diff --git a/includes/data/facts.yml b/includes/data/facts.yml index 522b7446c..e7a718686 100644 --- a/includes/data/facts.yml +++ b/includes/data/facts.yml @@ -2,12 +2,12 @@ facts: - name: users fields: - name: user accounts - value: 7039 + value: 6967 - name: PI groups - value: 1096 + value: 1102 desc: "from all Stanford's seven Schools, SLAC, Stanford Institutes, _etc._" - name: owner groups - value: 203 + value: 200 - name: interfaces icon: sitemap fields: @@ -24,7 +24,7 @@ facts: desc: 18.73 (FP32) PFLOPs - name: CPU cores value: 53488 - desc: "**4** CPU generations (**14** CPU models)" + desc: "**4** CPU generations (**13** CPU models)" - name: GPUs value: 756 desc: "**4** GPU generations (**12** GPU models)" @@ -32,7 +32,7 @@ facts: icon: server fields: - name: compute nodes - value: 1701 + value: 1707 desc: "**19** server models (from **3** different manufacturers)" - name: racks value: 37 @@ -41,7 +41,7 @@ facts: icon: plug fields: - name: kW - value: 570.61 + value: 535.15 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: 5670 - desc: spanning about **30.13 km** + value: 5687 + desc: spanning about **30.15 km** - name: Ethernet switches value: 53 - name: scheduler @@ -71,22 +71,22 @@ facts: - name: Slurm partitions value: 178 - name: CPU.hours/day - value: 45327 + value: 47630 desc: over **5 years** of computing in a single day - name: /month fmt: "${:,.0f}" - value: 3028620.8000 + value: 3182496.0992 desc: to run the same workload on t2.large on-demand cloud instances - name: partitions fields: - name: normal - nodes: 179 - cores: 4820 + nodes: 187 + cores: 5012 desc: compute nodes details: | - 57 nodes w/ 20-core (Intel E5-2640v4), 128 GB RAM, EDR IB - - 28 nodes w/ 24-core (Intel 5118), 191 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 - 70 nodes w/ 32-core (AMD 7502), 256 GB RAM, HDR IB access: public @@ -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: 1478 - cores: 47592 + nodes: 1477 + cores: 47912 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 - - 356 nodes w/ 24-core (Intel 5118), 191 GB RAM, EDR IB + - 348 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 - - 240 nodes w/ 32-core (AMD 7543), 256 GB RAM, HDR IB + - 244 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 @@ -162,8 +162,8 @@ facts: - 3 nodes w/ 64-core (Intel 6130), 3072 GB RAM, EDR IB - 1 nodes w/ 64-core (AMD 7502), 4096 GB RAM, HDR IB - 2 nodes w/ 64-core (AMD 7543), 4096 GB RAM, HDR IB - - 19 nodes w/ 128-core (AMD 7763), 1024 GB RAM, HDR IB + - 20 nodes w/ 128-core (AMD 7763), 1024 GB RAM, HDR IB - 36 nodes w/ 128-core (AMD 7742), 1024 GB RAM, HDR IB - 7 nodes w/ 128-core (AMD 7662), 1024 GB RAM, HDR IB, 8x Tesla A100_SXM4 GPUs - - 7 nodes w/ 128-core (AMD 7763), 1024 GB RAM, HDR IB, 8x Tesla A100_SXM4 GPUs + - 9 nodes w/ 128-core (AMD 7763), 1024 GB RAM, HDR IB, 8x Tesla A100_SXM4 GPUs access: private diff --git a/includes/data/software.yml b/includes/data/software.yml index 49ea65871..098b35d13 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -683,16 +683,14 @@ software_modules: - {description: Simple password manager using gpg and ordinary unix directories., markedDefault: false, versionName: 1.7.4} - categories: system, tools - defaultVersionName: 7.81.0 + defaultVersionName: 8.4.0 description: curl is an open source command line tool and library for transferring data with URL syntax. package: curl url: https://curl.haxx.se/ versions: - {description: curl is an open source command line tool and library for transferring - data with URL syntax., markedDefault: false, versionName: 7.54.0} - - {description: curl is an open source command line tool and library for transferring - data with URL syntax., markedDefault: false, versionName: 7.81.0} + data with URL syntax., markedDefault: false, versionName: 8.4.0} - categories: system, libs defaultVersionName: 1.4.1 description: Epoxy is a library for handling OpenGL function pointer management @@ -3417,6 +3415,8 @@ software_modules: the Python programming language., markedDefault: false, versionName: 0.24.2_py36} - {description: Scikit-learn is a free software machine learning library for the Python programming language., markedDefault: false, versionName: 1.0.2_py39} + - {description: Scikit-learn is a free software machine learning library for + the Python programming language., markedDefault: false, versionName: 1.3.2_py39} - {description: Scikit-learn is a free software machine learning library for the Python programming language., markedDefault: true, versionName: 0.19.1_py27} - categories: math, optimization @@ -4379,13 +4379,13 @@ software_modules: - {description: Python API for comprehensive GWAS analysis using GEMMA., markedDefault: false, versionName: 0.8.9_py39} - categories: biology, cryo-em - defaultVersionName: '2.1' + defaultVersionName: 4.0.1 description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). package: relion - url: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page + url: https://github.com/3dem/relion versions: - description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach @@ -4405,6 +4405,15 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: '2.1' + - description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) + is a stand-alone computer program that employs an empirical Bayesian approach + to refinement of (multiple) 3D reconstructions or 2D class averages in electron + cryo-microscopy (cryo-EM). + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: 4.0.1 - categories: biology, genomics defaultVersionName: 2.10.0 description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.' @@ -4910,6 +4919,12 @@ software_modules: properties: arch: {gpu: 1} versionName: 1.5.0 + - description: MotionCor2 is a multi-GPU accelerated program which corrects + anisotropic image motion at the single pixel level. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 1.6.4 - description: MotionCor2 is a multi-GPU accelerated program which corrects anisotropic image motion at the single pixel level. markedDefault: true @@ -4917,7 +4932,7 @@ software_modules: arch: {gpu: 1} versionName: 1.3.1 - categories: biology, cryo-em - defaultVersionName: 0.2.4_py36 + defaultVersionName: 0.2.5_py39 description: A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. package: py-topaz @@ -4930,6 +4945,13 @@ software_modules: properties: arch: {gpu: 1} versionName: 0.2.4_py36 + - description: A pipeline for particle detection in cryo-electron microscopy + images using convolutional neural networks trained from positive and unlabeled + examples. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 0.2.5_py39 - categories: biology, genomics defaultVersionName: 3.0.2_py27 description: Assessing genome assembly and annotation completeness with Benchmarking @@ -5774,24 +5796,30 @@ software_modules: and integer arrays that support high throughput read and write random access., markedDefault: false, versionName: 1.0.0} - categories: devel, compiler - defaultVersionName: '2019' - description: Intel C++ Compiler, also known as icc or icl, is a group of C and - C++ compilers from Intel - package: icc - url: https://software.intel.com/en-us/c-compilers + defaultVersionName: 7.0.0 + description: The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler, + package: llvm + url: http://llvm.org versions: - - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of - C and C++ compilers from Intel', family: compiler_c, markedDefault: false, - versionName: 2017.u2} - - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of - C and C++ compilers from Intel', family: compiler_c, markedDefault: false, - versionName: 2018.u1} - - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of - C and C++ compilers from Intel', family: compiler_c, markedDefault: false, - versionName: '2018'} - - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of - C and C++ compilers from Intel', family: compiler_c, markedDefault: false, - versionName: '2019'} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 3.8.1} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 4.0.0} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 5.0.0} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 9.0.1} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 15.0.3} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: true, versionName: 7.0.0} - categories: devel, data defaultVersionName: 1.12.3 description: Parallel netCDF (PnetCDF) is a parallel I/O library for accessing @@ -5811,41 +5839,39 @@ software_modules: properties: parallel: {mpi: 1} versionName: 1.12.3 - - categories: devel, lib - defaultVersionName: 4.2.2 - description: ZeroMQ (also spelled ØMQ, 0MQ or ZMQ) is a high-performance asynchronous - messaging library, aimed at use in distributed or concurrent applications. - package: zeromq - url: http://zeromq.org + - categories: devel, data + defaultVersionName: 4.0.1 + description: Redis is an open source, in-memory data structure store, used as + a database, cache and message broker. + package: redis + url: https://redis.io versions: - - {description: 'ZeroMQ (also spelled ØMQ, 0MQ or ZMQ) is a high-performance - asynchronous messaging library, aimed at use in distributed or concurrent - applications.', markedDefault: false, versionName: 4.2.2} - - categories: devel, debug - defaultVersionName: 3.14.0 - description: Valgrind is an instrumentation framework for building dynamic analysis - tools. - package: valgrind - url: http://valgrind.org/ + - {description: 'Redis is an open source, in-memory data structure store, used + as a database, cache and message broker.', markedDefault: false, versionName: 4.0.1} + - categories: devel, lib + defaultVersionName: 2.1.12 + description: The libevent API provides a mechanism to execute a callback function + when a specific event occurs on a file descriptor or after a timeout has been + reached. + package: libevent + url: https://libevent.org versions: - - {description: Valgrind is an instrumentation framework for building dynamic - analysis tools., markedDefault: false, versionName: 3.14.0} - - categories: devel, language - defaultVersionName: 2.7.13 - description: Python is an interpreted, interactive, object-oriented programming - language. - package: python - url: https://www.python.org + - {description: The libevent API provides a mechanism to execute a callback + function when a specific event occurs on a file descriptor or after a timeout + has been reached., markedDefault: false, versionName: 2.1.12} + - categories: devel, lib + defaultVersionName: 1.0.0 + description: CNMeM is a simple library to help the Deep Learning frameworks + manage CUDA memory. + package: cnmem + url: https://github.com/NVIDIA/ncmem versions: - - {description: 'Python is an interpreted, interactive, object-oriented programming - language.', family: python, help: 'https://www.sherlock.stanford.edu/docs/software/using/python', - markedDefault: false, versionName: 3.6.1} - - {description: 'Python is an interpreted, interactive, object-oriented programming - language.', family: python, help: 'https://www.sherlock.stanford.edu/docs/software/using/python', - markedDefault: false, versionName: 3.9.0} - - {description: 'Python is an interpreted, interactive, object-oriented programming - language.', family: python, help: 'https://www.sherlock.stanford.edu/docs/software/using/python', - markedDefault: true, versionName: 2.7.13} + - description: CNMeM is a simple library to help the Deep Learning frameworks + manage CUDA memory. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 1.0.0 - categories: devel, data defaultVersionName: 4.3.1 description: NetCDF is a set of software libraries and self-describing, machine-independent @@ -5892,6 +5918,22 @@ software_modules: - {description: 'Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.', markedDefault: false, versionName: 1.18.2} + - categories: devel, language + defaultVersionName: 7.0.6_py39 + description: Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins. + package: py-notebook + url: https://jupyter.org + versions: + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: false, versionName: 5.7.16_py27} + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: false, versionName: 6.4.10_py36} + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: false, versionName: 7.0.6_py39} - categories: devel, lib defaultVersionName: 1.2.0_py39 description: Parsl is a flexible and scalable parallel programming library for @@ -6004,6 +6046,17 @@ software_modules: - {description: Erlang is a programming language used to build massively scalable soft real-time systems with requirements on high availability., markedDefault: false, versionName: '21.3'} + - categories: devel, parser + defaultVersionName: 2.7.7 + description: ANTLR (ANother Tool for Language Recognition) is a powerful parser + generator for reading, processing, executing, or translating structured text + or binary files. + package: antlr + url: https://xerces.apache.org/xerces-c/index.html + versions: + - {description: 'ANTLR (ANother Tool for Language Recognition) is a powerful + parser generator for reading, processing, executing, or translating structured + text or binary files.', markedDefault: false, versionName: 2.7.7} - categories: devel, lib defaultVersionName: 4.5.0 description: libctl is a library for supporting flexible control files in scientific @@ -6027,6 +6080,17 @@ software_modules: markedDefault: false, versionName: 1.3.1_py36} - {description: netcdf4-python is a Python interface to the netCDF C library., markedDefault: true, versionName: 1.3.1_py27} + - categories: devel, data + defaultVersionName: 4.8.0 + description: The NCO toolkit manipulates and analyzes data stored in netCDF-accessible + formats. + package: nco + url: http://nco.sourceforge.net/ + versions: + - {description: The NCO toolkit manipulates and analyzes data stored in netCDF-accessible + formats., markedDefault: false, versionName: 5.0.6} + - {description: The NCO toolkit manipulates and analyzes data stored in netCDF-accessible + formats., markedDefault: true, versionName: 4.8.0} - categories: devel, lib defaultVersionName: 0.12.1 description: Collection of C++ software abstractions that enable architecture @@ -6041,47 +6105,30 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: 0.12.1 - - categories: devel, compiler - defaultVersionName: '21.5' - description: NVIDIA HPC Software Development Kit (SDK) including C, C++, and - Fortran compilers. - package: nvhpc - url: https://developer.nvidia.com/hpc-sdk + - categories: devel, data + defaultVersionName: 4.5.4 + description: NetCDF is a set of software libraries and self-describing, machine-independent + data formats that support the creation, access, and sharing of array-oriented + scientific data. This module provides Fortran libraries. + package: netcdf-fortran + url: https://www.unidata.ucar.edu/software/netcdf versions: - - description: NVIDIA HPC Software Development Kit (SDK) including C, C++, and - Fortran compilers. - family: mpi - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '21.7' - - description: NVIDIA HPC Software Development Kit (SDK) including C, C++, and - Fortran compilers. - family: mpi - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '22.3' - - description: NVIDIA HPC Software Development Kit (SDK) including C, C++, and - Fortran compilers. - family: mpi + - description: NetCDF is a set of software libraries and self-describing, machine-independent + data formats that support the creation, access, and sharing of array-oriented + scientific data. This module provides Fortran libraries. markedDefault: false properties: - arch: {gpu: 1} parallel: {mpi: 1} - versionName: '23.3' - - {description: 'NVIDIA HPC Software Development Kit (SDK) including C, C++, - and Fortran compilers.', family: compiler_f, markedDefault: true, versionName: '21.5'} - - categories: devel, lib - defaultVersionName: 2.0.0 - description: libtree prints shared object dependencies as a tree. - package: libtree - url: https://github.com/haampie/libtree + versionName: 4.5.4 + - categories: devel, engine + defaultVersionName: 8.4.371.22 + description: V8 is Google’s open source high-performance JavaScript and WebAssembly + engine, written in C++. + package: v8 + url: https://v8.dev versions: - - {description: libtree prints shared object dependencies as a tree., markedDefault: false, - versionName: 2.0.0} + - {description: 'V8 is Google’s open source high-performance JavaScript and + WebAssembly engine, written in C++.', markedDefault: false, versionName: 8.4.371.22} - categories: devel, networking defaultVersionName: 0.24.0_py39 description: Python bindinbgs for UCX. @@ -6089,17 +6136,14 @@ software_modules: url: https://github.com/rapidsai/ucx-py versions: - {description: Python bindinbgs for UCX., markedDefault: false, versionName: 0.24.0_py39} - - categories: devel, parser - defaultVersionName: 2.7.7 - description: ANTLR (ANother Tool for Language Recognition) is a powerful parser - generator for reading, processing, executing, or translating structured text - or binary files. - package: antlr - url: https://xerces.apache.org/xerces-c/index.html + - categories: devel, lib + defaultVersionName: 2.0.0 + description: libtree prints shared object dependencies as a tree. + package: libtree + url: https://github.com/haampie/libtree versions: - - {description: 'ANTLR (ANother Tool for Language Recognition) is a powerful - parser generator for reading, processing, executing, or translating structured - text or binary files.', markedDefault: false, versionName: 2.7.7} + - {description: libtree prints shared object dependencies as a tree., markedDefault: false, + versionName: 2.0.0} - categories: devel, data defaultVersionName: 3.4.0_py27 description: Python bindings for Google's Protocol Buffers data interchange @@ -6178,21 +6222,19 @@ software_modules: versions: - {description: Ninja is a small build system with a focus on speed., markedDefault: false, versionName: 1.9.0} - - categories: devel, data - defaultVersionName: 4.5.4 - description: NetCDF is a set of software libraries and self-describing, machine-independent - data formats that support the creation, access, and sharing of array-oriented - scientific data. This module provides Fortran libraries. - package: netcdf-fortran - url: https://www.unidata.ucar.edu/software/netcdf + - categories: devel, language + defaultVersionName: 5.36.1 + description: Perl 5 is a highly capable, feature-rich programming language with + over 29 years of development. + package: perl + url: https://www.perl.org versions: - - description: NetCDF is a set of software libraries and self-describing, machine-independent - data formats that support the creation, access, and sharing of array-oriented - scientific data. This module provides Fortran libraries. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 4.5.4 + - {description: 'Perl 5 is a highly capable, feature-rich programming language + with over 29 years of development.', help: 'https://www.sherlock.stanford.edu/docs/software/using/perl', + markedDefault: false, versionName: 5.26.0} + - {description: 'Perl 5 is a highly capable, feature-rich programming language + with over 29 years of development.', help: 'https://www.sherlock.stanford.edu/docs/software/using/perl', + markedDefault: false, versionName: 5.36.1} - categories: devel, language defaultVersionName: 1.9.0 description: Julia is a high-level, high-performance dynamic programming language @@ -6235,28 +6277,36 @@ software_modules: - {description: 'NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.', markedDefault: false, versionName: 4.8.1} - - categories: devel, language - defaultVersionName: 5.36.1 - description: Perl 5 is a highly capable, feature-rich programming language with - over 29 years of development. - package: perl - url: https://www.perl.org + - categories: devel, lib + defaultVersionName: 3.7.13 + description: RabbitMQ is an open-source message broker. + package: rabbitmq + url: http://rabbitmq.com versions: - - {description: 'Perl 5 is a highly capable, feature-rich programming language - with over 29 years of development.', help: 'https://www.sherlock.stanford.edu/docs/software/using/perl', - markedDefault: false, versionName: 5.26.0} - - {description: 'Perl 5 is a highly capable, feature-rich programming language - with over 29 years of development.', help: 'https://www.sherlock.stanford.edu/docs/software/using/perl', - markedDefault: false, versionName: 5.36.1} - - categories: devel, engine - defaultVersionName: 8.4.371.22 - description: V8 is Google’s open source high-performance JavaScript and WebAssembly - engine, written in C++. - package: v8 - url: https://v8.dev + - {description: RabbitMQ is an open-source message broker., markedDefault: false, + versionName: 3.7.13} + - categories: devel, build + defaultVersionName: 3.24.2 + description: CMake is an extensible, open-source system that manages the build + process in an operating system and in a compiler-independent manner. + package: cmake + url: https://www.cmake.org versions: - - {description: 'V8 is Google’s open source high-performance JavaScript and - WebAssembly engine, written in C++.', markedDefault: false, versionName: 8.4.371.22} + - {description: 'CMake is an extensible, open-source system that manages the + build process in an operating system and in a compiler-independent manner.', + markedDefault: false, versionName: 3.8.1} + - {description: 'CMake is an extensible, open-source system that manages the + build process in an operating system and in a compiler-independent manner.', + markedDefault: false, versionName: 3.11.1} + - {description: 'CMake is an extensible, open-source system that manages the + build process in an operating system and in a compiler-independent manner.', + markedDefault: false, versionName: 3.13.1} + - {description: 'CMake is an extensible, open-source system that manages the + build process in an operating system and in a compiler-independent manner.', + markedDefault: false, versionName: 3.20.3} + - {description: 'CMake is an extensible, open-source system that manages the + build process in an operating system and in a compiler-independent manner.', + markedDefault: false, versionName: 3.24.2} - categories: devel, language defaultVersionName: 0.29.28_py39 description: Cython is an optimising static compiler for both the Python programming @@ -6276,29 +6326,21 @@ software_modules: - {description: Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex)., markedDefault: false, versionName: 0.29.28_py39} - - categories: devel, data - defaultVersionName: 2.0.1_py39 - description: pandas is an open source, BSD-licensed library providing high-performance, - easy-to-use data structures and data analysis tools for the Python programming - language. - package: py-pandas - url: https://pandas.pydata.org/ + - categories: devel, language + defaultVersionName: 1.72.0 + description: A language empowering everyone to build reliable and efficient + software. + package: rust + url: https://www.rust-lang.org/ versions: - - {description: 'pandas is an open source, BSD-licensed library providing high-performance, - easy-to-use data structures and data analysis tools for the Python programming - language.', family: pandas, markedDefault: false, versionName: 0.23.0_py27} - - {description: 'pandas is an open source, BSD-licensed library providing high-performance, - easy-to-use data structures and data analysis tools for the Python programming - language.', family: pandas, markedDefault: false, versionName: 0.23.0_py36} - - {description: 'pandas is an open source, BSD-licensed library providing high-performance, - easy-to-use data structures and data analysis tools for the Python programming - language.', family: pandas, markedDefault: false, versionName: 1.0.3_py36} - - {description: 'pandas is an open source, BSD-licensed library providing high-performance, - easy-to-use data structures and data analysis tools for the Python programming - language.', family: pandas, markedDefault: false, versionName: 1.3.1_py39} - - {description: 'pandas is an open source, BSD-licensed library providing high-performance, - easy-to-use data structures and data analysis tools for the Python programming - language.', family: pandas, markedDefault: false, versionName: 2.0.1_py39} + - {description: A language empowering everyone to build reliable and efficient + software., markedDefault: false, versionName: 1.35.0} + - {description: A language empowering everyone to build reliable and efficient + software., markedDefault: false, versionName: 1.56.1} + - {description: A language empowering everyone to build reliable and efficient + software., markedDefault: false, versionName: 1.63.0} + - {description: A language empowering everyone to build reliable and efficient + software., markedDefault: false, versionName: 1.72.0} - categories: devel, language defaultVersionName: '20180301' description: Manticore is a high-level parallel programming language aimed at @@ -6339,28 +6381,41 @@ software_modules: properties: arch: {gpu: 1} versionName: 0.7.5 - - categories: devel, build - defaultVersionName: 3.24.2 - description: CMake is an extensible, open-source system that manages the build - process in an operating system and in a compiler-independent manner. - package: cmake - url: https://www.cmake.org + - categories: devel, mpi + defaultVersionName: '2019' + description: Intel® MPI Library is a multi-fabric message passing library that + implements the Message Passing Interface, version 3.1 (MPI-3.1) specification. + package: impi + url: https://software.intel.com/en-us/intel-mpi-library versions: - - {description: 'CMake is an extensible, open-source system that manages the - build process in an operating system and in a compiler-independent manner.', - markedDefault: false, versionName: 3.8.1} - - {description: 'CMake is an extensible, open-source system that manages the - build process in an operating system and in a compiler-independent manner.', - markedDefault: false, versionName: 3.11.1} - - {description: 'CMake is an extensible, open-source system that manages the - build process in an operating system and in a compiler-independent manner.', - markedDefault: false, versionName: 3.13.1} - - {description: 'CMake is an extensible, open-source system that manages the - build process in an operating system and in a compiler-independent manner.', - markedDefault: false, versionName: 3.20.3} - - {description: 'CMake is an extensible, open-source system that manages the - build process in an operating system and in a compiler-independent manner.', - markedDefault: false, versionName: 3.24.2} + - description: Intel® MPI Library is a multi-fabric message passing library + that implements the Message Passing Interface, version 3.1 (MPI-3.1) specification. + family: mpi + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 2017.u2 + - description: Intel® MPI Library is a multi-fabric message passing library + that implements the Message Passing Interface, version 3.1 (MPI-3.1) specification. + family: mpi + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 2018.u1 + - description: Intel® MPI Library is a multi-fabric message passing library + that implements the Message Passing Interface, version 3.1 (MPI-3.1) specification. + family: mpi + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '2018' + - description: Intel® MPI Library is a multi-fabric message passing library + that implements the Message Passing Interface, version 3.1 (MPI-3.1) specification. + family: mpi + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '2019' - categories: devel, lib defaultVersionName: 3.4.0 description: 'Eigen is a C++ template library for linear algebra: matrices, @@ -6426,60 +6481,6 @@ software_modules: system.', family: bazel, markedDefault: false, versionName: 0.26.1} - {description: 'Bazel is a fast, scalable, multi-language and extensible build system.', family: bazel, markedDefault: false, versionName: 0.29.1} - - categories: devel, lib - defaultVersionName: 3.7.13 - description: RabbitMQ is an open-source message broker. - package: rabbitmq - url: http://rabbitmq.com - versions: - - {description: RabbitMQ is an open-source message broker., markedDefault: false, - versionName: 3.7.13} - - categories: devel, mpi - defaultVersionName: '2019' - description: Intel® MPI Library is a multi-fabric message passing library that - implements the Message Passing Interface, version 3.1 (MPI-3.1) specification. - package: impi - url: https://software.intel.com/en-us/intel-mpi-library - versions: - - description: Intel® MPI Library is a multi-fabric message passing library - that implements the Message Passing Interface, version 3.1 (MPI-3.1) specification. - family: mpi - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 2017.u2 - - description: Intel® MPI Library is a multi-fabric message passing library - that implements the Message Passing Interface, version 3.1 (MPI-3.1) specification. - family: mpi - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 2018.u1 - - description: Intel® MPI Library is a multi-fabric message passing library - that implements the Message Passing Interface, version 3.1 (MPI-3.1) specification. - family: mpi - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '2018' - - description: Intel® MPI Library is a multi-fabric message passing library - that implements the Message Passing Interface, version 3.1 (MPI-3.1) specification. - family: mpi - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '2019' - - categories: devel, lib - defaultVersionName: 2.1.12 - description: The libevent API provides a mechanism to execute a callback function - when a specific event occurs on a file descriptor or after a timeout has been - reached. - package: libevent - url: https://libevent.org - versions: - - {description: The libevent API provides a mechanism to execute a callback - function when a specific event occurs on a file descriptor or after a timeout - has been reached., markedDefault: false, versionName: 2.1.12} - categories: devel, lib defaultVersionName: 1.79.0 description: Boost is a set of libraries for the C++ programming language that @@ -6525,6 +6526,16 @@ software_modules: properties: parallel: {mpi: 1} versionName: 1.79.0 + - categories: devel, lib + defaultVersionName: 4.2.2 + description: ZeroMQ (also spelled ØMQ, 0MQ or ZMQ) is a high-performance asynchronous + messaging library, aimed at use in distributed or concurrent applications. + package: zeromq + url: http://zeromq.org + versions: + - {description: 'ZeroMQ (also spelled ØMQ, 0MQ or ZMQ) is a high-performance + asynchronous messaging library, aimed at use in distributed or concurrent + applications.', markedDefault: false, versionName: 4.2.2} - categories: devel, lib defaultVersionName: '2019' description: Intel® Threading Building Blocks (Intel® TBB) is a widely used @@ -6545,6 +6556,32 @@ software_modules: - {description: Intel® Threading Building Blocks (Intel® TBB) is a widely used C++ library for shared-memory parallel programming and heterogeneous computing (intra-node distributed memory programming)., markedDefault: false, versionName: '2019'} + - categories: devel, build + defaultVersionName: 1.8.0 + description: Bazelisk is a wrapper for Bazel written in Go. + package: bazelisk + url: https://github.com/bazelbuild/bazelisk + versions: + - {description: Bazelisk is a wrapper for Bazel written in Go., family: bazel, + markedDefault: false, versionName: 1.3.0} + - {description: Bazelisk is a wrapper for Bazel written in Go., family: bazel, + markedDefault: false, versionName: 1.8.0} + - categories: devel, language + defaultVersionName: 5.4.1_py27 + description: IPython is a command shell for interactive computing in multiple + programming languages, originally developed for the Python programming language. + package: py-ipython + url: https://ipython.org + versions: + - {description: 'IPython is a command shell for interactive computing in multiple + programming languages, originally developed for the Python programming language.', + markedDefault: false, versionName: 6.1.0_py36} + - {description: 'IPython is a command shell for interactive computing in multiple + programming languages, originally developed for the Python programming language.', + markedDefault: false, versionName: 8.3.0_py39} + - {description: 'IPython is a command shell for interactive computing in multiple + programming languages, originally developed for the Python programming language.', + markedDefault: true, versionName: 5.4.1_py27} - categories: devel, lib defaultVersionName: 0.35.0_py27 description: Numba is a compiler for Python array and numerical functions that @@ -6565,31 +6602,41 @@ software_modules: - {description: Numba is a compiler for Python array and numerical functions that gives you the power to speed up your applications with high performance functions written directly in Python.., markedDefault: true, versionName: 0.35.0_py27} - - categories: devel, language - defaultVersionName: 1.72.0 - description: A language empowering everyone to build reliable and efficient - software. - package: rust - url: https://www.rust-lang.org/ - versions: - - {description: A language empowering everyone to build reliable and efficient - software., markedDefault: false, versionName: 1.35.0} - - {description: A language empowering everyone to build reliable and efficient - software., markedDefault: false, versionName: 1.56.1} - - {description: A language empowering everyone to build reliable and efficient - software., markedDefault: false, versionName: 1.63.0} - - {description: A language empowering everyone to build reliable and efficient - software., markedDefault: false, versionName: 1.72.0} - - categories: devel, build - defaultVersionName: 1.8.0 - description: Bazelisk is a wrapper for Bazel written in Go. - package: bazelisk - url: https://github.com/bazelbuild/bazelisk + - categories: devel, data + defaultVersionName: 4.9.0 + description: NetCDF is a set of software libraries and self-describing, machine-independent + data formats that support the creation, access, and sharing of array-oriented + scientific data. This module provides C libraries. + package: netcdf-c + url: https://www.unidata.ucar.edu/software/netcdf versions: - - {description: Bazelisk is a wrapper for Bazel written in Go., family: bazel, - markedDefault: false, versionName: 1.3.0} - - {description: Bazelisk is a wrapper for Bazel written in Go., family: bazel, - markedDefault: false, versionName: 1.8.0} + - description: NetCDF is a set of software libraries and self-describing, machine-independent + data formats that support the creation, access, and sharing of array-oriented + scientific data. This module provides C libraries. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 4.9.0 + - categories: devel, lib + defaultVersionName: 0.20.0_py39 + description: scikit-image is a collection of algorithms for image processing. + package: py-scikit-image + url: http://scikit-image.org/ + versions: + - {description: scikit-image is a collection of algorithms for image processing., + markedDefault: false, versionName: 0.13.0_py27} + - {description: scikit-image is a collection of algorithms for image processing., + markedDefault: false, versionName: 0.14.0_py27} + - {description: scikit-image is a collection of algorithms for image processing., + markedDefault: false, versionName: 0.15.0_py27} + - {description: scikit-image is a collection of algorithms for image processing., + markedDefault: false, versionName: 0.15.0_py36} + - {description: scikit-image is a collection of algorithms for image processing., + markedDefault: false, versionName: 0.17.2_py36} + - {description: scikit-image is a collection of algorithms for image processing., + markedDefault: false, versionName: 0.19.3_py39} + - {description: scikit-image is a collection of algorithms for image processing., + markedDefault: false, versionName: 0.20.0_py39} - categories: devel, framework defaultVersionName: 5.8.2 description: Global Arrays (GA) is a Partitioned Global Address Space (PGAS) @@ -6617,17 +6664,22 @@ software_modules: versions: - {description: Kerl is a tool to easily build and install Erlang/OTP instances., markedDefault: false, versionName: 1.8.5} - - categories: devel, language - defaultVersionName: 7.3.0 - description: 'PHP (recursive acronym for PHP: Hypertext Preprocessor) is an - open source general-purpose scripting language that is especially suited for - web development.' - package: php - url: http://www.php.net + - categories: devel, data + defaultVersionName: 3.4.0 + description: Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, + platform-neutral, extensible mechanism for serializing structured data. + package: protobuf + url: https://developers.google.com/protocol-buffers/ versions: - - {description: 'PHP (recursive acronym for PHP: Hypertext Preprocessor) is - an open source general-purpose scripting language that is especially suited - for web development.', markedDefault: false, versionName: 7.3.0} + - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, + platform-neutral, extensible mechanism for serializing structured data.', + markedDefault: false, versionName: 3.20.0} + - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, + platform-neutral, extensible mechanism for serializing structured data.', + markedDefault: false, versionName: '21.9'} + - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, + platform-neutral, extensible mechanism for serializing structured data.', + markedDefault: true, versionName: 3.4.0} - categories: devel, compiler defaultVersionName: 2.2.0 description: AMD Optimizing C/C++ Compiler - AOCC is a highly optimized C, C++ @@ -6648,26 +6700,22 @@ software_modules: url: https://www.gnu.org/software/gdb/ versions: - {description: GDB is the GNU Project debugger., markedDefault: false, versionName: 8.2.1} - - categories: devel, lib - defaultVersionName: 0.20.0_py39 - description: scikit-image is a collection of algorithms for image processing. - package: py-scikit-image - url: http://scikit-image.org/ + - categories: devel, language + defaultVersionName: 1.0.0_py27 + description: Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins. + package: py-jupyter + url: https://jupyter.org versions: - - {description: scikit-image is a collection of algorithms for image processing., - markedDefault: false, versionName: 0.13.0_py27} - - {description: scikit-image is a collection of algorithms for image processing., - markedDefault: false, versionName: 0.14.0_py27} - - {description: scikit-image is a collection of algorithms for image processing., - markedDefault: false, versionName: 0.15.0_py27} - - {description: scikit-image is a collection of algorithms for image processing., - markedDefault: false, versionName: 0.15.0_py36} - - {description: scikit-image is a collection of algorithms for image processing., - markedDefault: false, versionName: 0.17.2_py36} - - {description: scikit-image is a collection of algorithms for image processing., - markedDefault: false, versionName: 0.19.3_py39} - - {description: scikit-image is a collection of algorithms for image processing., - markedDefault: false, versionName: 0.20.0_py39} + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: false, versionName: 1.0.0_py36} + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: false, versionName: 1.0.0_py39} + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: true, versionName: 1.0.0_py27} - categories: devel, data defaultVersionName: 1.10.6 description: HDF5 is a data model, library, and file format for storing and @@ -6705,45 +6753,68 @@ software_modules: properties: parallel: {mpi: 1} versionName: 1.10.6 - - categories: devel, language - defaultVersionName: 3.1.2 - description: A dynamic, open source programming language with a focus on simplicity - and productivity. It has an elegant syntax that is natural to read and easy - to write. - package: ruby - url: https://www.ruby-lang.org + - categories: devel, lib + defaultVersionName: 23.04.00_py39 + description: Python interface for RMM + package: py-rmm + url: https://github.com/rapidsai/rmm versions: - - {description: 'A dynamic, open source programming language with a focus on - simplicity and productivity. It has an elegant syntax that is natural to - read and easy to write.', markedDefault: false, versionName: 2.4.1} - - {description: 'A dynamic, open source programming language with a focus on - simplicity and productivity. It has an elegant syntax that is natural to - read and easy to write.', markedDefault: false, versionName: 2.7.1} - - {description: 'A dynamic, open source programming language with a focus on - simplicity and productivity. It has an elegant syntax that is natural to - read and easy to write.', markedDefault: false, versionName: 3.1.2} - - categories: devel, data - defaultVersionName: 4.0.1 - description: Redis is an open source, in-memory data structure store, used as - a database, cache and message broker. - package: redis - url: https://redis.io + - description: Python interface for RMM + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 23.04.00_py39 + - categories: devel, networking + defaultVersionName: 1.12.1 + description: UCX is a communication library implementing high-performance messaging + for MPI/PGAS frameworks. + package: ucx + url: http://www.openucx.org versions: - - {description: 'Redis is an open source, in-memory data structure store, used - as a database, cache and message broker.', markedDefault: false, versionName: 4.0.1} - - categories: devel, language - defaultVersionName: 2.2.2 - description: GNU Guile is the preferred extension system for the GNU Project, - which features an implementation of the Scheme programming language. - package: guile - url: https://www.gnu.org/software/guile/ + - {description: UCX is a communication library implementing high-performance + messaging for MPI/PGAS frameworks., markedDefault: false, versionName: 1.3.1} + - description: UCX is a communication library implementing high-performance + messaging for MPI/PGAS frameworks. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 1.8.1 + - description: UCX is a communication library implementing high-performance + messaging for MPI/PGAS frameworks. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 1.9.0 + - description: UCX is a communication library implementing high-performance + messaging for MPI/PGAS frameworks. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 1.10.0 + - description: UCX is a communication library implementing high-performance + messaging for MPI/PGAS frameworks. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 1.12.1 + - categories: devel, lib + defaultVersionName: 3.1.0 + description: CUTLASS is a collection of CUDA C++ template abstractions for implementing + high-performance matrix-multiplication (GEMM) at all levels and scales within + CUDA. + package: cutlass + url: https://github.com/NVIDIA/cutlass versions: - - {description: 'GNU Guile is the preferred extension system for the GNU Project, - which features an implementation of the Scheme programming language.', markedDefault: false, - versionName: 2.0.11} - - {description: 'GNU Guile is the preferred extension system for the GNU Project, - which features an implementation of the Scheme programming language.', markedDefault: false, - versionName: 2.2.2} + - {description: CUTLASS is a collection of CUDA C++ template abstractions for + implementing high-performance matrix-multiplication (GEMM) at all levels + and scales within CUDA., markedDefault: false, versionName: 0.1.0} + - description: CUTLASS is a collection of CUDA C++ template abstractions for + implementing high-performance matrix-multiplication (GEMM) at all levels + and scales within CUDA. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 3.1.0 - categories: devel, data analytics defaultVersionName: 3.1.0 description: The Apache Hadoop software library is a framework that allows for @@ -6950,17 +7021,22 @@ software_modules: properties: arch: {gpu: 1} versionName: 9.0.176 - - categories: devel, lib - defaultVersionName: 23.04.00_py39 - description: Python interface for RMM - package: py-rmm - url: https://github.com/rapidsai/rmm + - categories: devel, language + defaultVersionName: 4.0.7_py39 + description: Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins. + package: py-jupyterlab + url: https://jupyter.org versions: - - description: Python interface for RMM - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 23.04.00_py39 + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: false, versionName: 0.33.12_py27} + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: false, versionName: 3.0.9_py36} + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: false, versionName: 4.0.7_py39} - categories: devel, build defaultVersionName: 0.51.1_py36 description: Meson is an open source build system meant to be both extremely @@ -6984,16 +7060,14 @@ software_modules: - {description: 'C++ wrappers for SIMD intrinsics and parallelized, optimized mathematical functions (SSE, AVX, NEON, AVX512)', markedDefault: false, versionName: 8.1.0} - - categories: devel, language - defaultVersionName: 8.6.5 - description: Haskell is a statically typed, purely functional programming language - with type inference and lazy evaluation. - package: haskell - url: https://www.haskell.org/ + - categories: devel, data + defaultVersionName: 0.13.3 + description: Hiredis is a minimalistic C client library for the Redis database. + package: hiredis + url: https://github.com/redis/hiredis versions: - - {description: 'Haskell is a statically typed, purely functional programming - language with type inference and lazy evaluation.', markedDefault: false, - versionName: 8.6.5} + - {description: Hiredis is a minimalistic C client library for the Redis database., + markedDefault: false, versionName: 0.13.3} - categories: devel, lib defaultVersionName: 3.1.0_py39 description: Python interface for CUTLASS @@ -7005,48 +7079,28 @@ software_modules: properties: arch: {gpu: 1} versionName: 3.1.0_py39 - - categories: devel, networking - defaultVersionName: 1.12.1 - description: UCX is a communication library implementing high-performance messaging - for MPI/PGAS frameworks. - package: ucx - url: http://www.openucx.org + - categories: devel, lib + defaultVersionName: 0.3.0 + description: libcircle is an API for distributing embarrassingly parallel workloads + using self-stabilization. + package: libcircle + url: https://github.com/hpc/libcircle versions: - - {description: UCX is a communication library implementing high-performance - messaging for MPI/PGAS frameworks., markedDefault: false, versionName: 1.3.1} - - description: UCX is a communication library implementing high-performance - messaging for MPI/PGAS frameworks. + - description: libcircle is an API for distributing embarrassingly parallel + workloads using self-stabilization. markedDefault: false properties: - arch: {gpu: 1} - versionName: 1.8.1 - - description: UCX is a communication library implementing high-performance - messaging for MPI/PGAS frameworks. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 1.9.0 - - description: UCX is a communication library implementing high-performance - messaging for MPI/PGAS frameworks. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 1.10.0 - - description: UCX is a communication library implementing high-performance - messaging for MPI/PGAS frameworks. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 1.12.1 - - categories: devel, lib - defaultVersionName: 1.10.0 - description: CUB is a flexible library of cooperative threadblock primitives - and other utilities for CUDA kernel programming. - package: cub - url: https://nvlabs.github.io/cub/ - versions: - - description: CUB is a flexible library of cooperative threadblock primitives - and other utilities for CUDA kernel programming. + parallel: {mpi: 1} + versionName: 0.3.0 + - categories: devel, lib + defaultVersionName: 1.10.0 + description: CUB is a flexible library of cooperative threadblock primitives + and other utilities for CUDA kernel programming. + package: cub + url: https://nvlabs.github.io/cub/ + versions: + - description: CUB is a flexible library of cooperative threadblock primitives + and other utilities for CUDA kernel programming. markedDefault: false properties: arch: {gpu: 1} @@ -7057,25 +7111,6 @@ software_modules: properties: arch: {gpu: 1} versionName: 1.10.0 - - categories: devel, data - defaultVersionName: 0.13.3 - description: Hiredis is a minimalistic C client library for the Redis database. - package: hiredis - url: https://github.com/redis/hiredis - versions: - - {description: Hiredis is a minimalistic C client library for the Redis database., - markedDefault: false, versionName: 0.13.3} - - categories: devel, lib - defaultVersionName: 1.10.1 - description: Apache Ant is a Java library and command-line tool whose mission - is to drive processes described in build files as targets and extension points - dependent upon each other. - package: ant - url: https://ant.apache.org/ - versions: - - {description: Apache Ant is a Java library and command-line tool whose mission - is to drive processes described in build files as targets and extension - points dependent upon each other., markedDefault: false, versionName: 1.10.1} - categories: devel, networking defaultVersionName: 1.30.0 description: GASNet is a language-independent, low-level networking layer that @@ -7092,6 +7127,17 @@ software_modules: properties: parallel: {mpi: 1} versionName: 1.30.0 + - categories: devel, lib + defaultVersionName: 1.10.1 + description: Apache Ant is a Java library and command-line tool whose mission + is to drive processes described in build files as targets and extension points + dependent upon each other. + package: ant + url: https://ant.apache.org/ + versions: + - {description: Apache Ant is a Java library and command-line tool whose mission + is to drive processes described in build files as targets and extension + points dependent upon each other., markedDefault: false, versionName: 1.10.1} - categories: devel, compiler defaultVersionName: '19.10' description: PGI compilers and tools, including Open MPI (Community Edition). @@ -7100,6 +7146,14 @@ software_modules: versions: - {description: 'PGI compilers and tools, including Open MPI (Community Edition).', family: mpi, markedDefault: false, versionName: '19.10'} + - categories: devel, profiling + defaultVersionName: 3.3.462 + description: AMD uProf is a performance analysis tool for applications. + package: amd-uprof + url: https://developer.amd.com/amd-uprof/ + versions: + - {description: AMD uProf is a performance analysis tool for applications., + markedDefault: false, versionName: 3.3.462} - categories: devel, lib defaultVersionName: 1.0.4 description: The Light-weight Group Library provides methods for MPI codes to @@ -7113,27 +7167,6 @@ software_modules: properties: parallel: {mpi: 1} versionName: 1.0.4 - - categories: devel, lib - defaultVersionName: 0.3.0 - description: libcircle is an API for distributing embarrassingly parallel workloads - using self-stabilization. - package: libcircle - url: https://github.com/hpc/libcircle - versions: - - description: libcircle is an API for distributing embarrassingly parallel - workloads using self-stabilization. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 0.3.0 - - categories: devel, build - defaultVersionName: '2.38' - description: The GNU Binutils are a collection of binary tools. - package: binutils - url: https://www.gnu.org/software/binutils/ - versions: - - {description: The GNU Binutils are a collection of binary tools., markedDefault: false, - versionName: '2.38'} - categories: devel, lib defaultVersionName: 0.3.2_py39 description: schwimmbad provides a uniform interface to parallel processing @@ -7159,14 +7192,54 @@ software_modules: properties: parallel: {mpi: 1} versionName: 0.3.2_py39 - - categories: devel, profiling - defaultVersionName: 3.3.462 - description: AMD uProf is a performance analysis tool for applications. - package: amd-uprof - url: https://developer.amd.com/amd-uprof/ + - categories: devel, build + defaultVersionName: '2.38' + description: The GNU Binutils are a collection of binary tools. + package: binutils + url: https://www.gnu.org/software/binutils/ versions: - - {description: AMD uProf is a performance analysis tool for applications., - markedDefault: false, versionName: 3.3.462} + - {description: The GNU Binutils are a collection of binary tools., markedDefault: false, + versionName: '2.38'} + - categories: devel, data + defaultVersionName: 2.0.1_py39 + description: pandas is an open source, BSD-licensed library providing high-performance, + easy-to-use data structures and data analysis tools for the Python programming + language. + package: py-pandas + url: https://pandas.pydata.org/ + versions: + - {description: 'pandas is an open source, BSD-licensed library providing high-performance, + easy-to-use data structures and data analysis tools for the Python programming + language.', family: pandas, markedDefault: false, versionName: 0.23.0_py27} + - {description: 'pandas is an open source, BSD-licensed library providing high-performance, + easy-to-use data structures and data analysis tools for the Python programming + language.', family: pandas, markedDefault: false, versionName: 0.23.0_py36} + - {description: 'pandas is an open source, BSD-licensed library providing high-performance, + easy-to-use data structures and data analysis tools for the Python programming + language.', family: pandas, markedDefault: false, versionName: 1.0.3_py36} + - {description: 'pandas is an open source, BSD-licensed library providing high-performance, + easy-to-use data structures and data analysis tools for the Python programming + language.', family: pandas, markedDefault: false, versionName: 1.3.1_py39} + - {description: 'pandas is an open source, BSD-licensed library providing high-performance, + easy-to-use data structures and data analysis tools for the Python programming + language.', family: pandas, markedDefault: false, versionName: 2.0.1_py39} + - categories: devel, language + defaultVersionName: 3.1.2 + description: A dynamic, open source programming language with a focus on simplicity + and productivity. It has an elegant syntax that is natural to read and easy + to write. + package: ruby + url: https://www.ruby-lang.org + versions: + - {description: 'A dynamic, open source programming language with a focus on + simplicity and productivity. It has an elegant syntax that is natural to + read and easy to write.', markedDefault: false, versionName: 2.4.1} + - {description: 'A dynamic, open source programming language with a focus on + simplicity and productivity. It has an elegant syntax that is natural to + read and easy to write.', markedDefault: false, versionName: 2.7.1} + - {description: 'A dynamic, open source programming language with a focus on + simplicity and productivity. It has an elegant syntax that is natural to + read and easy to write.', markedDefault: false, versionName: 3.1.2} - categories: devel, lib defaultVersionName: 3.0.12 description: SWIG is an interface compiler that connects programs written in @@ -7177,21 +7250,15 @@ software_modules: - {description: 'SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, and Tcl.', markedDefault: false, versionName: 3.0.12} - - categories: devel, data - defaultVersionName: 4.9.0 - description: NetCDF is a set of software libraries and self-describing, machine-independent - data formats that support the creation, access, and sharing of array-oriented - scientific data. This module provides C libraries. - package: netcdf-c - url: https://www.unidata.ucar.edu/software/netcdf + - categories: devel, debug + defaultVersionName: 3.14.0 + description: Valgrind is an instrumentation framework for building dynamic analysis + tools. + package: valgrind + url: http://valgrind.org/ versions: - - description: NetCDF is a set of software libraries and self-describing, machine-independent - data formats that support the creation, access, and sharing of array-oriented - scientific data. This module provides C libraries. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 4.9.0 + - {description: Valgrind is an instrumentation framework for building dynamic + analysis tools., markedDefault: false, versionName: 3.14.0} - categories: devel, lib defaultVersionName: 2.7.1_py27 description: The h5py package is a Pythonic interface to the HDF5 binary data @@ -7209,19 +7276,15 @@ software_modules: data format., markedDefault: false, versionName: 3.7.0_py39} - {description: The h5py package is a Pythonic interface to the HDF5 binary data format., markedDefault: true, versionName: 2.7.1_py27} - - categories: devel, lib - defaultVersionName: 1.0.0 - description: CNMeM is a simple library to help the Deep Learning frameworks - manage CUDA memory. - package: cnmem - url: https://github.com/NVIDIA/ncmem + - categories: devel, framework + defaultVersionName: 0.18.0_py39 + description: Kedro is an open-source Python framework for creating reproducible, + maintainable and modular data science code. + package: py-kedro + url: https://kedro.readthedocs.io/ versions: - - description: CNMeM is a simple library to help the Deep Learning frameworks - manage CUDA memory. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 1.0.0 + - {description: 'Kedro is an open-source Python framework for creating reproducible, + maintainable and modular data science code.', markedDefault: false, versionName: 0.18.0_py39} - categories: devel, language defaultVersionName: 1.8.0_131 description: Java is a general-purpose computer programming language that is @@ -7320,39 +7383,28 @@ software_modules: parallel: {mpi: 1} versionName: 4.1.2 - categories: devel, language - defaultVersionName: 1.0.0_py27 - description: Jupyter is a browser-based interactive notebook for programming, - mathematics, and data science. It supports a number of languages via plugins. - package: py-jupyter - url: https://jupyter.org + defaultVersionName: 8.6.5 + description: Haskell is a statically typed, purely functional programming language + with type inference and lazy evaluation. + package: haskell + url: https://www.haskell.org/ versions: - - {description: 'Jupyter is a browser-based interactive notebook for programming, - mathematics, and data science. It supports a number of languages via plugins.', - markedDefault: false, versionName: 1.0.0_py36} - - {description: 'Jupyter is a browser-based interactive notebook for programming, - mathematics, and data science. It supports a number of languages via plugins.', - markedDefault: false, versionName: 1.0.0_py39} - - {description: 'Jupyter is a browser-based interactive notebook for programming, - mathematics, and data science. It supports a number of languages via plugins.', - markedDefault: true, versionName: 1.0.0_py27} - - categories: devel, lib - defaultVersionName: 3.1.0 - description: CUTLASS is a collection of CUDA C++ template abstractions for implementing - high-performance matrix-multiplication (GEMM) at all levels and scales within - CUDA. - package: cutlass - url: https://github.com/NVIDIA/cutlass + - {description: 'Haskell is a statically typed, purely functional programming + language with type inference and lazy evaluation.', markedDefault: false, + versionName: 8.6.5} + - categories: devel, language + defaultVersionName: 2.2.2 + description: GNU Guile is the preferred extension system for the GNU Project, + which features an implementation of the Scheme programming language. + package: guile + url: https://www.gnu.org/software/guile/ versions: - - {description: CUTLASS is a collection of CUDA C++ template abstractions for - implementing high-performance matrix-multiplication (GEMM) at all levels - and scales within CUDA., markedDefault: false, versionName: 0.1.0} - - description: CUTLASS is a collection of CUDA C++ template abstractions for - implementing high-performance matrix-multiplication (GEMM) at all levels - and scales within CUDA. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 3.1.0 + - {description: 'GNU Guile is the preferred extension system for the GNU Project, + which features an implementation of the Scheme programming language.', markedDefault: false, + versionName: 2.0.11} + - {description: 'GNU Guile is the preferred extension system for the GNU Project, + which features an implementation of the Scheme programming language.', markedDefault: false, + versionName: 2.2.2} - categories: devel, language defaultVersionName: 5.3.4 description: Lua is a powerful, efficient, lightweight, embeddable scripting @@ -7376,44 +7428,36 @@ software_modules: properties: arch: {gpu: 1} versionName: 23.04.00 - - categories: devel, runtime - defaultVersionName: 1.3.2 - description: StarPU is a unified runtime system that offers support for heterogeneous - multicore architectures - package: starpu - url: https://gforge.inria.fr/projects/starpu/ + - categories: devel, language + defaultVersionName: 7.3.0 + description: 'PHP (recursive acronym for PHP: Hypertext Preprocessor) is an + open source general-purpose scripting language that is especially suited for + web development.' + package: php + url: http://www.php.net versions: - - description: StarPU is a unified runtime system that offers support for heterogeneous - multicore architectures - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 1.3.2 + - {description: 'PHP (recursive acronym for PHP: Hypertext Preprocessor) is + an open source general-purpose scripting language that is especially suited + for web development.', markedDefault: false, versionName: 7.3.0} - categories: devel, compiler - defaultVersionName: 7.0.0 - description: The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler, - package: llvm - url: http://llvm.org + defaultVersionName: '2019' + description: Intel C++ Compiler, also known as icc or icl, is a group of C and + C++ compilers from Intel + package: icc + url: https://software.intel.com/en-us/c-compilers versions: - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 3.8.1} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 4.0.0} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 5.0.0} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 9.0.1} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 15.0.3} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: true, versionName: 7.0.0} + - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of + C and C++ compilers from Intel', family: compiler_c, markedDefault: false, + versionName: 2017.u2} + - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of + C and C++ compilers from Intel', family: compiler_c, markedDefault: false, + versionName: 2018.u1} + - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of + C and C++ compilers from Intel', family: compiler_c, markedDefault: false, + versionName: '2018'} + - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of + C and C++ compilers from Intel', family: compiler_c, markedDefault: false, + versionName: '2019'} - categories: devel, data analytics defaultVersionName: 0.3_py27 description: 'Launching and controlling spark on HPC clusters ' @@ -7450,23 +7494,43 @@ software_modules: - {description: 'Intel Fortran Compiler, also known as ifort, is a group of Fortran compilers from Intel', family: compiler_f, markedDefault: false, versionName: '2019'} - - categories: devel, lib - defaultVersionName: 1.12.1 - description: Light-weight, simple and fast XML parser for C++ with XPath support. - package: pugixml - url: http://pugixml.org/ + - categories: devel, runtime + defaultVersionName: 1.3.2 + description: StarPU is a unified runtime system that offers support for heterogeneous + multicore architectures + package: starpu + url: https://gforge.inria.fr/projects/starpu/ versions: - - {description: 'Light-weight, simple and fast XML parser for C++ with XPath - support.', markedDefault: false, versionName: 1.12.1} - - categories: devel, framework - defaultVersionName: 0.18.0_py39 - description: Kedro is an open-source Python framework for creating reproducible, - maintainable and modular data science code. - package: py-kedro - url: https://kedro.readthedocs.io/ + - description: StarPU is a unified runtime system that offers support for heterogeneous + multicore architectures + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.3.2 + - categories: devel, IDE + defaultVersionName: 4.16.1 + description: Run VS Code on any machine anywhere and access it in the browser. + package: code-server + url: https://github.com/coder/code-server + versions: + - {description: Run VS Code on any machine anywhere and access it in the browser., + markedDefault: false, versionName: 4.16.1} + - categories: devel, language + defaultVersionName: 2.7.13 + description: Python is an interpreted, interactive, object-oriented programming + language. + package: python + url: https://www.python.org versions: - - {description: 'Kedro is an open-source Python framework for creating reproducible, - maintainable and modular data science code.', markedDefault: false, versionName: 0.18.0_py39} + - {description: 'Python is an interpreted, interactive, object-oriented programming + language.', family: python, help: 'https://www.sherlock.stanford.edu/docs/software/using/python', + markedDefault: false, versionName: 3.6.1} + - {description: 'Python is an interpreted, interactive, object-oriented programming + language.', family: python, help: 'https://www.sherlock.stanford.edu/docs/software/using/python', + markedDefault: false, versionName: 3.9.0} + - {description: 'Python is an interpreted, interactive, object-oriented programming + language.', family: python, help: 'https://www.sherlock.stanford.edu/docs/software/using/python', + markedDefault: true, versionName: 2.7.13} - categories: devel, lib defaultVersionName: 2.2.2 description: Copy-hiding array abstraction to automatically migrate data between @@ -7481,38 +7545,14 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: 2.2.2 - - categories: devel, data - defaultVersionName: 3.4.0 - description: Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, - platform-neutral, extensible mechanism for serializing structured data. - package: protobuf - url: https://developers.google.com/protocol-buffers/ - versions: - - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, - platform-neutral, extensible mechanism for serializing structured data.', - markedDefault: false, versionName: 3.20.0} - - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, - platform-neutral, extensible mechanism for serializing structured data.', - markedDefault: false, versionName: '21.9'} - - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, - platform-neutral, extensible mechanism for serializing structured data.', - markedDefault: true, versionName: 3.4.0} - - categories: devel, language - defaultVersionName: 5.4.1_py27 - description: IPython is a command shell for interactive computing in multiple - programming languages, originally developed for the Python programming language. - package: py-ipython - url: https://ipython.org + - categories: devel, lib + defaultVersionName: 1.12.1 + description: Light-weight, simple and fast XML parser for C++ with XPath support. + package: pugixml + url: http://pugixml.org/ versions: - - {description: 'IPython is a command shell for interactive computing in multiple - programming languages, originally developed for the Python programming language.', - markedDefault: false, versionName: 6.1.0_py36} - - {description: 'IPython is a command shell for interactive computing in multiple - programming languages, originally developed for the Python programming language.', - markedDefault: false, versionName: 8.3.0_py39} - - {description: 'IPython is a command shell for interactive computing in multiple - programming languages, originally developed for the Python programming language.', - markedDefault: true, versionName: 5.4.1_py27} + - {description: 'Light-weight, simple and fast XML parser for C++ with XPath + support.', markedDefault: false, versionName: 1.12.1} - categories: devel, compiler defaultVersionName: '110.81' description: Standard ML of New Jersey (abbreviated SML/NJ) is a compiler for @@ -7522,15 +7562,37 @@ software_modules: versions: - {description: Standard ML of New Jersey (abbreviated SML/NJ) is a compiler for the Standard ML '97 programming language., markedDefault: false, versionName: '110.81'} - - categories: devel, data - defaultVersionName: 4.8.0 - description: The NCO toolkit manipulates and analyzes data stored in netCDF-accessible - formats. - package: nco - url: http://nco.sourceforge.net/ + - categories: devel, compiler + defaultVersionName: '21.5' + description: NVIDIA HPC Software Development Kit (SDK) including C, C++, and + Fortran compilers. + package: nvhpc + url: https://developer.nvidia.com/hpc-sdk versions: - - {description: The NCO toolkit manipulates and analyzes data stored in netCDF-accessible - formats., markedDefault: false, versionName: 5.0.6} - - {description: The NCO toolkit manipulates and analyzes data stored in netCDF-accessible - formats., markedDefault: true, versionName: 4.8.0} + - description: NVIDIA HPC Software Development Kit (SDK) including C, C++, and + Fortran compilers. + family: mpi + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '21.7' + - description: NVIDIA HPC Software Development Kit (SDK) including C, C++, and + Fortran compilers. + family: mpi + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '22.3' + - description: NVIDIA HPC Software Development Kit (SDK) including C, C++, and + Fortran compilers. + family: mpi + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '23.3' + - {description: 'NVIDIA HPC Software Development Kit (SDK) including C, C++, + and Fortran compilers.', family: compiler_f, markedDefault: true, versionName: '21.5'} diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index 552e46f86..291c57133 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,69 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + 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 + + + New version: biology/relion version 4.0.1 + RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). + https://github.com/3dem/relion + https://www.sherlock.stanford.edu/docs/software/list/?add:v=4.0.1#relion + biology, cryo-em + kilian@stanford.edu (Kilian Cavalotti) + Tue, 24 Oct 2023 16:24:43 -0700 + + + New module: devel/code-server version 4.16.1 + Run VS Code on any machine anywhere and access it in the browser. + https://github.com/coder/code-server + https://www.sherlock.stanford.edu/docs/software/list/?add:v=4.16.1#code-server + devel, IDE + kilian@stanford.edu (Kilian Cavalotti) + Wed, 11 Oct 2023 11:47:39 -0700 + + + New version: system/curl version 8.4.0 + curl is an open source command line tool and library for transferring data with URL syntax. + https://curl.haxx.se/ + https://www.sherlock.stanford.edu/docs/software/list/?add:v=8.4.0#curl + system, tools + kilian@stanford.edu (Kilian Cavalotti) + Wed, 11 Oct 2023 08:43:26 -0700 + + + New version: devel/code-server version 4.16.1 + Run VS Code on any machine anywhere and access it in the browser. + https://github.com/coder/code-server + https://www.sherlock.stanford.edu/docs/software/list/?add:v=4.16.1#code-server + devel, IDE + mthartma@stanford.edu (Mike Hartman) + Tue, 10 Oct 2023 08:02:44 -0700 + New version: system/hwloc version 2.9.3 The Portable Hardware Locality (hwloc) software package provides a portable abstraction of the hierarchical topology of modern architectures. @@ -167,41 +230,5 @@ kilian@stanford.edu (Kilian Cavalotti) Fri, 18 Aug 2023 13:56:51 -0700 - - New module: system/jansson version 2.13.1 - C library for encoding, decoding and manipulating JSON data. - https://github.com/akheron/jansson - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.13.1#jansson - system, libs - kilian@stanford.edu (Kilian Cavalotti) - Mon, 14 Aug 2023 08:29:17 -0700 - - - New module: physics/swash version 9.01a - SWASH (an acronym of Simulating WAves till SHore) is a non-hydrostatic wave-flow model. - https://swash.sourceforge.io/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=9.01a#swash - physics, geoscience - kilian@stanford.edu (Kilian Cavalotti) - Thu, 20 Jul 2023 17:09:20 -0700 - - - New module: biology/py-vcf2gwas version 0.8.9_py39 - Python API for comprehensive GWAS analysis using GEMMA. - https://github.com/frankvogt/vcf2gwas - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.8.9_py39#py-vcf2gwas - biology, genomics - kilian@stanford.edu (Kilian Cavalotti) - Mon, 17 Jul 2023 18:23:53 -0700 - - - New module: biology/gemma version 0.98.5 - 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. - https://github.com/genetics-statistics/GEMMA - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.98.5#gemma - biology, genomics - kilian@stanford.edu (Kilian Cavalotti) - Mon, 17 Jul 2023 18:23:37 -0700 -