Package ListΒΆ
This is a list of things you can install using Spack. It is automatically generated based on the packages in this Spack version.
Spack currently has 5619 mainline packages:
3dtk¶
- Homepage:
- Spack package:
- Versions:
- trunk, 1.2
- Build Dependencies:
- cmake, ninja, boost, suite-sparse, zlib, libpng, eigen, cgal, gl, glew, freeglut, opencv, cuda
- Link Dependencies:
- boost, suite-sparse, zlib, libpng, eigen, cgal, gl, glew, freeglut, opencv, cuda
- Description:
- The 3D Toolkit provides algorithms and methods to process 3D point clouds. It includes automatic high-accurate registration (6D simultaneous localization and mapping, 6D SLAM) and other tools, e.g., a fast 3D viewer, plane extraction software, etc. Several file formats for the point clouds are natively supported, new formats can be implemented easily.
3proxy¶
- Homepage:
- Spack package:
- Versions:
- 0.8.13, 0.8.12, 0.8.11
- Build Dependencies:
- autoconf, automake, libtool, m4
- Description:
- 3proxy - tiny free proxy server
abduco¶
- Homepage:
- Spack package:
- Versions:
- 0.6, 0.5, 0.4
- Description:
- abduco provides session management i.e. it allows programs to be run independently from its controlling terminal. That is programs can be detached - run in the background - and then later reattached. Together with dvtm it provides a simpler and cleaner alternative to tmux or screen.
abi-compliance-checker¶
- Homepage:
- Spack package:
- Versions:
- 2.3, 2.2, 2.1
- Build Dependencies:
- abi-dumper, perl, binutils, universal-ctags
- Link Dependencies:
- abi-dumper, perl, binutils, universal-ctags
- Description:
- A tool for checking backward compatibility of a C/C++ library API.
abi-dumper¶
- Homepage:
- Spack package:
- Versions:
- 1.1, 1.0, 0.99.19
- Build Dependencies:
- perl, elfutils, binutils, universal-ctags, vtable-dumper
- Link Dependencies:
- perl, elfutils, binutils, universal-ctags, vtable-dumper
- Description:
- ABI Dumper is a tool to dump ABI of an ELF object containing DWARF debug info.
abinit¶
- Homepage:
- Spack package:
- Versions:
- 9.4.2, 8.10.3, 8.10.2, 8.8.2, 8.6.3, 8.2.2, 8.0.8b
- Build Dependencies:
- atompaw, blas, lapack, mpi, scalapack, fftw-api, netcdf-fortran, netcdf-c, hdf5, wannier90, libxc, libxml2
- Link Dependencies:
- atompaw, blas, lapack, mpi, scalapack, fftw-api, netcdf-fortran, netcdf-c, hdf5, wannier90, libxc, libxml2
- Description:
- ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time- Dependent Density Functional Theory (for molecules). In addition to the main ABINIT code, different utility programs are provided.
abseil-cpp¶
- Homepage:
- Spack package:
- Versions:
- 20200923.2, 20200923.1, 20200225.2, 20200225.1, 20190808, 20181200, 20180600
- Build Dependencies:
- cmake
- Description:
- Abseil Common Libraries (C++)
abyss¶
- Homepage:
- Spack package:
- Versions:
- 2.1.4, 2.0.2, 1.5.2
- Build Dependencies:
- autoconf, automake, mpi, boost, sparsehash, sqlite, libtool
- Link Dependencies:
- mpi, boost, sparsehash, sqlite, libtool
- Run Dependencies:
- bwa
- Description:
- ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size.
accfft¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cuda, cmake, fftw, parallel-netcdf
- Link Dependencies:
- cuda, fftw, parallel-netcdf
- Description:
- AccFFT extends existing FFT libraries for CUDA-enabled Graphics Processing Units (GPUs) to distributed memory clusters
acct¶
- Homepage:
- Spack package:
- Versions:
- 6.6.4, 6.6.3, 6.6.2
- Description:
- Utilities for monitoring process activities.
accumulo¶
- Homepage:
- Spack package:
- Versions:
- 2.0.0, 1.9.3, 1.9.2
- Build Dependencies:
- java, maven
- Run Dependencies:
- java
- Description:
- Apache Accumulo is a sorted, distributed key/value store that provides robust, scalable data storage and retrieval.
ace¶
- Homepage:
- Spack package:
- Versions:
- 6.5.12, 6.5.6, 6.5.1, 6.5.0
- Description:
- ACE is an open-source framework that provides many components and patterns for developing high-performance, distributed real-time and embedded systems. ACE provides powerful, yet efficient abstractions for sockets, demultiplexing loops, threads, synchronization primitives.
ack¶
- Homepage:
- Spack package:
- Versions:
- 2.22, 2.18, 2.16, 2.14
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Description:
- ack 2.14 is a tool like grep, optimized for programmers. Designed for programmers with large heterogeneous trees of source code, ack is written purely in portable Perl 5 and takes advantage of the power of Perl's regular expressions.
acl¶
- Homepage:
- Spack package:
- Versions:
- 2.2.53, 2.2.52, 2.2.51, 2.2.50, 2.2.49, 2.2.48
- Build Dependencies:
- m4, autoconf, automake, libtool, attr, gettext
- Link Dependencies:
- attr, gettext
- Description:
- Commands for Manipulating POSIX Access Control Lists.
acpica-tools¶
- Homepage:
- Spack package:
- Versions:
- 20200528, 20200430
- Build Dependencies:
- flex, bison
- Description:
- Debian packaging for the ACPICA user space tools
acpid¶
- Homepage:
- Spack package:
- Versions:
- 2.0.28, 2.0.27, 2.0.26, 2.0.25, 2.0.24
- Build Dependencies:
- autoconf, automake, libtool, m4
- Description:
- ACPID used to try to handle events internally. Rather than try to climb an ever-growing mountain, ACPID now lets YOU define what events to handle. Any event that publishes itself to /proc/acpi/event can be handled. ACPID reads a set of configuration files which define event->action pairs. This is how you make it do stuff. See the man page for details.
activeharmony¶
- Homepage:
- Spack package:
- Versions:
- 4.6.0, 4.5
- Description:
- Active Harmony: a framework for auto-tuning (the automated search for values to improve the performance of a target application).
activemq¶
- Homepage:
- Spack package:
- Versions:
- 5.14.0
- Description:
- Apache ActiveMQ is a high performance Apache 2.0 licensed Message Broker and JMS 1.1 implementation.
acts¶
- Homepage:
- Spack package:
- Versions:
- main, master, 8.03.0, 8.02.0, 8.01.0, 8.00.0, 7.00.0, 6.00.0, 5.00.0, 4.01.0, 4.00.0, 3.00.0, 2.00.0, 1.02.1, 1.02.0, 1.01.0, 1.00.0, 0.32.0, 0.31.0, 0.30.0, 0.29.0, 0.28.0, 0.27.1, 0.27.0, 0.26.0, 0.25.2, 0.25.1, 0.25.0, 0.24.0, 0.23.0, 0.22.1, 0.22.0, 0.21.0, 0.20.0, 0.19.0, 0.18.0, 0.17.0, 0.16.0, 0.15.0, 0.14.0, 0.13.0, 0.12.1, 0.12.0, 0.11.1, 0.11.0, 0.10.5, 0.10.4, 0.10.3, 0.10.2, 0.10.1, 0.10.0, 0.09.5, 0.09.4, 0.09.3, 0.09.2, 0.09.1, 0.09.0, 0.08.2, 0.08.1, 0.08.0
- Build Dependencies:
- cuda, cmake, boost, dd4hep, eigen, geant4, hepmc3, heppdt, intel-tbb, nlohmann-json, pythia8, root
- Link Dependencies:
- cuda, boost, dd4hep, geant4, hepmc3, heppdt, intel-tbb, nlohmann-json, pythia8, root
- Description:
- A Common Tracking Software (Acts) This project contains an experiment- independent set of track reconstruction tools. The main philosophy is to provide high-level track reconstruction modules that can be used for any tracking detector. The description of the tracking detector's geometry is optimized for efficient navigation and quick extrapolation of tracks. Converters for several common geometry description languages exist. Having a highly performant, yet largely customizable implementation of track reconstruction algorithms was a primary objective for the design of this toolset. Additionally, the applicability to real-life HEP experiments plays major role in the development process. Apart from algorithmic code, this project also provides an event data model for the description of track parameters and measurements. Key features of this project include: tracking geometry description which can be constructed from TGeo, DD4Hep, or GDML input, simple and efficient event data model, performant and highly flexible algorithms for track propagation and fitting, basic seed finding algorithms.
addrwatch¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2, 1.0.1
- Build Dependencies:
- libevent, libpcap
- Link Dependencies:
- libevent, libpcap
- Description:
- A tool similar to arpwatch for IPv4/IPv6 and ethernet address pairing monitoring.
adept-utils¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1, 1.0
- Build Dependencies:
- cmake, boost, mpi
- Link Dependencies:
- boost, mpi
- Description:
- Utility libraries for LLNL performance tools.
adf¶
- Homepage:
- Spack package:
- Versions:
- 2017.113
- Description:
- Amsterdam Density Functional (ADF) is a program for first-principles electronic structure calculations that makes use of density functional theory.
adiak¶
- Homepage:
- Spack package:
- Versions:
- 0.3.0-alpha, 0.2.1, 0.1.1
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- Adiak collects metadata about HPC application runs and provides it to tools.
adios¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.13.1, 1.13.0, 1.12.0, 1.11.1, 1.11.0, 1.10.0, 1.9.0
- Build Dependencies:
- autoconf, automake, m4, libtool, python, mpi, zlib, bzip2, szip, sz, zfp, lz4, c-blosc, hdf5, netcdf-c, libevpath, dataspaces
- Link Dependencies:
- mpi, zlib, bzip2, szip, sz, zfp, lz4, c-blosc, hdf5, netcdf-c, libevpath, dataspaces
- Description:
- The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.
adios2¶
- Homepage:
- Spack package:
- Versions:
- master, 2.7.1, 2.7.0, 2.6.0, 2.5.0, 2.4.0, 2.3.1
- Build Dependencies:
- cmake, pkgconfig, libffi, libfabric, mpi, libzmq, dataspaces, hdf5, c-blosc, bzip2, libpng, zfp, sz, python, py-numpy, py-mpi4py
- Link Dependencies:
- libffi, libfabric, mpi, libzmq, dataspaces, hdf5, c-blosc, bzip2, libpng, zfp, sz
- Run Dependencies:
- python, py-numpy, py-mpi4py
- Test Dependencies:
- python
- Description:
- The Adaptable Input Output System version 2, developed in the Exascale Computing Program
adlbx¶
- Homepage:
- Spack package:
- Versions:
- master, 1.0.0, 0.9.2, 0.9.1
- Build Dependencies:
- exmcutils, autoconf, automake, libtool, m4, mpi
- Link Dependencies:
- exmcutils, mpi
- Description:
- ADLB/X: Master-worker library + work stealing and data dependencies
admixtools¶
- Homepage:
- Spack package:
- Versions:
- 7.0.1, 7.0, 6.0, 5.1, 5.0, 1.0.1, 1.0
- Build Dependencies:
- lapack, gsl
- Link Dependencies:
- lapack, gsl
- Description:
- The ADMIXTOOLS package implements 5 methods described in Patterson et al. (2012) Ancient Admixture in Human History. Details of the methods and algorithm can be found in this paper..
adms¶
- Homepage:
- Spack package:
- Versions:
- master, 2.3.7
- Build Dependencies:
- bison, flex, perl-xml-libxml
- Description:
- ADMS is a code generator that converts electrical compact device models specified in high-level description language into ready-to-compile c code for the API of spice simulators.
adol-c¶
- Homepage:
- Spack package:
- Versions:
- master, 2.7.2, 2.7.1, 2.7.0, 2.6.3, 2.6.2, 2.6.1, 2.6.0, 2.5.2, 2.5.1, 2.5.0
- Build Dependencies:
- automake, autoconf, libtool, m4, boost
- Link Dependencies:
- boost
- Description:
- A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading.
advancecomp¶
- Homepage:
- Spack package:
- Versions:
- 2.1, 2.0, 1.23, 1.22
- Build Dependencies:
- autoconf, automake, libtool, m4
- Link Dependencies:
- zlib
- Description:
- AdvanceCOMP contains recompression utilities for your .zip archives, .png images, .mng video clips and .gz files.
adwaita-icon-theme¶
- Homepage:
- Spack package:
- Versions:
- 3.38.0
- Build Dependencies:
- gdk-pixbuf, librsvg
- Description:
- Mostly private use system icons.
aegean¶
- Homepage:
- Spack package:
- Versions:
- 0.15.2
- Build Dependencies:
- genometools
- Link Dependencies:
- genometools
- Description:
- The AEGeAn Toolkit is designed for the Analysis and Evaluation of Genome Annotations. The toolkit includes a variety of analysis programs as well as a C library whose API provides access to AEGeAn's core functions and data structures.
aeskeyfind¶
- Homepage:
- Spack package:
- Versions:
- master
- Description:
- This program illustrates automatic techniques for locating 128-bit and 256-bit AES keys in a captured memory image.
aespipe¶
- Homepage:
- Spack package:
- Versions:
- 2.4f, 2.4e, 2.4d, 2.4c, 2.4b, 2.3e, 2.3d
- Description:
- aespipe program is AES encrypting or decrypting pipe. It reads from standard input and writes to standard output.
agrep¶
- Homepage:
- Spack package:
- Versions:
- 3.41
- Description:
- AGREP - an approximate GREP. Fast searching files for a string or regular expression, with approximate matching capabilities and user- definable records. Developed 1989-1991 by Udi Manber, Sun Wu et al. at the University of Arizona.
akantu¶
- Homepage:
- Spack package:
- Versions:
- master, 3.0.0
- Build Dependencies:
- cmake, boost, lapack, python, py-numpy, py-scipy, py-pybind11, mumps, netlib-scalapack, petsc, mpi, scotch
- Link Dependencies:
- boost, lapack, mumps, netlib-scalapack, petsc, mpi, scotch
- Run Dependencies:
- python, py-numpy, py-scipy, py-pybind11
- Description:
- Akantu means a little element in Kinyarwanda, a Bantu language. From now on it is also an opensource object-oriented Finite Element library which has the ambition to be generic and efficient.
albany¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake, mpi, trilinos
- Link Dependencies:
- mpi, trilinos
- Description:
- Albany is an implicit, unstructured grid, finite element code for the solution and analysis of multiphysics problems. The Albany repository on the GitHub site contains hundreds of regression tests and examples that demonstrate the code's capabilities on a wide variety of problems including fluid mechanics, solid mechanics (elasticity and plasticity), ice-sheet flow, quantum device modeling, and many other applications.
albert¶
- Homepage:
- Spack package:
- Versions:
- 4.0a_opt4, 4.0a
- Build Dependencies:
- readline
- Link Dependencies:
- readline
- Description:
- Albert is an interactive program to assist the specialist in the study of nonassociative algebra.
alembic¶
- Homepage:
- Spack package:
- Versions:
- 1.7.16
- Build Dependencies:
- cmake, openexr, hdf5, boost, zlib, py-ilmbase
- Link Dependencies:
- openexr, hdf5, boost, zlib, py-ilmbase
- Description:
- Alembic is an open computer graphics interchange framework. Alembic distills complex, animated scenes into a non-procedural, application- independent set of baked geometric results.
alglib¶
- Homepage:
- Spack package:
- Versions:
- 3.11.0
- Description:
- ALGLIB is a cross-platform numerical analysis and data processing library.
allpaths-lg¶
- Homepage:
- Spack package:
- Versions:
- 52488
- Description:
- ALLPATHS-LG is our original short read assembler and it works on both small and large (mammalian size) genomes.
alluxio¶
- Homepage:
- Spack package:
- Versions:
- 2.2.1, 2.2.0
- Run Dependencies:
- java
- Description:
- Alluxio (formerly known as Tachyon) is a virtual distributed storage system. It bridges the gap between computation frameworks and storage systems, enabling computation applications to connect to numerous storage systems through a common interface.
alpaka¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.6.0, 0.5.0, 0.4.0
- Build Dependencies:
- cuda, cmake, boost
- Link Dependencies:
- cuda, boost
- Description:
- Abstraction Library for Parallel Kernel Acceleration.
alps¶
- Homepage:
- Spack package:
- Versions:
- 2.3.0
- Build Dependencies:
- cmake, boost, fftw, hdf5, lapack, python, py-numpy, py-scipy, py-matplotlib
- Link Dependencies:
- boost, fftw, hdf5, lapack, python, py-numpy, py-scipy
- Run Dependencies:
- python, py-numpy, py-scipy, py-matplotlib
- Description:
- Algorithms for Physics Simulations Tags: Condensed Matter Physics, Computational Physics
alquimia¶
- Homepage:
- Spack package:
- Versions:
- develop, xsdk-0.6.0, xsdk-0.5.0, xsdk-0.4.0, xsdk-0.3.0, xsdk-0.2.0
- Build Dependencies:
- cmake, mpi, hdf5, pflotran, petsc
- Link Dependencies:
- mpi, hdf5, pflotran, petsc
- Description:
- Alquimia is an interface that exposes the capabilities of mature geochemistry codes such as CrunchFlow and PFLOTRAN
alsa-lib¶
- Homepage:
- Spack package:
- Versions:
- 1.2.3.2, 1.2.2, 1.1.4.1
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. alsa-lib contains the user space library that developers compile ALSA applications against.
aluminum¶
- Homepage:
- Spack package:
- Versions:
- master, 1.0.0, 0.7.0, 0.6.0, 0.5.0, 0.4.0, 0.3.3, 0.3.2, 0.2.1-1, 0.2.1, 0.2, 0.1
- Build Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, cmake, mpi, nccl, hwloc, cub, hipcub, ninja
- Link Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, mpi, nccl, hwloc, cub, hipcub
- Description:
- Aluminum provides a generic interface to high-performance communication libraries, with a focus on allreduce algorithms. Blocking and non- blocking algorithms and GPU-aware algorithms are supported. Aluminum also contains custom implementations of select algorithms to optimize for certain situations.
ambari¶
- Homepage:
- Spack package:
- Versions:
- 2.7.5, 2.7.4, 2.7.3, 2.7.1
- Build Dependencies:
- python, py-setuptools, py-coilmq
- Run Dependencies:
- python, py-coilmq
- Test Dependencies:
- py-mock
- Description:
- Apache Ambari is a tool for provisioning, managing, and monitoring Apache Hadoop clusters. Ambari consists of a set of RESTful APIs and a browser-based management interface.
amber¶
- Homepage:
- Spack package:
- Versions:
- 20, 18, 16
- Build Dependencies:
- cuda, zlib, bzip2, flex, bison, netcdf-fortran, mpi
- Link Dependencies:
- cuda, zlib, bzip2, netcdf-fortran, mpi
- Description:
- Amber is a suite of biomolecular simulation programs together with Amber tools. A manual download is required for Ambers. Spack will search your current directory for the download files. Alternatively, add the files to a mirror so that Spack can find them. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html Note: Only certain versions of ambertools are compatible with amber. Only the latter version of ambertools for each amber version is supported.
amdblis¶
- Homepage:
- Spack package:
- Versions:
- 3.0, 2.2
- Build Dependencies:
- python
- Run Dependencies:
- python
- Description:
- AMD Optimized BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. The framework was designed to isolate essential kernels of computation that, when optimized, immediately enable optimized implementations of most of its commonly used and computationally intensive operations.
amdfftw¶
- Homepage:
- Spack package:
- Versions:
- 3.0, 2.2
- Build Dependencies:
- mpi, llvm-openmp, texinfo
- Link Dependencies:
- mpi, llvm-openmp, texinfo
- Description:
- FFTW (AMD Optimized version) is a comprehensive collection of fast C routines for computing the Discrete Fourier Transform (DFT) and various special cases thereof. It is an open-source implementation of the Fast Fourier transform algorithm. It can compute transforms of real and complex-values arrays of arbitrary size and dimension. AMD Optimized FFTW is the optimized FFTW implementation targeted for AMD CPUs. For single precision build, please use precision value as float. Example : spack install amdfftw precision=float
amdlibflame¶
- Homepage:
- Spack package:
- Versions:
- 3.0, 2.2
- Build Dependencies:
- blas
- Link Dependencies:
- blas
- Description:
- libFLAME (AMD Optimized version) is a portable library for dense matrix computations, providing much of the functionality present in Linear Algebra Package (LAPACK). It includes a compatibility layer, FLAPACK, which includes complete LAPACK implementation. The library provides scientific and numerical computing communities with a modern, high- performance dense linear algebra library that is extensible, easy to use, and available under an open source license. libFLAME is a C-only implementation and does not depend on any external FORTRAN libraries including LAPACK. There is an optional backward compatibility layer, lapack2flame that maps LAPACK routine invocations to their corresponding native C implementations in libFLAME. This allows legacy applications to start taking advantage of libFLAME with virtually no changes to their source code. In combination with BLIS library which includes optimizations for the AMD EPYC processor family, libFLAME enables running high performing LAPACK functionalities on AMD platform.
amdlibm¶
- Homepage:
- Spack package:
- Versions:
- 3.0, 2.2
- Build Dependencies:
- scons, python
- Link Dependencies:
- mpfr
- Run Dependencies:
- python
- Description:
- AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor-based machines. It provides many routines from the list of standard C99 math functions. Applications can link into AMD LibM library and invoke math functions instead of compiler's math functions for better accuracy and performance.
amdscalapack¶
- Homepage:
- Spack package:
- Versions:
- 3.0, 2.2
- Build Dependencies:
- cmake, mpi, lapack, blas
- Link Dependencies:
- mpi, lapack, blas
- Description:
- ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. It depends on external libraries including BLAS and LAPACK for Linear Algebra computations. AMD's optimized version of ScaLAPACK enables using BLIS and LibFLAME library that have optimized dense matrix functions and solvers for AMD EPYC processor family CPUs.
amg¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.2, 1.1, 1.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- AMG is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. The driver provided with AMG builds linear systems for various 3-dimensional problems.
amg2013¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- AMG2013 is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. It has been derived directly from the BoomerAMG solver in the hypre library, a large linear solver library that is being developed in the Center for Applied Scientific Computing (CASC) at LLNL.
amgx¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0, 2.0.1, 2.0.0
- Build Dependencies:
- cuda, cmake, mpi, mkl, magma
- Link Dependencies:
- cuda, mpi, mkl, magma
- Description:
- AmgX provides a simple path to accelerated core solver technology on NVIDIA GPUs. AmgX provides up to 10x acceleration to the computationally intense linear solver portion of simulations, and is especially well suited for implicit unstructured methods. It is a high performance, state-of-the-art library and includes a flexible solver composition system that allows a user to easily construct complex nested solvers and preconditioners.
aml¶
- Homepage:
- Spack package:
- Versions:
- develop, master, 0.1.0
- Build Dependencies:
- numactl, m4, autoconf, automake, libtool
- Link Dependencies:
- numactl
- Description:
- AML: Building Blocks for Memory Management.
amp¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake, blas, lapack, boost, hdf5, hypre, libmesh, netcdf-c, petsc, silo, sundials, trilinos, zlib, mpi
- Link Dependencies:
- blas, lapack, boost, hdf5, hypre, libmesh, netcdf-c, petsc, silo, sundials, trilinos, zlib, mpi
- Description:
- The Advanced Multi-Physics (AMP) package. The Advanced Multi-Physics (AMP) package is an open source parallel object-oriented computational framework that is designed with single and multi-domain multi-physics applications in mind.
ampliconnoise¶
- Homepage:
- Spack package:
- Versions:
- 1.29
- Build Dependencies:
- mpi, gsl
- Link Dependencies:
- mpi, gsl
- Description:
- AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons.
amr-wind¶
- Homepage:
- Spack package:
- Versions:
- main
- Build Dependencies:
- cuda, cmake, mpi, amrex, hypre, netcdf-c, masa, openfast
- Link Dependencies:
- cuda, mpi, amrex, hypre, netcdf-c, masa, openfast
- Description:
- AMR-Wind is a massively parallel, block-structured adaptive-mesh, incompressible flow sover for wind turbine and wind farm simulations.
amrex¶
- Homepage:
- Spack package:
- Versions:
- develop, 21.05, 21.04, 21.03, 21.02, 21.01, 20.12, 20.11, 20.10, 20.09, 20.08, 20.07, 20.06, 20.05, 20.04, 20.03, 20.02, 20.01, 19.10, 19.08, 18.10.1, 18.10, 18.09.1
- Build Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, cmake, mpi, sundials, python, hdf5, rocrand
- Link Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, mpi, sundials, hdf5, hypre, petsc
- Description:
- AMReX is a publicly available software framework designed for building massively parallel block- structured adaptive mesh refinement (AMR) applications.
amrvis¶
- Homepage:
- Spack package:
- Versions:
- main
- Build Dependencies:
- gmake, mpi, libsm, libice, libxpm, libx11, libxt, libxext, motif, flex, bison
- Link Dependencies:
- mpi, libsm, libice, libxpm, libx11, libxt, libxext, motif, flex, bison
- Description:
- Amrvis is a visualization package specifically designed to read and display output and profiling data from codes built on the AMReX framework.
anaconda2¶
- Homepage:
- Spack package:
- Versions:
- 2019.10, 2019.07, 2019.03, 2018.12, 5.3.1, 5.3.0, 5.2.0, 5.1.0, 5.0.1, 5.0.0.1, 5.0.0, 4.4.0, 4.3.1, 4.3.0, 4.2.0, 4.1.1, 4.1.0, 4.0.0, 2.5.0, 2.4.1, 2.4.0
- Description:
- Anaconda is a free and open-source distribution of the Python and R programming languages for scientific computing, that aims to simplify package management and deployment. Package versions are managed by the package management system conda.
anaconda3¶
- Homepage:
- Spack package:
- Versions:
- 2020.11, 2020.07, 2020.02, 2019.10, 2019.07, 2019.03, 2018.12, 5.3.1, 5.3.0, 5.2.0, 5.1.0, 5.0.1, 5.0.0.1, 5.0.0, 4.4.0, 4.3.1, 4.3.0, 4.2.0, 4.1.1, 4.1.0, 4.0.0, 2.5.0, 2.4.1, 2.4.0, 2.3.0, 2.2.0, 2.1.0, 2.0.1, 2.0.0
- Description:
- Anaconda is a free and open-source distribution of the Python and R programming languages for scientific computing, that aims to simplify package management and deployment. Package versions are managed by the package management system conda.
andi¶
- Homepage:
- Spack package:
- Versions:
- 0.10
- Build Dependencies:
- m4, autoconf, automake, libtool, gsl, libdivsufsort
- Link Dependencies:
- gsl, libdivsufsort
- Description:
- andi is used for for estimating the evolutionary distance between closely related genomes.
angsd¶
- Homepage:
- Spack package:
- Versions:
- 0.933, 0.921, 0.919
- Build Dependencies:
- htslib, zlib, lzma, curl
- Link Dependencies:
- htslib, zlib, lzma, curl
- Run Dependencies:
- r
- Description:
- Angsd is a program for analysing NGS data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.
ant¶
- Homepage:
- Spack package:
- Versions:
- 1.10.7, 1.10.6, 1.10.5, 1.10.4, 1.10.3, 1.10.2, 1.10.1, 1.10.0, 1.9.9, 1.9.8, 1.9.7, 1.9.6
- Build Dependencies:
- java
- Link Dependencies:
- java
- 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
antimony¶
- Homepage:
- Spack package:
- Versions:
- 2.8, 2.7, 2.6, 2.5, 2.4, 2.2, 2.0
- Build Dependencies:
- cmake, sbml, swig, qt, python
- Link Dependencies:
- sbml, swig, qt, python
- Description:
- Human readable language for modifying sbml
antlr¶
- Homepage:
- Spack package:
- Versions:
- 2.7.7
- Build Dependencies:
- python, java
- Run Dependencies:
- python, java
- Description:
- ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files. It's widely used to build languages, tools, and frameworks. From a grammar, ANTLR generates a parser that can build and walk parse trees.
ants¶
- Homepage:
- Spack package:
- Versions:
- 2.3.5, 2.2.0
- Build Dependencies:
- cmake
- Link Dependencies:
- zlib
- Description:
- ANTs extracts information from complex datasets that include imaging. Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to which ANTs developers contribute.
aocc¶
- Homepage:
- Spack package:
- Versions:
- 3.0.0, 2.3.0, 2.2.0
- Build Dependencies:
- libxml2, zlib, ncurses, libtool, texinfo
- Link Dependencies:
- libxml2, zlib, ncurses, libtool, texinfo
- Description:
- The AOCC compiler system is a high performance, production quality code generation tool. The AOCC environment provides various options to developers when building and optimizing C, C++, and Fortran applications targeting 32-bit and 64-bit Linux platforms. The AOCC compiler system offers a high level of advanced optimizations, multi-threading and processor support that includes global optimization, vectorization, inter-procedural analyses, loop transformations, and code generation. AMD also provides highly optimized libraries, which extract the optimal performance from each x86 processor core when utilized. The AOCC Compiler Suite simplifies and accelerates development and tuning for x86 applications. Please install only if you agree to terms and conditions depicted under : http://developer.amd.com/wordpress/media/files/AOCC_EULA.pdf Example for installation: 'spack install aocc +license-agreed'
aocl-sparse¶
- Homepage:
- Spack package:
- Versions:
- 3.0, 2.2
- Build Dependencies:
- cmake, boost
- Link Dependencies:
- boost
- Description:
- AOCL-Sparse is a library that contains basic linear algebra subroutines for sparse matrices and vectors optimized for AMD EPYC family of processors. It is designed to be used with C and C++. Current functionality of sparse library supports SPMV function with CSR and ELLPACK formats.
aoflagger¶
- Homepage:
- Spack package:
- Versions:
- 2.10.0
- Build Dependencies:
- cmake, casacore, fftw, boost, libxml2, lapack, cfitsio
- Link Dependencies:
- casacore, fftw, boost, libxml2, lapack, cfitsio
- Description:
- RFI detector and quality analysis for astronomical radio observations.
aom¶
- Homepage:
- Spack package:
- Versions:
- v1.0.0-errata1
- Build Dependencies:
- cmake, yasm
- Link Dependencies:
- yasm
- Description:
- Alliance for Open Media AOM AV1 Codec Library
aomp¶
- Homepage:
- Spack package:
- Versions:
- 3.10.0, 3.9.0, 3.8.0, 3.7.0, 3.5.0
- Build Dependencies:
- cmake, python, py-setuptools, mesa18, py-pip, py-wheel, perl-data-dumper, awk, elfutils, libffi, hsakmt-roct, comgr, hsa-rocr-dev, rocm-device-libs, hip, hip-rocclr, rocm-gdb
- Link Dependencies:
- mesa18, elfutils, libffi
- Run Dependencies:
- py-wheel, hsakmt-roct, hsa-rocr-dev, rocm-device-libs, hip, rocm-gdb
- Description:
- llvm openmp compiler from AMD.
apachetop¶
- Homepage:
- Spack package:
- Versions:
- 0.19.7, 0.18.4, 0.17.4, 0.15.6
- Build Dependencies:
- autoconf, automake, libtool, m4, readline
- Link Dependencies:
- readline
- Description:
- ApacheTop watches a logfile generated by Apache (in standard common or combined logformat, and generates human-parsable output in realtime.) See the INSTALL file for ./configure options (there's a few newly added since v0.11)
apcomp¶
- Homepage:
- Spack package:
- Versions:
- master, 0.0.1
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- A multi use-case image compositor
ape¶
- Homepage:
- Spack package:
- Versions:
- 2.2.1
- Build Dependencies:
- gsl, libxc
- Link Dependencies:
- gsl, libxc
- Description:
- A tool for generating atomic pseudopotentials within a Density- Functional Theory framework
aperture-photometry¶
- Homepage:
- Spack package:
- Versions:
- 2.8.4, 2.8.2
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- Aperture Photometry Tool APT is software for astronomical research
apex¶
- Homepage:
- Spack package:
- Versions:
- develop, master, 2.4.0, 2.3.2, 2.3.1, 2.3.0, 2.2.0
- Build Dependencies:
- cmake, binutils, activeharmony, otf2, mpi, gperftools, jemalloc, papi, cuda, boost
- Link Dependencies:
- binutils, activeharmony, otf2, mpi, gperftools, jemalloc, papi, cuda, boost
- Description:
- Autonomic Performance Environment for eXascale (APEX).
apfel¶
- Homepage:
- Spack package:
- Versions:
- 3.0.4
- Build Dependencies:
- swig, python, lhapdf
- Link Dependencies:
- swig
- Run Dependencies:
- python, lhapdf
- Description:
- APFEL is a library able to perform DGLAP evolution up to NNLO in QCD and to NLO in QED, both with pole and MSbar masses. The coupled DGLAP QCD+QED evolution equations are solved in x-space by means of higher order interpolations and Runge-Kutta techniques.
apple-libunwind¶
- Homepage:
- Spack package:
- Description:
- Placeholder package for Apple's analogue to non-GNU libunwind
apple-libuuid¶
- Homepage:
- Spack package:
- Versions:
- 1353.100.2
- Description:
- Placeholder package for Apple's analogue to non-GNU libuuid
applewmproto¶
- Homepage:
- Spack package:
- Versions:
- 1.4.2
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Apple Rootless Window Management Extension. This extension defines a protcol that allows X window managers to better interact with the Mac OS X Aqua user interface when running X11 in a rootless mode.
appres¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- libx11, libxt, xproto, pkgconfig, util-macros
- Link Dependencies:
- libx11, libxt, xproto
- Description:
- The appres program prints the resources seen by an application (or subhierarchy of an application) with the specified class and instance names. It can be used to determine which resources a particular program will load.
apr¶
- Homepage:
- Spack package:
- Versions:
- 1.7.0, 1.6.2, 1.5.2
- Link Dependencies:
- uuid
- Description:
- Apache portable runtime.
apr-util¶
- Homepage:
- Spack package:
- Versions:
- 1.6.1, 1.6.0, 1.5.4
- Build Dependencies:
- apr, expat, iconv, openssl, gdbm, postgresql, sqlite, unixodbc
- Link Dependencies:
- apr, expat, iconv, openssl, gdbm, postgresql, sqlite, unixodbc
- Description:
- Apache Portable Runtime Utility
aragorn¶
- Homepage:
- Spack package:
- Versions:
- 1.2.38, 1.2.36
- Description:
- ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.
arbor¶
- Homepage:
- Spack package:
- Versions:
- master, 0.5
- Build Dependencies:
- cuda, cmake, nlohmann-json, libxml2, mpi, py-mpi4py, python, py-numpy, py-pybind11, py-sphinx, py-svgwrite
- Link Dependencies:
- cuda, nlohmann-json, libxml2, mpi
- Run Dependencies:
- py-mpi4py, python, py-numpy, py-pybind11
- Description:
- Arbor is a high-performance library for computational neuroscience simulations.
arborx¶
- Homepage:
- Spack package:
- Versions:
- master, 1.0, 0.9-beta
- Build Dependencies:
- cmake, mpi, kokkos, trilinos
- Link Dependencies:
- mpi, kokkos, trilinos
- Description:
- ArborX is a performance-portable library for geometric search
archer¶
- Homepage:
- Spack package:
- Versions:
- 2.0.0, 1.0.0
- Build Dependencies:
- cmake, llvm, ninja, llvm-openmp-ompt
- Link Dependencies:
- llvm, llvm-openmp-ompt
- Description:
- ARCHER, a data race detection tool for large OpenMP applications.
argobots¶
- Homepage:
- Spack package:
- Versions:
- main, 1.1, 1.0.1, 1.0
- Build Dependencies:
- m4, autoconf, automake, libtool, valgrind, libunwind
- Link Dependencies:
- valgrind, libunwind
- Description:
- Argobots, which was developed as a part of the Argo project, is a lightweight runtime system that supports integrated computation and data movement with massive concurrency. It will directly leverage the lowest- level constructs in the hardware and OS: lightweight notification mechanisms, data movement engines, memory mapping, and data placement strategies. It consists of an execution model and a memory model.
argon2¶
- Homepage:
- Spack package:
- Versions:
- 20190702, 20171227, 20161029
- Description:
- Argon2 is a password-hashing function that summarizes the state of the art in the design of memory-hard functions and can be used to hash passwords for credential storage, key derivation, or other applications.
argp-standalone¶
- Homepage:
- Spack package:
- Versions:
- 1.3
- Description:
- Standalone version of the argp interface from glibc for parsing unix- style arguments.
args¶
- Homepage:
- Spack package:
- Versions:
- 6.2.3, 6.2.2, 6.2.1
- Build Dependencies:
- cmake
- Description:
- A simple header-only C++ argument parser library. Supposed to be flexible and powerful, and attempts to be compatible with the functionality of the Python standard argparse library (though not necessarily the API).
argtable¶
- Homepage:
- Spack package:
- Versions:
- 2-13
- Description:
- Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.
aria2¶
- Homepage:
- Spack package:
- Versions:
- 1.35.0, 1.34.0
- Build Dependencies:
- libxml2, libssh2, libgcrypt, zlib, c-ares, sqlite
- Link Dependencies:
- libxml2, libssh2, libgcrypt, zlib, c-ares, sqlite
- Description:
- An ultra fast download utility
arm¶
- Homepage:
- Spack package:
- Versions:
- 20.2.1
- Description:
- Arm Compiler combines the optimized tools and libraries from Arm with a modern LLVM-based compiler framework.
arm-forge¶
- Homepage:
- Spack package:
- Versions:
- 21.0
- Description:
- Arm Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and Fortran applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.
armadillo¶
- Homepage:
- Spack package:
- Versions:
- 10.5.0, 9.800.3, 8.100.1, 7.950.1
- Build Dependencies:
- cmake, arpack-ng, blas, lapack, superlu, hdf5
- Link Dependencies:
- arpack-ng, blas, lapack, superlu, hdf5
- Description:
- Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use.
arpack-ng¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.8.0, 3.7.0, 3.6.3, 3.6.2, 3.6.0, 3.5.0, 3.4.0, 3.3.0
- Build Dependencies:
- blas, lapack, automake, autoconf, libtool, cmake, mpi
- Link Dependencies:
- blas, lapack, mpi
- Description:
- ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Important Features: * Reverse Communication Interface. * Single and Double Precision Real Arithmetic Versions for Symmetric, Non-symmetric, Standard or Generalized Problems. * Single and Double Precision Complex Arithmetic Versions for Standard or Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems. * Routines for The Singular Value Decomposition. * Example driver routines that may be used as templates to implement numerous Shift-Invert strategies for all problem types, data types and precision. This project is a joint project between Debian, Octave and Scilab in order to provide a common and maintained version of arpack. Indeed, no single release has been published by Rice university for the last few years and since many software (Octave, Scilab, R, Matlab...) forked it and implemented their own modifications, arpack-ng aims to tackle this by providing a common repository and maintained versions. arpack-ng is replacing arpack almost everywhere.
arrayfire¶
- Homepage:
- Spack package:
- Versions:
- master, 3.7.3, 3.7.2, 3.7.0
- Build Dependencies:
- cuda, cmake, boost, fftw-api, blas, cudnn, opencl, fontconfig, glfw
- Link Dependencies:
- cuda, boost, fftw-api, blas, cudnn, opencl, fontconfig, glfw
- Description:
- ArrayFire is a high performance software library for parallel computing with an easy-to-use API. Its array based function set makes parallel programming more accessible.
arrow¶
- Homepage:
- Spack package:
- Versions:
- 0.17.1, 0.15.1, 0.15.0, 0.14.1, 0.12.1, 0.11.0, 0.9.0, 0.8.0
- Build Dependencies:
- cuda, cmake, boost, flatbuffers, python, py-numpy, rapidjson, snappy, zlib, zstd, thrift, orc
- Link Dependencies:
- cuda, boost, flatbuffers, python, py-numpy, rapidjson, snappy, zlib, zstd, thrift, orc
- Description:
- A cross-language development platform for in-memory data. This package contains the C++ bindings.
asagi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1, 1.0
- Build Dependencies:
- cmake, mpi, netcdf-c, numactl
- Link Dependencies:
- mpi, netcdf-c, numactl
- Description:
- a pArallel Server for Adaptive GeoInformation.
ascent¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.7.1, 0.7.0, 0.6.0
- Build Dependencies:
- cuda, cmake, conduit, python, py-numpy, py-pip, mpi, py-mpi4py, babelflow, parallelmergetree, vtk-h, mfem, adios, dray, py-sphinx, py-sphinx-rtd-theme
- Link Dependencies:
- cuda, conduit, python, mpi, py-mpi4py, babelflow, parallelmergetree, vtk-h, mfem, adios, dray
- Run Dependencies:
- python, py-numpy, py-pip
- Description:
- Ascent is an open source many-core capable lightweight in situ visualization and analysis infrastructure for multi-physics HPC simulations.
asciidoc¶
- Homepage:
- Spack package:
- Versions:
- master, 9.1.0, 9.0.5, 9.0.4, 9.0.3, 9.0.2, 8.6.10, 8.6.9
- Build Dependencies:
- libxml2, libxslt, docbook-xml, docbook-xsl, python
- Run Dependencies:
- libxml2, libxslt, docbook-xml, docbook-xsl, python
- Description:
- A presentable text document format for writing articles, UNIX man pages and other small to medium sized documents.
asciidoc-py3¶
- Homepage:
- Spack package:
- Versions:
- 9.0.3, 9.0.2
- Build Dependencies:
- python, libxml2, libxslt, docbook-xml, docbook-xsl
- Run Dependencies:
- python, libxml2, libxslt, docbook-xml, docbook-xsl
- Description:
- Python 3 port of Asciidoc Python. AsciiDoc is a text document format for writing notes, documentation, articles, books, ebooks, slideshows, web pages, man pages and blogs. AsciiDoc files can be translated to many formats including HTML, PDF, EPUB, man page.
asdcplib¶
- Homepage:
- Spack package:
- Versions:
- 2_10_35, 2_10_34, 2_10_33, 2_10_32
- Build Dependencies:
- m4, autoconf, automake, libtool, openssl
- Link Dependencies:
- openssl
- Description:
- AS-DCP and AS-02 File Access Library.
asdf-cxx¶
- Homepage:
- Spack package:
- Versions:
- 7.2.1, 7.2.0, 7.1.0, 7.0.0, 6.3.0, 6.0.0, 5.0.0, 4.0.1, 3.1.0, 3.0.0, 2.6.1, 2.5.1, 2.5.0, 2.4.1, 2.4.0, 2.3.1, 2.2.1, 2.1.1, 2.1.0, 1.1.0, 1.0.0
- Build Dependencies:
- cmake, bzip2, openssl, py-numpy, python, swig, yaml-cpp, zlib
- Link Dependencies:
- bzip2, openssl, yaml-cpp, zlib
- Run Dependencies:
- py-numpy, python
- Description:
- ASDF - Advanced Scientific Data Format, a C++ implementation
aspa¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- lapack, blas, mpi, hdf5
- Link Dependencies:
- lapack, blas, mpi, hdf5
- Description:
- A fundamental premise in ExMatEx is that scale-bridging performed in heterogeneous MPMD materials science simulations will place important demands upon the exascale ecosystem that need to be identified and quantified.
aspcud¶
- Homepage:
- Spack package:
- Versions:
- 1.9.5, 1.9.4
- Build Dependencies:
- cmake, boost, re2c, clingo
- Link Dependencies:
- clingo
- Description:
- Aspcud: Package dependency solver Aspcud is a solver for package dependencies. A package universe and a request to install, remove, or upgrade packages have to be encoded in the CUDF format. Such a CUDF document can then be passed to aspcud along with an optimization criteria to obtain a solution to the given package problem.
aspect¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.2.0, 2.1.0, 2.0.1, 2.0.0
- Build Dependencies:
- cmake, dealii, dealii-parameter-gui, libdap4
- Link Dependencies:
- dealii, dealii-parameter-gui, libdap4
- Description:
- Parallel and extensible Finite Element code to simulate convection in the Earth's mantle and elsewhere.
aspell¶
- Homepage:
- Spack package:
- Versions:
- 0.60.6.1
- Description:
- GNU Aspell is a Free and Open Source spell checker designed to eventually replace Ispell.
aspell6-de¶
- Homepage:
- Spack package:
- Versions:
- 6-de-20030222-1
- Build Dependencies:
- aspell
- Run Dependencies:
- aspell
- Description:
- German (de) dictionary for aspell.
aspell6-en¶
- Homepage:
- Spack package:
- Versions:
- 2017.01.22-0
- Build Dependencies:
- aspell
- Run Dependencies:
- aspell
- Description:
- English (en) dictionary for aspell.
aspell6-es¶
- Homepage:
- Spack package:
- Versions:
- 1.11-2
- Build Dependencies:
- aspell
- Run Dependencies:
- aspell
- Description:
- Spanish (es) dictionary for aspell.
aspera-cli¶
- Homepage:
- Spack package:
- Versions:
- 3.7.7
- Description:
- The Aspera CLI client for the Fast and Secure Protocol (FASP).
assimp¶
- Homepage:
- Spack package:
- Versions:
- master, 5.0.1, 4.0.1
- Build Dependencies:
- cmake, boost
- Link Dependencies:
- boost
- Description:
- Open Asset Import Library (Assimp) is a portable Open Source library to import various well-known 3D model formats in a uniform manner.
astra¶
- Homepage:
- Spack package:
- Versions:
- 2020-02-03
- Build Dependencies:
- libxcb, libx11
- Link Dependencies:
- libxcb, libx11
- Description:
- A Space Charge Tracking Algorithm.
astral¶
- Homepage:
- Spack package:
- Versions:
- 5.6.1, 4.10.7
- Build Dependencies:
- java, zip
- Run Dependencies:
- java
- Description:
- ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.
astyle¶
- Homepage:
- Spack package:
- Versions:
- 3.1, 3.0.1, 2.06, 2.05.1, 2.04
- Description:
- A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code.
at-spi2-atk¶
- Homepage:
- Spack package:
- Versions:
- 2.38.0, 2.34.2, 2.26.2, 2.26.1
- Build Dependencies:
- meson, ninja, pkgconfig, at-spi2-core, atk
- Link Dependencies:
- at-spi2-core, atk
- Description:
- The At-Spi2 Atk package contains a library that bridges ATK to At-Spi2 D-Bus service.
at-spi2-core¶
- Homepage:
- Spack package:
- Versions:
- 2.40.1, 2.38.0, 2.36.0, 2.28.0
- Build Dependencies:
- meson, ninja, glib, dbus, gettext, libx11, libxi, libxtst, recordproto, inputproto, fixesproto, pkgconfig, python, gobject-introspection
- Link Dependencies:
- glib, dbus, gettext, libx11, libxi, libxtst, recordproto, inputproto, fixesproto, gobject-introspection
- Description:
- The At-Spi2 Core package provides a Service Provider Interface for the Assistive Technologies available on the GNOME platform and a library against which applications can be linked.
atf¶
- Homepage:
- Spack package:
- Versions:
- 0.21, 0.20, 0.19
- Build Dependencies:
- m4, autoconf, automake, libtool
- Description:
- ATF, or Automated Testing Framework, is a collection of libraries to write test programs in C, C++ and POSIX shell.
athena¶
- Homepage:
- Spack package:
- Versions:
- master, 4.2
- Build Dependencies:
- autoconf, automake, libtool, m4, mpi, fftw
- Link Dependencies:
- mpi, fftw
- Description:
- Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD). It was developed primarily for studies of the interstellar medium, star formation, and accretion flows.
atk¶
- Homepage:
- Spack package:
- Versions:
- 2.36.0, 2.30.0, 2.28.1, 2.20.0, 2.14.0
- Build Dependencies:
- meson, glib, gettext, pkgconfig, gobject-introspection, libffi
- Link Dependencies:
- glib, gettext, gobject-introspection, libffi
- Description:
- ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
atlas¶
- Homepage:
- Spack package:
- Versions:
- 3.11.41, 3.11.39, 3.11.34, 3.10.3, 3.10.2
- Description:
- Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines in the LAPACK library.
atmi¶
- Homepage:
- Spack package:
- Versions:
- 4.2.0, 4.1.0, 4.0.0, 3.10.0, 3.9.0, 3.8.0, 3.7.0, 3.5.0
- Build Dependencies:
- cmake
- Link Dependencies:
- comgr, hsa-rocr-dev, libelf
- Description:
- Asynchronous Task and Memory Interface, or ATMI, is a runtime framework and programming model for heterogeneous CPU-GPU systems. It provides a consistent, declarative API to create task graphs on CPUs and GPUs (integrated and discrete).
atom-dft¶
- Homepage:
- Spack package:
- Versions:
- 4.2.6
- Build Dependencies:
- libgridxc, xmlf90
- Link Dependencies:
- libgridxc, xmlf90
- Description:
- ATOM is a program for DFT calculations in atoms and pseudopotential generation.
atompaw¶
- Homepage:
- Spack package:
- Versions:
- 4.1.1.0, 4.0.0.13, 3.1.0.3
- Build Dependencies:
- lapack, blas, libxc
- Link Dependencies:
- lapack, blas, libxc
- Description:
- A Projector Augmented Wave (PAW) code for generating atom-centered functions. Official website: http://pwpaw.wfu.edu User's guide: ~/doc/atompaw-usersguide.pdf
atop¶
- Homepage:
- Spack package:
- Versions:
- 2.5.0, 2.4.0, 2.3.0, 2.2.6, 2.2-3
- Build Dependencies:
- zlib, ncurses
- Link Dependencies:
- zlib, ncurses
- Description:
- Atop is an ASCII full-screen performance monitor for Linux
attr¶
- Homepage:
- Spack package:
- Versions:
- 2.4.48, 2.4.47, 2.4.46
- Description:
- Commands for Manipulating Filesystem Extended Attributes
audacious¶
- Homepage:
- Spack package:
- Versions:
- 4.0.2, 4.0.1, 4.0, 3.10.1, 3.10
- Build Dependencies:
- m4, autoconf, automake, libtool, gettext, glib, qt
- Link Dependencies:
- gettext, iconv, glib, qt
- Description:
- A lightweight and versatile audio player.
audacity¶
- Homepage:
- Spack package:
- Versions:
- 2.4.2, 2.4.1, 2.4.0
- Build Dependencies:
- cmake, wxwidgets
- Link Dependencies:
- wxwidgets
- Description:
- Audacity is a cross-platform multitrack audio editor. It allows you to record sounds directly or to import files in various formats. It features a few simple effects, all of the editing features you should need, and unlimited undo. The GUI was built with wxWidgets and the audio I/O supports PulseAudio, OSS and ALSA under Linux.
audit-userspace¶
- Homepage:
- Spack package:
- Versions:
- 2.8.5, 2.8.4, 2.8.3, 2.8.2
- Build Dependencies:
- autoconf, automake, libtool, m4, openldap, swig
- Link Dependencies:
- openldap, swig
- Description:
- Linux audit userspace
augustus¶
- Homepage:
- Spack package:
- Versions:
- 3.4.0, 3.3.2, 3.3.1-tag1, 3.3, 3.2.3
- Build Dependencies:
- perl, python, bamtools, gsl, boost, zlib, htslib, bcftools, samtools, curl, sqlite, mysql-client, mysqlpp, lp-solve, suite-sparse
- Link Dependencies:
- bamtools, gsl, boost, zlib, htslib, bcftools, samtools, curl, sqlite, mysql-client, mysqlpp, lp-solve, suite-sparse
- Run Dependencies:
- perl, python
- Description:
- AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
authd¶
- Homepage:
- Spack package:
- Versions:
- 1.4.4
- Description:
- authd is a small and fast RFC 1413 ident protocol daemon with both xinetd server and interactive modes that supports IPv6 and IPv4 as well as the more popular features of pidentd.
authselect¶
- Homepage:
- Spack package:
- Versions:
- 1.2.1, 1.2, 1.1
- Build Dependencies:
- autoconf, automake, libtool, m4, popt
- Link Dependencies:
- popt
- Description:
- Select authentication and indentity profile to use on the system.
autoconf¶
- Homepage:
- Spack package:
- Versions:
- 2.71, 2.70, 2.69, 2.62, 2.59, 2.13
- Build Dependencies:
- m4, perl
- Run Dependencies:
- m4, perl
- Description:
- Autoconf -- system configuration part of autotools
autoconf-archive¶
- Homepage:
- Spack package:
- Versions:
- 2019.01.06
- Description:
- The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf.
autodock-gpu¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cuda
- Link Dependencies:
- cuda
- Description:
- AutoDock-GPU: AutoDock for GPUs and other accelerators. OpenCL and Cuda accelerated version of AutoDock 4.2.6. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units.
autodock-vina¶
- Homepage:
- Spack package:
- Versions:
- 1_1_2
- Build Dependencies:
- boost
- Link Dependencies:
- boost
- Description:
- AutoDock Vina is an open-source program for doing molecular docking
autofact¶
- Homepage:
- Spack package:
- Versions:
- 3_4
- Run Dependencies:
- perl, perl-bioperl, perl-io-string, perl-libwww-perl, blast-legacy
- Description:
- An Automatic Functional Annotation and Classification Tool
autogen¶
- Homepage:
- Spack package:
- Versions:
- 5.18.12
- Build Dependencies:
- pkgconfig, guile, libxml2
- Link Dependencies:
- guile, libxml2
- Description:
- AutoGen is a tool designed to simplify the creation and maintenance of programs that contain large amounts of repetitious text. It is especially valuable in programs that have several blocks of text that must be kept synchronized.
automaded¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- cmake, mpi, boost, callpath
- Link Dependencies:
- mpi, boost, callpath
- Description:
- AutomaDeD (Automata-based Debugging for Dissimilar parallel tasks) is a tool for automatic diagnosis of performance and correctness problems in MPI applications. It creates control-flow models of each MPI process and, when a failure occurs, these models are leveraged to find the origin of problems automatically. MPI calls are intercepted (using wrappers) to create the models. When an MPI application hangs, AutomaDeD creates a progress-dependence graph that helps finding the process (or group of processes) that caused the hang.
automake¶
- Homepage:
- Spack package:
- Versions:
- 1.16.3, 1.16.2, 1.16.1, 1.15.1, 1.15, 1.14.1, 1.13.4, 1.11.6
- Build Dependencies:
- autoconf, perl
- Run Dependencies:
- perl
- Description:
- Automake -- make file builder part of autotools
avizo¶
- Homepage:
- Spack package:
- Versions:
- 2020.1, 2019.4, 2019.3, 9.7.0
- Description:
- Avizo is a 3D analysis software for scientific and industrial data. Wherever three-dimensional imaging data sets need to be processed, in materials science, geosciences or engineering applications, Avizo offers abundant state-of-the-art image data processing, exploration and analysis features within an intuitive workflow and easy-to-use graphical user interface.
aws-parallelcluster¶
- Homepage:
- Spack package:
- Versions:
- 2.10.4, 2.10.3, 2.10.2, 2.10.1, 2.10.0, 2.9.1, 2.9.0, 2.8.1, 2.8.0, 2.7.0, 2.6.1, 2.6.0, 2.5.1, 2.5.0
- Build Dependencies:
- python, py-future, py-ipaddress, py-configparser, py-tabulate, py-pyyaml, py-jinja2, py-boto3, py-setuptools, py-enum34
- Run Dependencies:
- python, py-future, py-ipaddress, py-configparser, py-tabulate, py-pyyaml, py-jinja2, py-boto3, py-setuptools, py-enum34
- Description:
- AWS ParallelCluster is an AWS supported Open Source cluster management tool to deploy and manage HPC clusters in the AWS cloud.
awscli¶
- Homepage:
- Spack package:
- Versions:
- 1.16.308, 1.16.179
- Build Dependencies:
- python, py-setuptools, py-botocore, py-docutils, py-rsa, py-s3transfer, py-argparse, py-pyyaml, py-colorama
- Run Dependencies:
- python, py-botocore, py-docutils, py-rsa, py-s3transfer, py-argparse, py-pyyaml, py-colorama
- Test Dependencies:
- py-nose, py-mock
- Description:
- This package provides a unified command line interface to Amazon Web Services
axel¶
- Homepage:
- Spack package:
- Versions:
- 2.16.1
- Build Dependencies:
- m4, autoconf, automake, libtool, pkgconfig, gettext, openssl
- Link Dependencies:
- gettext, openssl
- Description:
- Axel is a light command line download accelerator for Linux and Unix
axl¶
- Homepage:
- Spack package:
- Versions:
- master, 0.4.0, 0.3.0, 0.2.0, 0.1.1
- Build Dependencies:
- cmake, kvtree
- Link Dependencies:
- kvtree
- Description:
- Asynchronous transfer library
axom¶
- Homepage:
- Spack package:
- Versions:
- develop, main, 0.5.0, 0.4.0, 0.3.3, 0.3.2, 0.3.1, 0.3.0, 0.2.9
- Build Dependencies:
- cuda, cmake, mpi, conduit, hdf5, lua, scr, kvtree, dtcmp, raja, umpire, mfem, python, cppcheck, doxygen, graphviz, py-sphinx, py-shroud, llvm
- Link Dependencies:
- cuda, mpi, conduit, hdf5, lua, scr, kvtree, dtcmp, raja, umpire, mfem, python, cppcheck, doxygen, graphviz, py-sphinx, py-shroud
- Description:
- Axom provides a robust, flexible software infrastructure for the development of multi-physics applications and computational tools.
babelflow¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1, 1.0.0
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- BabelFlow is an Embedded Domain Specific Language to describe algorithms using a task graph abstraction which allows them to be executed on top of one of several available runtime systems.
babeltrace¶
- Homepage:
- Spack package:
- Versions:
- 1.2.4
- Build Dependencies:
- glib, uuid, popt
- Link Dependencies:
- glib, uuid, popt
- Description:
- Babeltrace is a trace viewer and converter reading and writing the Common Trace Format (CTF). Its main use is to pretty-print CTF traces into a human-readable text output ordered by time.
backupninja¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- autoconf, automake, libtool, m4, bash, gawk
- Description:
- Backupninja backup tool.
bam-readcount¶
- Homepage:
- Spack package:
- Versions:
- 0.8.0
- Build Dependencies:
- cmake
- Description:
- Bam-readcount generates metrics at single nucleotide positions.
bamaddrg¶
- Homepage:
- Spack package:
- Versions:
- 0.1
- Build Dependencies:
- bamtools
- Description:
- bamaddrg adds read groups to input BAM files, streams BAM output on stdout
bamdst¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Bamdst is a a lightweight bam file depth statistical tool.
bamtools¶
- Homepage:
- Spack package:
- Versions:
- 2.5.1, 2.5.0, 2.4.1, 2.4.0, 2.3.0, 2.2.3
- Build Dependencies:
- cmake
- Link Dependencies:
- zlib
- Description:
- C++ API & command-line toolkit for working with BAM data.
bamutil¶
- Homepage:
- Spack package:
- Versions:
- 1.0.13
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.
bannergrab¶
- Homepage:
- Spack package:
- Versions:
- master
- Description:
- Bannergrab is a simple tool, designed to collect information from network services. It can do this using two different methods; grab the connection banners and send triggers and collect the responses. Bannergrab defaults to sending triggers.
barrnap¶
- Homepage:
- Spack package:
- Versions:
- 0.8, 0.7, 0.6
- Run Dependencies:
- hmmer
- Description:
- Barrnap predicts the location of ribosomal RNA genes in genomes.
bart¶
- Homepage:
- Spack package:
- Versions:
- 0.7.00, 0.6.00, 0.5.00
- Build Dependencies:
- cuda, libpng, fftw, blas, lapack, python
- Link Dependencies:
- cuda, libpng, fftw, blas, lapack
- Run Dependencies:
- py-numpy, py-matplotlib, python
- Description:
- BART: Toolbox for Computational Magnetic Resonance Imaging
bash¶
- Homepage:
- Spack package:
- Versions:
- 5.1, 5.0, 4.4, 4.3
- Build Dependencies:
- ncurses, readline, iconv
- Link Dependencies:
- ncurses, readline, iconv
- Description:
- The GNU Project's Bourne Again SHell.
bash-completion¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.7, 2.3
- Build Dependencies:
- automake, autoconf, libtool
- Run Dependencies:
- bash
- Description:
- Programmable completion functions for bash.
bashtop¶
- Homepage:
- Spack package:
- Versions:
- 0.8.17, 0.8.16, 0.8.15, 0.8.14, 0.8.13, 0.8.12, 0.8.11, 0.8.10, 0.8.9, 0.8.8
- Description:
- Linux resource monitor.
bat¶
- Homepage:
- Spack package:
- Versions:
- 0.13.0, 0.12.1
- Build Dependencies:
- rust
- Link Dependencies:
- rust
- Description:
- A cat(1) clone with wings.
batctl¶
- Homepage:
- Spack package:
- Versions:
- 2019.5, 2019.4, 2019.3, 2019.2
- Build Dependencies:
- libnl
- Link Dependencies:
- libnl
- Description:
- B.A.T.M.A.N. advanced control and management tool
bats¶
- Homepage:
- Spack package:
- Versions:
- 0.4.0
- Description:
- Bats is a TAP-compliant testing framework for Bash.
bazel¶
- Homepage:
- Spack package:
- Versions:
- 4.0.0, 3.7.2, 3.7.1, 3.7.0, 3.6.0, 3.5.1, 3.5.0, 3.4.1, 3.4.0, 3.3.1, 3.3.0, 3.2.0, 3.1.0, 3.0.0, 2.2.0, 2.1.1, 2.1.0, 2.0.1, 2.0.0, 1.2.1, 1.2.0, 1.1.0, 1.0.1, 1.0.0, 0.29.1, 0.29.0, 0.28.1, 0.28.0, 0.27.2, 0.27.1, 0.27.0, 0.26.1, 0.26.0, 0.25.3, 0.25.2, 0.25.1, 0.25.0, 0.24.1, 0.24.0, 0.23.2, 0.23.1, 0.23.0, 0.22.0, 0.21.0, 0.20.0, 0.19.2, 0.19.1, 0.19.0, 0.18.1, 0.18.0, 0.17.2, 0.17.1, 0.16.1, 0.16.0, 0.15.2, 0.15.1, 0.15.0, 0.14.1, 0.14.0, 0.13.1, 0.13.0, 0.12.0, 0.11.1, 0.11.0, 0.10.1, 0.10.0, 0.9.0, 0.8.1, 0.8.0, 0.7.0, 0.6.1, 0.6.0, 0.5.4, 0.5.3, 0.5.2, 0.5.1, 0.5.0, 0.4.5, 0.4.4, 0.4.3, 0.4.2, 0.4.1, 0.4.0, 0.3.2, 0.3.1, 0.3.0
- Build Dependencies:
- java, python, zip
- Run Dependencies:
- java, python, zip
- Description:
- Bazel is an open-source build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.
bbcp¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- zlib, openssl, libnsl
- Link Dependencies:
- zlib, openssl, libnsl
- Description:
- Securely and quickly copy data from source to target
bbmap¶
- Homepage:
- Spack package:
- Versions:
- 38.63, 37.36
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- Short read aligner for DNA and RNA-seq data.
bc¶
- Homepage:
- Spack package:
- Versions:
- 1.07
- Build Dependencies:
- ed, texinfo
- Description:
- bc is an arbitrary precision numeric processing language. Syntax is similar to C, but differs in many substantial areas. It supports interactive execution of statements.
bcache¶
- Homepage:
- Spack package:
- Versions:
- 1.0.8, 1.0.7, 1.0.6, 1.0.5, 1.0.4
- Build Dependencies:
- uuid, util-linux, gettext, pkgconfig
- Link Dependencies:
- uuid, util-linux, gettext
- Description:
- Bcache is a patch for the Linux kernel to use SSDs to cache other block devices.
bcftools¶
- Homepage:
- Spack package:
- Versions:
- 1.12, 1.10.2, 1.9, 1.8, 1.7, 1.6, 1.4, 1.3.1, 1.2
- Build Dependencies:
- gsl, perl, htslib
- Link Dependencies:
- gsl, htslib
- Run Dependencies:
- py-matplotlib, perl
- Description:
- BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF- compressed.
bcl2fastq2¶
- Homepage:
- Spack package:
- Versions:
- 2.20.0.422, 2.19.1.403
- Build Dependencies:
- boost, cmake, libxml2, libxslt, libgcrypt, zlib
- Link Dependencies:
- boost, libxml2, libxslt, libgcrypt, zlib
- Description:
- The bcl2fastq2 Conversion Software converts base call (BCL) files from a sequencing run into FASTQ files.
bdftopcf¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- libxfont, pkgconfig, xproto, fontsproto, util-macros
- Link Dependencies:
- libxfont, xproto, fontsproto
- Description:
- bdftopcf is a font compiler for the X server and font server. Fonts in Portable Compiled Format can be read by any architecture, although the file is structured to allow one particular architecture to read them directly without reformatting. This allows fast reading on the appropriate machine, but the files are still portable (but read more slowly) on other machines.
bdii¶
- Homepage:
- Spack package:
- Versions:
- 5.2.25, 5.2.24
- Run Dependencies:
- openldap
- Description:
- The Berkeley Database Information Index (BDII) consists of a standard LDAP database which is updated by an external process. The update process obtains LDIF from a number of sources and merges them. It then compares this to the contents of the database and creates an LDIF file of the differences. This is then used to update the database.
bdw-gc¶
- Homepage:
- Spack package:
- Versions:
- 8.0.0, 7.6.0, 7.4.4
- Build Dependencies:
- libatomic-ops
- Link Dependencies:
- libatomic-ops
- Description:
- The Boehm-Demers-Weiser conservative garbage collector is a garbage collecting replacement for C malloc or C++ new.
beagle¶
- Homepage:
- Spack package:
- Versions:
- 5.1, 5.0, 4.1
- Run Dependencies:
- java
- Description:
- Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
beakerlib¶
- Homepage:
- Spack package:
- Versions:
- 1.20, 1.19, 1.18.1
- Description:
- BeakerLib is a shell-level integration testing library, providing convenience functions which simplify writing, running and analysis of integration and blackbox tests.
bear¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0, 2.0.4
- Build Dependencies:
- cmake, python
- Link Dependencies:
- python
- Description:
- Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems.
beast-tracer¶
- Homepage:
- Spack package:
- Versions:
- 1.7.1
- Build Dependencies:
- ant, java
- Run Dependencies:
- java
- Description:
- Tracer is a graphical tool for visualization and diagnostics of MCMC output.
beast1¶
- Homepage:
- Spack package:
- Versions:
- 1.10.4, 1.8.4
- Build Dependencies:
- libbeagle
- Link Dependencies:
- libbeagle
- Run Dependencies:
- java, libbeagle
- Description:
- BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
beast2¶
- Homepage:
- Spack package:
- Versions:
- 2.5.2, 2.4.6
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely orientated towards rooted, time- measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.
bedops¶
- Homepage:
- Spack package:
- Versions:
- 2.4.35, 2.4.34, 2.4.30
- Description:
- BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
bedtools2¶
- Homepage:
- Spack package:
- Versions:
- 2.29.2, 2.27.1, 2.27.0, 2.26.0, 2.25.0, 2.23.0
- Build Dependencies:
- zlib, bzip2, xz, python
- Link Dependencies:
- zlib, bzip2, xz
- Description:
- Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.
beforelight¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- libx11, libxscrnsaver, libxt, pkgconfig, util-macros
- Link Dependencies:
- libx11, libxscrnsaver, libxt
- Description:
- The beforelight program is a sample implementation of a screen saver for X servers supporting the MIT-SCREEN-SAVER extension. It is only recommended for use as a code sample, as it does not include features such as screen locking or configurability.
benchmark¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.5.0, 1.4.1, 1.4.0, 1.3.0, 1.2.0, 1.1.0, 1.0.0
- Build Dependencies:
- cmake
- Description:
- A microbenchmark support library
berkeley-db¶
- Homepage:
- Spack package:
- Versions:
- 18.1.40, 18.1.32, 6.2.32, 6.1.29, 6.0.35, 5.3.28
- Description:
- Oracle Berkeley DB
bertini¶
- Homepage:
- Spack package:
- Versions:
- 1.5
- Build Dependencies:
- flex, bison, gmp, mpfr, mpi
- Link Dependencies:
- gmp, mpfr, mpi
- Description:
- Bertini is a general-purpose solver, written in C, that was created for research about polynomial continuation. It solves for the numerical solution of systems of polynomial equations using homotopy continuation.
bgpdump¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- m4, autoconf, automake, libtool, bzip2
- Link Dependencies:
- bzip2
- Description:
- Utility and C Library for parsing MRT files
bib2xhtml¶
- Homepage:
- Spack package:
- Versions:
- 3.0-79-ge935
- Run Dependencies:
- texlive
- Description:
- bib2xhtml is a program that converts BibTeX files into HTML.
bigreqsproto¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Big Requests Extension. This extension defines a protocol to enable the use of requests that exceed 262140 bytes in length.
bind9¶
- Homepage:
- Spack package:
- Versions:
- 9_14_6
- Build Dependencies:
- pkgconfig
- Link Dependencies:
- libuv, openssl, libiconv
- Description:
- BIND 9 has evolved to be a very flexible, full-featured DNS system.
binutils¶
- Homepage:
- Spack package:
- Versions:
- 2.36.1, 2.35.2, 2.35.1, 2.35, 2.34, 2.33.1, 2.32, 2.31.1, 2.29.1, 2.28, 2.27, 2.26, 2.25.1, 2.25, 2.24, 2.23.2, 2.20.1
- Build Dependencies:
- zlib, diffutils, gettext, m4, bison, texinfo
- Link Dependencies:
- zlib, gettext
- Description:
- GNU binutils, which contain the linker, assembler, objdump and others
bioawk¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- zlib, bison
- Link Dependencies:
- zlib
- Description:
- Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
biobambam2¶
- Homepage:
- Spack package:
- Versions:
- 2.0.177
- Build Dependencies:
- autoconf, automake, libtool, m4, libmaus2
- Link Dependencies:
- libmaus2
- Description:
- Tools for early stage alignment file processing
biobloom¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- boost, sdsl-lite, sparsehash, zlib
- Link Dependencies:
- boost, sdsl-lite, sparsehash, zlib
- Description:
- BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorize sequences.
biopieces¶
- Homepage:
- Spack package:
- Versions:
- 2016-04-12
- Build Dependencies:
- perl, perl-module-build, perl-bit-vector, perl-svg, perl-termreadkey, perl-time-hires, perl-dbi, perl-xml-parser, perl-carp-clan, perl-class-inspector, perl-html-parser, perl-libwww-perl, perl-soap-lite, perl-uri, perl-inline, perl-inline-c, perl-parse-recdescent, perl-perl-version, perl-db-file, perl-dbd-mysql, ruby, ruby-gnuplot, ruby-narray, ruby-rubyinline, ruby-terminal-table, python, blast-plus, muscle, mummer, blat, vmatch, bowtie, bwa, usearch, velvet, idba, ray, scan-for-matches
- Link Dependencies:
- ruby, ruby-gnuplot, ruby-narray, ruby-rubyinline, ruby-terminal-table, blast-plus, muscle, mummer, blat, vmatch, bowtie, bwa, usearch, velvet, idba, ray, scan-for-matches
- Run Dependencies:
- perl, perl-module-build, perl-bit-vector, perl-svg, perl-termreadkey, perl-time-hires, perl-dbi, perl-xml-parser, perl-carp-clan, perl-class-inspector, perl-html-parser, perl-libwww-perl, perl-soap-lite, perl-uri, perl-inline, perl-inline-c, perl-parse-recdescent, perl-perl-version, perl-db-file, perl-dbd-mysql, python
- Description:
- The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks.
bird¶
- Homepage:
- Spack package:
- Versions:
- 2.0.2, 2.0.1
- Build Dependencies:
- autoconf, automake, libtool, m4, flex, bison, ncurses, readline
- Link Dependencies:
- ncurses, readline
- Description:
- The BIRD project aims to develop a dynamic IP routing daemon with full support of all modern routing protocols, easy to use configuration interface and powerful route filtering language, primarily targeted on (but not limited to) Linux and other UNIX-like systems and distributed under the GNU General Public License.
bismark¶
- Homepage:
- Spack package:
- Versions:
- 0.19.0, 0.18.2
- Run Dependencies:
- bowtie2, perl, samtools
- Description:
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states
bison¶
- Homepage:
- Spack package:
- Versions:
- 3.7.6, 3.7.5, 3.7.4, 3.7.3, 3.7.2, 3.7.1, 3.7, 3.6.4, 3.6.3, 3.6.2, 3.6.1, 3.6, 3.5.3, 3.5.2, 3.5.1, 3.5, 3.4.2, 3.4.1, 3.3.2, 3.0.5, 3.0.4, 2.7
- Build Dependencies:
- diffutils, m4, perl
- Run Dependencies:
- m4
- Description:
- Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
bitlbee¶
- Homepage:
- Spack package:
- Versions:
- 3.6-1, 3.6, 3.5-2
- Build Dependencies:
- glib, gnutls, libgcrypt
- Link Dependencies:
- glib, gnutls, libgcrypt
- Description:
- An IRC to other chat networks gateway.
bitmap¶
- Homepage:
- Spack package:
- Versions:
- 1.0.8
- Build Dependencies:
- libx11, libxmu, libxaw, libxt, xbitmaps, xproto, pkgconfig, util-macros
- Link Dependencies:
- libx11, libxmu, libxaw, libxt, xbitmaps, xproto
- Description:
- bitmap, bmtoa, atobm - X bitmap (XBM) editor and converter utilities.
bitsery¶
- Homepage:
- Spack package:
- Versions:
- 5.1.0
- Build Dependencies:
- cmake
- Description:
- Header only C++ binary serialization library. It is designed around the networking requirements for real-time data delivery, especially for games.
blaspp¶
- Homepage:
- Spack package:
- Versions:
- master, 2021.04.01, 2020.10.02, 2020.10.01, 2020.10.00
- Build Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, cmake, blas, llvm-openmp, rocblas
- Link Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, blas, llvm-openmp, rocblas
- Description:
- C++ API for the Basic Linear Algebra Subroutines. Developed by the Innovative Computing Laboratory at the University of Tennessee, Knoxville.
blasr¶
- Homepage:
- Spack package:
- Versions:
- 5.3.1
- Build Dependencies:
- ncurses, hdf5, htslib, zlib, boost, pbbam, blasr-libcpp, python
- Link Dependencies:
- ncurses, hdf5, htslib, zlib, boost, pbbam, blasr-libcpp
- Description:
- The PacBio long read aligner.
blasr-libcpp¶
- Homepage:
- Spack package:
- Versions:
- 5.3.1
- Build Dependencies:
- pbbam, hdf5, python
- Link Dependencies:
- pbbam, hdf5
- Description:
- Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences.
blast-legacy¶
- Homepage:
- Spack package:
- Versions:
- 2.2.26
- Build Dependencies:
- tcsh
- Description:
- Legacy NCBI BLAST distribution -- no longer supported. Contains older programs including `blastall'
blast-plus¶
- Homepage:
- Spack package:
- Versions:
- 2.11.0, 2.9.0, 2.8.1, 2.7.1, 2.6.0, 2.2.30
- Build Dependencies:
- jpeg, libpng, freetype, gnutls, openssl, zlib, bzip2, lzo, pcre, python, perl, lmdb
- Link Dependencies:
- jpeg, libpng, freetype, gnutls, openssl, zlib, bzip2, lzo, pcre, python, perl, lmdb
- Description:
- Basic Local Alignment Search Tool.
blast2go¶
- Homepage:
- Spack package:
- Versions:
- 5.2.5
- Build Dependencies:
- bash, java
- Run Dependencies:
- blast-plus
- Description:
- Blast2GO is a bioinformatics platform for high-quality functional annotation and analysis of genomic datasets.
blat¶
- Homepage:
- Spack package:
- Versions:
- 35
- Build Dependencies:
- libpng
- Link Dependencies:
- libpng
- Description:
- BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm.
blaze¶
- Homepage:
- Spack package:
- Versions:
- master, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 2.0, 1.5, 1.4, 1.3, 1.2, 1.1, 1.0
- Build Dependencies:
- cmake, blas
- Link Dependencies:
- blas
- Description:
- Blaze is an open-source, high-performance C++ math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and ease of use of a domain- specific language with HPC-grade performance, making it one of the most intuitive and fastest C++ math libraries available.
blis¶
- Homepage:
- Spack package:
- Versions:
- master, 0.8.1, 0.8.0, 0.7.0, 0.6.1, 0.6.0, 0.5.0, 0.4.0, 0.3.2, 0.3.1, 0.3.0, 0.2.2
- Build Dependencies:
- python
- Run Dependencies:
- python
- Description:
- BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. The framework was designed to isolate essential kernels of computation that, when optimized, immediately enable optimized implementations of most of its commonly used and computationally intensive operations. BLIS is written in ISO C99 and available under a new/modified/3-clause BSD license. While BLIS exports a new BLAS-like API, it also includes a BLAS compatibility layer which gives application developers access to BLIS implementations via traditional BLAS routine calls. An object-based API unique to BLIS is also available.
bliss¶
- Homepage:
- Spack package:
- Versions:
- 0.73
- Build Dependencies:
- gmp, libtool
- Link Dependencies:
- gmp
- Description:
- bliss: A Tool for Computing Automorphism Groups and Canonical Labelings of Graphs
blitz¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2, 1.0.1, 1.0.0
- Build Dependencies:
- python
- Description:
- N-dimensional arrays for C++
blktrace¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0, 1.1.0, 1.0.5, 1.0.4, 1.0.3, 1.0.2
- Build Dependencies:
- libaio
- Link Dependencies:
- libaio
- Description:
- blktrace is a block layer IO tracing mechanism which provides detailed information about request queue operations up to user space. There are three major components: a kernel component, a utility to record the i/o trace information for the kernel to user space, and utilities to analyse and view the trace information.
bloaty¶
- Homepage:
- Spack package:
- Versions:
- 1.1
- Build Dependencies:
- cmake
- Description:
- Bloaty McBloatface: a size profiler for binaries.
blogbench¶
- Homepage:
- Spack package:
- Versions:
- 1.1, 1.0
- Description:
- A filesystem benchmark tool that simulates a realistic load.
blt¶
- Homepage:
- Spack package:
- Versions:
- develop, main, 0.4.0, 0.3.6, 0.3.5, 0.3.0, 0.2.5, 0.2.0
- Run Dependencies:
- cmake
- Description:
- BLT is a streamlined CMake-based foundation for Building, Linking and Testing large-scale high performance computing (HPC) applications.
bmake¶
- Homepage:
- Spack package:
- Versions:
- 20200710, 20180512, 20171207
- Description:
- Portable version of NetBSD make(1).
bmi¶
- Homepage:
- Spack package:
- Versions:
- main
- Build Dependencies:
- autoconf, automake
- Description:
- a communications framework and network abstraction layer
bml¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.3.1, 1.3.0, 1.2.3, 1.2.2, 1.1.0
- Build Dependencies:
- cmake, blas, lapack, mpi, python
- Link Dependencies:
- blas, lapack, mpi
- Description:
- The basic matrix library (bml) is a collection of various matrix data formats (in dense and sparse) and their associated algorithms for basic matrix operations.
bohrium¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.9.1, 0.9.0
- Build Dependencies:
- cuda, cmake, python, boost, opencl, netlib-lapack, blas, opencv, py-numpy, swig, py-cython, zlib
- Link Dependencies:
- cuda, python, boost, opencl, netlib-lapack, blas, opencv, zlib
- Run Dependencies:
- python, py-numpy
- Test Dependencies:
- python, py-numpy
- Description:
- Library for automatic acceleration of array operations
boinc-client¶
- Homepage:
- Spack package:
- Versions:
- 7.16.5
- Build Dependencies:
- autoconf, automake, libtool, m4, curl, openssl, freeglut, libsm, libice, libxmu, libxi, libx11, libjpeg, wxwidgets, libnotify, sqlite
- Link Dependencies:
- curl, openssl, freeglut, libsm, libice, libxmu, libxi, libx11, libjpeg, wxwidgets, libnotify, sqlite
- Description:
- BOINC is a platform for high-throughput computing on a large scale (thousands or millions of computers). It can be used for volunteer computing (using consumer devices) or grid computing (using organizational resources). It supports virtualized, parallel, and GPU- based applications.
bolt¶
- Homepage:
- Spack package:
- Versions:
- main, 2.0, 1.0.1, 1.0
- Build Dependencies:
- cmake, argobots, autoconf, automake, libtool
- Link Dependencies:
- argobots
- Description:
- BOLT targets a high-performing OpenMP implementation, especially specialized for fine-grain parallelism. Unlike other OpenMP implementations, BOLT utilizes a lightweight threading model for its underlying threading mechanism. It currently adopts Argobots, a new holistic, low-level threading and tasking runtime, in order to overcome shortcomings of conventional OS-level threads. The current BOLT implementation is based on the OpenMP runtime in LLVM, and thus it can be used with LLVM/Clang, Intel OpenMP compiler, and GCC.
bonniepp¶
- Homepage:
- Spack package:
- Versions:
- 1.98
- Description:
- Bonnie++ is a benchmark suite that is aimed at performing a number of simple tests of hard drive and file system performance.
bookleaf-cpp¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.0.2, 2.0.1, 2.0
- Build Dependencies:
- cmake, caliper, parmetis, silo, typhon, mpi, yaml-cpp
- Link Dependencies:
- caliper, parmetis, silo, typhon, mpi, yaml-cpp
- Description:
- BookLeaf is a 2D unstructured hydrodynamics mini-app.
boost¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.76.0, 1.75.0, 1.74.0, 1.73.0, 1.72.0, 1.71.0, 1.70.0, 1.69.0, 1.68.0, 1.67.0, 1.66.0, 1.65.1, 1.65.0, 1.64.0, 1.63.0, 1.62.0, 1.61.0, 1.60.0, 1.59.0, 1.58.0, 1.57.0, 1.56.0, 1.55.0, 1.54.0, 1.53.0, 1.52.0, 1.51.0, 1.50.0, 1.49.0, 1.48.0, 1.47.0, 1.46.1, 1.46.0, 1.45.0, 1.44.0, 1.43.0, 1.42.0, 1.41.0, 1.40.0, 1.39.0, 1.38.0, 1.37.0, 1.36.0, 1.35.0, 1.34.1, 1.34.0
- Build Dependencies:
- icu4c, python, mpi, bzip2, zlib, py-numpy
- Link Dependencies:
- icu4c, python, mpi, bzip2, zlib
- Run Dependencies:
- py-numpy
- Description:
- Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.
boostmplcartesianproduct¶
- Homepage:
- Spack package:
- Versions:
- 20161205
- Description:
- Cartesian_product is an extension to the Boost.MPL library and as such requires a version of the Boost libraries on your system.
botan¶
- Homepage:
- Spack package:
- Versions:
- 2.18.1, 2.18.0, 2.17.3, 2.17.2, 2.17.1, 2.17.0, 2.16.0, 2.15.0, 2.14.0, 2.13.0, 2.12.1, 2.12.0, 2.11.0
- Build Dependencies:
- python, py-sphinx
- Description:
- Crypto and TLS for Modern C++
bowtie¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0, 1.2.3, 1.2.2_p1, 1.2.2, 1.2.1.1, 1.2.1, 1.2.0, 1.2
- Build Dependencies:
- tbb, zlib
- Link Dependencies:
- tbb, zlib
- Description:
- Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
bowtie2¶
- Homepage:
- Spack package:
- Versions:
- 2.4.2, 2.4.1, 2.3.5.1, 2.3.5, 2.3.4.1, 2.3.1, 2.3.0, 2.2.5
- Build Dependencies:
- tbb, readline, zlib
- Link Dependencies:
- tbb, readline, zlib, simde
- Run Dependencies:
- perl, python
- Description:
- Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
boxlib¶
- Homepage:
- Spack package:
- Versions:
- 16.12.2
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- BoxLib, a software framework for massively parallel block-structured adaptive mesh refinement (AMR) codes.
bpp-core¶
- Homepage:
- Spack package:
- Versions:
- 2.4.1, 2.2.0
- Build Dependencies:
- cmake
- Description:
- Bio++ core library.
bpp-phyl¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- cmake, bpp-core, bpp-seq
- Link Dependencies:
- bpp-core, bpp-seq
- Description:
- Bio++ phylogeny library.
bpp-phyl-omics¶
- Homepage:
- Spack package:
- Versions:
- 2.4.1, 2.4.0, 2.3.2, 2.3.1, 2.3.0
- Build Dependencies:
- cmake, bpp-core, bpp-phyl, bpp-seq, bpp-seq-omics
- Link Dependencies:
- bpp-core, bpp-phyl, bpp-seq, bpp-seq-omics
- Description:
- Bio++ Phylogenetic Omics Library
bpp-seq¶
- Homepage:
- Spack package:
- Versions:
- 2.4.1, 2.2.0
- Build Dependencies:
- cmake, bpp-core
- Link Dependencies:
- bpp-core
- Description:
- Bio++ seq library.
bpp-seq-omics¶
- Homepage:
- Spack package:
- Versions:
- 2.4.1, 2.4.0, 2.3.2, 2.3.1, 2.3.0
- Build Dependencies:
- cmake, bpp-core, bpp-seq
- Link Dependencies:
- bpp-core, bpp-seq
- Description:
- Bio++ Sequence Omics Library
bpp-suite¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- cmake, texinfo, bpp-core, bpp-seq, bpp-phyl
- Link Dependencies:
- bpp-core, bpp-seq, bpp-phyl
- Description:
- BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.
bracken¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- perl, python, perl-exporter-tiny, perl-list-moreutils, perl-parallel-forkmanager
- Link Dependencies:
- perl, python, perl-exporter-tiny, perl-list-moreutils, perl-parallel-forkmanager
- Run Dependencies:
- perl, python
- Description:
- Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
braker¶
- Homepage:
- Spack package:
- Versions:
- 2.1.6, 2.1.4, 1.11
- Build Dependencies:
- perl, perl-scalar-util-numeric, perl-parallel-forkmanager, perl-file-which, perl-yaml, perl-hash-merge, perl-logger-simple, perl-file-homedir, augustus, genemark-et, bamtools, samtools, diamond
- Link Dependencies:
- augustus, genemark-et, bamtools, samtools, diamond
- Run Dependencies:
- perl, perl-scalar-util-numeric, perl-parallel-forkmanager, perl-file-which, perl-yaml, perl-hash-merge, perl-logger-simple, perl-file-homedir
- Description:
- BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS
branson¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.82, 0.81, 0.8
- Build Dependencies:
- cmake, mpi, boost, metis, parmetis
- Link Dependencies:
- mpi, boost, metis, parmetis
- Description:
- Branson's purpose is to study different algorithms for parallel Monte Carlo transport. Currently it contains particle passing and mesh passing methods for domain decomposition.
breakdancer¶
- Homepage:
- Spack package:
- Versions:
- master, 1.4.5
- Build Dependencies:
- cmake, zlib
- Link Dependencies:
- zlib, ncurses
- Run Dependencies:
- perl-statistics-descriptive, perl-math-cdf, perl-gdgraph, perl-gdgraph-histogram, perl-list-moreutils, perl-exporter-tiny
- Description:
- BreakDancer-1.3.6, released under GPLv3, is a perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs..
bref3¶
- Homepage:
- Spack package:
- Versions:
- 2019-11-25, 2019-07-12, 2018-01-27
- Run Dependencies:
- java
- Description:
- Bref3: Converts from VCF format to bref3 format.
breseq¶
- Homepage:
- Spack package:
- Versions:
- 0.33.2, 0.33.1, 0.31.1
- Build Dependencies:
- autoconf, automake, libtool, m4
- Link Dependencies:
- zlib
- Run Dependencies:
- bedtools2, r
- Description:
- breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes.
bridger¶
- Homepage:
- Spack package:
- Versions:
- 2014-12-01
- Build Dependencies:
- boost
- Link Dependencies:
- boost
- Run Dependencies:
- perl
- Description:
- Bridger : An Efficient De novo Transcriptome Assembler For RNA-Seq Data
brigand¶
- Homepage:
- Spack package:
- Versions:
- master, 1.3.0, 1.2.0, 1.1.0, 1.0.0
- Build Dependencies:
- cmake
- Description:
- Brigand Meta-programming library
brltty¶
- Homepage:
- Spack package:
- Versions:
- 6.0, 5.6, 5.5, 5.4
- Build Dependencies:
- autoconf, automake, libtool, m4, expat
- Link Dependencies:
- expat, alsa-lib
- Description:
- BRLTTY is a background process (daemon) providing access to the Linux/Unix console (when in text mode) for a blind person using a refreshable braille display.
brotli¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7
- Build Dependencies:
- cmake
- Description:
- Brotli is a generic-purpose lossless compression algorithm
brpc¶
- Homepage:
- Spack package:
- Versions:
- 0.9.7, 0.9.6, 0.9.5
- Build Dependencies:
- cmake, gflags, protobuf, leveldb, openssl
- Link Dependencies:
- gflags, protobuf, leveldb, openssl
- Description:
- An industrial-grade RPC framework used throughout Baidu, with 1,000,000+ instances(not counting clients) and thousands kinds of services, called "baidu-rpc" inside Baidu. Only C++ implementatioo on is opensourced right now.
brynet¶
- Homepage:
- Spack package:
- Versions:
- 1.10.0, 1.0.8, 1.0.7, 1.0.6
- Build Dependencies:
- cmake
- Description:
- Header Only Cross platform high performance TCP network library using C++ 11.
bsseeker2¶
- Homepage:
- Spack package:
- Versions:
- 2.1.8, 2.1.7, 2.1.2
- Build Dependencies:
- python, py-pysam
- Run Dependencies:
- python, py-pysam
- Description:
- A versatile aligning pipeline for bisulfite sequencing data.
bubblewrap¶
- Homepage:
- Spack package:
- Versions:
- 0.4.0, 0.3.3, 0.3.2, 0.3.1
- Build Dependencies:
- autoconf, automake, libtool, m4, libcap
- Link Dependencies:
- libcap
- Description:
- Unprivileged sandboxing tool
bucky¶
- Homepage:
- Spack package:
- Versions:
- 1.4.4
- Description:
- BUCKy is a free program to combine molecular data from multiple loci. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian concordance analysis.
bumpversion¶
- Homepage:
- Spack package:
- Versions:
- 0.5.3, 0.5.0
- Build Dependencies:
- python, py-setuptools
- Run Dependencies:
- python
- Description:
- Version-bump your software with a single command.
busco¶
- Homepage:
- Spack package:
- Versions:
- 4.1.3, 3.0.1, 2.0.1
- Build Dependencies:
- python, blast-plus, hmmer, augustus, py-biopython
- Link Dependencies:
- blast-plus, hmmer, augustus
- Run Dependencies:
- python, py-biopython
- Description:
- Assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
busybox¶
- Homepage:
- Spack package:
- Versions:
- 1.31.1, 1.31.0, 1.30.1, 1.30.0
- Description:
- BusyBox combines tiny versions of many common UNIX utilities into a single small executable. It provides replacements for most of the utilities you usually find in GNU fileutils, shellutils, etc
butter¶
- Homepage:
- Spack package:
- Versions:
- 0.3.3
- Build Dependencies:
- perl, samtools, bowtie
- Link Dependencies:
- samtools, bowtie
- Run Dependencies:
- perl
- Description:
- butter: Bowtie UTilizing iTerative placEment of Repetitive small rnas. A wrapper for bowtie to produce small RNA-seq alignments where multimapped small RNAs tend to be placed near regions of confidently high density.
butterflypack¶
- Homepage:
- Spack package:
- Versions:
- master, 1.2.1, 1.2.0, 1.1.0, 1.0.3, 1.0.1, 1.0.0
- Build Dependencies:
- cmake, mpi, blas, lapack, scalapack, arpack-ng
- Link Dependencies:
- mpi, blas, lapack, scalapack, arpack-ng
- Description:
- ButterflyPACK is a mathematical software for rapidly solving large-scale dense linear systems that exhibit off-diagonal rank-deficiency. These systems arise frequently from boundary element methods, or factorization phases in finite-difference/finite-element methods. ButterflyPACK relies on low-rank or butterfly formats under Hierarchical matrix, HODLR or other hierarchically nested frameworks to compress, factor and solve the linear system in quasi-linear time. The computationally most intensive phase, factorization, is accelerated via randomized linear algebras. The butterfly format, originally inspired by the butterfly data flow in fast Fourier Transform, is a linear algebra tool well-suited for compressing matrices arising from high-frequency wave equations or highly oscillatory integral operators.
bwa¶
- Homepage:
- Spack package:
- Versions:
- 0.7.17, 0.7.15, 0.7.13, 0.7.12
- Build Dependencies:
- zlib, sse2neon
- Link Dependencies:
- zlib, sse2neon
- Description:
- Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
bwtool¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- libbeato
- Link Dependencies:
- libbeato
- Description:
- bwtool is a command-line utility for bigWig files.
byacc¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- m4, autoconf, automake, libtool
- Description:
- Berkeley Yacc is an LALR(1) parser generator. Berkeley Yacc has been made as compatible as possible with AT&T Yacc. Berkeley Yacc can accept any input specification that conforms to the AT&T Yacc documentation. Specifications that take advantage of undocumented features of AT&T Yacc will probably be rejected.
byobu¶
- Homepage:
- Spack package:
- Versions:
- 5.131, 5.127, 5.125, 5.123
- Build Dependencies:
- tmux
- Run Dependencies:
- tmux
- Description:
- Byobu: Text-based window manager and terminal multiplexer.
byte-unixbench¶
- Homepage:
- Spack package:
- Versions:
- 5.1.3
- Description:
- UnixBench is the original BYTE UNIX benchmark suite.
byteman¶
- Homepage:
- Spack package:
- Versions:
- 4.0.12, 4.0.11, 4.0.10, 4.0.9, 4.0.8, 4.0.7
- Build Dependencies:
- java, maven
- Run Dependencies:
- java
- Description:
- Byteman is a tool which makes it easy to trace, monitor and test the behaviour of Java application and JDK runtime code.
bzip2¶
- Homepage:
- Spack package:
- Versions:
- 1.0.8, 1.0.7, 1.0.6
- Build Dependencies:
- diffutils
- Description:
- bzip2 is a freely available, patent free high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
c-ares¶
- Homepage:
- Spack package:
- Versions:
- master, 1.15.0, 1.13.0
- Build Dependencies:
- cmake
- Description:
- c-ares: A C library for asynchronous DNS requests
c-blosc¶
- Homepage:
- Spack package:
- Versions:
- 1.21.0, 1.17.0, 1.16.3, 1.15.0, 1.12.1, 1.11.1, 1.9.2, 1.9.1, 1.9.0, 1.8.1, 1.8.0
- Build Dependencies:
- cmake, snappy, zlib, zstd, lz4
- Link Dependencies:
- snappy, zlib, zstd, lz4
- Description:
- Blosc, an extremely fast, multi-threaded, meta-compressor library
c-blosc2¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.0.0.rc1
- Build Dependencies:
- cmake, lizard, lz4, snappy, zlib, zstd
- Link Dependencies:
- lizard, lz4, snappy, zlib, zstd
- Description:
- Next generation c-blosc with a new API, a new container and other bells and whistles
c-lime¶
- Homepage:
- Spack package:
- Versions:
- 2-3-9
- Description:
- LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII and/or binary data.
ca-certificates-mozilla¶
- Homepage:
- Spack package:
- Versions:
- 2021-04-13, 2021-01-19, 2020-12-08, 2020-10-14, 2020-07-22, 2020-06-24, 2020-01-01, 2019-11-27, 2019-10-16, 2019-08-28
- Description:
- The Mozilla CA certificate store in PEM format
cabana¶
- Homepage:
- Spack package:
- Versions:
- master, 0.3.0, 0.2.0, 0.1.0-rc0, 0.1.0
- Build Dependencies:
- cmake, kokkos-legacy, kokkos, mpi
- Link Dependencies:
- kokkos-legacy, kokkos, mpi
- Description:
- The Exascale Co-Design Center for Particle Applications Toolkit
cachefilesd¶
- Homepage:
- Spack package:
- Versions:
- 0.10.10, 0.10.9, 0.10.7, 0.10.6, 0.10.5
- Description:
- The cachefilesd daemon manages the caching files and directory that are that are used by network file systems such a AFS and NFS to do persistent caching to the local disk.
caffe¶
- Homepage:
- Spack package:
- Versions:
- 1.0, rc5, rc4, rc3, rc2
- Build Dependencies:
- cmake, boost, cuda, blas, protobuf, glog, gflags, hdf5, opencv, leveldb, lmdb, python, py-numpy, matlab
- Link Dependencies:
- boost, cuda, blas, protobuf, glog, gflags, hdf5, opencv, leveldb, lmdb, python, matlab
- Run Dependencies:
- python, py-numpy
- Description:
- Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors.
cairo¶
- Homepage:
- Spack package:
- Versions:
- 1.17.2, 1.16.0, 1.14.12, 1.14.8, 1.14.0
- Build Dependencies:
- libx11, libxext, libxrender, libxcb, python, libpng, librsvg, glib, pixman, automake, autoconf, libtool, m4, freetype, pkgconfig, fontconfig
- Link Dependencies:
- libx11, libxext, libxrender, libxcb, libpng, librsvg, glib, pixman, freetype, fontconfig
- Description:
- Cairo is a 2D graphics library with support for multiple output devices.
cairomm¶
- Homepage:
- Spack package:
- Versions:
- 1.6.4, 1.6.2
- Build Dependencies:
- cairo, libsigcpp
- Link Dependencies:
- cairo, libsigcpp
- Description:
- Cairomm is a C++ wrapper for the cairo graphics library.
caliper¶
- Homepage:
- Spack package:
- Versions:
- master, 2.5.0, 2.4.0, 2.3.0, 2.2.0, 2.1.1, 2.0.1, 1.9.1, 1.9.0, 1.8.0, 1.7.0
- Build Dependencies:
- cuda, cmake, adiak, papi, libpfm4, mpi, unwind, elfutils, sosflow, python
- Link Dependencies:
- cuda, adiak, papi, libpfm4, mpi, unwind, elfutils, sosflow
- Description:
- Caliper is a program instrumentation and performance measurement framework. It is designed as a performance analysis toolbox in a library, allowing one to bake performance analysis capabilities directly into applications and activate them at runtime.
callflow¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.1.2, 1.1.1, 1.1.0
- Build Dependencies:
- python, py-setuptools, py-numpy, py-scipy, py-pandas, py-hatchet, py-statsmodels, py-scikit-learn, py-colorlog, py-jsonschema, py-matplotlib, py-networkx, py-ipython, py-flask-socketio, py-flask-cors
- Run Dependencies:
- python, py-setuptools, py-numpy, py-scipy, py-pandas, py-hatchet, py-statsmodels, py-scikit-learn, py-colorlog, py-jsonschema, py-matplotlib, py-networkx, py-ipython, py-flask-socketio, py-flask-cors
- Description:
- CallFlow is an interactive visual analysis tool that provides a high- level overview of CCTs together with semantic refinement operations to progressively explore the CCTs.
callpath¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4, 1.0.2, 1.0.1
- Build Dependencies:
- cmake, libdwarf, dyninst, adept-utils, mpi
- Link Dependencies:
- elf, libdwarf, dyninst, adept-utils, mpi
- Description:
- Library for representing callpaths consistently in distributed-memory performance tools.
camellia¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- cmake, trilinos, moab, hdf5, mpi
- Link Dependencies:
- trilinos, moab, hdf5, mpi
- Description:
- Camellia: user-friendly MPI-parallel adaptive finite element package, with support for DPG and other hybrid methods, built atop Trilinos.
camp¶
- Homepage:
- Spack package:
- Versions:
- master, 0.1.0
- Build Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, cmake, cub
- Link Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, cub
- Description:
- Compiler agnostic metaprogramming library providing concepts, type operations and tuples for C++ and cuda
camx¶
- Homepage:
- Spack package:
- Versions:
- 6.50
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Comprehensive Air Quality Model with Extensions.
canal¶
- Homepage:
- Spack package:
- Versions:
- 1.1.4, 1.1.3, 1.1.2
- Build Dependencies:
- java, maven
- Run Dependencies:
- java
- Description:
- Alibaba MySQL binlog incremental subscription & consumer components.
candle-benchmarks¶
- Homepage:
- Spack package:
- Versions:
- 0.1
- Build Dependencies:
- python, py-theano, py-keras, py-matplotlib, py-tqdm, py-scikit-learn, opencv, py-mdanalysis, py-mpi4py, py-h5py, py-requests
- Link Dependencies:
- python, opencv
- Run Dependencies:
- python, py-theano, py-keras, py-matplotlib, py-tqdm, py-scikit-learn, py-mdanalysis, py-mpi4py, py-h5py, py-requests
- Description:
- ECP-CANDLE Benchmarks
cantera¶
- Homepage:
- Spack package:
- Versions:
- 2.4.0, 2.3.0, 2.2.1
- Build Dependencies:
- scons, fmt, googletest, eigen, boost, sundials, blas, lapack, python, py-cython, py-numpy, py-scipy, py-3to2, py-unittest2, py-unittest2py3k, matlab
- Link Dependencies:
- fmt, googletest, eigen, boost, sundials, blas, lapack
- Run Dependencies:
- python, py-numpy, py-scipy, py-3to2, py-unittest2, py-unittest2py3k, matlab
- Description:
- Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes.
canu¶
- Homepage:
- Spack package:
- Versions:
- 2.0, 1.8, 1.7.1, 1.7, 1.5
- Build Dependencies:
- boost
- Link Dependencies:
- boost
- Run Dependencies:
- gnuplot, java, perl
- Description:
- A single molecule sequence assembler for genomes large and small.
cap3¶
- Homepage:
- Spack package:
- Versions:
- 2015-02-11
- Description:
- CAP3 is DNA Sequence Assembly Program
capnproto¶
- Homepage:
- Spack package:
- Versions:
- 0.8.0, 0.7.0
- Description:
- Cap'n Proto is an insanely fast data interchange format and capability- based RPC system.
capstone¶
- Homepage:
- Spack package:
- Versions:
- master, 4.0.2, 4.0.1, next
- Build Dependencies:
- cmake
- Description:
- Capstone is a lightweight multi-platform, multi-architecture disassembly framework.
cardioid¶
- Homepage:
- Spack package:
- Versions:
- develop, elecfem
- Build Dependencies:
- cmake, blas, lapack, mpi, cuda, mfem, hypre, perl
- Link Dependencies:
- blas, lapack, mpi, cuda, mfem, hypre
- Description:
- Cardiac simulation suite.
care¶
- Homepage:
- Spack package:
- Versions:
- develop, master, 0.3.0, 0.2.0
- Build Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, cmake, blt, camp, umpire, raja, chai, cub
- Link Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, camp, umpire, raja, chai, cub
- Description:
- Algorithms for chai managed arrays.
casacore¶
- Homepage:
- Spack package:
- Versions:
- 3.4.0, 3.3.0, 3.2.0, 3.1.2, 3.1.1, 3.1.0, 3.0.0, 2.4.1
- Build Dependencies:
- cmake, readline, flex, bison, blas, lapack, cfitsio, wcslib, fftw, hdf5, python, boost, py-numpy
- Link Dependencies:
- readline, blas, lapack, cfitsio, wcslib, fftw, hdf5, python, boost, py-numpy
- Test Dependencies:
- sofa-c
- Description:
- A suite of c++ libraries for radio astronomy data processing.
cask¶
- Homepage:
- Spack package:
- Versions:
- 0.8.1, 0.7.4
- Build Dependencies:
- emacs
- Run Dependencies:
- emacs
- Description:
- Cask is a project management tool for Emacs Lisp to automate the package development cycle; development, dependencies, testing, building, packaging and more.
casper¶
- Homepage:
- Spack package:
- Versions:
- 0.8.2
- Build Dependencies:
- jellyfish, boost
- Link Dependencies:
- jellyfish, boost
- Description:
- CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.
cassandra¶
- Homepage:
- Spack package:
- Versions:
- 4.0-alpha2, 4.0-alpha1, 3.11.6, 3.11.5
- Build Dependencies:
- java
- Run Dependencies:
- java
- Description:
- Apache Cassandra is a highly-scalable partitioned row store. Rows are organized into tables with a required primary key.
catalyst¶
- Homepage:
- Spack package:
- Versions:
- 5.6.0, 5.5.2, 5.5.1, 5.5.0, 5.4.1, 5.4.0, 5.3.0, 5.2.0, 5.1.2, 5.0.1, 4.4.0
- Build Dependencies:
- cmake, python, git, mpi, py-numpy, py-mpi4py, gl, osmesa, glx
- Link Dependencies:
- python, mpi, gl, osmesa, glx
- Run Dependencies:
- python, py-numpy, py-mpi4py
- Description:
- Catalyst is an in situ use case library, with an adaptable application programming interface (API), that orchestrates the alliance between simulation and analysis and/or visualization tasks.
catch2¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.0.0-preview3, 2.13.4, 2.13.3, 2.13.2, 2.13.1, 2.13.0, 2.12.4, 2.12.3, 2.12.1, 2.12.0, 2.11.3, 2.11.2, 2.11.1, 2.11.0, 2.10.2, 2.10.1, 2.10.0, 2.9.2, 2.9.1, 2.9.0, 2.8.0, 2.7.2, 2.7.1, 2.7.0, 2.6.1, 2.6.0, 2.5.0, 2.4.2, 2.4.1, 2.4.0, 2.3.0, 2.2.3, 2.2.2, 2.2.1, 2.1.0, 2.0.1, 1.12.1, 1.12.0, 1.11.0, 1.10.0, 1.9.7, 1.9.6, 1.9.5, 1.9.4, 1.9.3, 1.9.2, 1.9.1, 1.9.0, 1.8.2, 1.8.1, 1.8.0, 1.7.2, 1.7.1, 1.7.0, 1.6.1, 1.6.0, 1.5.9, 1.5.0, 1.4.0, 1.3.5, 1.3.0
- Build Dependencies:
- cmake
- Description:
- Catch2 is a multi-paradigm test framework for C++, which also supports Objective-C (and maybe C).
cbc¶
- Homepage:
- Spack package:
- Versions:
- 2.10.5
- Build Dependencies:
- coinutils, osi, cgl
- Link Dependencies:
- coinutils, osi, cgl
- Description:
- Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable.
cbench¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0
- Build Dependencies:
- mpi, blas, lapack, fftw
- Link Dependencies:
- mpi, blas, lapack, fftw
- Description:
- Cbench is intended as a relatively straightforward toolbox of tests, benchmarks, applications, utilities, and framework to hold them together with the goal to facilitate scalable testing, benchmarking, and analysis of a Linux parallel compute cluster.
cbflib¶
- Homepage:
- Spack package:
- Versions:
- 0.9.2
- Build Dependencies:
- m4
- Description:
- CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files.
cblas¶
- Homepage:
- Spack package:
- Versions:
- 2015-06-06
- Build Dependencies:
- blas
- Link Dependencies:
- blas
- Description:
- The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations.
cbtf¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.9.4.1, 1.9.4, 1.9.3
- Build Dependencies:
- cmake, rpcsvc-proto, boost, mrnet, xerces-c, libxml2
- Link Dependencies:
- rpcsvc-proto, libtirpc, boost, mrnet, xerces-c, libxml2
- Description:
- CBTF project contains the base code for CBTF that supports creating components, component networks and the support to connect these components and component networks into sequential and distributed network tools.
cbtf-krell¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.9.4.1, 1.9.4, 1.9.3
- Build Dependencies:
- cmake, rpcsvc-proto, binutils, boost, dyninst, mrnet, xerces-c, cbtf, libmonitor, libunwind, papi, llvm-openmp-ompt, openmpi, mpich, mvapich2, mpt, python, gotcha
- Link Dependencies:
- libtirpc, binutils, boost, dyninst, mrnet, xerces-c, cbtf, libmonitor, libunwind, papi, llvm-openmp-ompt, openmpi, mpich, mvapich2, mpt, gotcha
- Run Dependencies:
- mrnet, cbtf, libmonitor, papi, python
- Description:
- CBTF Krell project contains collector and runtime contributions to the CBTF project. These contributions include many performance data collectors and support libraries as well as some example tools that drive the data collection at HPC levels of scale.
cbtf-lanl¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.9.4.1, 1.9.4, 1.9.3
- Build Dependencies:
- cmake, mrnet, xerces-c, cbtf, cbtf-krell
- Link Dependencies:
- mrnet, xerces-c, cbtf, cbtf-krell
- Description:
- CBTF LANL project contains a memory tool and data center type system command monitoring tool.
cc65¶
- Homepage:
- Spack package:
- Versions:
- 2.18, 2.17, 2.16, 2.15, 2.14
- Description:
- cc65 is a complete cross development package for 65(C)02 systems, including a powerful macro assembler, a C compiler, linker, librarian and several other tools.
ccache¶
- Homepage:
- Spack package:
- Versions:
- 4.3, 4.2.1, 4.2, 4.1, 4.0, 3.7.11, 3.7.9, 3.7.1, 3.3.4, 3.3.3, 3.3.2, 3.3.1, 3.3, 3.2.9
- Build Dependencies:
- cmake, zstd, gperf, libxslt, zlib
- Link Dependencies:
- zstd, gperf, libxslt, zlib
- Description:
- ccache is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again.
ccfits¶
- Homepage:
- Spack package:
- Versions:
- 2.5, 2.4
- Build Dependencies:
- cfitsio
- Link Dependencies:
- cfitsio
- Description:
- CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++. It is written in ANSI C++ and implemented using the C++ Standard Library with namespaces, exception handling, and member template functions.
ccls¶
- Homepage:
- Spack package:
- Versions:
- 0.20201025
- Build Dependencies:
- cmake, llvm, rapidjson
- Link Dependencies:
- llvm, rapidjson
- Description:
- C/C++ language server
ccs-qcd¶
- Homepage:
- Spack package:
- Versions:
- master, 1.2.1
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- This program benchmarks the performance of a linear equation solver with a large sparse coefficient matrix appering in a lattice QCD probrem. Lattice QCD describes the property of protons, neutrons and neucleons in terms of more fundamental interacting elementary particles gluon and quarks.
cctools¶
- Homepage:
- Spack package:
- Versions:
- 7.2.10, 7.2.4, 7.2.3, 7.2.2, 7.2.1, 7.1.7, 7.1.5, 7.1.3, 7.1.2, 7.1.0, 7.0.18, 6.1.1
- Build Dependencies:
- openssl, perl, python, readline, gettext, swig, zlib
- Link Dependencies:
- openssl, readline, gettext, swig, zlib
- Run Dependencies:
- perl, python
- Description:
- The Cooperative Computing Tools (cctools) enable large scale distributed computations to harness hundreds to thousands of machines from clusters, clouds, and grids.
cdbfasta¶
- Homepage:
- Spack package:
- Versions:
- 2017-03-16
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Fast indexing and retrieval of fasta records from flat file databases
cdd¶
- Homepage:
- Spack package:
- Versions:
- 0.61a
- Build Dependencies:
- libtool
- Description:
- The program cdd+ (cdd, respectively) is a C++ (ANSI C) implementation of the Double Description Method [MRTT53] for generating all vertices (i.e. extreme points) and extreme rays of a general convex polyhedron given by a system of linear inequalities
cddlib¶
- Homepage:
- Spack package:
- Versions:
- 0.94h
- Build Dependencies:
- gmp, libtool
- Link Dependencies:
- gmp
- Description:
- The C-library cddlib is a C implementation of the Double Description Method of Motzkin et al. for generating all vertices (i.e. extreme points) and extreme rays of a general convex polyhedron in R^d given by a system of linear inequalities
cdecimal¶
- Homepage:
- Spack package:
- Versions:
- 2.3
- Description:
- cdecimal is a fast drop-in replacement for the decimal module in Python's standard library.
cdhit¶
- Homepage:
- Spack package:
- Versions:
- 4.8.1, 4.6.8
- Build Dependencies:
- perl
- Link Dependencies:
- zlib
- Run Dependencies:
- perl
- Description:
- CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
cdo¶
- Homepage:
- Spack package:
- Versions:
- 1.9.10, 1.9.9, 1.9.8, 1.9.7.1, 1.9.6, 1.9.5, 1.9.4, 1.9.3, 1.9.2, 1.9.1, 1.9.0, 1.8.2, 1.7.2
- Build Dependencies:
- pkgconfig, netcdf-c, hdf5, grib-api, eccodes, szip, udunits, libxml2, proj, curl, fftw-api, magics, uuid
- Link Dependencies:
- netcdf-c, hdf5, grib-api, eccodes, szip, udunits, libxml2, proj, curl, fftw-api, magics, uuid
- Description:
- CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
ceed¶
- Homepage:
- Spack package:
- Versions:
- 3.0.0, 2.0.0, 1.0.0
- Build Dependencies:
- libceed, occa, nek5000, nektools, gslib, nekbone, nekcem, petsc, hypre, hpgmg, magma, pumi, mfem, laghos, remhos, suite-sparse
- Link Dependencies:
- libceed, occa, nek5000, nektools, gslib, nekbone, nekcem, petsc, hypre, hpgmg, magma, pumi, mfem, laghos, remhos, suite-sparse
- Description:
- Ceed is a collection of benchmarks, miniapps, software libraries and APIs for efficient high-order finite element and spectral element discretizations for exascale applications developed in the Department of Energy (DOE) and partially supported by the Exascale Computing Project (ECP). This is a Spack bundle package that installs the CEED software components.
cereal¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0, 1.2.2, 1.2.1, 1.2.0, 1.1.2, 1.1.1, 1.1.0, 1.0.0, 0.9.1
- Build Dependencies:
- cmake
- Description:
- cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.
ceres-solver¶
- Homepage:
- Spack package:
- Versions:
- 2.0.0, 1.14.0, 1.12.0
- Build Dependencies:
- cmake, eigen, lapack, glog
- Link Dependencies:
- eigen, lapack, glog
- Description:
- Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems. It can be used to solve Non- linear Least Squares problems with bounds constraints and general unconstrained optimization problems. It is a mature, feature rich, and performant library that has been used in production at Google since 2010.
cfitsio¶
- Homepage:
- Spack package:
- Versions:
- 3.49, 3.48, 3.47, 3.45, 3.42, 3.41, 3.37
- Build Dependencies:
- curl, bzip2
- Link Dependencies:
- curl, bzip2
- Description:
- CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
cgal¶
- Homepage:
- Spack package:
- Versions:
- 5.0.3, 5.0, 4.13, 4.12, 4.11, 4.9.1, 4.9, 4.7, 4.6.3
- Build Dependencies:
- cmake, boost, gmp, mpfr, zlib, qt, eigen
- Link Dependencies:
- boost, gmp, mpfr, zlib, qt, eigen
- Description:
- The Computational Geometry Algorithms Library (CGAL) is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics.
cgdb¶
- Homepage:
- Spack package:
- Versions:
- 0.7.0
- Build Dependencies:
- ncurses, readline, flex, bison, texinfo
- Link Dependencies:
- ncurses, readline
- Description:
- A curses front-end to GDB
cgdcbxd¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2, 1.0.1
- Build Dependencies:
- autoconf, automake, libtool, m4, libcgroup, libmnl
- Link Dependencies:
- libcgroup, libmnl
- Description:
- cgdcbxd is a daemon used to monitor DCB netlink events and manage the net_prio control group subsystem. The daemon keeps the hierarchy and priority mappings in sync with DCBX Application events
cget¶
- Homepage:
- Spack package:
- Versions:
- 0.1.9
- Build Dependencies:
- python, py-setuptools, py-six, py-click, py-subprocess32
- Run Dependencies:
- python, py-six, py-click, py-subprocess32
- Description:
- Cmake package retrieval.
cgl¶
- Homepage:
- Spack package:
- Versions:
- 0.60.3
- Build Dependencies:
- coinutils, osi, clp
- Link Dependencies:
- coinutils, osi, clp
- Description:
- The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver.
cgm¶
- Homepage:
- Spack package:
- Versions:
- 16.0, 13.1.1, 13.1.0, 13.1
- Build Dependencies:
- mpi, oce
- Link Dependencies:
- mpi, oce
- Description:
- The Common Geometry Module, Argonne (CGMA) is a code library which provides geometry functionality used for mesh generation and other applications.
cgns¶
- Homepage:
- Spack package:
- Versions:
- develop, master, 4.2.0, 4.1.2, 4.1.1, 4.1.0, 4.0.0, 3.4.1, 3.4.0, 3.3.1, 3.3.0
- Build Dependencies:
- cmake, hdf5, mpi
- Link Dependencies:
- hdf5, mpi
- Description:
- The CFD General Notation System (CGNS) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.
chai¶
- Homepage:
- Spack package:
- Versions:
- develop, master, 2.3.0, 2.2.2, 2.2.1, 2.2.0, 2.1.1, 2.1.0, 2.0.0, 1.2.0, 1.1.0, 1.0
- Build Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, cmake, blt, umpire, raja
- Link Dependencies:
- llvm-amdgpu, hsa-rocr-dev, hip, cuda, umpire, raja
- Description:
- Copy-hiding array interface for data migration between memory spaces
changa¶
- Homepage:
- Spack package:
- Versions:
- master, 3.4
- Build Dependencies:
- charmpp
- Link Dependencies:
- charmpp
- Description:
- ChaNGa (Charm N-body GrAvity solver) is a code to perform collisionless N-body simulations. It can perform cosmological simulations with periodic boundary conditions in comoving coordinates or simulations of isolated stellar systems. It also can include hydrodynamics using the Smooth Particle Hydrodynamics (SPH) technique. It uses a Barnes-Hut tree to calculate gravity, with hexadecapole expansion of nodes and Ewald summation for periodic forces. Timestepping is done with a leapfrog integrator with individual timesteps for each particle.
channelflow¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- cmake, eigen, fftw, mpi, hdf5, netcdf-c, boost
- Link Dependencies:
- eigen, fftw, mpi, hdf5, netcdf-c, boost
- Description:
- Channelflow is a software system for numerical analysis of the incompressible fluid flow in channel geometries, written in C++.
chapel¶
- Homepage:
- Spack package:
- Versions:
- 1.24.1, 1.24.0, 1.23.0, 1.22.1, 1.22.0, 1.21.0, 1.20.0, 1.19.0, 1.18.0
- Description:
- Chapel is a modern programming language that is parallel, productive, portable, scalable and open-source.
chaplin¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Description:
- The FORTRAN library CHAPLIN enables you to numerically evaluate Harmonic polylogarithms up to weight 4 for any complex argument.
charliecloud¶
- Homepage:
- Spack package:
- Versions:
- master, 0.23, 0.22, 0.21, 0.19, 0.18
- Build Dependencies:
- m4, autoconf, automake, libtool, rsync, py-sphinx, py-sphinx-rtd-theme
- Run Dependencies:
- python, py-lark-parser, py-requests
- Test Dependencies:
- bats
- Description:
- Lightweight user-defined software stacks for HPC.
charmpp¶
- Homepage:
- Spack package:
- Versions:
- main, 6.10.2, 6.10.1, 6.10.0, 6.9.0, 6.8.2, 6.8.1, 6.8.0, 6.7.1, 6.7.0, 6.6.1, 6.6.0, 6.5.1
- Build Dependencies:
- mpi, papi, cuda, ucx, slurm, openmpi, automake, autoconf
- Link Dependencies:
- mpi, papi, cuda, ucx, slurm, openmpi, automake, autoconf
- Description:
- Charm++ is a parallel programming framework in C++ supported by an adaptive runtime system, which enhances user productivity and allows programs to run portably from small multicore computers (your laptop) to the largest supercomputers.
chatterbug¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0
- Build Dependencies:
- mpi, scorep
- Link Dependencies:
- mpi, scorep
- Description:
- A suite of communication-intensive proxy applications that mimic commonly found communication patterns in HPC codes. These codes can be used as synthetic codes for benchmarking, or for trace generation using Score-P / OTF2.
check¶
- Homepage:
- Spack package:
- Versions:
- 0.12.0, 0.11.0, 0.10.0
- Description:
- Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.
chgcentre¶
- Homepage:
- Spack package:
- Versions:
- 1.6
- Build Dependencies:
- cmake, casacore, gsl
- Link Dependencies:
- casacore, gsl
- Description:
- The chgcentre tool can be used to change the phase centre of a measurement set.
chill¶
- Homepage:
- Spack package:
- Versions:
- master, 0.3
- Build Dependencies:
- boost, rose, autoconf, automake, libtool, m4, iegenlib, bison, flex, python, isl, gmp
- Link Dependencies:
- python
- Run Dependencies:
- rose, iegenlib
- Description:
- A polyheadral compiler for autotuning
chlorop¶
- Homepage:
- Spack package:
- Versions:
- 1.1
- Run Dependencies:
- awk
- Description:
- Chlorop predicts the presence of chloroplast transit peptides in protein sequences and the location of potential cTP cleavage sites. You will need to obtain the tarball by visiting the URL and completing the form. You can then either run spack install with the tarball in the directory, or add it to a mirror. You will need to set the CHLOROTMP environment variable to the full path of the directory you want chlorop to use as a temporary directory.
chombo¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.2
- Build Dependencies:
- blas, lapack, gmake, mpi, hdf5
- Link Dependencies:
- blas, lapack, mpi, hdf5
- Description:
- The Chombo package provides a set of tools for implementing finite difference and finite-volume methods for the solution of partial differential equations on block-structured adaptively refined logically rectangular (i.e. Cartesian) grids.
chrony¶
- Homepage:
- Spack package:
- Versions:
- 3.5.1, 3.5, 3.4, 3.3
- Build Dependencies:
- ruby-asciidoctor, bison
- Link Dependencies:
- ruby-asciidoctor
- Description:
- chrony is a versatile implementation of the Network Time Protocol (NTP). It can synchronise the system clock with NTP servers, reference clocks(e.g. GPS receiver), and manual input using wristwatch and keyboard.
chrpath¶
- Homepage:
- Spack package:
- Versions:
- 0.16
- Description:
- chrpath: Modifies the dynamic library load path (rpath and runpath) of compiled programs and libraries.
cinch¶
- Homepage:
- Spack package:
- Versions:
- master, 1.0
- Description:
- Cinch is a set of utilities and configuration options designed to make cmake builds easy to use and manage.
circos¶
- Homepage:
- Spack package:
- Versions:
- 0.69-6
- Run Dependencies:
- perl, perl-clone, perl-config-general, perl-exporter-tiny, perl-font-ttf, perl-gd, perl-io-string, perl-list-moreutils, perl-math-round, perl-math-bezier, perl-math-vecstat, perl-params-validate, perl-readonly, perl-regexp-common, perl-set-intspan, perl-statistics-basic, perl-svg, perl-text-format
- Description:
- Circos is a software package for visualizing data and information.
cistem¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0-beta
- Build Dependencies:
- wxwidgets, fftw
- Link Dependencies:
- wxwidgets, fftw
- Description:
- cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
citcoms¶
- Homepage:
- Spack package:
- Versions:
- master, 3.3.1, 3.2.0
- Build Dependencies:
- mpi, zlib, automake, autoconf, libtool, m4, hc, cuda, hdf5
- Link Dependencies:
- mpi, zlib, hc, cuda, hdf5
- Run Dependencies:
- python
- Description:
- CitcomS is a finite element code designed to solve compressible thermochemical convection problems relevant to Earth's mantle.
cityhash¶
- Homepage:
- Spack package:
- Versions:
- master, 2013-07-31
- Description:
- CityHash, a family of hash functions for strings.
ck¶
- Homepage:
- Spack package:
- Versions:
- 0.6.2, 0.6.1, 0.6.0, 0.5.2, 0.5.1, 0.5.0
- Build Dependencies:
- java, maven
- Run Dependencies:
- java
- Description:
- CK calculates class-level and metric-level code metrics in Java projects by means of static analysis (i.e. no need for compiled code).
clamav¶
- Homepage:
- Spack package:
- Versions:
- 0.101.2
- Build Dependencies:
- pkgconfig, json-c, openssl, pcre, yara, zlib, bzip2
- Link Dependencies:
- json-c, openssl, pcre, yara, zlib, bzip2, curl
- Description:
- Open source antivirus engine for detecting trojans, viruses, malware & other malicious threats.
clamr¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- cmake, mpi, mpe
- Link Dependencies:
- mpi, mpe
- Description:
- The CLAMR code is a cell-based adaptive mesh refinement (AMR) mini-app developed as a testbed for hybrid algorithm development using MPI and OpenCL GPU code.
clapack¶
- Homepage:
- Spack package:
- Versions:
- 3.2.1
- Build Dependencies:
- atlas
- Link Dependencies:
- atlas
- Description:
- CLAPACK is a f2c'ed version of LAPACK. The CLAPACK library was built using a Fortran to C conversion utility called f2c. The entire Fortran 77 LAPACK library is run through f2c to obtain C code, and then modified to improve readability. CLAPACK's goal is to provide LAPACK for someone who does not have access to a Fortran compiler.
clara¶
- Homepage:
- Spack package:
- Versions:
- 1.1.5, 1.1.4, 1.1.3, 1.1.2, 1.1.1, 1.1.0
- Build Dependencies:
- cmake
- Description:
- A simple to use, composable, command line parser for C++ 11 and beyond.
claw¶
- Homepage:
- Spack package:
- Versions:
- master, 2.0.2, 2.0.1, 2.0, 1.2.3, 1.2.2, 1.2.1, 1.2.0, 1.1.0
- Build Dependencies:
- cmake, ant, bison, flex, java, libxml2
- Link Dependencies:
- java, libxml2
- Description:
- CLAW Compiler targets performance portability problem in climate and weather application written in Fortran. From a single source code, it generates architecture specific code decorated with OpenMP or OpenACC
cleaveland4¶
- Homepage:
- Spack package:
- Versions:
- 4.4
- Build Dependencies:
- perl, perl-math-cdf, bowtie, viennarna, r, samtools
- Link Dependencies:
- bowtie, viennarna, samtools
- Run Dependencies:
- perl, perl-math-cdf, r
- Description:
- CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA targets
cleverleaf¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake, samrai, hdf5, boost
- Link Dependencies:
- samrai, hdf5, boost
- Description:
- CleverLeaf is a hydrodynamics mini-app that extends CloverLeaf with Adaptive Mesh Refinement using the SAMRAI toolkit from Lawrence Livermore National Laboratory. The primary goal of CleverLeaf is to evaluate the application of AMR to the Lagrangian-Eulerian hydrodynamics scheme used by CloverLeaf.
clfft¶
- Homepage:
- Spack package:
- Versions:
- 2.12.2
- Build Dependencies:
- cmake, opencl, boost
- Link Dependencies:
- opencl, boost
- Description:
- a software library containing FFT functions written in OpenCL
clhep¶
- Homepage:
- Spack package:
- Versions:
- 2.4.4.0, 2.4.1.3, 2.4.1.2, 2.4.1.0, 2.4.0.4, 2.4.0.2, 2.4.0.1, 2.4.0.0, 2.3.4.6, 2.3.4.5, 2.3.4.4, 2.3.4.3, 2.3.4.2, 2.3.3.2, 2.3.3.1, 2.3.3.0, 2.3.2.2, 2.3.1.1, 2.3.1.0, 2.3.0.0, 2.2.0.8, 2.2.0.5, 2.2.0.4
- Build Dependencies:
- cmake
- Description:
- CLHEP is a C++ Class Library for High Energy Physics.
cli11¶
- Homepage:
- Spack package:
- Versions:
- 1.9.1
- Build Dependencies:
- cmake
- Description:
- CLI11 is a command line parser for C++11 and beyond that provides a rich feature set with a simple and intuitive interface.
clinfo¶
- Homepage:
- Spack package:
- Versions:
- 2.2.18.04.06
- Build Dependencies:
- opencl
- Link Dependencies:
- opencl
- Description:
- Print all known information about all available OpenCL platforms and devices in the system.
clingo¶
- Homepage:
- Spack package:
- Versions:
- master, 5.5.0, 5.4.1, 5.4.0, 5.3.0, 5.2.2, spack
- Build Dependencies:
- cmake, doxygen, re2c, bison, python, py-cffi
- Link Dependencies:
- python
- Run Dependencies:
- python, py-cffi
- Description:
- Clingo: A grounder and solver for logic programs Clingo is part of the Potassco project for Answer Set Programming (ASP). ASP offers a simple and powerful modeling language to describe combinatorial problems as logic programs. The clingo system then takes such a logic program and computes answer sets representing solutions to the given problem.
clingo-bootstrap¶
- Homepage:
- Spack package:
- Versions:
- master, 5.5.0, 5.4.1, 5.4.0, 5.3.0, 5.2.2, spack
- Build Dependencies:
- cmake, doxygen, re2c, bison, python, py-cffi
- Link Dependencies:
- python
- Run Dependencies:
- python, py-cffi
- Description:
- Clingo with some options used for bootstrapping
cln¶
- Homepage:
- Spack package:
- Versions:
- master, 1.3.6, 1.3.5, 1.3.4, 1.3.3, 1.3.2, 1.3.1, 1.3.0, 1.2.2, 1.2.1, 1.2.0
- Build Dependencies:
- autoconf, automake, libtool, m4, gmp, texinfo, gettext
- Link Dependencies:
- gmp
- Description:
- CLN is a library for efficient computations with all kinds of numbers in arbitrary precision. It features number classes for unlimited length integers, rationals, arbitrary precision floating point numbers and much more.
cloc¶
- Homepage:
- Spack package:
- Versions:
- 1.84, 1.80, 1.74
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Description:
- Count, or compute differences of, physical lines of source code in the given files (may be archives such as compressed tarballs or zip files) and/or recursively below the given directories.
cloog¶
- Homepage:
- Spack package:
- Versions:
- 0.18.1, 0.18.0, 0.17.0
- Build Dependencies:
- gmp, isl
- Link Dependencies:
- gmp, isl
- Description:
- CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra.
cloverleaf¶
- Homepage:
- Spack package:
- Versions:
- 1.1
- Build Dependencies:
- mpi, cuda
- Link Dependencies:
- mpi, cuda
- Description:
- Proxy Application. CloverLeaf is a miniapp that solves the compressible Euler equations on a Cartesian grid, using an explicit, second-order accurate method.
cloverleaf3d¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Proxy Application. CloverLeaf3D is 3D version of the CloverLeaf mini- app. CloverLeaf is a mini-app that solves the compressible Euler equations on a Cartesian grid, using an explicit, second-order accurate method.
clp¶
- Homepage:
- Spack package:
- Versions:
- 1.17.6, 1.17.4, 1.16.11
- Build Dependencies:
- coinutils, osi
- Link Dependencies:
- coinutils, osi
- Description:
- Clp (Coin-or linear programming) is an open-source linear programming solver written in C++.
clustal-omega¶
- Homepage:
- Spack package:
- Versions:
- 1.2.4
- Build Dependencies:
- argtable
- Link Dependencies:
- argtable
- Description:
- Clustal Omega: the last alignment program you'll ever need.
clustalw¶
- Homepage:
- Spack package:
- Versions:
- 2.1
- Description:
- Multiple alignment of nucleic acid and protein sequences.
cmake¶
- Homepage:
- Spack package:
- Versions:
- 3.20.3, 3.20.2, 3.20.1, 3.20.0, 3.19.8, 3.19.7, 3.19.6, 3.19.5, 3.19.4, 3.19.3, 3.19.2, 3.19.1, 3.19.0, 3.18.6, 3.18.5, 3.18.4, 3.18.3, 3.18.2, 3.18.1, 3.18.0, 3.17.5, 3.17.4, 3.17.3, 3.17.1, 3.17.0, 3.16.9, 3.16.8, 3.16.7, 3.16.6, 3.16.5, 3.16.4, 3.16.3, 3.16.2, 3.16.1, 3.16.0, 3.15.7, 3.15.6, 3.15.5, 3.15.4, 3.15.3, 3.15.2, 3.15.1, 3.15.0, 3.14.7, 3.14.6, 3.14.5, 3.14.4, 3.14.3, 3.14.2, 3.14.1, 3.14.0, 3.13.5, 3.13.4, 3.13.3, 3.13.2, 3.13.1, 3.13.0, 3.12.4, 3.12.3, 3.12.2, 3.12.1, 3.12.0, 3.11.4, 3.11.3, 3.11.2, 3.11.1, 3.11.0, 3.10.3, 3.10.2, 3.10.1, 3.10.0, 3.9.6, 3.9.4, 3.9.2, 3.9.0, 3.8.2, 3.8.1, 3.8.0, 3.7.2, 3.7.1, 3.6.1, 3.6.0, 3.5.2, 3.5.1, 3.5.0, 3.4.3, 3.4.0, 3.3.1, 3.1.0, 3.0.2, 2.8.10.2
- Build Dependencies:
- curl, expat, zlib, bzip2, xz, libarchive, libuv, rhash, qt, python, py-sphinx, openssl, ncurses
- Link Dependencies:
- curl, expat, zlib, bzip2, xz, libarchive, libuv, rhash, qt, openssl, ncurses
- Description:
- A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
cmaq¶
- Homepage:
- Spack package:
- Versions:
- 5.3.1, 5.3
- Description:
- Code base for the U.S. EPA's Community Multiscale Air Quality Model (CMAQ).
cmark¶
- Homepage:
- Spack package:
- Versions:
- 0.29.0, 0.28.3, 0.28.2, 0.28.1, 0.28.0, 0.27.1
- Build Dependencies:
- cmake
- Description:
- cmark is the C reference implementation of CommonMark, a rationalized version of Markdown syntax with a spec.
cminpack¶
- Homepage:
- Spack package:
- Versions:
- master, 1.3.6
- Build Dependencies:
- cmake, blas
- Link Dependencies:
- blas
- Description:
- This is a C version of the minpack minimization package. Minpack includes software for solving nonlinear equations and nonlinear least squares problems.
cmocka¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1, 1.1.0
- Build Dependencies:
- cmake
- Description:
- Unit-testing framework in pure C
cmockery¶
- Homepage:
- Spack package:
- Versions:
- 0.1.2, 0.1.1, 0.1.0
- Build Dependencies:
- m4, autoconf, automake, libtool
- Description:
- A lightweight library to simplify and generalize the process of writing unit tests for C applications.
cmor¶
- Homepage:
- Spack package:
- Versions:
- 3.4.0, 3.3.0, 3.2.0, 3.1.2
- Build Dependencies:
- uuid, netcdf-c, udunits, hdf5, python, py-numpy
- Link Dependencies:
- uuid, netcdf-c, udunits, hdf5, python
- Run Dependencies:
- python, py-numpy
- Description:
- Climate Model Output Rewriter is used to produce CF-compliant netCDF files. The structure of the files created by the library and the metadata they contain fulfill the requirements of many of the climate community's standard model experiments.
cnmem¶
- Homepage:
- Spack package:
- Versions:
- git
- Build Dependencies:
- cmake
- Description:
- CNMem mempool for CUDA devices
cnpy¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- cmake
- Link Dependencies:
- zlib
- Description:
- cnpy: library to read/write .npy and .npz files in C/C++.
cntk¶
- Homepage:
- Spack package:
- Versions:
- master, 2.0
- Build Dependencies:
- libzip, openblas, mpi, boost, protobuf, kaldi, opencv, cuda, cub, cudnn, nccl, cntk1bitsgd, multiverso
- Link Dependencies:
- libzip, openblas, mpi, boost, protobuf, kaldi, opencv, cuda, cub, cudnn, nccl, cntk1bitsgd, multiverso
- Description:
- The Microsoft Cognitive Toolkit is a unified deep-learning toolkit that describes neural networks as a series of computational steps via a directed graph.
cntk1bitsgd¶
- Homepage:
- Spack package:
- Versions:
- master, c8b77d
- Description:
- CNTK1bitSGD is the header-only 1-bit stochastic gradient descent (1bit- SGD) library for the Computational Network Toolkit (CNTK).
cnvnator¶
- Homepage:
- Spack package:
- Versions:
- 0.3.3
- Build Dependencies:
- samtools, htslib, root, bzip2, curl, lzma, zlib
- Link Dependencies:
- samtools, htslib, root, bzip2, curl, lzma, zlib
- Description:
- A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads.
codar-cheetah¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.1.0, 1.0.0, 0.5
- Build Dependencies:
- python
- Run Dependencies:
- python
- Description:
- CODAR Cheetah: The CODAR Experiment Harness for Exascale science applications.
code-server¶
- Homepage:
- Spack package:
- Versions:
- 3.4.1, 3.1.1, 3.1.0
- Build Dependencies:
- git
- Link Dependencies:
- git
- Description:
- code-server is VS Code running on a remote server, accessible through the browser.
codec2¶
- Homepage:
- Spack package:
- Versions:
- 0.9.2
- Build Dependencies:
- cmake
- Description:
- Open source speech codec designed for communications quality speech between 450 and 3200 bit/s. The main application is low bandwidth HF/VHF digital radio.
codes¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.1.0, 1.0.0
- Build Dependencies:
- autoconf, automake, libtool, m4, pkgconfig, bison, flex, mpi, ross, sst-dumpi
- Link Dependencies:
- mpi, ross, sst-dumpi
- Description:
- CO-Design of multi-layer Exascale Storage (CODES) simulation framework
coevp¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- mpi, silo, flann, lapack
- Link Dependencies:
- mpi, silo, flann, lapack
- Description:
- CoEVP is a scale-bridging proxy application for embedded viscoplasticity applications. It is created and maintained by The Exascale Co-Design Center for Materials in Extreme Environments (ExMatEx). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement it as needed to test performance of new architectures, programming models, etc. Due to the size and complexity of the studied models, as well as restrictions on distribution, the currently available LULESH proxy application provides the coarse-scale model implementation and the ASPA proxy application provides the adaptive sampling support.
cohmm¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- gnuplot
- Link Dependencies:
- gnuplot
- Description:
- An anticipated important use-case for next-generation supercomputing is multiscale modeling, in which continuum equations for large-scale material deformation are augmented with high-fidelity, fine-scale simulations that provide constitutive data on demand.
coin3d¶
- Homepage:
- Spack package:
- Versions:
- 3.1.0, 3.0.0, 2.0.0
- Build Dependencies:
- boost, doxygen, perl
- Link Dependencies:
- glu, gl, libsm, libxext, libice, uuid, libxcb, libxau
- Description:
- Coin is an OpenGL-based, 3D graphics library that has its roots in the Open Inventor 2.1 API, which Coin still is compatible with.
coinhsl¶
- Homepage:
- Spack package:
- Versions:
- 2019.05.21, 2015.06.23, 2014.01.17, 2014.01.10
- Build Dependencies:
- blas
- Link Dependencies:
- blas
- Description:
- CoinHSL is a collection of linear algebra libraries (KB22, MA27, MA28, MA54, MA57, MA64, MA77, MA86, MA97, MC19, MC34, MC64, MC68, MC69, MC78, MC80, OF01, ZB01, ZB11) bundled for use with IPOPT and other applications that use these HSL routines. Note: CoinHSL is licensed software. You will need to request a license from Research Councils UK and download a .tar.gz archive of CoinHSL yourself. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
coinutils¶
- Homepage:
- Spack package:
- Versions:
- 2.11.4
- Description:
- CoinUtils is an open-source collection of classes and helper functions that are generally useful to multiple COIN-OR projects.
collectd¶
- Homepage:
- Spack package:
- Versions:
- 5.12.0, 5.11.0, 5.10.0
- Test Dependencies:
- valgrind
- Description:
- The system statistics collection daemon.
collier¶
- Homepage:
- Spack package:
- Versions:
- 1.2.5, 1.2.4, 1.2.3, 1.2.2, 1.2.1, 1.2.0, 1.1, 1.0
- Build Dependencies:
- cmake
- Description:
- COLLIER: A Complex One-Loop LIbrary with Extended Regularizations
colm¶
- Homepage:
- Spack package:
- Versions:
- 0.12.0
- Description:
- Colm Programming Language Colm is a programming language designed for the analysis and transformation of computer languages. Colm is influenced primarily by TXL. It is in the family of program transformation languages.
colordiff¶
- Homepage:
- Spack package:
- Versions:
- 1.0.19, 1.0.18
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Description:
- Colorful diff utility.
comd¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.1
- Build Dependencies:
- mpi, graphviz
- Link Dependencies:
- mpi, graphviz
- Description:
- CoMD is a reference implementation of classical molecular dynamics algorithms and workloads as used in materials science. It is created and maintained by The Exascale Co-Design Center for Materials in Extreme Environments (ExMatEx). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement it as needed to test performance of new architectures, programming models, etc. New versions of CoMD will be released to incorporate the lessons learned from the co-design process.
comgr¶
- Homepage:
- Spack package:
- Versions:
- master, 4.2.0, 4.1.0, 4.0.0, 3.10.0, 3.9.0, 3.8.0, 3.7.0, 3.5.0
- Build Dependencies:
- cmake, llvm-amdgpu, rocm-device-libs, rocm-cmake
- Link Dependencies:
- zlib, z3, ncurses
- Description:
- This provides various Lightning Compiler related services. It currently contains one library, the Code Object Manager (Comgr)
commons-lang¶
- Homepage:
- Spack package:
- Versions:
- 2.6, 2.4
- Build Dependencies:
- jdk
- Run Dependencies:
- jdk, java
- Description:
- The standard Java libraries fail to provide enough methods for manipulation of its core classes. Apache Commons Lang provides these extra methods. Lang provides a host of helper utilities for the java.lang API, notably String manipulation methods, basic numerical methods, object reflection, concurrency, creation and serialization and System properties. Additionally it contains basic enhancements to java.util.Date and a series of utilities dedicated to help with building methods, such as hashCode, toString and equals.
commons-lang3¶
- Homepage:
- Spack package:
- Versions:
- 3.7
- Build Dependencies:
- jdk
- Run Dependencies:
- jdk, java
- Description:
- The standard Java libraries fail to provide enough methods for manipulation of its core classes. Apache Commons Lang provides these extra methods. Lang provides a host of helper utilities for the java.lang API, notably String manipulation methods, basic numerical methods, object reflection, concurrency, creation and serialization and System properties. Additionally it contains basic enhancements to java.util.Date and a series of utilities dedicated to help with building methods, such as hashCode, toString and equals.
commons-logging¶
- Homepage:
- Spack package:
- Versions:
- 1.2, 1.1.3, 1.1.1
- Build Dependencies:
- jdk
- Run Dependencies:
- jdk, java
- Description:
- When writing a library it is very useful to log information. However there are many logging implementations out there, and a library cannot impose the use of a particular one on the overall application that the library is a part of. The Logging package is an ultra-thin bridge between different logging implementations. A library that uses the commons-logging API can be used with any logging implementation at runtime. Commons-logging comes with support for a number of popular logging implementations, and writing adapters for others is a reasonably simple task.
compadre¶
- Homepage:
- Spack package:
- Versions:
- master, 1.3.0
- Build Dependencies:
- cmake, kokkos, kokkos-kernels, mpi
- Link Dependencies:
- kokkos, kokkos-kernels, mpi
- Description:
- The Compadre Toolkit provides a performance portable solution for the parallel evaluation of computationally dense kernels. The toolkit specifically targets the Generalized Moving Least Squares (GMLS) approach, which requires the inversion of small dense matrices. The result is a set of weights that provide the information needed for remap or entries that constitute the rows of some globally sparse matrix.
compiz¶
- Homepage:
- Spack package:
- Versions:
- 0.7.8
- Build Dependencies:
- libxcb, libxcomposite, libxfixes, libxdamage, libxrandr, libxinerama, libice, libsm, libxml2, libxslt, libxrender, libpng, glib, gconf
- Link Dependencies:
- libxcb, libxcomposite, libxfixes, libxdamage, libxrandr, libxinerama, libice, libsm, libxml2, libxslt, libxrender, libpng, glib, gconf
- Description:
- compiz - OpenGL window and compositing manager. Compiz is an OpenGL compositing manager that use GLX_EXT_texture_from_pixmap for binding redirected top-level windows to texture objects. It has a flexible plug- in system and it is designed to run well on most graphics hardware.