Merge branch 'main' into dependabot/github_actions/rojopolis/spellche…

…ck-github-actions-0.35.0
stanford-rc · Jan 8, 2024 · 47cd346 · 47cd346
2 parents be757bf + 6e3c871
commit 47cd346
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diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
@@ -43,7 +43,7 @@ jobs:
         uses: actions/checkout@v4
       - name: list changed yaml files
         id: changedfiles
-        uses: tj-actions/changed-files@v40
+        uses: tj-actions/changed-files@v41
         with:
           files: |
             **.yml
@@ -63,7 +63,7 @@ jobs:
         uses: actions/checkout@v4
       - name: list changed markdown files
         id: changedfiles
-        uses: tj-actions/changed-files@v40
+        uses: tj-actions/changed-files@v41
         with:
           files: '**.md'
       - name: lint markdown files
@@ -81,7 +81,7 @@ jobs:
         uses: actions/checkout@v4
       - name: list changed markdown files
         id: changedfiles
-        uses: tj-actions/changed-files@v40
+        uses: tj-actions/changed-files@v41
         with:
           files: '**.md'
       - uses: rojopolis/[email protected]

diff --git a/includes/data/facts.yml b/includes/data/facts.yml
@@ -2,9 +2,9 @@ facts:
   - name: users
     fields:
       - name: user accounts
-        value: 7020
+        value: 7150
       - name: PI groups
-        value: 1109
+        value: 1119
         desc: "from all Stanford's seven Schools, SLAC, Stanford Institutes, _etc._"
       - name: owner groups
         value: 201
@@ -20,28 +20,28 @@ facts:
     fields:
       - name: PFLOPs (FP64)
         fmt: "{:0.2f}"
-        value: 5.00
-        desc: 18.73 (FP32) PFLOPs
+        value: 5.34
+        desc: 19.42 (FP32) PFLOPs
       - name: CPU cores
-        value: 53488
+        value: 55216
         desc: "**4** CPU generations (**13** CPU models)"
       - name: GPUs
-        value: 756
+        value: 784
         desc: "**4** GPU generations (**12** GPU models)"
   - name: hardware
     icon: server
     fields:
       - name: compute nodes
-        value: 1718
+        value: 1722
         desc: "**19** server models (from **3** different manufacturers)"
       - name: racks
         value: 37
-        desc: "**1,147** rack units"
+        desc: "**1,178** rack units"
   - name: energy
     icon: plug
     fields:
       - name: kW
-        value: 516.49
+        value: 633.67
         desc: total power usage
       - name: PDUs
         value: 57
@@ -50,7 +50,7 @@ facts:
     fields:
       - name: "`$SCRATCH`"
         desc: parallel, distributed filesystem, delivering over **200 GB/s** of I/O bandwidth
-        value: 7921067654840320
+        value: 8834817281064960
       - name: "`$OAK`"
         desc: long term research data storage
         value: 51280561781604352
@@ -61,8 +61,8 @@ facts:
         value: 104
         desc: across **2** Infiniband fabrics (EDR, HDR)
       - name: Infiniband cables
-        value: 5706
-        desc: spanning about **30.17 km**
+        value: 5716
+        desc: spanning about **30.19 km**
       - name: Ethernet switches
         value: 53
   - name: scheduler
@@ -71,11 +71,11 @@ facts:
       - name: Slurm partitions
         value: 178
       - name: CPU.hours/day
-        value: 46190
+        value: 47495
         desc: over **5 years** of computing in a single day
       - name: /month
         fmt: "${:,.0f}"
-        value: 3086246.9088
+        value: 3173488.1888
         desc: to run the same workload on t2.large on-demand cloud instances
 
   - name: partitions
@@ -123,8 +123,8 @@ facts:
                 - 2 nodes w/ 32-core (AMD 7502P), 256 GB RAM, HDR IB, 4x Tesla V100S PCIe GPUs
         access: public
       - name: owners
-        nodes: 1488
-        cores: 48360
+        nodes: 1492
+        cores: 48488
         desc: privately-owned nodes
         details: |
                 - 146 nodes w/ 20-core (Intel E5-2640v4), 128 GB RAM, EDR IB
@@ -147,7 +147,7 @@ facts:
                 - 75 nodes w/ 24-core (Intel 5118), 384 GB RAM, EDR IB
                 - 1 nodes w/ 24-core (Intel 5118), 512 GB RAM, EDR IB
                 - 1 nodes w/ 24-core (Intel 5118), 768 GB RAM, EDR IB, 8x Tesla V100_SXM2 GPUs
-                - 252 nodes w/ 32-core (AMD 7543), 256 GB RAM, HDR IB
+                - 256 nodes w/ 32-core (AMD 7543), 256 GB RAM, HDR IB
                 - 360 nodes w/ 32-core (AMD 7502), 256 GB RAM, HDR IB
                 - 13 nodes w/ 32-core (AMD 7502P), 256 GB RAM, HDR IB, 4x Geforce RTX_2080Ti GPUs
                 - 15 nodes w/ 32-core (AMD 7502P), 256 GB RAM, HDR IB, 4x Geforce RTX_3090 GPUs

diff --git a/includes/data/software.yml b/includes/data/software.yml
@@ -1361,7 +1361,7 @@ software_modules:
       - {description: GStreamer is a library for constructing graphs of media-handling
           components., markedDefault: false, versionName: 1.12.0}
     - categories: system, file transfer
-      defaultVersionName: 1.59.1
+      defaultVersionName: 1.65.0
       description: 'Rclone is a command line program to sync files and directories
         to and from: Google Drive, Amazon S3, Dropbox, Google Cloud Storage, Amazon
         Drive, Microsoft One Drive, Hubic, Backblaze B2, Yandex Disk, or the local
@@ -1372,23 +1372,15 @@ software_modules:
       - {description: 'Rclone is a command line program to sync files and directories
           to and from: Google Drive, Amazon S3, Dropbox, Google Cloud Storage, Amazon
           Drive, Microsoft One Drive, Hubic, Backblaze B2, Yandex Disk, or the local
-          filesystem.', markedDefault: false, versionName: '1.39'}
-      - {description: 'Rclone is a command line program to sync files and directories
-          to and from: Google Drive, Amazon S3, Dropbox, Google Cloud Storage, Amazon
-          Drive, Microsoft One Drive, Hubic, Backblaze B2, Yandex Disk, or the local
-          filesystem.', markedDefault: false, versionName: 1.43.1}
-      - {description: 'Rclone is a command line program to sync files and directories
-          to and from: Google Drive, Amazon S3, Dropbox, Google Cloud Storage, Amazon
-          Drive, Microsoft One Drive, Hubic, Backblaze B2, Yandex Disk, or the local
-          filesystem.', markedDefault: false, versionName: 1.49.5}
+          filesystem.', markedDefault: false, versionName: 1.55.1}
       - {description: 'Rclone is a command line program to sync files and directories
           to and from: Google Drive, Amazon S3, Dropbox, Google Cloud Storage, Amazon
           Drive, Microsoft One Drive, Hubic, Backblaze B2, Yandex Disk, or the local
-          filesystem.', markedDefault: false, versionName: 1.55.1}
+          filesystem.', markedDefault: false, versionName: 1.59.1}
       - {description: 'Rclone is a command line program to sync files and directories
           to and from: Google Drive, Amazon S3, Dropbox, Google Cloud Storage, Amazon
           Drive, Microsoft One Drive, Hubic, Backblaze B2, Yandex Disk, or the local
-          filesystem.', markedDefault: false, versionName: 1.59.1}
+          filesystem.', markedDefault: false, versionName: 1.65.0}
     - categories: system, libs
       defaultVersionName: 2.3.3
       description: The libseccomp library provides an easy to use, platform independent,
@@ -2093,14 +2085,16 @@ software_modules:
       - {description: 'git-annex allows managing files with git, without checking
           the file contents into git.', markedDefault: false, versionName: '8.20210622'}
     - categories: system, tools
-      defaultVersionName: 0.9.1_py39
+      defaultVersionName: 0.10.0_py39
       description: matlab-proxy is a Python package which enables you to launch MATLAB
         and access it from a web browser.
       package: py-matlab-proxy
       url: https://github.com/mathworks/matlab-proxy
       versions:
       - {description: matlab-proxy is a Python package which enables you to launch
           MATLAB and access it from a web browser., markedDefault: false, versionName: 0.9.1_py39}
+      - {description: matlab-proxy is a Python package which enables you to launch
+          MATLAB and access it from a web browser., markedDefault: false, versionName: 0.10.0_py39}
     - categories: system, tools
       defaultVersionName: '20200731'
       description: Tools for working with Chromium development.
@@ -3736,6 +3730,9 @@ software_modules:
       versions:
       - {description: GEOS (Geometry Engine - Open Source) is a C++ port of Java Topology
           Suite (JTS)., markedDefault: false, versionName: 3.11.0}
+      - {description: GEOS is a C/C++ library for computational geometry with a focus
+          on algorithms used in geographic information systems (GIS) software., markedDefault: false,
+        versionName: 3.12.1}
       - {description: GEOS (Geometry Engine - Open Source) is a C++ port of Java Topology
           Suite (JTS)., markedDefault: true, versionName: 3.6.2}
     - categories: physics, astronomy
@@ -4502,6 +4499,9 @@ software_modules:
       - {description: kallisto is a program for quantifying abundances of transcripts
           from RNA-Seq data using high-throughput sequencing reads., markedDefault: false,
         versionName: 0.46.1}
+      - {description: kallisto is a program for quantifying abundances of transcripts
+          from RNA-Seq data using high-throughput sequencing reads., markedDefault: false,
+        versionName: 0.50.1}
       - {description: kallisto is a program for quantifying abundances of transcripts
           from RNA-Seq data using high-throughput sequencing reads., markedDefault: true,
         versionName: 0.44.0}
@@ -7015,7 +7015,7 @@ software_modules:
       versions:
       - {description: 'Jupyter is a browser-based interactive notebook for programming,
           mathematics, and data science. It supports a number of languages via plugins.',
-        markedDefault: false, versionName: 3.0.9_py36}
+        markedDefault: false, versionName: 2.3.2_py36}
       - {description: 'Jupyter is a browser-based interactive notebook for programming,
           mathematics, and data science. It supports a number of languages via plugins.',
         markedDefault: false, versionName: 4.0.8_py39}

diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml
@@ -5,6 +5,42 @@
 <description>Sherlock software update feed</description>
 <link>https://www.sherlock.stanford.edu/docs/software/list</link>
 <atom:link href="https://www.sherlock.stanford.edu/docs/software/updates.xml" rel="self" type="application/rss+xml"/>
+    <item>
+        <title>New version: physics/geos version 3.12.1</title>
+        <description>GEOS is a C/C++ library for computational geometry with a focus on algorithms used in geographic information systems (GIS) software.</description>
+        <link>https://libgeos.org</link>
+        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.12.1#geos</guid>
+        <category>physics, geoscience</category>
+        <author>[email protected] (Kilian Cavalotti)</author>
+        <pubDate>Tue, 12 Dec 2023 11:17:10 -0800</pubDate>
+    </item>
+    <item>
+        <title>New version: biology/kallisto version 0.50.1</title>
+        <description>kallisto is a program for quantifying abundances of transcripts from RNA-Seq data using high-throughput sequencing reads.</description>
+        <link>https://pachterlab.github.io/kallisto/</link>
+        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.50.1#kallisto</guid>
+        <category>biology, genomics</category>
+        <author>[email protected] (Kilian Cavalotti)</author>
+        <pubDate>Wed, 29 Nov 2023 13:50:00 -0800</pubDate>
+    </item>
+    <item>
+        <title>New version: system/py-matlab-proxy version 0.10.0_py39</title>
+        <description>matlab-proxy is a Python package which enables you to launch MATLAB and access it from a web browser.</description>
+        <link>https://github.com/mathworks/matlab-proxy</link>
+        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.10.0_py39#py-matlab-proxy</guid>
+        <category>system, tools</category>
+        <author>[email protected] (Kilian Cavalotti)</author>
+        <pubDate>Wed, 29 Nov 2023 10:37:32 -0800</pubDate>
+    </item>
+    <item>
+        <title>New version: system/rclone version 1.65.0</title>
+        <description>Rclone is a command line program to sync files and directories to and from</description>
+        <link>https://rclone.org</link>
+        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.65.0#rclone</guid>
+        <category>system, file transfer</category>
+        <author>[email protected] (Kilian Cavalotti)</author>
+        <pubDate>Tue, 28 Nov 2023 07:59:13 -0800</pubDate>
+    </item>
     <item>
         <title>New module: devel/darshan version 3.4.4</title>
         <description>Darshan is a scalable HPC I/O characterization tool.</description>
@@ -41,15 +77,6 @@
         <author>[email protected] (Kilian Cavalotti)</author>
         <pubDate>Thu, 16 Nov 2023 13:18:43 -0800</pubDate>
     </item>
-    <item>
-        <title>New module: devel/py-jupyterlab version 3.0.9_py36</title>
-        <description>Jupyter is a browser-based interactive notebook for programming, mathematics, and data science. It supports a number of languages via plugins.</description>
-        <link>https://jupyter.org</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.0.9_py36#py-jupyterlab</guid>
-        <category>devel, language</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Thu, 16 Nov 2023 13:18:22 -0800</pubDate>
-    </item>
     <item>
         <title>New module: devel/py-jupyterlab version 4.0.8_py39</title>
         <description>Jupyter is a browser-based interactive notebook for programming, mathematics, and data science. It supports a number of languages via plugins.</description>
@@ -212,68 +239,5 @@
         <author>[email protected] (Kilian Cavalotti)</author>
         <pubDate>Fri, 15 Sep 2023 08:08:08 -0700</pubDate>
     </item>
-    <item>
-        <title>New version: devel/rust version 1.72.0</title>
-        <description>A language empowering everyone to build reliable and efficient software.</description>
-        <link>https://www.rust-lang.org/</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.72.0#rust</guid>
-        <category>devel, language</category>
-        <author>[email protected] (Mike Hartman)</author>
-        <pubDate>Tue, 12 Sep 2023 12:48:07 -0700</pubDate>
-    </item>
-    <item>
-        <title>New module: biology/dorado version 0.3.4</title>
-        <description>Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.</description>
-        <link>https://github.com/nanoporetech/dorado</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.3.4#dorado</guid>
-        <category>biology, genomics</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Thu, 7 Sep 2023 08:58:33 -0700</pubDate>
-    </item>
-    <item>
-        <title>New module: biology/ncbi-vdb version 3.0.7</title>
-        <description>NCBI VDB is the database engine used by NCBI SRA tools.</description>
-        <link>https://github.com/ncbi/ncbi-vdb</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.0.7#ncbi-vdb</guid>
-        <category>biology, genomics</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Thu, 7 Sep 2023 08:55:47 -0700</pubDate>
-    </item>
-    <item>
-        <title>New version: devel/dotnet version 6.0.413</title>
-        <description>.NET is a free, cross-platform, open source developer platform for building many different types of applications.</description>
-        <link>https://dotnet.microsoft.com/</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=6.0.413#dotnet</guid>
-        <category>devel, framework</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Thu, 31 Aug 2023 13:44:20 -0700</pubDate>
-    </item>
-    <item>
-        <title>New version: biology/shapeit version 4.2.2</title>
-        <description>SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data.</description>
-        <link>https://odelaneau.github.io/shapeit4/</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=4.2.2#shapeit</guid>
-        <category>biology, genomics</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Tue, 29 Aug 2023 17:23:19 -0700</pubDate>
-    </item>
-    <item>
-        <title>New version: biology/sra-tools version 3.0.7</title>
-        <description>The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.</description>
-        <link>https://github.com/ncbi/sra-tools</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.0.7#sra-tools</guid>
-        <category>biology, genomics</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Tue, 29 Aug 2023 12:16:28 -0700</pubDate>
-    </item>
-    <item>
-        <title>New version: biology/freesurfer version 7.4.1</title>
-        <description>An open source software suite for processing and analyzing (human) brain MRI images.</description>
-        <link>https://surfer.nmr.mgh.harvard.edu/</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=7.4.1#freesurfer</guid>
-        <category>biology, neurology</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Mon, 28 Aug 2023 11:15:04 -0700</pubDate>
-    </item>
 </channel>
 </rss>
diff --git a/src/docs/user-guide/images/file_explorer_btn1.png b/src/docs/user-guide/images/file_explorer_btn1.png
diff --git a/src/docs/user-guide/images/file_explorer_btn2.png b/src/docs/user-guide/images/file_explorer_btn2.png
diff --git a/src/docs/user-guide/images/ood_code-server.png b/src/docs/user-guide/images/ood_code-server.png
diff --git a/src/docs/user-guide/images/ood_dashboard.png b/src/docs/user-guide/images/ood_dashboard.png
diff --git a/src/docs/user-guide/images/ood_juplab.png b/src/docs/user-guide/images/ood_juplab.png
diff --git a/src/docs/user-guide/images/ood_matlab.png b/src/docs/user-guide/images/ood_matlab.png
diff --git a/src/docs/user-guide/images/ood_rstudio.png b/src/docs/user-guide/images/ood_rstudio.png
diff --git a/src/docs/user-guide/images/ood_sess_support.png b/src/docs/user-guide/images/ood_sess_support.png
diff --git a/src/docs/user-guide/images/ood_shell.png b/src/docs/user-guide/images/ood_shell.png
diff --git a/src/docs/user-guide/images/ood_tb.png b/src/docs/user-guide/images/ood_tb.png
diff --git a/src/docs/user-guide/ondemand.md b/src/docs/user-guide/ondemand.md
@@ -320,7 +320,7 @@ To create a custom kernel for a virtual environment using Python 3.x:
 
     ```none
     $ pip3 install ipykernel
-    $ python3 -m install --user --name env --display-name "My Env"
+    $ python3 -m ipykernel install --user --name env --display-name "My Env"
     ```
 
     This will create a kernel for the environment `env`. It will appear as `My