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| align="center" | [https://software.intel.com/intel-advisor-xe advisor/2018.3] | | align="center" | [https://software.intel.com/intel-advisor-xe advisor/2018.3] | ||
| align="center" | tools | |||
| align="center" | | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Vectorization Optimization and Thread Prototyping - Vectorize and thread code or performance dies - Easy workflow + data + tips = faster code faster - Prioritize, Prototype and Predict performance gain Homepage: https://software.intel.com/intel-advisor-xe Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div> | |||
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| align="center" | [https://software.intel.com/intel-advisor-xe advisor/2019.3] | |||
| align="center" | tools | | align="center" | tools | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 or gcc/6.4.0 or intel/2016.4 or intel/2017.1 or intel/2017.5<br />'''Description:''' </div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 or gcc/6.4.0 or intel/2016.4 or intel/2017.1 or intel/2017.5<br />'''Description:''' </div> | ||
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| align="center" | [http://www.boost.org/ boost/1.68.0] | |||
| align="center" | tools | |||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools<br />'''Prerequisites:''' gcc/7.3.0<br />'''Description:''' </div> | |||
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| align="center" | [http://bowtie-bio.sourceforge.net/index.shtml bowtie/1.1.2] | | align="center" | [http://bowtie-bio.sourceforge.net/index.shtml bowtie/1.1.2] | ||
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| align="center" | tools | | align="center" | tools | ||
| align="center" | [[CUDA]] | | align="center" | [[CUDA]] | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. Homepage: https://developer.nvidia.com/cuda-toolkit Keyword:tools CC-Wiki: CUDA<br />'''Prerequisites:''' gcc/7.3.0<br />'''Description:''' </div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. Homepage: https://developer.nvidia.com/cuda-toolkit Keyword:tools CC-Wiki: CUDA<br />'''Prerequisites:''' gcc/7.3.0 or pgi/19.4<br />'''Description:''' </div> | ||
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| align="center" | [https://developer.nvidia.com/cuda-toolkit cuda/7.5.18] | | align="center" | [https://developer.nvidia.com/cuda-toolkit cuda/7.5.18] | ||
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| align="center" | tools | | align="center" | tools | ||
| align="center" | [[CUDA]] | | align="center" | [[CUDA]] | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. - Homepage: https://developer.nvidia.com/cuda-toolkit Keyword:tools CC-Wiki: CUDA<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or pgi/17.3<br />'''Description:''' </div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. - Homepage: https://developer.nvidia.com/cuda-toolkit Keyword:tools CC-Wiki: CUDA<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or pgi/16.9 or pgi/17.3<br />'''Description:''' </div> | ||
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| align="center" | [https://developer.nvidia.com/cuda-toolkit cuda/9.0.176] | | align="center" | [https://developer.nvidia.com/cuda-toolkit cuda/9.0.176] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program - Homepage: http://research-pub.gene.com/gmap/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program - Homepage: http://research-pub.gene.com/gmap/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div> | ||
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| align="center" | [https://www.google.ca/search?q=gmpich gmpich/2019.05] | |||
| align="center" | - | |||
| align="center" | | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: gcc and GFortran based compiler toolchain, including MPICH for MPI support. Homepage: (none)<br />'''Prerequisites:''' -<br />'''Description:''' </div> | |||
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| align="center" | [http://www.golang.org go/1.10.3] | | align="center" | [http://www.golang.org go/1.10.3] | ||
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| align="center" | math | | align="center" | math | ||
| align="center" | | | align="center" | | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: http://xianyi.github.com/OpenBLAS/ Keyword:math<br />'''Prerequisites:''' gcc/6.4.0<br />'''Description:''' </div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: http://xianyi.github.com/OpenBLAS/ Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or gcc/6.4.0<br />'''Description:''' </div> | ||
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| align="center" | [http://opencolorio.org/ opencolorio/1.0.9] | | align="center" | [http://opencolorio.org/ opencolorio/1.0.9] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. Homepage: http://code.google.com/p/openpgm/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. Homepage: http://code.google.com/p/openpgm/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div> | ||
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| align="center" | [http://opensees.berkeley.edu/ opensees/3.0.0] | |||
| align="center" | - | |||
| align="center" | | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. This version is built using DISTRIBUTED_MP platform setting. Homepage: http://opensees.berkeley.edu/<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1<br />'''Description:''' </div> | |||
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| align="center" | [http://opensees.berkeley.edu/ opensees/3.0.2] | |||
| align="center" | - | |||
| align="center" | | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. This version is built using DISTRIBUTED_MP platform setting. Homepage: http://opensees.berkeley.edu/<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1<br />'''Description:''' </div> | |||
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| align="center" | [http://cec.mpg.de/forum/ orca/4.0.0.2] | | align="center" | [http://cec.mpg.de/forum/ orca/4.0.0.2] | ||
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| align="center" | [http://www.pgroup.com/ pgi/13.10] | | align="center" | [http://www.pgroup.com/ pgi/13.10] | ||
| align="center" | tools | |||
| align="center" | | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++ and Fortran compilers from The Portland Group - PGI Homepage: http://www.pgroup.com/<br />'''Prerequisites:''' -<br />'''Description:''' </div> | |||
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| align="center" | [http://www.pgroup.com/ pgi/16.9] | |||
| align="center" | tools | | align="center" | tools | ||
| align="center" | | | align="center" | | ||
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| align="center" | [http://www.pgroup.com/ pgi/17.3] | | align="center" | [http://www.pgroup.com/ pgi/17.3] | ||
| align="center" | tools | |||
| align="center" | | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++ and Fortran compilers from The Portland Group - PGI Homepage: http://www.pgroup.com/<br />'''Prerequisites:''' -<br />'''Description:''' </div> | |||
|- | |||
| align="center" | [http://www.pgroup.com/ pgi/19.4] | |||
| align="center" | tools | | align="center" | tools | ||
| align="center" | | | align="center" | | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pilon is an automated genome assembly improvement and variant detection tool To run pilon, please use: java -jar $EBROOTPILON/pilon-1.22.jar ... Use -Xmx Java option to adjust memory as in: java -Xmx8G -jar $EBROOTPILON/pilon-1.22.jar ... Homepage: https://github.com/broadinstitute/pilon Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pilon is an automated genome assembly improvement and variant detection tool To run pilon, please use: java -jar $EBROOTPILON/pilon-1.22.jar ... Use -Xmx Java option to adjust memory as in: java -Xmx8G -jar $EBROOTPILON/pilon-1.22.jar ... Homepage: https://github.com/broadinstitute/pilon Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div> | ||
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| align="center" | [https://github.com/broadinstitute/pilon pilon/1.23] | |||
| align="center" | bio | |||
| align="center" | | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pilon is an automated genome assembly improvement and variant detection tool To run pilon, please use: java -jar $EBROOTPILON/pilon-1.23.jar ... Use -Xmx Java option to adjust memory as in: java -Xmx8G -jar $EBROOTPILON/pilon-1.23.jar ... Homepage: https://github.com/broadinstitute/pilon Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div> | |||
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| align="center" | [http://pngu.mgh.harvard.edu/~purcell/plink/ plink/1.07] | | align="center" | [http://pngu.mgh.harvard.edu/~purcell/plink/ plink/1.07] | ||
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| align="center" | [[R]] | | align="center" | [[R]] | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ Keyword:tools CC-Wiki: R<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ Keyword:tools CC-Wiki: R<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div> | ||
|- | |||
| align="center" | [http://www.r-project.org/ r/3.5.2] | |||
| align="center" | tools | |||
| align="center" | [[R]] | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ Keyword:tools CC-Wiki: R<br />'''Prerequisites:''' gcc/7.3.0<br />'''Description:''' </div> | |||
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| align="center" | [https://github.com/isovic/racon/ racon/20170719] | | align="center" | [https://github.com/isovic/racon/ racon/20170719] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server, bringing the power and productivity of the RStudio IDE to server-based deployments of R. Homepage: https://www.rstudio.com/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server, bringing the power and productivity of the RStudio IDE to server-based deployments of R. Homepage: https://www.rstudio.com/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div> | ||
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| align="center" | [https://www.rstudio.com/ rstudio-server/1.2.1335] | |||
| align="center" | tools | |||
| align="center" | | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server, bringing the power and productivity of the RStudio IDE to server-based deployments of R. Homepage: https://www.rstudio.com/ Keyword:tools<br />'''Prerequisites:''' gcc/7.3.0<br />'''Description:''' </div> | |||
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| align="center" | [https://itk.org rtk/1.4.0] | | align="center" | [https://itk.org rtk/1.4.0] | ||
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| align="center" | | | align="center" | | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Homepage: http://www.tcl.tk/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Homepage: http://www.tcl.tk/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div> | ||
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| align="center" | [http://wiki.tcl.tk/1877 tktable/2.10] | |||
| align="center" | tools | |||
| align="center" | | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tcl is a simple-to-learn yet very powerful language. Its syntax is described in just a dozen rules, but it has all the features needed to rapidly create useful programs in almost any field of application - on a wide variety of international platforms. Tk is a graphical toolkit for Tcl. It allows you to develop graphical applications that run on Windows, Linux, MacOS X and many other platforms. And not just from Tcl - Tk can be used from many languages including C, Ruby, Perl, Python and Lua. Homepage: http://wiki.tcl.tk/1877 Keyword:tools<br />'''Prerequisites:''' gcc/7.3.0<br />'''Description:''' </div> | |||
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| align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm/2.0c] | | align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm/2.0c] | ||
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| align="center" | [http://software.intel.com/en-us/intel-vtune-amplifier-xe vtune/2018.3] | | align="center" | [http://software.intel.com/en-us/intel-vtune-amplifier-xe vtune/2018.3] | ||
| align="center" | tools | |||
| align="center" | | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. Homepage: http://software.intel.com/en-us/intel-vtune-amplifier-xe Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div> | |||
|- | |||
| align="center" | [http://software.intel.com/en-us/intel-vtune-amplifier-xe vtune/2019.3] | |||
| align="center" | tools | | align="center" | tools | ||
| align="center" | | | align="center" | | ||