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Ginsburg is currently running Red Hat Enterprise Linux release 8.2.
The table below shows software already installed on the cluster system-wide.
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Name | Version | Location / Module | Category |
|---|---|---|---|
| AFNI | 23.1.05 | module load AFNI/23.1.05 | Analysis of Functional Neuro Images |
Anaconda Python 3.11.5 2023.09 | Python 3.11.5 | module load anaconda/3-2023.09 | Python for Scientific Computing |
Anaconda Python 2.7.16 2019.10 | Python 2.7.16 | module load anaconda/2-2019.10 | Python for Scientific Computing |
| ancestry_hmm | ancestry_hmm | module load ancestry_hmm/0.94 | Program designed to infer adaptive introgression from population genomic data. |
| ANTs | 2.4.4 | module load ANTs/2.4.4 | ANTs computes high-dimensional mappings to capture the statistics of brain structure and function |
BCFtools | 1.18 | module load bcftools/1.18 | Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants |
cactus | 2.6.7 | module load cactus/2.6.7 | Comparative Genomics Toolkit |
candi | 9.4.2-r3 | module load candi/9.4.2-r3 | The |
cuda | 12.0 | module load cuda12.0/toolkit | GPU Computing |
| cudnn | 8.0 | module load cudnn8.0-cuda11.1 | CUDA Deep Neural Network library |
| freesurfer | 7.4 | module load freesurfer/7.4 | Brain imaging software |
| FSL | 6.0.5.2 | module load FSL/6.0.5.2 | Analysis tools for FMRI, MRI and DTI brain imaging data |
| gcc | 13.0.1 | module load gcc/13.0.1 | Compiler - C / C++ |
| glpk | 5.0 | module load glpk/5.0 | C library for solving large-scale linear programming (LP), mixed integer programming (MIP) |
| gurobi | 10.0.3 | module load gurobi/10/0/3 | Prescriptive analytics platform and a decision-making technology |
| hdf5 | 1.10.1 | module load hdf5/1.10.1 | High performance data software library & file format |
| htslib | 1.19 | module load htslib/1.19 | A C library for reading/writing high-throughput sequencing data |
| Intel oneAPI toolkit | various | module load intel-oneAPI-toolkit <library> | Core set of tools and libraries for developing high-performance, data-centric applications across diverse architectures. |
| intel-parallel-studio | 2020 Update 4 | module load intel-parallel-studio/2020 | Intel Compiler |
| julia | 1.5.3 | module load julia/1.5.3 | Programming Language |
| knitro | 13.2.0 | module load knitro/13.2.0 | Software package for solving large scale nonlinear mathematical optimization problems; short for "Nonlinear Interior point Trust Region Optimization" |
| lastz | 1.04.15 | module load lastz/1.04.15 | A program for aligning DNA sequences, a pairwise aligner. |
| LBPM | 22.08 | module load LBPM/22.08 | Model flow processes based on digital rock physics |
| leptonica | 1.83.0 | module load leptonica/1.83.0 | A ipedagogically-oriented open source library containing software that is broadly useful for image processing and image analysis |
| libRadtran | 2.0.5 | modulel load libRadtran/2.0.5 | A library for radiative transfer |
| Mathematica | 13.2 | module load Mathematica/13.2 | Numerical Computing |
| Matlab | 2023a | module load matlab/2023a | Numerical Computing |
| metis | 5.1.0 | module load metis/5.1.0 | A set of serial programs for partitioning graphs, partitioning finite element meshes. |
| MUMPS | 5.6.2 | module load mumps/5.6.2 | MUltifrontal Massively Parallel Sparse direct Solver |
| netcdf-fortran-intel | 4.5.3 | module load netcdf-fortran-intel/4.5.3 | Array Interface Library |
| netcdf/gcc | 4.7.4 | module load netcdf/gcc/64/gcc/64/4.7.4 | Array Interface Library |
| Nextflow | 23.10.0 | module load nextflow/23.10.0 | Enables scalable and reproducible scientific workflows using software containers. |
| occsw | V2022.3 | module load ocssw | Ocean Color Science Software, CLI version |
| octave | 5.2.0 | module load octave | Installed on all compute nodes, start with 'octave'. Mathematics-oriented syntax with built-in 2D/3D plotting and visualization |
| OpenFOAM | v2206 | module load OpenFOAM/v2206 | Computational fluid dynamics. |
| openmpi | 4.1.5a1 | openmpi/gcc/64/4.1.5a1 | OpenMPI Compiler |
| Quantum Espresso | 7.2 | module load QE/7.2 | Quantum Espresso |
| R | 3.6.3 | module load R/3.6.3 | Programming Language |
| R | 4.3.1 | module load R/4.3.1 | Programming Language |
| samtools | 1.19 | module load samtools/1.19 | Suite of programs for interacting with high-throughput sequencing data |
ScaLAPACK | 2.2.0 | module load scalapack/2.2.0 | Scalable Linear Algebra PACKage |
| Schrodinger | 2024-1 | module load schrodinger/2024-1 | Modeling, analysis and computational tasks |
SeaDAS | 9.0.1 | module load seadas/9.0.1 | A comprehensive software package for the processing, display, analysis, and quality control of ocean color data. Requires XQuartz on a Mac or Mobaxterm on Windows. |
| Singularity | 3.7.1 | module load singularity/3.7.1 | Run Docker-like containers |
| Stata | 18 | module load stata/18 | General-purpose statistical software |
| stopos | 0.93 | module load stopos | Create and manage computing tasks |
| tesseract | 5.3.1 | module load tesseract | OCR |
| VCFTools | 0.1.17 | module load vcftools/0.1.17 | A set of tools written in Perl and C++ for working with VCF files |
| vim | 9.1 | module load vim/9.1 | vi improved test editor |
Visual Studio Code Server | Not a module | A server side Integrated Development Environment hosted on Ginsburg compute nodes | |
| WIEN2k | WIEN2k_21.1 | module load WIEN2k_21.1 | Perform electronic structure calculations of solids using density functional theory. |
| workbench | 1.5.0 | module load workbench/1.5.0 | Visualization and Discovery tool used to map neuro-imaging data |
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Once done, you will be able to open files in your Ginsburg folder the same as you do ones on your local computer.
| Info |
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It's possible that the next time you try to use the tunnel you've just made, you may not be able to re-connect. The connection may keep trying endlessly, or finally fail with an error. This is because the srun session in the first step has placed you on another node different from the one where you created the tunnel. IF that happens, follow the steps below: 1) In your local VSCode app (if you use a local copy of VS Code and not the browser-based window version), unregister/delete all of your existing tunnels. We’ll be making a new one. 2) Login to Ginsburg. Do not start an srun session yet. 3) Delete your invisible vscode settings folders in your home directory (" 4) Start an srun session as described above, type "code tunnel", and follow all of the directions as normal. Open VScode in the web browser first. It will take a moment as the new tunnel is created. If you only use VS Code in the browser, you are now done. 5) If you prefer to use a local copy of VS Code on your computer, you can now connect to this tunnel in it. |