + GPUs](../../Scientific_Computing/Supported_Applications/TensorFlow_on_GPUs.md) And programming toolkits: diff --git a/docs/Scientific_Computing/Supported_Applications/Cylc.md b/docs/Scientific_Computing/Supported_Applications/Cylc.md index 2dfbcc1cc..295fda908 100644 --- a/docs/Scientific_Computing/Supported_Applications/Cylc.md +++ b/docs/Scientific_Computing/Supported_Applications/Cylc.md @@ -11,21 +11,6 @@ zendesk_article_id: 5254610390415 zendesk_section_id: 360000040076 --- - -[//]: <> (APPS PAGE BOILERPLATE START) -{% set app_name = page.title | trim %} -{% set app = applications[app_name] %} -{% include "partials/appHeader.md" %} -[//]: <> (APPS PAGE BOILERPLATE END) - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) - ## What is Cylc [Cylc](https://cylc.github.io/) is a **general purpose workflow engine** @@ -52,9 +37,7 @@ documentation](https://cylc.github.io/documentation/) for more elaborate examples, including some with a cycling (repeated) graph pattern. One of the strengths of Cylc is that simple workflows can be executed simply while allowing for very complex workflows, with thousands of tasks, -which may be repeated ad infinitum.  - -  +which may be repeated ad infinitum. ## SSH configuration @@ -64,16 +47,16 @@ done so you need to allow ssh to connect to other hosts on the HPC cluster without prompting for a passphrase (all HPC nodes see the same filesystem, so this is easy): -- run **`ssh-keygen`** to generate a public/private key pair with **no +- run **`ssh-keygen`** to generate a public/private key pair with **no passphrase** (when it asks for a passphrase, just hit enter) -- add your own public key to your authorized keys +- add your own public key to your authorized keys file: **`cat .ssh/id_rsa.pub >> .ssh/authorized_keys`**  -- check that your **keys, authorized\_keys file, ssh +- check that your **keys, authorized\_keys file, ssh directory, **and** home directory** all have sufficiently secure file permissions. If not, `ssh` will silently revert to requiring password entry. See for example  -- make sure your **home directory** has a maximum +- make sure your **home directory** has a maximum of **750** permissions Now you should be able to run **`ssh mahuika02`**(for example) without @@ -84,7 +67,7 @@ being asked for a passphrase. Cylc has been installed on Māui and Mahuika, there is no need to load any module, -``` sl +``` sh $ which cylc /opt/nesi/share/bin/cylc ``` @@ -93,7 +76,7 @@ $ which cylc Be aware that the default version -``` sl +``` sh $ cylc version 7.9.1 ``` @@ -103,7 +86,7 @@ changed significantly at version 8. **New Cylc users should use version 8 or later**, -``` sl +``` sh $ cylc list-versions 7.9.1 @@ -128,14 +111,14 @@ At the time of writing, the latest version is 8.0.1. To demonstrate Cylc, let's start with a workflow, which we call "simple", -``` sl +``` sh $ mkdir -p ~/cylc-src/simple $ cd ~/cylc-src/simple ``` Create/edit the following **flow.cylc** file containing -``` sl +``` sh [scheduling] # Define the tasks and when they should run [[graph]] R1 = """ # R1 means run this graph once @@ -159,7 +142,7 @@ Create/edit the following **flow.cylc** file containing In the above example, we have three tasks (taskA, taskB and taskC), which run under SLURM (hence platform = mahuika-slurm). Type -``` sl +``` sh cylc config --platform-names ``` @@ -170,13 +153,13 @@ to see a list of platforms. The SLURM settings for taskA are in the Cylc takes command lines. Type  -``` sl +``` sh $ cylc help all ``` to see the available commands. Type  -``` sl +``` sh $ cylc help install # or cylc install --help ``` @@ -189,13 +172,13 @@ directory. Due to limited disk space in home directories on NeSI, Cylc has been configured to symlink the standard run directories to project directories, if $PROJECT is defined. Hence, you need to set -``` sl +``` sh $ export PROJECT=nesi99999 # CHANGE ``` Then install the workflow with -``` sl +``` sh cylc install simple ``` @@ -203,24 +186,24 @@ cylc install simple It's a good idea to check that there are no syntax errors in flow.cylc, -``` sl +``` sh $ cylc validate simple Valid for cylc-8.0.1 ``` ## Looking at the workflow graph -A useful command is  +A useful command is -``` sl +``` sh $ cylc graph simple ``` which will generate a png file, generally in the /tmp directory with a name like /tmp/tmpzq3bjktw.PNG. Take note of the name of the png file. -To visualise the file you can type  +To visualise the file you can type -``` sl +``` sh $ display  /tmp/tmpzq3bjktw.PNG # ADJUST the file name ``` @@ -236,13 +219,13 @@ The "1" indicates that this workflow graph is executed only once. Every Cylc action can be executed via the command line. Alternatively, you can invoke each action through a **terminal user interface** (tui),  -``` sl +``` sh $ cylc tui simple ``` Another alternative, is to use the **graphical user interface** -``` sl +``` sh $ cylc gui ``` @@ -264,7 +247,7 @@ First open ssh tunnelling, so that a given port on your local machine (e.g. your laptop) maps to the Cylc UI Server’s port on the HPC. On your local machine, type -``` sl +``` sh $ ssh -N -L PORT:localhost:PORT HOST ``` @@ -278,14 +261,14 @@ connection without logging you into the shell. Then ssh to the host (e.g. mahuika) -``` sl +``` sh $ ssh HOST ``` and add the following to **$HOME/.cylc/uiserver/jupyter\_config.py** on the **HOST**. -``` sl +``` sh c.ServerApp.open_browser=False c.ServerApp.port=PORT ``` @@ -295,13 +278,13 @@ tunnel. You're now ready to fire up the web graphical interface -``` sl +``` sh $ cylc gui ``` Just copy the URL that looks like -``` sl +``` sh http://127.0.0.1:PORT/cylc?token=TOKEN ``` @@ -312,7 +295,7 @@ chosen above.) To execute the workflow type -``` sl +``` sh $ cylc play --no-detach simple ``` @@ -322,7 +305,7 @@ can see its output in your terminal. Without this option it will Command -``` sl +``` sh $ cylc scan ``` @@ -330,17 +313,17 @@ will list all running and installed workflows. ## Checking the output -``` sl +``` sh $ cylc cat-log simple//1/taskA # note // between workflow and task ID ``` of the first cycle of taskA. The "1" refers to the task iteration, or cycle point. Our simple workflow only has one iteration (as dictated by -the R1 graph above).  +the R1 graph above). ## How to clean or remove a workflow -``` sl +``` sh $ cylc clean simple ``` @@ -352,7 +335,7 @@ Cylc will create a directory under $HOME/cylc-run. On NeSI, the output of the runs will be stored in the project directory, with a symbolic link pointing from the user home directory to the project directory -``` sl +``` sh $ ls -l $HOME/cylc-run/simple/run1 lrwxrwxrwx 1 pletzera pletzera 54 Aug  5 03:19 /home/pletzera/cylc-run/simple/run1 -> /nesi/nobackup/nesi99999/pletzera/cylc-run/simple/run1 ``` @@ -362,4 +345,4 @@ lrwxrwxrwx 1 pletzera pletzera 54 Aug  5 03:19 /home/pletzera/cylc-run/simple/r More can be found about Cylc [here](https://cylc.github.io/cylc-doc/nightly/html/tutorial/index.html), including what Cylc is and how you can leverage Cylc to submit parallel -jobs. \ No newline at end of file +jobs. diff --git a/docs/Scientific_Computing/Supported_Applications/Keras.md b/docs/Scientific_Computing/Supported_Applications/Keras.md index 0ed55bb5a..281f95f73 100644 --- a/docs/Scientific_Computing/Supported_Applications/Keras.md +++ b/docs/Scientific_Computing/Supported_Applications/Keras.md @@ -11,27 +11,12 @@ zendesk_article_id: 360001075936 zendesk_section_id: 360000040076 --- - -[//]: <> (APPS PAGE BOILERPLATE START) -{% set app_name = page.title | trim %} -{% set app = applications[app_name] %} -{% include "partials/appHeader.md" %} -[//]: <> (APPS PAGE BOILERPLATE END) - - -[//]: <> (REMOVE ME IF PAGE VALIDATED) -[//]: <> (vvvvvvvvvvvvvvvvvvvv) -!!! warning - This page has been automatically migrated and may contain formatting errors. -[//]: <> (^^^^^^^^^^^^^^^^^^^^) -[//]: <> (REMOVE ME IF PAGE VALIDATED) - Keras is a modular and extensible API for building neural networks in Python. Keras is included with TensorFlow. Note that there are [CPU -and](../../Scientific_Computing/Supported_Applications/TensorFlow on CPUs.md) [GPU +and](../../Scientific_Computing/Supported_Applications/TensorFlow_on_CPUs.md) [GPU versions](https://support.nesi.org.nz/hc/en-gb/articles/360000990436-TensorFlow) of TensorFlow, here we'll use TensorFlow 1.10 for GPUs, which is available -as an environment module.  +as an environment module. Keras can be used to solve a wide set of problems using artificial neural networks, including pattern recognition. Ultimately, a neural @@ -41,7 +26,7 @@ neurons, which are modelled after biological neurons. The connections between neurons have different "weights", which when submitted to different stimuli will output different signals. With sufficient training, we can teach a neural network to acquire the correct weights, -i.e. adjust the weights until the desired output is produced.  +i.e. adjust the weights until the desired output is produced. ## Counting dots in images @@ -54,7 +39,7 @@ Start by generating images of dots.  We'll generate 1000 images for our training set and 100 images to test our predictions. On Mahuika type the following commands to generate the training and testing data sets: -``` sl +``` sh wget https://raw.githubusercontent.com/mkienzle/MachineLearning/master/Scripts/ProduceSyntheticData/DrawDots.R ml R/3.6.1-gimkl-2018b Rscript DrawDots.R -n 1000 -r 0 -R 5 -s 123 -o train -c train.csv -w 40 @@ -64,7 +49,7 @@ Rscript DrawDots.R -n 100 -r 0 -R 5 -s 234 -o test -c test.csv -w 40 The images are saved under directories train/ and test/, respectively. An example of image is test/img49.jpg. -``` sl +``` sh display test/img49.jpg ``` @@ -80,7 +65,7 @@ The images need to be slightly manipulated. For instance we expect all the images to be black and white so we can collapse the red, green and blue channel into one. We'll need OpenCV to this task: -``` sl +``` sh pip install opencv-python --user ``` @@ -88,7 +73,7 @@ pip install opencv-python --user Our neural network -``` sl +``` sh wget https://raw.githubusercontent.com/mkienzle/MachineLearning/master/Scripts/Conv2D/classify.py ``` @@ -99,7 +84,7 @@ flattened as a 1D array and a dense layer, which returns an estimate of the number of dots as a single floating point number, is added. The corresponding lines in classify.py look like (Python code): -``` sl +``` sh clf = keras.Sequential() clf.add( keras.layers.Conv2D(32, kernel_size=(3,3), strides=(1,1),                              padding='same', data_format='channels_last', activation='relu') ) @@ -114,8 +99,6 @@ clf.add( keras.layers.Flatten() ) clf.add( keras.layers.Dense(1) ) ``` -  - We're now ready to train and test our model: ``` sl @@ -134,7 +117,7 @@ python classify.py --testDir=test --trainDir=train --save=someResults.png Copy-paste the above and save in file classify.sl. Submit the Slurm script classify.sl -``` sl +``` sh sbatch classify.sl ``` @@ -143,7 +126,7 @@ sbatch classify.sl Upon completion of the run, expect to find file someResults.png in the same directory as classify.py. This file contains the predictions for the first 50 test images, which will vary for each training but the -result will look like:  +result will look like: ![someResults.png](../../assets/images/Keras.png) @@ -153,12 +136,4 @@ inferred values are to be rounded to the nearest integer. Plot titles in red indicate failures. Among the 100 test images, the correct number of dots was found in 90 percent of the cases (the accuracy will change with each training due to the randomness of the process). The predicted -number of dots should be off by no more than one unit in most cases.  - -  - -  - -  - -  \ No newline at end of file +number of dots should be off by no more than one unit in most cases. diff --git a/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md b/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md index 4b2b9829c..6f53dfee9 100644 --- a/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md +++ b/docs/Scientific_Computing/Supported_Applications/Lambda Stack.md @@ -11,12 +11,6 @@ zendesk_article_id: 360002558216 zendesk_section_id: 360000040076 --- - -[//]: <> (APPS PAGE BOILERPLATE START) -{% set app_name = page.title | trim %} -{% set app = applications[app_name] %} -{% include "partials/appHeader.md" %} -[//]: <> (APPS PAGE BOILERPLATE END) ## Introduction [Lambda diff --git a/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md b/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md index f551f0a35..efef9650b 100644 --- a/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md +++ b/docs/Scientific_Computing/Supported_Applications/Software Installation Request.md @@ -11,12 +11,6 @@ zendesk_article_id: 360000361675 zendesk_section_id: 360000040076 --- - -[//]: <> (APPS PAGE BOILERPLATE START) -{% set app_name = page.title | trim %} -{% set app = applications[app_name] %} -{% include "partials/appHeader.md" %} -[//]: <> (APPS PAGE BOILERPLATE END) To request that we install a scientific application (either a new application, or a new version of an already installed application), please [email our support diff --git a/docs/redirect_map.yml b/docs/redirect_map.yml index 5a982bcd5..54e18f2a4 100644 --- a/docs/redirect_map.yml +++ b/docs/redirect_map.yml @@ -177,16 +177,12 @@ hc/en-gb/articles/360000931775-National-Data-Transfer-Platform.md: Storage/Data_ hc/en-gb/articles/360000931775.md: Storage/Data_Transfer_Services/National_Data_Transfer_Platform.md hc/en-gb/articles/360000980375-Trinity.md: Scientific_Computing/Supported_Applications/Trinity.md hc/en-gb/articles/360000980375.md: Scientific_Computing/Supported_Applications/Trinity.md -hc/en-gb/articles/360000990436-TensorFlow-on-GPUs.md: Scientific_Computing/Supported_Applications/TensorFlow - on GPUs.md -hc/en-gb/articles/360000990436.md: Scientific_Computing/Supported_Applications/TensorFlow - on GPUs.md +hc/en-gb/articles/360000990436-TensorFlow-on-GPUs.md: Scientific_Computing/Supported_Applications/TensorFlow_on_GPUs.md +hc/en-gb/articles/360000990436.md: Scientific_Computing/Supported_Applications/TensorFlow_on_GPUs.md hc/en-gb/articles/360000995575-Thread-Placement-and-Thread-Affinity.md: Scientific_Computing/HPC_Software_Environment/Thread_Placement_and_Thread_Affinity.md hc/en-gb/articles/360000995575.md: Scientific_Computing/HPC_Software_Environment/Thread_Placement_and_Thread_Affinity.md -hc/en-gb/articles/360000997675-TensorFlow-on-CPUs.md: Scientific_Computing/Supported_Applications/TensorFlow - on CPUs.md -hc/en-gb/articles/360000997675.md: Scientific_Computing/Supported_Applications/TensorFlow - on CPUs.md +hc/en-gb/articles/360000997675-TensorFlow-on-CPUs.md: Scientific_Computing/Supported_Applications/TensorFlow_on_CPUs.md +hc/en-gb/articles/360000997675.md: Scientific_Computing/Supported_Applications/TensorFlow_on_CPUs.md hc/en-gb/articles/360001002956-ParaView.md: Scientific_Computing/Supported_Applications/ParaView.md hc/en-gb/articles/360001002956.md: Scientific_Computing/Supported_Applications/ParaView.md hc/en-gb/articles/360001008136-Debugging.md: Scientific_Computing/Profiling_and_Debugging/Debugging.md @@ -255,10 +251,8 @@ hc/en-gb/articles/360001316356-Slurm-Interactive-Sessions.md: Scientific_Computi hc/en-gb/articles/360001316356.md: Scientific_Computing/Running_Jobs_on_Maui_and_Mahuika/Slurm_Interactive_Sessions.md hc/en-gb/articles/360001330415-Checksums.md: Scientific_Computing/Running_Jobs_on_Maui_and_Mahuika/Checksums.md hc/en-gb/articles/360001330415.md: Scientific_Computing/Running_Jobs_on_Maui_and_Mahuika/Checksums.md -hc/en-gb/articles/360001332675-Find-execution-hot-spots-with-VTune.md: Scientific_Computing/Supported_Applications/Find - execution hot spots with VTune.md -hc/en-gb/articles/360001332675.md: Scientific_Computing/Supported_Applications/Find - execution hot spots with VTune.md +hc/en-gb/articles/360001332675-Find-execution-hot-spots-with-VTune.md: Scientific_Computing/Supported_Applications/VTune.md +hc/en-gb/articles/360001332675.md: Scientific_Computing/Supported_Applications/VTune.md hc/en-gb/articles/360001343015-TurboVNC.md: Scientific_Computing/Supported_Applications/TurboVNC.md hc/en-gb/articles/360001343015.md: Scientific_Computing/Supported_Applications/TurboVNC.md hc/en-gb/articles/360001385735-What-is-an-allocation-.md: Getting_Started/Accounts-Projects_and_Allocations/What_is_an_allocation.md diff --git a/typos.txt b/typos.txt index 5d1949c82..13b0e04a2 100644 --- a/typos.txt +++ b/typos.txt @@ -1,1581 +1,1802 @@ -# | sort | uniq -c | sort -rnk1 - -361 SBATCH -261 zendesk -200 nesi -126 nz -116 CPUs -110 sl -86 https -63 mem -58 mahuika -58 JupyterLab -56 cpus -51 admonation -50 VASP -49 ntasks -45 XC -40 releasenote -38 gimkl -35 ANSYS -34 py -33 filesystem -30 WRF -30 slurm -30 jupyter -29 MobaXterm -28 Hyperthreading -28 conda -28 Ancil -27 hyperthreading -25 Tuakiri -25 cd -23 gpus -23 config -22 www -22 TurboVNC -22 RStudio -22 programme -22 Cylc -21 gpu -21 DCV -21 Dask -21 AlphaFold -20 ParaView -20 nomultithread -20 intel -20 Fortran -20 cpu -19 sbatch -19 CPUS -18 pre -18 GATK -18 DTN -17 VTune -17 NIWA -16 rclone -16 mpi -16 HDF -16 Conda -15 maui -15 localhost -15 GROMACS -15 filesystems -15 datasets -15 CESM -15 Broadwell -14 WinSCP -14 TMPDIR -14 ORCA -14 hpc -14 globus -13 NetCDF -13 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+ 1 Benchmarks's + 1 Benchmarking + 1 behavirour + 1 bedMethyl + 1 BDD + 1 batchsolve + 1 batchoptions + 1 basecall + 1 baremetal + 1 barcoding + 1 barcodes + 1 barcoded + 1 backtraces + 1 Backplane + 1 backfilled + 1 backends + 1 Backend + 1 BABA + 1 awk + 1 AveCPU + 1 Availablity + 1 autosaves + 1 autodelete + 1 attemps + 1 atomistic + 1 ATL + 1 atk's + 1 aswcli + 1 AssocGrpCPURunMinutes + 1 assember + 1 asn's + 1 ASE's + 1 ASE + 1 ascii + 1 asav + 1 ArrayJob + 1 ARPACK + 1 ArgumentParser + 1 args + 1 ares's + 1 archaeal + 1 APPBIN + 1 APOA + 1 apoa + 1 APIs + 1 api's + 1 APDL + 1 apache + 1 Aotearoa's + 1 Aotearoa + 1 ansysedt + 1 ANother + 1 ANnoTation + 1 anf + 1 ancilliary + 1 anaLyses + 1 amplicon + 1 Amon + 1 alphabetcial + 1 aln + 1 AllocGres + 1 AllocCPUS + 1 allocator + 1 ALignment + 1 ALgebraic + 1 al + 1 AgResearch’s + 1 aedt + 1 Admonations + 1 Admonation + 1 adjustTimeStep + 1 Additionnally + 1 Acroynym + 1 accuracies + 1 Accessability + 1 ACC + 1 ABI + 1 ABBA From 63cda394817f11b08b4dfbdab0ffac282327c5bc Mon Sep 17 00:00:00 2001 From: cal Date: Fri, 8 Dec 2023 18:16:01 +1300 Subject: [PATCH 10/14] gatk update --- docs/Scientific_Computing/Supported_Applications/GATK.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/Scientific_Computing/Supported_Applications/GATK.md b/docs/Scientific_Computing/Supported_Applications/GATK.md index 15edfc798..6a8fa3ccb 100644 --- a/docs/Scientific_Computing/Supported_Applications/GATK.md +++ b/docs/Scientific_Computing/Supported_Applications/GATK.md @@ -16,6 +16,7 @@ zendesk_section_id: 360000040076 {% set app = applications[app_name] %} {% include "partials/appHeader.md" %} [//]: <> (APPS PAGE BOILERPLATE END) + The Genome Analysis Toolkit (GATK), developed at the [Broad Institute](http://www.broadinstitute.org/), provides a wide variety of tools focusing primarily on variant discovery and genotyping. It is @@ -32,10 +33,9 @@ of Java is already included as part of the GATK module, you will not need to load a Java module separately. !!! note - -- `--time` and `--mem` defined in the following example are just place - holders. -- Please load the GATK version of your choice + - `--time` and `--mem` defined in the following example are just place + holders. + - Please load the GATK version of your choice ``` sl #!/bin/bash -e From a2874db40b530f86e3278c6cf66d7d7c112be07b Mon Sep 17 00:00:00 2001 From: cal Date: Fri, 8 Dec 2023 18:19:26 +1300 Subject: [PATCH 11/14] change template --- docs/Scientific_Computing/Supported_Applications/index.md | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/docs/Scientific_Computing/Supported_Applications/index.md b/docs/Scientific_Computing/Supported_Applications/index.md index d2d2ec03a..336e0324d 100644 --- a/docs/Scientific_Computing/Supported_Applications/index.md +++ b/docs/Scientific_Computing/Supported_Applications/index.md @@ -1,13 +1,8 @@ --- title: Supported Applications +template: supportedApplications.html --- - -[//]: <> (APPS PAGE BOILERPLATE START) -{% set app_name = page.title | trim %} -{% set app = applications[app_name] %} -{% include "partials/appHeader.md" %} -[//]: <> (APPS PAGE BOILERPLATE END) === "Mahuika" On Mahuika, and Ancillary nodes (both Mahuika and Māui) software packages are provided using 'lmod' an implementation of Environment Modules with [additional features](https://lmod.readthedocs.io/en/latest/010_user.html). From 3567bee909fb0cf7b14e36b445772f2ebd5acb33 Mon Sep 17 00:00:00 2001 From: cal Date: Wed, 13 Dec 2023 14:19:50 +1300 Subject: [PATCH 12/14] add js --- overrides/partials/supportedApplicationsList.html | 2 ++ 1 file changed, 2 insertions(+) diff --git a/overrides/partials/supportedApplicationsList.html b/overrides/partials/supportedApplicationsList.html index 487098a89..26ad37a29 100644 --- a/overrides/partials/supportedApplicationsList.html +++ b/overrides/partials/supportedApplicationsList.html @@ -1,5 +1,7 @@
    + +
    From 0f36223e2d1197bff02c8dc9bb2cd1c1ad465482 Mon Sep 17 00:00:00 2001 From: cal Date: Fri, 15 Dec 2023 16:04:21 +1300 Subject: [PATCH 13/14] mvp for supported apps page. --- .../Supported_Applications/index.md | 9 ++--- .../stylesheets/supportedApplications.css | 17 ++++++++ overrides/partials/appCard.html | 39 ++++++++++--------- overrides/partials/appHeader.md | 2 + overrides/partials/appNetworkLicence.html | 2 - .../partials/supportedApplicationsList.html | 2 + overrides/supportedApplications.html | 13 ++++++- 7 files changed, 57 insertions(+), 27 deletions(-) diff --git a/docs/Scientific_Computing/Supported_Applications/index.md b/docs/Scientific_Computing/Supported_Applications/index.md index 0ab4dc585..0a19fc08f 100644 --- a/docs/Scientific_Computing/Supported_Applications/index.md +++ b/docs/Scientific_Computing/Supported_Applications/index.md @@ -1,11 +1,10 @@ --- title: Supported Applications +template: supportedApplications.html --- - - - -=== "Mahuika" +For more information on environment-modules see [Finding Software](../HPC_Software_Environment/Finding_Software.md). + diff --git a/docs/assets/stylesheets/supportedApplications.css b/docs/assets/stylesheets/supportedApplications.css index c0269ec46..7163eabc5 100644 --- a/docs/assets/stylesheets/supportedApplications.css +++ b/docs/assets/stylesheets/supportedApplications.css @@ -61,6 +61,19 @@ color: var(--md-primary-bg-color); background-color: #972220; } + +.grid.flex-card-parent { + display: flex; + flex-direction: row; + flex-wrap: wrap; + align-content: stretch; + align-items: stretch; + justify-content: space-between; +} + +.flex-card { + flex-grow: 1; +} .app-list-header { display: inline; } @@ -248,3 +261,7 @@ div#updated { #srchbar{ border-right:0; } +.md-source-file{ + display: none; + /* This is lazy */ +} \ No newline at end of file diff --git a/overrides/partials/appCard.html b/overrides/partials/appCard.html index 92a9c4982..9d59092d1 100644 --- a/overrides/partials/appCard.html +++ b/overrides/partials/appCard.html @@ -25,15 +25,18 @@

    {{ app_name }}

    {{ app.description }}

    -
    - {% include "partials/appVersion.html" -%} -
    - Links +
    +
    +
    Available Modules
    + {% include "partials/appVersion.html" -%} +
    +
    +
    Links
    -
    - {% if app.licence_type %} - - - -

    Licence {{ app_name }} is {{ app.licence_type }} software.

    - {% if app.licences %} -

    Access to a valid licence token is required to run {{ app_name }}, a list of which can be found - here.

    - {% endif %} - - {% endif %} + {% if app.licence_type %} +
    +
    Licence
    + +

    Licence {{ app_name }} is {{ app.licence_type }} software.

    + {% if app.network_licences %} +

    Access to a valid licence token is required to run {{ app_name }}. + {% include "partials/appNetworkLicence.html" -%} + {% endif %} +

    + {% endif %} +
    \ No newline at end of file diff --git a/overrides/partials/appHeader.md b/overrides/partials/appHeader.md index 3831c73c6..e6a7de53a 100644 --- a/overrides/partials/appHeader.md +++ b/overrides/partials/appHeader.md @@ -21,6 +21,8 @@ ## Licences +

    The following network licence servers can be accessed from the NeSI cluster.

    {% include "partials/appNetworkLicence.html" -%} +

    If you do not have access, or want a server connected {% include "partials/support_request.html" %}.

    {% endif -%} diff --git a/overrides/partials/appNetworkLicence.html b/overrides/partials/appNetworkLicence.html index dc5703328..696e3aa2e 100644 --- a/overrides/partials/appNetworkLicence.html +++ b/overrides/partials/appNetworkLicence.html @@ -1,5 +1,3 @@ -

    The following network licence servers can be accessed from the NeSI cluster.

    -

    If you do not have access, or want a server connected {% include "partials/support_request.html" %}.

    diff --git a/overrides/partials/supportedApplicationsList.html b/overrides/partials/supportedApplicationsList.html index 26ad37a29..7a33d9c1d 100644 --- a/overrides/partials/supportedApplicationsList.html +++ b/overrides/partials/supportedApplicationsList.html @@ -27,4 +27,6 @@
    +

    If the application you are looking for is not here you can make software installation request or try compiling it yourself.

    + You can help contribute to this list by tagging software here. diff --git a/overrides/supportedApplications.html b/overrides/supportedApplications.html index e93ce231a..ab8512e38 100644 --- a/overrides/supportedApplications.html +++ b/overrides/supportedApplications.html @@ -1,9 +1,18 @@ {% extends "base.html" -%} {% block head -%} {% endblock -%} +{% block libs %} + {{ super() }} + + + +{% endblock -%} +{% block styles %} +{{ super() }} + +{% endblock -%} + {% block content -%} {{ super() }} {% include "partials/supportedApplicationsList.html" %} -

    If the application you are looking for is not here you can make software installation request or try compiling it yourself.

    -You can help contribute to this list by tagging software here. {% endblock %} \ No newline at end of file From 51b119e99d100018a083c84fb5d7103349b803a2 Mon Sep 17 00:00:00 2001 From: cal Date: Fri, 15 Dec 2023 16:07:49 +1300 Subject: [PATCH 14/14] unbreak check --- checks/run_meta_check.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/checks/run_meta_check.py b/checks/run_meta_check.py index 67632376f..ae0bcac82 100755 --- a/checks/run_meta_check.py +++ b/checks/run_meta_check.py @@ -135,9 +135,6 @@ def check_article_titles(path, meta, contents): check_title(page_title(path, meta, contents)) -def supported(path, meta, contents): - - all_checks = [check_expected_parameters, check_article_titles]