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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 | 8.4.1 | module load seadas/8.4.1 | 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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The latest version of OpenMPI on Insomnia is Ginsburg is 4.1.5a1, which is provided by Nvidia Mellanox and optimized for the MOFED stack, and is installed on each compute node to increase performance. You will receive the following warnings when using mpirun/mpiexec:
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singularity pull --name rstudio.simg docker://rocker/rstudio:4.3.1 |
In order for RStudio to start in a browser via an interactive session you will need the IP address of the compute node. Note that the IP below will likely be different for you:
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IP_ADDR=`hostname -i` echo $IP_ADDR 10.197.16.39 |
From RStudio 4.2 and later, some added security features require binding of a locally created database file to the database in the container. Don't forget to change the password.
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mkdir -p run var-lib-rstudio-server printf 'provider=sqlite\ndirectory=/var/lib/rstudio-server\n' > database.conf PASSWORD='CHANGEME' singularity exec \ --bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server,database.conf:/etc/rstudio/database.conf \ rstudio.simg \ /usr/lib/rstudio-server/bin/rserver --auth-none=0 --auth-pam-helper-path=pam-helper --server-user=$USER |
This will run the Rstudio server in a Singularity container.
PART 2: Port forwarding and access from your browser
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