From eb2f5fed90b2dc059760095617c0ca52eac36425 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Sun, 4 Feb 2024 23:24:05 -0800 Subject: [PATCH 01/15] docs: updated facts --- includes/data/facts.yml | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/includes/data/facts.yml b/includes/data/facts.yml index 86e6ddafa..fbcef96e9 100644 --- a/includes/data/facts.yml +++ b/includes/data/facts.yml @@ -2,9 +2,9 @@ facts: - name: users fields: - name: user accounts - value: 7048 + value: 7054 - name: PI groups - value: 1114 + value: 1115 desc: "from all Stanford's seven Schools, SLAC, Stanford Institutes, _etc._" - name: owner groups value: 201 @@ -41,7 +41,7 @@ facts: icon: plug fields: - name: kW - value: 575.14 + value: 564.70 desc: total power usage - name: PDUs value: 57 @@ -61,33 +61,33 @@ facts: value: 104 desc: across **2** Infiniband fabrics (EDR, HDR) - name: Infiniband cables - value: 5736 - desc: spanning about **30.22 km** + value: 5740 + desc: spanning about **30.23 km** - name: Ethernet switches value: 53 - name: scheduler icon: chart-bar fields: - name: Slurm partitions - value: 179 + value: 178 - name: CPU.hours/day - value: 48550 + value: 47065 desc: over **5 years** of computing in a single day - name: /month fmt: "${:,.0f}" - value: 3243922.1824 + value: 3144742.5536 desc: to run the same workload on t2.large on-demand cloud instances - name: partitions fields: - name: normal - nodes: 187 - cores: 5012 + nodes: 195 + cores: 5236 desc: compute nodes details: | - 57 nodes w/ 20-core (Intel E5-2640v4), 128 GB RAM, EDR IB - - 36 nodes w/ 24-core (Intel 5118), 191 GB RAM, EDR IB - - 24 nodes w/ 32-core (AMD 7543), 256 GB RAM, HDR IB + - 40 nodes w/ 24-core (Intel 5118), 191 GB RAM, EDR IB + - 28 nodes w/ 32-core (AMD 7543), 256 GB RAM, HDR IB - 70 nodes w/ 32-core (AMD 7502), 256 GB RAM, HDR IB access: public - name: dev @@ -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: 1501 - cores: 48872 + nodes: 1493 + cores: 48648 desc: privately-owned nodes details: | - 146 nodes w/ 20-core (Intel E5-2640v4), 128 GB RAM, EDR IB @@ -142,12 +142,12 @@ facts: - 1 nodes w/ 20-core (Intel E5-2640v4), 512 GB RAM, EDR IB, 8x Geforce TITAN_Xp GPUs - 2 nodes w/ 20-core (Intel E5-2640v4), 512 GB RAM, EDR IB, 8x Geforce TITAN_V GPUs - 2 nodes w/ 20-core (Intel E5-2640v4), 1024 GB RAM, EDR IB, 4x Geforce TITAN_Xp GPUs - - 348 nodes w/ 24-core (Intel 5118), 191 GB RAM, EDR IB + - 344 nodes w/ 24-core (Intel 5118), 191 GB RAM, EDR IB - 2 nodes w/ 24-core (Intel 5118), 191 GB RAM, EDR IB, 4x Tesla V100 PCIe GPUs - 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 - - 264 nodes w/ 32-core (AMD 7543), 256 GB RAM, HDR IB + - 260 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 From aa1e5dab93cbfb6f2c6f46a5c4e32bfa9abc5052 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Mon, 5 Feb 2024 10:13:18 -0800 Subject: [PATCH 02/15] docs: updated software list --- includes/data/software.yml | 916 +++++++++++++++++----------------- src/docs/software/updates.xml | 63 +-- 2 files changed, 495 insertions(+), 484 deletions(-) diff --git a/includes/data/software.yml b/includes/data/software.yml index c102e55c2..53a1a6156 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -325,15 +325,16 @@ software_modules: versions: - {description: GNU Midnight Commander is a visual file manager., markedDefault: false, versionName: 4.8.29} - - categories: system, libs - defaultVersionName: 1.8.2 - description: Libgcrypt is a general purpose cryptographic library originally - based on code from GnuPG. - package: libgcrypt - url: https://www.gnupg.org/software/libgcrypt + - categories: system, compression + defaultVersionName: 1.5.2 + description: Zstandard, or zstd, is a fast lossless compression algorithm, targeting + real-time compression scenarios at zlib-level and better compression ratios. + package: zstd + url: https://github.com/facebook/zstd versions: - - {description: Libgcrypt is a general purpose cryptographic library originally - based on code from GnuPG., markedDefault: false, versionName: 1.8.2} + - {description: 'Zstandard, or zstd, is a fast lossless compression algorithm, + targeting real-time compression scenarios at zlib-level and better compression + ratios.', markedDefault: false, versionName: 1.5.2} - categories: system, tools defaultVersionName: 2.2.3 description: Expat is a stream-oriented XML parser library written in C. @@ -342,18 +343,16 @@ software_modules: versions: - {description: Expat is a stream-oriented XML parser library written in C., markedDefault: false, versionName: 2.2.3} - - categories: system, job management - defaultVersionName: 1.1.2 - description: DRMAA for Slurm Workload Manager (Slurm) is an implementation of - Open Grid Forum Distributed Resource Management Application API (DRMAA) version - 1 for submission and control of jobs to Slurm. - package: slurm-drmaa - url: https://github.com/natefoo/slurm-drmaa + - categories: system, libs + defaultVersionName: 2.3.3 + description: The libseccomp library provides an easy to use, platform independent, + interface to the Linux Kernel's syscall filtering mechanism.. + package: libseccomp + url: https://github.com/seccomp/libseccomp versions: - - {description: DRMAA for Slurm Workload Manager (Slurm) is an implementation - of Open Grid Forum Distributed Resource Management Application API (DRMAA) - version 1 for submission and control of jobs to Slurm., markedDefault: false, - versionName: 1.1.2} + - {description: 'The libseccomp library provides an easy to use, platform independent, + interface to the Linux Kernel''s syscall filtering mechanism..', markedDefault: false, + versionName: 2.3.3} - categories: system, document management defaultVersionName: 2.7.3 description: Pandoc is a universal document converter. @@ -526,15 +525,17 @@ software_modules: versions: - {description: libuv is a multi-platform support library with a focus on asynchronous I/O., markedDefault: false, versionName: 1.38.1} - - categories: system, libs - defaultVersionName: 1.14.10 - description: Cairo is a 2D graphics library with support for multiple output - devices. - package: cairo - url: https://www.cairographics.org/ - versions: - - {description: Cairo is a 2D graphics library with support for multiple output - devices., markedDefault: false, versionName: 1.14.10} + - categories: system, containers + defaultVersionName: 0.3.13_py312 + description: Singularity Python (spython) is the Python API for working with + Singularity containers. + package: py-spython + url: https://github.com/singularityhub/singularity-cli + versions: + - {description: Singularity Python (spython) is the Python API for working with + Singularity containers., markedDefault: false, versionName: 0.3.13_py39} + - {description: Singularity Python (spython) is the Python API for working with + Singularity containers., markedDefault: false, versionName: 0.3.13_py312} - categories: system, tools defaultVersionName: 2.3.7 description: Motif is the toolkit for the Common Desktop Environment. @@ -626,24 +627,23 @@ software_modules: versions: - {description: GD is an open source code library for the dynamic creation of images by programmers., markedDefault: false, versionName: 2.2.5} - - categories: system, tools - defaultVersionName: '1.6' - description: jq is a lightweight and flexible command-line JSON processor. - package: jq - url: https://stedolan.github.io/jq/ + - categories: system, libs + defaultVersionName: 2.13.1 + description: C library for encoding, decoding and manipulating JSON data. + package: jansson + url: https://github.com/akheron/jansson versions: - - {description: jq is a lightweight and flexible command-line JSON processor., - markedDefault: false, versionName: '1.6'} + - {description: 'C library for encoding, decoding and manipulating JSON data.', + markedDefault: false, versionName: 2.13.1} - categories: system, libs - defaultVersionName: '8.40' - description: The PCRE library is a set of functions that implement regular expression - pattern matching using the same syntax and semantics as Perl 5. - package: pcre - url: http://www.pcre.org/ + defaultVersionName: 0.7.0 + description: yaml-cpp is a YAML parser and emitter in C++ matching the YAML + 1.2 spec. + package: yaml-cpp + url: https://github.com/jbeder/yaml-cpp versions: - - {description: The PCRE library is a set of functions that implement regular - expression pattern matching using the same syntax and semantics as Perl - 5., markedDefault: false, versionName: '8.40'} + - {description: yaml-cpp is a YAML parser and emitter in C++ matching the YAML + 1.2 spec., markedDefault: false, versionName: 0.7.0} - categories: system, libs defaultVersionName: '6.4' description: The ncurses (new curses) library is a free software emulation of @@ -691,14 +691,14 @@ software_modules: - {description: 'FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created.', markedDefault: false, versionName: '5.0'} - - categories: system, libs - defaultVersionName: 0.3.5 - description: C++ implementation of the Google logging module. - package: glog - url: https://github.com/google/glog + - categories: system, tools + defaultVersionName: 1.7.4 + description: Simple password manager using gpg and ordinary unix directories. + package: password-store + url: https://www.passwordstore.org/ versions: - - {description: C++ implementation of the Google logging module., markedDefault: false, - versionName: 0.3.5} + - {description: Simple password manager using gpg and ordinary unix directories., + markedDefault: false, versionName: 1.7.4} - categories: system, tools defaultVersionName: 8.4.0 description: curl is an open source command line tool and library for transferring @@ -995,14 +995,23 @@ software_modules: properties: arch: {gpu: 1} versionName: 2.2.18.04.06 - - categories: system, tools - defaultVersionName: 1.7.4 - description: Simple password manager using gpg and ordinary unix directories. - package: password-store - url: https://www.passwordstore.org/ + - categories: system, libs + defaultVersionName: 1.14.10 + description: Cairo is a 2D graphics library with support for multiple output + devices. + package: cairo + url: https://www.cairographics.org/ versions: - - {description: Simple password manager using gpg and ordinary unix directories., - markedDefault: false, versionName: 1.7.4} + - {description: Cairo is a 2D graphics library with support for multiple output + devices., markedDefault: false, versionName: 1.14.10} + - categories: system, libs + defaultVersionName: 0.6.21 + description: A library for parsing, editing, and saving EXIF data. + package: libexif + url: https://github.com/libexif/libexif + versions: + - {description: 'A library for parsing, editing, and saving EXIF data.', markedDefault: false, + versionName: 0.6.21} - categories: system, file transfer defaultVersionName: 3.19.0_py39 description: A command line wrapper over the Globus SDK for Python. @@ -1055,15 +1064,6 @@ software_modules: - {description: The Portable Hardware Locality (hwloc) software package provides a portable abstraction of the hierarchical topology of modern architectures., markedDefault: false, versionName: 2.9.3} - - categories: system, compression - defaultVersionName: '16.02' - description: p7zip is a Linux port of 7zip, a file archiver with high compression - ratio. - package: p7zip - url: https://sourceforge.net/projects/p7zip/ - versions: - - {description: 'p7zip is a Linux port of 7zip, a file archiver with high compression - ratio.', markedDefault: false, versionName: '16.02'} - categories: system, libs defaultVersionName: 1.4.4 description: JSON-GLib is a library providing serialization and deserialization @@ -1075,15 +1075,14 @@ software_modules: - {description: JSON-GLib is a library providing serialization and deserialization support for the JavaScript Object Notation (JSON) format described by RFC 4627., markedDefault: false, versionName: 1.4.4} - - categories: system, libs - defaultVersionName: 2.36.8 - description: The GdkPixbuf library provides facilities for loading images in - a variety of file formats. - package: gdk-pixbuf - url: https://git.gnome.org/browse/gdk-pixbuf + - categories: system, compression + defaultVersionName: 1.8.0 + description: LZ4 is lossless compression algorithm. + package: lz4 + url: https://www.lz4.org versions: - - {description: The GdkPixbuf library provides facilities for loading images - in a variety of file formats., markedDefault: false, versionName: 2.36.8} + - {description: LZ4 is lossless compression algorithm., markedDefault: false, + versionName: 1.8.0} - categories: system, language defaultVersionName: 8.6.6 description: Tcl (Tool Command Language) is a dynamic programming language, @@ -1096,24 +1095,31 @@ software_modules: suitable for web and desktop applications, networking, administration, testing. Tk is a graphical user interface toolkit.', markedDefault: false, versionName: 8.6.6} - categories: system, libs - defaultVersionName: 1.7.7 - description: Scalable I/O library for parallel access to task-local files. - package: sionlib - url: https://www.fz-juelich.de/en/ias/jsc/services/user-support/jsc-software-tools/sionlib + defaultVersionName: 2.36.8 + description: The GdkPixbuf library provides facilities for loading images in + a variety of file formats. + package: gdk-pixbuf + url: https://git.gnome.org/browse/gdk-pixbuf versions: - - description: Scalable I/O library for parallel access to task-local files. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 1.7.7 - - categories: system, libs - defaultVersionName: 2.9.91 - description: GConf is a system for storing application preferences. - package: gconf - url: https://projects.gnome.org/gconf + - {description: The GdkPixbuf library provides facilities for loading images + in a variety of file formats., markedDefault: false, versionName: 2.36.8} + - categories: system, tools + defaultVersionName: 1.3.26 + description: GraphicsMagick is the swiss army knife of image processing. + package: graphicsmagick + url: http://www.graphicsmagick.org/ versions: - - {description: GConf is a system for storing application preferences., markedDefault: false, - versionName: 2.9.91} + - {description: GraphicsMagick is the swiss army knife of image processing., + markedDefault: false, versionName: 1.3.26} + - categories: system, compression + defaultVersionName: '2.4' + description: A parallel implementation of gzip for modern multi-processor, multi-core + machines. + package: pigz + url: https://zlib.net/pigz/ + versions: + - {description: 'A parallel implementation of gzip for modern multi-processor, + multi-core machines.', markedDefault: false, versionName: '2.4'} - categories: system, libs defaultVersionName: 1.6.3 description: The Apache Portable Runtime is a supporting library for the Apache @@ -1141,15 +1147,6 @@ software_modules: versions: - {description: Remora is a tool to monitor runtime resource utilization., markedDefault: false, versionName: 1.8.5} - - categories: system, compression - defaultVersionName: '2.4' - description: A parallel implementation of gzip for modern multi-processor, multi-core - machines. - package: pigz - url: https://zlib.net/pigz/ - versions: - - {description: 'A parallel implementation of gzip for modern multi-processor, - multi-core machines.', markedDefault: false, versionName: '2.4'} - categories: system, libs defaultVersionName: 1.52.1 description: GObject introspection is a middleware layer between C libraries @@ -1159,6 +1156,14 @@ software_modules: versions: - {description: GObject introspection is a middleware layer between C libraries (using GObject) and language bindings., markedDefault: false, versionName: 1.52.1} + - categories: system, libs + defaultVersionName: 2.9.91 + description: GConf is a system for storing application preferences. + package: gconf + url: https://projects.gnome.org/gconf + versions: + - {description: GConf is a system for storing application preferences., markedDefault: false, + versionName: 2.9.91} - categories: system, file transfer defaultVersionName: 3.2.1_py39 description: HTTPie is a command-line HTTP client designed for testing, debugging, @@ -1169,15 +1174,6 @@ software_modules: - {description: 'HTTPie is a command-line HTTP client designed for testing, debugging, and generally interacting with APIs and HTTP servers.', markedDefault: false, versionName: 3.2.1_py39} - - categories: system, libs - defaultVersionName: 0.7.0 - description: yaml-cpp is a YAML parser and emitter in C++ matching the YAML - 1.2 spec. - package: yaml-cpp - url: https://github.com/jbeder/yaml-cpp - versions: - - {description: yaml-cpp is a YAML parser and emitter in C++ matching the YAML - 1.2 spec., markedDefault: false, versionName: 0.7.0} - categories: system, libs defaultVersionName: 1.6.1 description: The Apache Portable Runtime is a supporting library for the Apache @@ -1189,6 +1185,22 @@ software_modules: - {description: The Apache Portable Runtime is a supporting library for the Apache web server. It provides a set of APIs that map to the underlying operating system., markedDefault: false, versionName: 1.6.1} + - categories: system, compression + defaultVersionName: 3.5.2 + description: The libarchive project develops a portable, efficient C library + that can read and write streaming archives in a variety of formats. + package: libarchive + url: https://www.libarchive.org/ + versions: + - {description: 'The libarchive project develops a portable, efficient C library + that can read and write streaming archives in a variety of formats.', markedDefault: false, + versionName: 3.3.2} + - {description: 'The libarchive project develops a portable, efficient C library + that can read and write streaming archives in a variety of formats.', markedDefault: false, + versionName: 3.4.2} + - {description: 'The libarchive project develops a portable, efficient C library + that can read and write streaming archives in a variety of formats.', markedDefault: false, + versionName: 3.5.2} - categories: system, libs defaultVersionName: '1.16' description: Library for parsing command line options. @@ -1204,18 +1216,6 @@ software_modules: url: https://gitlab.freedesktop.org/xorg/lib/libpciaccess versions: - {description: Generic PCI access library., markedDefault: false, versionName: '0.16'} - - categories: system, cloud interface - defaultVersionName: 448.0.0 - description: Command-line interface for Google Cloud Platform products and services. - package: google-cloud-sdk - url: https://cloud.google.com/sdk - versions: - - {description: Command-line interface for Google Cloud Platform products and - services., markedDefault: false, versionName: 338.0.0} - - {description: Command-line interface for Google Cloud Platform products and - services., markedDefault: false, versionName: 400.0.0} - - {description: Command-line interface for Google Cloud Platform products and - services., markedDefault: false, versionName: 448.0.0} - categories: system, file management defaultVersionName: 2.8.0 description: rmlint finds space waste and other broken things on your filesystem @@ -1225,30 +1225,37 @@ software_modules: versions: - {description: rmlint finds space waste and other broken things on your filesystem and offers to remove it., markedDefault: false, versionName: 2.8.0} - - categories: system, compression - defaultVersionName: 3.5.2 - description: The libarchive project develops a portable, efficient C library - that can read and write streaming archives in a variety of formats. - package: libarchive - url: https://www.libarchive.org/ + - categories: system, tools + defaultVersionName: '1.6' + description: jq is a lightweight and flexible command-line JSON processor. + package: jq + url: https://stedolan.github.io/jq/ versions: - - {description: 'The libarchive project develops a portable, efficient C library - that can read and write streaming archives in a variety of formats.', markedDefault: false, - versionName: 3.3.2} - - {description: 'The libarchive project develops a portable, efficient C library - that can read and write streaming archives in a variety of formats.', markedDefault: false, - versionName: 3.4.2} - - {description: 'The libarchive project develops a portable, efficient C library - that can read and write streaming archives in a variety of formats.', markedDefault: false, - versionName: 3.5.2} + - {description: jq is a lightweight and flexible command-line JSON processor., + markedDefault: false, versionName: '1.6'} - categories: system, libs - defaultVersionName: '1.0' - description: Implementation of a minimal subset of the PMI1 and PMI2 specifications. - package: minipmi - url: https://github.com/kraused/minipmi + defaultVersionName: 1.6.29 + description: libpng is the official PNG reference library. It supports almost + all PNG features, is extensible, and has been extensively tested for over + 20 years. + package: libpng + url: http://libpng.sourceforge.net versions: - - {description: Implementation of a minimal subset of the PMI1 and PMI2 specifications., - markedDefault: false, versionName: '1.0'} + - {description: 'libpng is the official PNG reference library. It supports almost + all PNG features, is extensible, and has been extensively tested for over + 20 years.', markedDefault: false, versionName: 1.2.57} + - {description: 'libpng is the official PNG reference library. It supports almost + all PNG features, is extensible, and has been extensively tested for over + 20 years.', markedDefault: false, versionName: 1.6.29} + - categories: system, document processing + defaultVersionName: 9.53.2 + description: Ghostscript is an interpreter for the PostScript language and PDF + files. + package: ghostscript + url: https://ghostcript.com + versions: + - {description: Ghostscript is an interpreter for the PostScript language and + PDF files., markedDefault: false, versionName: 9.53.2} - categories: system, tools defaultVersionName: 7.0.7-2 description: ImageMagick is a free and open-source software suite for displaying, @@ -1259,26 +1266,22 @@ software_modules: - {description: 'ImageMagick is a free and open-source software suite for displaying, converting, and editing raster image and vector image files.', markedDefault: false, versionName: 7.0.7-2} - - categories: system, document processing - defaultVersionName: 9.53.2 - description: Ghostscript is an interpreter for the PostScript language and PDF - files. - package: ghostscript - url: https://ghostcript.com + - categories: system, libs + defaultVersionName: 2.61.2 + description: libsoup is an HTTP client/server library for GNOME. + package: libsoup + url: https://wiki.gnome.org/LibSoup versions: - - {description: Ghostscript is an interpreter for the PostScript language and - PDF files., markedDefault: false, versionName: 9.53.2} + - {description: libsoup is an HTTP client/server library for GNOME., markedDefault: false, + versionName: 2.61.2} - categories: system, libs - defaultVersionName: 0.9.1 - description: libxkbcommon is a keyboard keymap compiler and support library - which processes a reduced subset of keymaps as defined by the XKB (X Keyboard - Extension) specification. - package: libxkbcommon - url: https://github.com/xkbcommon/libxkbcommon + defaultVersionName: '1.0' + description: Implementation of a minimal subset of the PMI1 and PMI2 specifications. + package: minipmi + url: https://github.com/kraused/minipmi versions: - - {description: libxkbcommon is a keyboard keymap compiler and support library - which processes a reduced subset of keymaps as defined by the XKB (X Keyboard - Extension) specification., markedDefault: false, versionName: 0.9.1} + - {description: Implementation of a minimal subset of the PMI1 and PMI2 specifications., + markedDefault: false, versionName: '1.0'} - categories: system, scm defaultVersionName: 1.1.0 description: libgit2 is a portable, pure C implementation of the Git core methods @@ -1299,14 +1302,15 @@ software_modules: - {description: LZO is a portable lossless data compression library written in ANSI C., markedDefault: false, versionName: '2.10'} - categories: system, libs - defaultVersionName: 1.2.0 - description: libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL - API calls between multiple vendors. - package: libglvnd - url: https://github.com/NVIDIA/libglvnd + defaultVersionName: 0.8.14 + description: The libIDL package contains libraries for Interface Definition + Language files. This is a specification for defining portable interfaces. + package: libidl + url: https://github.com/GNOME/libIDL versions: - - {description: libglvnd is a vendor-neutral dispatch layer for arbitrating - OpenGL API calls between multiple vendors., markedDefault: false, versionName: 1.2.0} + - {description: The libIDL package contains libraries for Interface Definition + Language files. This is a specification for defining portable interfaces., + markedDefault: false, versionName: 0.8.14} - categories: system, libs defaultVersionName: 2.52.3 description: The GLib library provides core non-graphical functionality such @@ -1318,15 +1322,15 @@ software_modules: - {description: 'The GLib library provides core non-graphical functionality such as high level data types, Unicode manipulation, and an object and type system to C programs.', markedDefault: false, versionName: 2.52.3} - - categories: system, cloud interface - defaultVersionName: 2.0.50 - description: This package provides a unified command line interface to Amazon - Web Services. - package: aws-cli - url: https://github.com/aws/aws-cli + - categories: system, libs + defaultVersionName: 1.2.0 + description: libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL + API calls between multiple vendors. + package: libglvnd + url: https://github.com/NVIDIA/libglvnd versions: - - {description: This package provides a unified command line interface to Amazon - Web Services., markedDefault: false, versionName: 2.0.50} + - {description: libglvnd is a vendor-neutral dispatch layer for arbitrating + OpenGL API calls between multiple vendors., markedDefault: false, versionName: 1.2.0} - categories: system, libs defaultVersionName: 1.0.3 description: Portable uuid C library. @@ -1334,16 +1338,17 @@ software_modules: url: https://sourceforge.net/projects/libuuid versions: - {description: Portable uuid C library., markedDefault: false, versionName: 1.0.3} - - categories: system, compiler - defaultVersionName: 1.3.3 - description: MRC is a resource compiler that can create self-contained applications, - by including all the required data inside executable files. - package: mrc - url: https://github.com/mhekkel/mrc + - categories: system, benchmark + defaultVersionName: '3.2' + description: 'Heavy Peer To Peer: a MPI based benchmark for network diagnostic.' + package: hp2p + url: https://github.com/cea-hpc/hp2p versions: - - {description: 'MRC is a resource compiler that can create self-contained applications, - by including all the required data inside executable files.', markedDefault: false, - versionName: 1.3.3} + - description: 'Heavy Peer To Peer: a MPI based benchmark for network diagnostic.' + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '3.2' - categories: system, libs defaultVersionName: 2.1.14 description: talloc is a hierarchical, reference counted memory pool system @@ -1353,23 +1358,18 @@ software_modules: versions: - {description: 'talloc is a hierarchical, reference counted memory pool system with destructors.', markedDefault: false, versionName: 2.1.14} - - categories: system, compression - defaultVersionName: 1.5.1 - description: libzip is a C library for reading, creating, and modifying zip - archives. - package: libzip - url: http://libzip.org - versions: - - {description: 'libzip is a C library for reading, creating, and modifying - zip archives.', markedDefault: false, versionName: 1.5.1} - - categories: system, libs - defaultVersionName: 2.61.2 - description: libsoup is an HTTP client/server library for GNOME. - package: libsoup - url: https://wiki.gnome.org/LibSoup + - categories: system, cloud interface + defaultVersionName: 448.0.0 + description: Command-line interface for Google Cloud Platform products and services. + package: google-cloud-sdk + url: https://cloud.google.com/sdk versions: - - {description: libsoup is an HTTP client/server library for GNOME., markedDefault: false, - versionName: 2.61.2} + - {description: Command-line interface for Google Cloud Platform products and + services., markedDefault: false, versionName: 338.0.0} + - {description: Command-line interface for Google Cloud Platform products and + services., markedDefault: false, versionName: 400.0.0} + - {description: Command-line interface for Google Cloud Platform products and + services., markedDefault: false, versionName: 448.0.0} - categories: system, libs defaultVersionName: 1.12.0 description: GStreamer is a library for constructing graphs of media-handling @@ -1379,6 +1379,14 @@ software_modules: versions: - {description: GStreamer is a library for constructing graphs of media-handling components., markedDefault: false, versionName: 1.12.0} + - categories: system, libs + defaultVersionName: 2.9.4 + description: Libxml2 is a XML C parser and toolkit. + package: libxml2 + url: http://xmlsoft.org/ + versions: + - {description: Libxml2 is a XML C parser and toolkit., markedDefault: false, + versionName: 2.9.4} - categories: system, libs defaultVersionName: 3.0.4 description: wxWidgets is a C++ library that lets developers create applications @@ -1409,39 +1417,49 @@ software_modules: - {description: 'Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server.', markedDefault: false, versionName: 2.4.0} - - categories: system, compression - defaultVersionName: 5.2.3 - description: XZ Utils, the successor to LZMA Utils, is free general-purpose - data compression software with a high compression ratio. - package: xz - url: http://tukaani.org/xz/ + - categories: system, job management + defaultVersionName: 1.1.2 + description: DRMAA for Slurm Workload Manager (Slurm) is an implementation of + Open Grid Forum Distributed Resource Management Application API (DRMAA) version + 1 for submission and control of jobs to Slurm. + package: slurm-drmaa + url: https://github.com/natefoo/slurm-drmaa versions: - - {description: 'XZ Utils, the successor to LZMA Utils, is free general-purpose - data compression software with a high compression ratio.', markedDefault: false, - versionName: 5.2.3} - - categories: system, compression - defaultVersionName: 1.5.2 - description: Zstandard, or zstd, is a fast lossless compression algorithm, targeting - real-time compression scenarios at zlib-level and better compression ratios. - package: zstd - url: https://github.com/facebook/zstd + - {description: DRMAA for Slurm Workload Manager (Slurm) is an implementation + of Open Grid Forum Distributed Resource Management Application API (DRMAA) + version 1 for submission and control of jobs to Slurm., markedDefault: false, + versionName: 1.1.2} + - categories: system, libs + defaultVersionName: 2.1.2 + description: FTGL is a free cross-platform Open Source C++ library that uses + Freetype2 to simplify rendering fonts in OpenGL applications. + package: ftgl + url: https://sourceforge.net/projects/ftgl/ versions: - - {description: 'Zstandard, or zstd, is a fast lossless compression algorithm, - targeting real-time compression scenarios at zlib-level and better compression - ratios.', markedDefault: false, versionName: 1.5.2} + - {description: FTGL is a free cross-platform Open Source C++ library that uses + Freetype2 to simplify rendering fonts in OpenGL applications., markedDefault: false, + versionName: 2.1.2} - categories: system, libs - defaultVersionName: 4.0.8 - description: libtiff provides support for the Tag Image File Format (TIFF), - a widely used format for storing image data. - package: libtiff - url: http://simplesystems.org/libtiff/ + defaultVersionName: 1.7.7 + description: Scalable I/O library for parallel access to task-local files. + package: sionlib + url: https://www.fz-juelich.de/en/ias/jsc/services/user-support/jsc-software-tools/sionlib versions: - - {description: 'libtiff provides support for the Tag Image File Format (TIFF), - a widely used format for storing image data.', markedDefault: false, versionName: 4.4.0} - - {description: 'libtiff provides support for the Tag Image File Format (TIFF), - a widely used format for storing image data.', markedDefault: false, versionName: 4.5.0} - - {description: 'libtiff provides support for the Tag Image File Format (TIFF), - a widely used format for storing image data.', markedDefault: true, versionName: 4.0.8} + - description: Scalable I/O library for parallel access to task-local files. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.7.7 + - categories: system, scm + defaultVersionName: 2.0.696 + description: Secure, cross-platform Git credential storage with authentication + to GitHub, Azure Repos, and other popular Git hosting services. + package: git-credential-manager + url: https://github.com/GitCredentialManager/git-credential-manager + versions: + - {description: 'Secure, cross-platform Git credential storage with authentication + to GitHub, Azure Repos, and other popular Git hosting services.', markedDefault: false, + versionName: 2.0.696} - categories: system, libs defaultVersionName: 1.0.12 description: The Free Implementation of the Unicode Bidirectional Algorithm. @@ -1450,20 +1468,6 @@ software_modules: versions: - {description: The Free Implementation of the Unicode Bidirectional Algorithm., markedDefault: false, versionName: 1.0.12} - - categories: system, libs - defaultVersionName: 1.6.29 - description: libpng is the official PNG reference library. It supports almost - all PNG features, is extensible, and has been extensively tested for over - 20 years. - package: libpng - url: http://libpng.sourceforge.net - versions: - - {description: 'libpng is the official PNG reference library. It supports almost - all PNG features, is extensible, and has been extensively tested for over - 20 years.', markedDefault: false, versionName: 1.2.57} - - {description: 'libpng is the official PNG reference library. It supports almost - all PNG features, is extensible, and has been extensively tested for over - 20 years.', markedDefault: false, versionName: 1.6.29} - categories: system, libs defaultVersionName: 2.0.3 description: THE reference library for reading, displaying, writing and examining @@ -1503,15 +1507,16 @@ software_modules: -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.', markedDefault: false, versionName: 1.2.11} - - categories: system, libs - defaultVersionName: 2.14.19 - description: ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) featuring - mature C, C++ and Python bindings. - package: orbit - url: https://projects.gnome.org/ORBit2 + - categories: system, scm + defaultVersionName: 1.12.2 + description: Subversion is an open source version control system. + package: subversion + url: https://subversion.apache.org/ versions: - - {description: 'ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) - featuring mature C, C++ and Python bindings.', markedDefault: false, versionName: 2.14.19} + - {description: Subversion is an open source version control system., markedDefault: false, + versionName: 1.9.7} + - {description: Subversion is an open source version control system., markedDefault: false, + versionName: 1.12.2} - categories: system, document processing defaultVersionName: 0.47.0 description: Poppler is a PDF rendering library. @@ -1536,25 +1541,22 @@ software_modules: versions: - {description: C-based implementation of the GDI+ API, markedDefault: false, versionName: '5.6'} - - categories: system, scm - defaultVersionName: 1.12.2 - description: Subversion is an open source version control system. - package: subversion - url: https://subversion.apache.org/ + - categories: system, libs + defaultVersionName: 2.14.19 + description: ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) featuring + mature C, C++ and Python bindings. + package: orbit + url: https://projects.gnome.org/ORBit2 versions: - - {description: Subversion is an open source version control system., markedDefault: false, - versionName: 1.9.7} - - {description: Subversion is an open source version control system., markedDefault: false, - versionName: 1.12.2} - - categories: system, file management - defaultVersionName: 2.2.1 - description: FDUPES is a program for identifying or deleting duplicate files - residing within specified directories. - package: fdupes - url: https://github.com/adrianlopezroche/fdupes + - {description: 'ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) + featuring mature C, C++ and Python bindings.', markedDefault: false, versionName: 2.14.19} + - categories: system, libs + defaultVersionName: 1.6.2 + description: Hunspell is a spell checker. + package: hunspell + url: https://hunspell.github.io/ versions: - - {description: FDUPES is a program for identifying or deleting duplicate files - residing within specified directories., markedDefault: false, versionName: 2.2.1} + - {description: Hunspell is a spell checker., markedDefault: false, versionName: 1.6.2} - categories: system, libs defaultVersionName: 0.6.13 description: Libcroco is a standalone css2 parsing and manipulation library. @@ -1573,13 +1575,6 @@ software_modules: - {description: 'GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them.', markedDefault: false, versionName: 3.5.9} - - categories: system, libs - defaultVersionName: 1.6.2 - description: Hunspell is a spell checker. - package: hunspell - url: https://hunspell.github.io/ - versions: - - {description: Hunspell is a spell checker., markedDefault: false, versionName: 1.6.2} - categories: system, tools defaultVersionName: '7.7' description: The X.Org project provides an open source implementation of the @@ -1589,6 +1584,15 @@ software_modules: versions: - {description: The X.Org project provides an open source implementation of the X Window System., markedDefault: false, versionName: '7.7'} + - categories: system, file management + defaultVersionName: 2.2.1 + description: FDUPES is a program for identifying or deleting duplicate files + residing within specified directories. + package: fdupes + url: https://github.com/adrianlopezroche/fdupes + versions: + - {description: FDUPES is a program for identifying or deleting duplicate files + residing within specified directories., markedDefault: false, versionName: 2.2.1} - categories: system, tools defaultVersionName: '20200822' description: GNU parallel is a shell tool for executing jobs in parallel using @@ -1870,14 +1874,6 @@ software_modules: - {description: 'The IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line.', markedDefault: false, versionName: 3.9.6} - - categories: system, tools - defaultVersionName: 1.3.26 - description: GraphicsMagick is the swiss army knife of image processing. - package: graphicsmagick - url: http://www.graphicsmagick.org/ - versions: - - {description: GraphicsMagick is the swiss army knife of image processing., - markedDefault: false, versionName: 1.3.26} - categories: system, libs defaultVersionName: 2.24.0 description: ATK is the Accessibility Toolkit. It provides a set of generic @@ -1889,6 +1885,15 @@ software_modules: - {description: ATK is the Accessibility Toolkit. It provides a set of generic interfaces allowing accessibility technologies such as screen readers to interact with a graphical user interface., markedDefault: false, versionName: 2.24.0} + - categories: system, libs + defaultVersionName: 1.8.2 + description: Libgcrypt is a general purpose cryptographic library originally + based on code from GnuPG. + package: libgcrypt + url: https://www.gnupg.org/software/libgcrypt + versions: + - {description: Libgcrypt is a general purpose cryptographic library originally + based on code from GnuPG., markedDefault: false, versionName: 1.8.2} - categories: system, resource monitoring defaultVersionName: 3.0.2 description: Nvtop stands for NVidia TOP, a (h)top like task monitor for NVIDIA @@ -1915,15 +1920,18 @@ software_modules: arch: {gpu: 1} versionName: 3.0.2 - categories: system, libs - defaultVersionName: 2.3.3 - description: The libseccomp library provides an easy to use, platform independent, - interface to the Linux Kernel's syscall filtering mechanism.. - package: libseccomp - url: https://github.com/seccomp/libseccomp + defaultVersionName: 4.0.8 + description: libtiff provides support for the Tag Image File Format (TIFF), + a widely used format for storing image data. + package: libtiff + url: http://simplesystems.org/libtiff/ versions: - - {description: 'The libseccomp library provides an easy to use, platform independent, - interface to the Linux Kernel''s syscall filtering mechanism..', markedDefault: false, - versionName: 2.3.3} + - {description: 'libtiff provides support for the Tag Image File Format (TIFF), + a widely used format for storing image data.', markedDefault: false, versionName: 4.4.0} + - {description: 'libtiff provides support for the Tag Image File Format (TIFF), + a widely used format for storing image data.', markedDefault: false, versionName: 4.5.0} + - {description: 'libtiff provides support for the Tag Image File Format (TIFF), + a widely used format for storing image data.', markedDefault: true, versionName: 4.0.8} - categories: system, libs defaultVersionName: 3.0.7 description: OpenSSL is a full-featured toolkit for general-purpose cryptography @@ -1933,16 +1941,16 @@ software_modules: versions: - {description: OpenSSL is a full-featured toolkit for general-purpose cryptography and secure communication., markedDefault: false, versionName: 3.0.7} - - categories: system, libs - defaultVersionName: 2.1.2 - description: FTGL is a free cross-platform Open Source C++ library that uses - Freetype2 to simplify rendering fonts in OpenGL applications. - package: ftgl - url: https://sourceforge.net/projects/ftgl/ + - categories: system, compression + defaultVersionName: 5.2.3 + description: XZ Utils, the successor to LZMA Utils, is free general-purpose + data compression software with a high compression ratio. + package: xz + url: http://tukaani.org/xz/ versions: - - {description: FTGL is a free cross-platform Open Source C++ library that uses - Freetype2 to simplify rendering fonts in OpenGL applications., markedDefault: false, - versionName: 2.1.2} + - {description: 'XZ Utils, the successor to LZMA Utils, is free general-purpose + data compression software with a high compression ratio.', markedDefault: false, + versionName: 5.2.3} - categories: system, tools defaultVersionName: 5.9.1 description: QT is a cross-platform application framework that is used for developing @@ -1978,14 +1986,15 @@ software_modules: - {description: Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime., markedDefault: false, versionName: 5.20.1.19} - - categories: system, libs - defaultVersionName: 2.9.4 - description: Libxml2 is a XML C parser and toolkit. - package: libxml2 - url: http://xmlsoft.org/ + - categories: system, compression + defaultVersionName: 1.5.1 + description: libzip is a C library for reading, creating, and modifying zip + archives. + package: libzip + url: http://libzip.org versions: - - {description: Libxml2 is a XML C parser and toolkit., markedDefault: false, - versionName: 2.9.4} + - {description: 'libzip is a C library for reading, creating, and modifying + zip archives.', markedDefault: false, versionName: 1.5.1} - categories: system, containers defaultVersionName: 1.0.0rc2 description: libnvidia-container is a library and a simple CLI utility to automatically @@ -1999,17 +2008,15 @@ software_modules: properties: arch: {gpu: 1} versionName: 1.0.0rc2 - - categories: system, benchmark - defaultVersionName: '3.2' - description: 'Heavy Peer To Peer: a MPI based benchmark for network diagnostic.' - package: hp2p - url: https://github.com/cea-hpc/hp2p + - categories: system, cloud interface + defaultVersionName: 2.0.50 + description: This package provides a unified command line interface to Amazon + Web Services. + package: aws-cli + url: https://github.com/aws/aws-cli versions: - - description: 'Heavy Peer To Peer: a MPI based benchmark for network diagnostic.' - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '3.2' + - {description: This package provides a unified command line interface to Amazon + Web Services., markedDefault: false, versionName: 2.0.50} - categories: system, database defaultVersionName: '0.9998' description: ODBC driver for SQLite @@ -2018,15 +2025,16 @@ software_modules: versions: - {description: ODBC driver for SQLite, markedDefault: false, versionName: '0.9998'} - categories: system, libs - defaultVersionName: 0.8.14 - description: The libIDL package contains libraries for Interface Definition - Language files. This is a specification for defining portable interfaces. - package: libidl - url: https://github.com/GNOME/libIDL + defaultVersionName: 0.9.1 + description: libxkbcommon is a keyboard keymap compiler and support library + which processes a reduced subset of keymaps as defined by the XKB (X Keyboard + Extension) specification. + package: libxkbcommon + url: https://github.com/xkbcommon/libxkbcommon versions: - - {description: The libIDL package contains libraries for Interface Definition - Language files. This is a specification for defining portable interfaces., - markedDefault: false, versionName: 0.8.14} + - {description: libxkbcommon is a keyboard keymap compiler and support library + which processes a reduced subset of keymaps as defined by the XKB (X Keyboard + Extension) specification., markedDefault: false, versionName: 0.9.1} - categories: system, libs defaultVersionName: 0.9.7 description: Libunistring provides functions for manipulating Unicode strings @@ -2044,24 +2052,26 @@ software_modules: url: https://github.com/google/benchmark versions: - {description: A microbenchmark support library, markedDefault: false, versionName: 1.2.0} - - categories: system, scm - defaultVersionName: 2.0.696 - description: Secure, cross-platform Git credential storage with authentication - to GitHub, Azure Repos, and other popular Git hosting services. - package: git-credential-manager - url: https://github.com/GitCredentialManager/git-credential-manager - versions: - - {description: 'Secure, cross-platform Git credential storage with authentication - to GitHub, Azure Repos, and other popular Git hosting services.', markedDefault: false, - versionName: 2.0.696} - categories: system, libs - defaultVersionName: 2.13.1 - description: C library for encoding, decoding and manipulating JSON data. - package: jansson - url: https://github.com/akheron/jansson + defaultVersionName: '8.40' + description: The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. + package: pcre + url: http://www.pcre.org/ versions: - - {description: 'C library for encoding, decoding and manipulating JSON data.', - markedDefault: false, versionName: 2.13.1} + - {description: The PCRE library is a set of functions that implement regular + expression pattern matching using the same syntax and semantics as Perl + 5., markedDefault: false, versionName: '8.40'} + - categories: system, compiler + defaultVersionName: 1.3.3 + description: MRC is a resource compiler that can create self-contained applications, + by including all the required data inside executable files. + package: mrc + url: https://github.com/mhekkel/mrc + versions: + - {description: 'MRC is a resource compiler that can create self-contained applications, + by including all the required data inside executable files.', markedDefault: false, + versionName: 1.3.3} - categories: system, document processing defaultVersionName: 1.23.0 description: groff (GNU roff) is a typesetting system that reads plain text @@ -2139,13 +2149,13 @@ software_modules: - {description: Tools for working with Chromium development., markedDefault: false, versionName: '20200731'} - categories: system, libs - defaultVersionName: 0.6.21 - description: A library for parsing, editing, and saving EXIF data. - package: libexif - url: https://github.com/libexif/libexif + defaultVersionName: 0.3.5 + description: C++ implementation of the Google logging module. + package: glog + url: https://github.com/google/glog versions: - - {description: 'A library for parsing, editing, and saving EXIF data.', markedDefault: false, - versionName: 0.6.21} + - {description: C++ implementation of the Google logging module., markedDefault: false, + versionName: 0.3.5} - categories: system, testing defaultVersionName: 7.1.3_py39 description: 'pytest is a full-featured Python testing framework ' @@ -2155,13 +2165,14 @@ software_modules: - {description: 'pytest is a full-featured Python testing framework ', markedDefault: false, versionName: 7.1.3_py39} - categories: system, compression - defaultVersionName: 1.8.0 - description: LZ4 is lossless compression algorithm. - package: lz4 - url: https://www.lz4.org + defaultVersionName: '16.02' + description: p7zip is a Linux port of 7zip, a file archiver with high compression + ratio. + package: p7zip + url: https://sourceforge.net/projects/p7zip/ versions: - - {description: LZ4 is lossless compression algorithm., markedDefault: false, - versionName: 1.8.0} + - {description: 'p7zip is a Linux port of 7zip, a file archiver with high compression + ratio.', markedDefault: false, versionName: '16.02'} - categories: system, libs defaultVersionName: 3.2.1 description: libffi is a portable Foreign Function Interface library. @@ -4136,16 +4147,18 @@ software_modules: - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false, versionName: 2.13.1} - categories: biology, genomics - defaultVersionName: 2.2.3_py39 - description: A software package for animal pose estimation. - package: py-deeplabcut - url: http://deeplabcut.org + defaultVersionName: 3.0.7 + description: The SRA Toolkit and SDK from NCBI is a collection of tools and + libraries for using data in the INSDC Sequence Read Archives. + package: sra-tools + url: https://github.com/ncbi/sra-tools versions: - - description: A software package for animal pose estimation. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 2.2.3_py39 + - {description: The SRA Toolkit and SDK from NCBI is a collection of tools and + libraries for using data in the INSDC Sequence Read Archives., markedDefault: false, + versionName: 2.11.0} + - {description: The SRA Toolkit and SDK from NCBI is a collection of tools and + libraries for using data in the INSDC Sequence Read Archives., markedDefault: false, + versionName: 3.0.7} - categories: biology, genomics defaultVersionName: '202112.01' description: Sentieon Genomics software is a set of software tools that perform @@ -4188,15 +4201,14 @@ software_modules: from different cohorts, or time-series from the same subject.', markedDefault: false, versionName: '12'} - categories: biology, genomics - defaultVersionName: 0.12.0 - description: Highly-accurate & wicked fast transcript-level quantification from - RNA-seq reads using lightweight alignments. - package: salmon - url: https://combine-lab.github.io/salmon + defaultVersionName: 0.3.4 + description: Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads. + package: dorado + url: https://github.com/nanoporetech/dorado versions: - - {description: Highly-accurate & wicked fast transcript-level quantification - from RNA-seq reads using lightweight alignments., markedDefault: false, - versionName: 0.12.0} + - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4} - categories: biology, neurology defaultVersionName: 21.3.00 description: AFNI (Analysis of Functional NeuroImages) is a set of C programs @@ -4261,6 +4273,15 @@ software_modules: - {description: 'The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.', markedDefault: false, versionName: '20110325'} + - categories: biology, genomics + defaultVersionName: 4.2.7 + description: The BCL Convert App generates demultiplexed FASTQ files from a + run as input. + package: bcl-convert + url: https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html + versions: + - {description: The BCL Convert App generates demultiplexed FASTQ files from + a run as input., markedDefault: false, versionName: 4.2.7} - categories: biology, genomics defaultVersionName: 0.18.0_py39 description: Pysam is a python module for reading, manipulating and writing @@ -4487,31 +4508,21 @@ software_modules: - {description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences., markedDefault: false, versionName: 2.3.4.1} - categories: biology, genomics - defaultVersionName: '1.16' - description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF. - package: bcftools - url: https://github.com/samtools/bcftools + defaultVersionName: 3.3.1_py36 + description: Tools to process and analyze deep sequencing data. + package: py-deeptools + url: https://github.com/deeptools/deepTools/ versions: - - {description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, - versionName: '1.6'} - - {description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, - versionName: '1.8'} - - {description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, - versionName: '1.16'} - - categories: biology, genomics - defaultVersionName: 0.11.8 - description: FastQC aims to provide a simple way to do some quality control - checks on raw sequence data coming from high throughput sequencing pipelines. - package: fastqc - url: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + - {description: Tools to process and analyze deep sequencing data., markedDefault: false, + versionName: 3.3.1_py36} + - categories: biology, neurology + defaultVersionName: '20160502' + description: MRIcron is a cross-platform NIfTI format image viewer. + package: mricron + url: https://www.nitrc.org/projects/mricron versions: - - {description: FastQC aims to provide a simple way to do some quality control - checks on raw sequence data coming from high throughput sequencing pipelines., - markedDefault: false, versionName: 0.11.8} + - {description: MRIcron is a cross-platform NIfTI format image viewer., markedDefault: false, + versionName: '20160502'} - categories: biology, cryo-em defaultVersionName: 4.11.5 description: IMOD is a set of image processing, modeling and display programs @@ -4618,15 +4629,16 @@ software_modules: diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.', markedDefault: false, versionName: 3.0.3} - categories: biology, genomics - defaultVersionName: 0.38.1 - description: breseq is a computational pipeline for finding mutations relative - to a reference sequence in short-read DNA resequencing data. - package: breseq - url: http://barricklab.org/breseq + defaultVersionName: 0.98.5 + description: GEMMA is a software toolkit for fast application of linear mixed + models (LMMs) and related models to genome-wide association studies (GWAS) + and other large-scale data sets. + package: gemma + url: https://github.com/genetics-statistics/GEMMA versions: - - {description: breseq is a computational pipeline for finding mutations relative - to a reference sequence in short-read DNA resequencing data., markedDefault: false, - versionName: 0.38.1} + - {description: GEMMA is a software toolkit for fast application of linear mixed + models (LMMs) and related models to genome-wide association studies (GWAS) + and other large-scale data sets., markedDefault: false, versionName: 0.98.5} - categories: biology, neurology defaultVersionName: 7.4.1 description: An open source software suite for processing and analyzing (human) @@ -4645,27 +4657,26 @@ software_modules: - {description: An open source software suite for processing and analyzing (human) brain MRI images., markedDefault: false, versionName: 7.4.1} - categories: biology, genomics - defaultVersionName: 3.0.7 - description: The SRA Toolkit and SDK from NCBI is a collection of tools and - libraries for using data in the INSDC Sequence Read Archives. - package: sra-tools - url: https://github.com/ncbi/sra-tools + defaultVersionName: 0.38.1 + description: breseq is a computational pipeline for finding mutations relative + to a reference sequence in short-read DNA resequencing data. + package: breseq + url: http://barricklab.org/breseq versions: - - {description: The SRA Toolkit and SDK from NCBI is a collection of tools and - libraries for using data in the INSDC Sequence Read Archives., markedDefault: false, - versionName: 2.11.0} - - {description: The SRA Toolkit and SDK from NCBI is a collection of tools and - libraries for using data in the INSDC Sequence Read Archives., markedDefault: false, - versionName: 3.0.7} + - {description: breseq is a computational pipeline for finding mutations relative + to a reference sequence in short-read DNA resequencing data., markedDefault: false, + versionName: 0.38.1} - categories: biology, genomics - defaultVersionName: 0.3.4 - description: Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads. - package: dorado - url: https://github.com/nanoporetech/dorado + defaultVersionName: 2.2.3_py39 + description: A software package for animal pose estimation. + package: py-deeplabcut + url: http://deeplabcut.org versions: - - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4} + - description: A software package for animal pose estimation. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 2.2.3_py39 - categories: biology, neurology defaultVersionName: 5.0.10 description: FSL is a comprehensive library of analysis tools for FMRI, MRI @@ -4780,13 +4791,14 @@ software_modules: - {description: C library for high-throughput sequencing data formats., markedDefault: false, versionName: '1.16'} - categories: biology, genomics - defaultVersionName: 3.3.1_py36 - description: Tools to process and analyze deep sequencing data. - package: py-deeptools - url: https://github.com/deeptools/deepTools/ + defaultVersionName: 0.0.14 + description: The FASTX-Toolkit is a collection of command line tools for Short-Reads + FASTA/FASTQ files preprocessing. + package: fastx_toolkit + url: http://hannonlab.cshl.edu/fastx_toolkit/ versions: - - {description: Tools to process and analyze deep sequencing data., markedDefault: false, - versionName: 3.3.1_py36} + - {description: The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing., markedDefault: false, versionName: 0.0.14} - categories: biology, computational biology defaultVersionName: '3.8' description: Rosetta is the premier software suite for modeling macromolecular @@ -4936,14 +4948,15 @@ software_modules: - {description: The NBIA Data Retriever is an application to download radiology images from the TCIA Radiology Portal., markedDefault: false, versionName: '4.2'} - categories: biology, genomics - defaultVersionName: 0.0.14 - description: The FASTX-Toolkit is a collection of command line tools for Short-Reads - FASTA/FASTQ files preprocessing. - package: fastx_toolkit - url: http://hannonlab.cshl.edu/fastx_toolkit/ + defaultVersionName: 0.11.8 + description: FastQC aims to provide a simple way to do some quality control + checks on raw sequence data coming from high throughput sequencing pipelines. + package: fastqc + url: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ versions: - - {description: The FASTX-Toolkit is a collection of command line tools for - Short-Reads FASTA/FASTQ files preprocessing., markedDefault: false, versionName: 0.0.14} + - {description: FastQC aims to provide a simple way to do some quality control + checks on raw sequence data coming from high throughput sequencing pipelines., + markedDefault: false, versionName: 0.11.8} - categories: biology, genomics defaultVersionName: 0.5.0 description: Trim Galore! is a wrapper script to automate quality and adapter @@ -5080,14 +5093,22 @@ software_modules: of brain structure and function., markedDefault: false, versionName: 2.3.1} - {description: ANTs computes high-dimensional mappings to capture the statistics of brain structure and function., markedDefault: false, versionName: 2.4.0} - - categories: biology, neurology - defaultVersionName: '20160502' - description: MRIcron is a cross-platform NIfTI format image viewer. - package: mricron - url: https://www.nitrc.org/projects/mricron + - categories: biology, genomics + defaultVersionName: '1.16' + description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF. + package: bcftools + url: https://github.com/samtools/bcftools versions: - - {description: MRIcron is a cross-platform NIfTI format image viewer., markedDefault: false, - versionName: '20160502'} + - {description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, + versionName: '1.6'} + - {description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, + versionName: '1.8'} + - {description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, + versionName: '1.16'} - categories: biology, genomics defaultVersionName: 2.30.0 description: The bedtools utilities are a swiss-army knife of tools for a wide-range @@ -5127,6 +5148,16 @@ software_modules: versions: - {description: A Python framework for the analysis and visualization of trees., markedDefault: false, versionName: 3.0.0_py27} + - categories: biology, genomics + defaultVersionName: 0.12.0 + description: Highly-accurate & wicked fast transcript-level quantification from + RNA-seq reads using lightweight alignments. + package: salmon + url: https://combine-lab.github.io/salmon + versions: + - {description: Highly-accurate & wicked fast transcript-level quantification + from RNA-seq reads using lightweight alignments., markedDefault: false, + versionName: 0.12.0} - categories: biology, genomics defaultVersionName: 1.1.3_py27 description: Fit-Hi-C is a tool for assigning statistical confidence estimates @@ -5137,17 +5168,6 @@ software_modules: - {description: Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome architecture assays., markedDefault: false, versionName: 1.1.3_py27} - - categories: biology, genomics - defaultVersionName: 0.98.5 - description: GEMMA is a software toolkit for fast application of linear mixed - models (LMMs) and related models to genome-wide association studies (GWAS) - and other large-scale data sets. - package: gemma - url: https://github.com/genetics-statistics/GEMMA - versions: - - {description: GEMMA is a software toolkit for fast application of linear mixed - models (LMMs) and related models to genome-wide association studies (GWAS) - and other large-scale data sets., markedDefault: false, versionName: 0.98.5} - categories: biology, genomics defaultVersionName: 2.11.0 description: NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index a8c80a2e8..6c38e90ff 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,33 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New module: biology/bcl-convert version 4.2.7 + The BCL Convert App generates demultiplexed FASTQ files from a run as input. + https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html + https://www.sherlock.stanford.edu/docs/software/list/?add:v=4.2.7#bcl-convert + biology, genomics + kilian@stanford.edu (Kilian Cavalotti) + Mon, 5 Feb 2024 10:12:19 -0800 + + + New module: system/py-spython version 0.3.13_py312 + Singularity Python (spython) is the Python API for working with Singularity containers. + https://github.com/singularityhub/singularity-cli + https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.3.13_py312#py-spython + system, containers + kilian@stanford.edu (Kilian Cavalotti) + Thu, 25 Jan 2024 12:08:39 -0800 + + + New module: system/py-spython version 0.3.13_py39 + Singularity Python (spython) is the Python API for working with Singularity containers. + https://github.com/singularityhub/singularity-cli + https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.3.13_py39#py-spython + system, containers + kilian@stanford.edu (Kilian Cavalotti) + Thu, 25 Jan 2024 12:08:39 -0800 + New version: system/restic version 0.16.3 Fast, secure, efficient backup program. @@ -221,41 +248,5 @@ kilian@stanford.edu (Kilian Cavalotti) Thu, 16 Nov 2023 13:18:43 -0800 - - New module: devel/py-jupyterlab version 4.0.8_py39 - Jupyter is a browser-based interactive notebook for programming, mathematics, and data science. It supports a number of languages via plugins. - https://jupyter.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=4.0.8_py39#py-jupyterlab - devel, language - kilian@stanford.edu (Kilian Cavalotti) - Thu, 16 Nov 2023 13:18:22 -0800 - - - New version: math/py-scikit-learn version 1.3.2_py39 - Scikit-learn is a free software machine learning library for the Python programming language. - http://scikit-learn.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.3.2_py39#py-scikit-learn - math, machine learning - kilian@stanford.edu (Kilian Cavalotti) - Thu, 26 Oct 2023 12:10:01 -0700 - - - New version: biology/py-topaz version 0.2.5_py39 - A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. - https://github.com/tbepler/topaz - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.2.5_py39#py-topaz - biology, cryo-em - kilian@stanford.edu (Kilian Cavalotti) - Thu, 26 Oct 2023 12:09:44 -0700 - - - New version: biology/motioncor2 version 1.6.4 - MotionCor2 is a multi-GPU accelerated program which corrects anisotropic image motion at the single pixel level. - https://emcore.ucsf.edu/ucsf-motioncor2 - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.6.4#motioncor2 - biology, cryo-em - kilian@stanford.edu (Kilian Cavalotti) - Tue, 24 Oct 2023 16:45:17 -0700 - From f473c69d8b3808a618eaf3a1e58ec268b11fc8d4 Mon Sep 17 00:00:00 2001 From: bcritt1 <122565439+bcritt1@users.noreply.github.com> Date: Mon, 5 Feb 2024 14:34:42 -0800 Subject: [PATCH 03/15] Update node-features.md (#143) fix typo --- src/docs/advanced-topics/node-features.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/docs/advanced-topics/node-features.md b/src/docs/advanced-topics/node-features.md index b003dd5a1..a93360a9a 100644 --- a/src/docs/advanced-topics/node-features.md +++ b/src/docs/advanced-topics/node-features.md @@ -176,7 +176,7 @@ matching `OR` condition can be defined by enclosing the options within square brackets (`[`,`]`). For instance, the following options may be used to request a job to run on -nodes with the same frequency, either 2.5 GHz or 2/75GHz: +nodes with the same frequency, either 2.5 GHz or 2.75GHz: ``` none #SBATCH -C "[CPU_FRQ:2.50GHz|CPU_FRQ:2.75GHz]" From 0b5901435d043429986a398b5820240323ae06a8 Mon Sep 17 00:00:00 2001 From: bcritt1 <122565439+bcritt1@users.noreply.github.com> Date: Thu, 8 Feb 2024 14:16:56 -0800 Subject: [PATCH 04/15] Update R.md (#144) this workflow no longer works with system default R (3.5). --- src/docs/software/using/R.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/docs/software/using/R.md b/src/docs/software/using/R.md index 3b6c34da1..44b3716e0 100644 --- a/src/docs/software/using/R.md +++ b/src/docs/software/using/R.md @@ -371,7 +371,7 @@ and `gdal` modules, and try installing `sf` again: ``` none $ ml load physics udunits gdal geos -$ ml R +$ ml R/4.3.2 $ R > install.packages("sf") ``` From c517ae799864729ef5760b64b4c38ba9ab9c5de7 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Sun, 11 Feb 2024 23:23:50 -0800 Subject: [PATCH 05/15] docs: updated facts --- includes/data/facts.yml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/includes/data/facts.yml b/includes/data/facts.yml index fbcef96e9..b5fce8aed 100644 --- a/includes/data/facts.yml +++ b/includes/data/facts.yml @@ -1,10 +1,14 @@ +edr +100 +hdr +200 facts: - name: users fields: - name: user accounts - value: 7054 + value: 7082 - name: PI groups - value: 1115 + value: 1116 desc: "from all Stanford's seven Schools, SLAC, Stanford Institutes, _etc._" - name: owner groups value: 201 @@ -41,7 +45,7 @@ facts: icon: plug fields: - name: kW - value: 564.70 + value: 501.19 desc: total power usage - name: PDUs value: 57 @@ -61,7 +65,7 @@ facts: value: 104 desc: across **2** Infiniband fabrics (EDR, HDR) - name: Infiniband cables - value: 5740 + value: 5738 desc: spanning about **30.23 km** - name: Ethernet switches value: 53 @@ -71,11 +75,11 @@ facts: - name: Slurm partitions value: 178 - name: CPU.hours/day - value: 47065 + value: 45806 desc: over **5 years** of computing in a single day - name: /month fmt: "${:,.0f}" - value: 3144742.5536 + value: 3060616.2912 desc: to run the same workload on t2.large on-demand cloud instances - name: partitions From d4c7e9ef0cedb00a335b9d298424eb0e5d63cd3e Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Mon, 12 Feb 2024 07:51:27 -0800 Subject: [PATCH 06/15] docs: updated facts --- includes/data/facts.yml | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/includes/data/facts.yml b/includes/data/facts.yml index b5fce8aed..749ded1b9 100644 --- a/includes/data/facts.yml +++ b/includes/data/facts.yml @@ -1,12 +1,8 @@ -edr -100 -hdr -200 facts: - name: users fields: - name: user accounts - value: 7082 + value: 7085 - name: PI groups value: 1116 desc: "from all Stanford's seven Schools, SLAC, Stanford Institutes, _etc._" @@ -24,13 +20,13 @@ facts: fields: - name: PFLOPs (FP64) fmt: "{:0.2f}" - value: 5.00 - desc: 18.73 (FP32) PFLOPs + value: 5.44 + desc: 19.61 (FP32) PFLOPs - name: CPU cores - value: 53488 + value: 55600 desc: "**4** CPU generations (**13** CPU models)" - name: GPUs - value: 756 + value: 792 desc: "**4** GPU generations (**12** GPU models)" - name: hardware icon: server @@ -40,12 +36,12 @@ facts: desc: "**19** server models (from **3** different manufacturers)" - name: racks value: 37 - desc: "**1,147** rack units" + desc: "**1,186** rack units" - name: energy icon: plug fields: - name: kW - value: 501.19 + value: 548.42 desc: total power usage - name: PDUs value: 57 @@ -65,7 +61,7 @@ facts: value: 104 desc: across **2** Infiniband fabrics (EDR, HDR) - name: Infiniband cables - value: 5738 + value: 5739 desc: spanning about **30.23 km** - name: Ethernet switches value: 53 @@ -75,11 +71,11 @@ facts: - name: Slurm partitions value: 178 - name: CPU.hours/day - value: 45806 + value: 45679 desc: over **5 years** of computing in a single day - name: /month fmt: "${:,.0f}" - value: 3060616.2912 + value: 3052120.7296 desc: to run the same workload on t2.large on-demand cloud instances - name: partitions From 1645651295dcec6f25f27e619d79266eaa3c1c04 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Sun, 18 Feb 2024 23:23:48 -0800 Subject: [PATCH 07/15] docs: updated facts --- includes/data/facts.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/includes/data/facts.yml b/includes/data/facts.yml index 749ded1b9..dbee2c2a1 100644 --- a/includes/data/facts.yml +++ b/includes/data/facts.yml @@ -2,9 +2,9 @@ facts: - name: users fields: - name: user accounts - value: 7085 + value: 7116 - name: PI groups - value: 1116 + value: 1117 desc: "from all Stanford's seven Schools, SLAC, Stanford Institutes, _etc._" - name: owner groups value: 201 @@ -41,7 +41,7 @@ facts: icon: plug fields: - name: kW - value: 548.42 + value: 506.39 desc: total power usage - name: PDUs value: 57 @@ -71,11 +71,11 @@ facts: - name: Slurm partitions value: 178 - name: CPU.hours/day - value: 45679 + value: 44505 desc: over **5 years** of computing in a single day - name: /month fmt: "${:,.0f}" - value: 3052120.7296 + value: 2973675.0336 desc: to run the same workload on t2.large on-demand cloud instances - name: partitions From b66c3549b82a8ae8d58645c48f3c0448d686f1ef Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Wed, 21 Feb 2024 09:30:49 -0800 Subject: [PATCH 08/15] docs: updated software list --- includes/data/software.yml | 4 ++- src/docs/software/updates.xml | 54 ++++++----------------------------- 2 files changed, 12 insertions(+), 46 deletions(-) diff --git a/includes/data/software.yml b/includes/data/software.yml index 53a1a6156..eedf7bac1 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -4201,7 +4201,7 @@ software_modules: from different cohorts, or time-series from the same subject.', markedDefault: false, versionName: '12'} - categories: biology, genomics - defaultVersionName: 0.3.4 + defaultVersionName: 0.5.3 description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. package: dorado @@ -4209,6 +4209,8 @@ software_modules: versions: - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4} + - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads.', markedDefault: false, versionName: 0.5.3} - categories: biology, neurology defaultVersionName: 21.3.00 description: AFNI (Analysis of Functional NeuroImages) is a set of C programs diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index 6c38e90ff..db091b01b 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,15 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New version: biology/dorado version 0.5.3 + Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. + https://github.com/nanoporetech/dorado + https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.5.3#dorado + biology, genomics + kilian@stanford.edu (Kilian Cavalotti) + Wed, 21 Feb 2024 09:29:37 -0800 + New module: biology/bcl-convert version 4.2.7 The BCL Convert App generates demultiplexed FASTQ files from a run as input. @@ -203,50 +212,5 @@ kilian@stanford.edu (Kilian Cavalotti) Wed, 29 Nov 2023 10:37:32 -0800 - - New version: system/rclone version 1.65.0 - Rclone is a command line program to sync files and directories to and from - https://rclone.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.65.0#rclone - system, file transfer - kilian@stanford.edu (Kilian Cavalotti) - Tue, 28 Nov 2023 07:59:13 -0800 - - - New module: devel/darshan version 3.4.4 - Darshan is a scalable HPC I/O characterization tool. - https://www.mcs.anl.gov/research/projects/darshan/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.4.4#darshan - devel, profiling - kilian@stanford.edu (Kilian Cavalotti) - Thu, 16 Nov 2023 17:34:11 -0800 - - - New module: system/py-matlab-proxy version 0.9.1_py39 - matlab-proxy is a Python package which enables you to launch MATLAB and access it from a web browser. - https://github.com/mathworks/matlab-proxy - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.9.1_py39#py-matlab-proxy - system, tools - kilian@stanford.edu (Kilian Cavalotti) - Thu, 16 Nov 2023 13:19:14 -0800 - - - New version: system/py-globus-cli version 3.19.0_py39 - A command line wrapper over the Globus SDK for Python. - https://github.com/globus/globus-cli - https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.19.0_py39#py-globus-cli - system, file transfer - kilian@stanford.edu (Kilian Cavalotti) - Thu, 16 Nov 2023 13:18:58 -0800 - - - New version: math/rstudio version 2023.09.1 - RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. - http://www.rstudio.com - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2023.09.1#rstudio - math, statistics - kilian@stanford.edu (Kilian Cavalotti) - Thu, 16 Nov 2023 13:18:43 -0800 - From 327602a2379422a5a08c28e51b13bb4bcbd68085 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Wed, 21 Feb 2024 10:03:31 -0800 Subject: [PATCH 09/15] docs: updated software list --- includes/data/software.yml | 6 +++++- src/docs/software/updates.xml | 18 ++++++++++++++++++ 2 files changed, 23 insertions(+), 1 deletion(-) diff --git a/includes/data/software.yml b/includes/data/software.yml index eedf7bac1..2e6055401 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -175,7 +175,7 @@ software_modules: quality figures in a variety of hardcopy formats and interactive environments across platforms., family: matplotlib, markedDefault: true, versionName: 2.2.2_py27} - categories: viz, plotting - defaultVersionName: 2.4.1_py27 + defaultVersionName: 5.19.0_py312 description: Plotly's Python graphing library makes interactive, publication-quality graphs online. package: py-plotly @@ -183,6 +183,10 @@ software_modules: versions: - {description: 'Plotly''s Python graphing library makes interactive, publication-quality graphs online.', markedDefault: false, versionName: 2.4.1_py27} + - {description: 'Plotly''s Python graphing library makes interactive, publication-quality + graphs online.', markedDefault: false, versionName: 5.19.0_py39} + - {description: 'Plotly''s Python graphing library makes interactive, publication-quality + graphs online.', markedDefault: false, versionName: 5.19.0_py312} - categories: viz, imaging defaultVersionName: 9.2.0_py39 description: Pillow-SIMD is an optimized version of Pillow diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index db091b01b..c5546a045 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,24 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New version: viz/py-plotly version 5.19.0_py312 + Plotly's Python graphing library makes interactive, publication-quality graphs online. + https://plot.ly/python/ + https://www.sherlock.stanford.edu/docs/software/list/?add:v=5.19.0_py312#py-plotly + viz, plotting + kilian@stanford.edu (Kilian Cavalotti) + Wed, 21 Feb 2024 10:02:42 -0800 + + + New version: viz/py-plotly version 5.19.0_py39 + Plotly's Python graphing library makes interactive, publication-quality graphs online. + https://plot.ly/python/ + https://www.sherlock.stanford.edu/docs/software/list/?add:v=5.19.0_py39#py-plotly + viz, plotting + kilian@stanford.edu (Kilian Cavalotti) + Wed, 21 Feb 2024 10:02:42 -0800 + New version: biology/dorado version 0.5.3 Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. From c4dd18545d6560833cee25057470ec86c4e251d9 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Sun, 25 Feb 2024 23:24:07 -0800 Subject: [PATCH 10/15] docs: updated facts --- includes/data/facts.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/includes/data/facts.yml b/includes/data/facts.yml index dbee2c2a1..99cccbc78 100644 --- a/includes/data/facts.yml +++ b/includes/data/facts.yml @@ -2,9 +2,9 @@ facts: - name: users fields: - name: user accounts - value: 7116 + value: 7135 - name: PI groups - value: 1117 + value: 1119 desc: "from all Stanford's seven Schools, SLAC, Stanford Institutes, _etc._" - name: owner groups value: 201 @@ -41,7 +41,7 @@ facts: icon: plug fields: - name: kW - value: 506.39 + value: 596.96 desc: total power usage - name: PDUs value: 57 @@ -61,7 +61,7 @@ facts: value: 104 desc: across **2** Infiniband fabrics (EDR, HDR) - name: Infiniband cables - value: 5739 + value: 5740 desc: spanning about **30.23 km** - name: Ethernet switches value: 53 @@ -71,11 +71,11 @@ facts: - name: Slurm partitions value: 178 - name: CPU.hours/day - value: 44505 + value: 44222 desc: over **5 years** of computing in a single day - name: /month fmt: "${:,.0f}" - value: 2973675.0336 + value: 2954803.4112 desc: to run the same workload on t2.large on-demand cloud instances - name: partitions From a4df1f1216dc8dee66efbf81c32686575736d528 Mon Sep 17 00:00:00 2001 From: cagancayco Date: Tue, 27 Feb 2024 16:33:34 -0800 Subject: [PATCH 11/15] updating Rclone documentation (#146) * updating Rclone documentation --- src/docs/software/using/rclone.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/docs/software/using/rclone.md b/src/docs/software/using/rclone.md index b6e4e5566..874dc61f6 100644 --- a/src/docs/software/using/rclone.md +++ b/src/docs/software/using/rclone.md @@ -21,6 +21,13 @@ browser, so you will need to connect to Sherlock with **local port forwarding** (`ssh -L`). You only need to do this when you are configuring `rclone` for the first time. +!!! Note "Use local terminal for `rclone config`" + + **This method will not work in the Sherlock OnDemand shell.** You will need + to use your local machine's terminal to enable local port forwarding and to + allow `rclone` to communicate with your browser. On Linux and macOS, you + can use the Terminal app; on Windows, you can use the PowerShell app. + When running `rclone config` you will be prompted to enter names and values, indicated by the `>` symbol. To leave it empty, press Enter. From f7e8f975cbe5e4ce463baee544dd5b80596eacbe Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Sun, 3 Mar 2024 23:24:02 -0800 Subject: [PATCH 12/15] docs: updated facts --- includes/data/facts.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/includes/data/facts.yml b/includes/data/facts.yml index 99cccbc78..d1b47660a 100644 --- a/includes/data/facts.yml +++ b/includes/data/facts.yml @@ -2,9 +2,9 @@ facts: - name: users fields: - name: user accounts - value: 7135 + value: 7155 - name: PI groups - value: 1119 + value: 1121 desc: "from all Stanford's seven Schools, SLAC, Stanford Institutes, _etc._" - name: owner groups value: 201 @@ -41,7 +41,7 @@ facts: icon: plug fields: - name: kW - value: 596.96 + value: 548.15 desc: total power usage - name: PDUs value: 57 @@ -61,7 +61,7 @@ facts: value: 104 desc: across **2** Infiniband fabrics (EDR, HDR) - name: Infiniband cables - value: 5740 + value: 5737 desc: spanning about **30.23 km** - name: Ethernet switches value: 53 @@ -71,11 +71,11 @@ facts: - name: Slurm partitions value: 178 - name: CPU.hours/day - value: 44222 - desc: over **5 years** of computing in a single day + value: 41412 + desc: over **4 years** of computing in a single day - name: /month fmt: "${:,.0f}" - value: 2954803.4112 + value: 2766987.1616 desc: to run the same workload on t2.large on-demand cloud instances - name: partitions From e63790745bc3d0ba975af7aa1d79f5254a3b420b Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Wed, 6 Mar 2024 14:18:08 -0800 Subject: [PATCH 13/15] docs: updated software list --- includes/data/software.yml | 22 ++++++++++++++++- src/docs/software/updates.xml | 45 ++++++++++++++--------------------- 2 files changed, 39 insertions(+), 28 deletions(-) diff --git a/includes/data/software.yml b/includes/data/software.yml index 2e6055401..2cfa4fc38 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -2302,6 +2302,9 @@ software_modules: - {description: The SciPy library provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization., family: scipy, markedDefault: false, versionName: 1.10.1_py39} + - {description: The SciPy library provides many user-friendly and efficient + numerical routines such as routines for numerical integration and optimization., + family: scipy, markedDefault: false, versionName: 1.12.0_py312} - {description: The SciPy library provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization., family: scipy, markedDefault: true, versionName: 1.1.0_py27} @@ -3710,6 +3713,12 @@ software_modules: properties: arch: {gpu: 1} versionName: 4.7.0 + - description: OpenCV (Open Source Computer Vision Library) is an open source + computer vision and machine learning software library. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 4.9.0 - description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. markedDefault: true @@ -5155,7 +5164,7 @@ software_modules: - {description: A Python framework for the analysis and visualization of trees., markedDefault: false, versionName: 3.0.0_py27} - categories: biology, genomics - defaultVersionName: 0.12.0 + defaultVersionName: 1.10.0 description: Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments. package: salmon @@ -5164,6 +5173,9 @@ software_modules: - {description: Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments., markedDefault: false, versionName: 0.12.0} + - {description: Highly-accurate & wicked fast transcript-level quantification + from RNA-seq reads using lightweight alignments., markedDefault: false, + versionName: 1.10.0} - categories: biology, genomics defaultVersionName: 1.1.3_py27 description: Fit-Hi-C is a tool for assigning statistical confidence estimates @@ -7097,6 +7109,14 @@ software_modules: properties: arch: {gpu: 1} versionName: 12.2.0 + - description: CUDA is a parallel computing platform and application programming + interface (API) model created by Nvidia. It allows software developers and + software engineers to use a CUDA-enabled graphics processing unit (GPU) + for general purpose processing. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 12.4.0 - description: CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia. It allows software developers and software engineers to use a CUDA-enabled graphics processing unit (GPU) diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index c5546a045..de3debadf 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,24 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New version: biology/salmon version 1.10.0 + Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments. + https://combine-lab.github.io/salmon + https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.10.0#salmon + biology, genomics + kilian@stanford.edu (Kilian Cavalotti) + Wed, 6 Mar 2024 14:17:16 -0800 + + + New version: devel/cuda version 12.4.0 + CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia. It allows software developers and software engineers to use a CUDA-enabled graphics processing unit (GPU) for general purpose processing. + https://developer.nvidia.com/cuda-toolkit + https://www.sherlock.stanford.edu/docs/software/list/?add:v=12.4.0#cuda + devel, language + kilian@stanford.edu (Kilian Cavalotti) + Tue, 5 Mar 2024 14:39:10 -0800 + New version: viz/py-plotly version 5.19.0_py312 Plotly's Python graphing library makes interactive, publication-quality graphs online. @@ -203,32 +221,5 @@ kilian@stanford.edu (Kilian Cavalotti) Mon, 8 Jan 2024 14:23:50 -0800 - - New version: physics/geos version 3.12.1 - GEOS is a C/C++ library for computational geometry with a focus on algorithms used in geographic information systems (GIS) software. - https://libgeos.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.12.1#geos - physics, geoscience - kilian@stanford.edu (Kilian Cavalotti) - Tue, 12 Dec 2023 11:17:10 -0800 - - - New version: biology/kallisto version 0.50.1 - kallisto is a program for quantifying abundances of transcripts from RNA-Seq data using high-throughput sequencing reads. - https://pachterlab.github.io/kallisto/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.50.1#kallisto - biology, genomics - kilian@stanford.edu (Kilian Cavalotti) - Wed, 29 Nov 2023 13:50:00 -0800 - - - New version: system/py-matlab-proxy version 0.10.0_py39 - matlab-proxy is a Python package which enables you to launch MATLAB and access it from a web browser. - https://github.com/mathworks/matlab-proxy - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.10.0_py39#py-matlab-proxy - system, tools - kilian@stanford.edu (Kilian Cavalotti) - Wed, 29 Nov 2023 10:37:32 -0800 - From 56c8721d6da326a6541c07cae42698e8de6439e6 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Sun, 10 Mar 2024 23:23:57 -0700 Subject: [PATCH 14/15] docs: updated facts --- includes/data/facts.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/includes/data/facts.yml b/includes/data/facts.yml index d1b47660a..96f6872b9 100644 --- a/includes/data/facts.yml +++ b/includes/data/facts.yml @@ -2,9 +2,9 @@ facts: - name: users fields: - name: user accounts - value: 7155 + value: 7189 - name: PI groups - value: 1121 + value: 1124 desc: "from all Stanford's seven Schools, SLAC, Stanford Institutes, _etc._" - name: owner groups value: 201 @@ -41,7 +41,7 @@ facts: icon: plug fields: - name: kW - value: 548.15 + value: 558.16 desc: total power usage - name: PDUs value: 57 @@ -61,7 +61,7 @@ facts: value: 104 desc: across **2** Infiniband fabrics (EDR, HDR) - name: Infiniband cables - value: 5737 + value: 5739 desc: spanning about **30.23 km** - name: Ethernet switches value: 53 @@ -71,11 +71,11 @@ facts: - name: Slurm partitions value: 178 - name: CPU.hours/day - value: 41412 + value: 41145 desc: over **4 years** of computing in a single day - name: /month fmt: "${:,.0f}" - value: 2766987.1616 + value: 2749185.3376 desc: to run the same workload on t2.large on-demand cloud instances - name: partitions From fa48ab52f630acef04d194c57c5e28222281b167 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Sun, 17 Mar 2024 23:23:47 -0700 Subject: [PATCH 15/15] docs: updated facts --- includes/data/facts.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/includes/data/facts.yml b/includes/data/facts.yml index 96f6872b9..f5fab26ce 100644 --- a/includes/data/facts.yml +++ b/includes/data/facts.yml @@ -2,9 +2,9 @@ facts: - name: users fields: - name: user accounts - value: 7189 + value: 7190 - name: PI groups - value: 1124 + value: 1126 desc: "from all Stanford's seven Schools, SLAC, Stanford Institutes, _etc._" - name: owner groups value: 201 @@ -41,7 +41,7 @@ facts: icon: plug fields: - name: kW - value: 558.16 + value: 574.39 desc: total power usage - name: PDUs value: 57 @@ -61,8 +61,8 @@ facts: value: 104 desc: across **2** Infiniband fabrics (EDR, HDR) - name: Infiniband cables - value: 5739 - desc: spanning about **30.23 km** + value: 5733 + desc: spanning about **30.14 km** - name: Ethernet switches value: 53 - name: scheduler @@ -71,11 +71,11 @@ facts: - name: Slurm partitions value: 178 - name: CPU.hours/day - value: 41145 + value: 41542 desc: over **4 years** of computing in a single day - name: /month fmt: "${:,.0f}" - value: 2749185.3376 + value: 2775676.0256 desc: to run the same workload on t2.large on-demand cloud instances - name: partitions