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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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On Ginsburg, rstudio can be loaded by leveraging an interactive session, i.e., srun, and using a Singularity container via the Rocker Project which provides containers from where this tutorial comes . First you will need to download the Singularity image. This will require two terminal sessions. One session will be used to connect to a compute host and run rstudio. The other terminal session will be used to initiate SSH Port Forwarding/Tunneling to access the resource. The first step is to request an interactive session so you can run rstudio server from a compute node as follows. Please be sure to change your group as noted by "-A".
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srun -X -A <GROUP> --pty -t 0-01:00 -X /bin/bash OR, if you want a GPU node srun -X -A <GROUP> --pty -t 0-01:00 -X --gres=gpu:1 /bin/bash |
Load the Singularity module:
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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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