The confluence migration is currently ongoing. Please note that any modifications made right now will not be transferred or preserved in the new instance. Plan your activities accordingly to accommodate this limitation. For details on the migration please click here

Ginsburg is currently running Red Hat Enterprise Linux release 8.2.

The table below shows software already installed on the cluster system-wide.

The list may be partial and not totally up-to-date at any given time.

Use the following command to verify whether unlisted software/packages can be found on Ginsburg otherwise:


$ module avail


For a good guide on how to use environment modules to easily load your software environment, please see:

https://lmod.readthedocs.io/en/latest/010_user.html


Name

Version

Location / Module

Category

AFNI23.1.05module load AFNI/23.1.05Analysis 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_hmmancestry_hmmmodule load ancestry_hmm/0.94Program designed to infer adaptive introgression from population genomic data.
ANTs2.4.4module load ANTs/2.4.4ANTs 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 candi.sh shell script downloads, configures, builds, and installs deal.II with common dependencies on linux-based systems

cuda

12.0

module load cuda12.0/toolkit

GPU Computing

cudnn8.0module load cudnn8.0-cuda11.1CUDA Deep Neural Network library
freesurfer7.4module load freesurfer/7.4Brain imaging software
FSL6.0.5.2module load FSL/6.0.5.2Analysis tools for FMRI, MRI and DTI brain imaging data
gcc13.0.1module load gcc/13.0.1Compiler - C / C++
glpk5.0module load glpk/5.0C library for solving large-scale linear programming (LP), mixed integer programming (MIP)
gurobi10.0.3module load gurobi/10/0/3Prescriptive analytics platform and a decision-making technology 
hdf51.10.1module load hdf5/1.10.1High 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/2020Intel Compiler 
julia1.5.3module load julia/1.5.3Programming Language
knitro13.2.0module load knitro/13.2.0Software package for solving large scale nonlinear mathematical optimization problems; short for "Nonlinear Interior point Trust Region Optimization"
lastz1.04.15module load lastz/1.04.15A program for aligning DNA sequences, a pairwise aligner.
LBPM22.08module load LBPM/22.08Model flow processes based on digital rock physics
leptonica

1.83.0

module load leptonica/1.83.0A ipedagogically-oriented open source library containing software that is broadly useful for image processing and image analysis 
libRadtran2.0.5modulel load libRadtran/2.0.5A library for radiative transfer
Mathematica13.2module load Mathematica/13.2Numerical Computing
Matlab2023amodule load matlab/2023aNumerical 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-intel4.5.3

module load netcdf-fortran-intel/4.5.3

Array Interface Library
netcdf/gcc4.7.4module load netcdf/gcc/64/gcc/64/4.7.4Array Interface Library
Nextflow

23.10.0

module load nextflow/23.10.0Enables scalable and reproducible scientific workflows using software containers.
occswV2022.3module load ocsswOcean Color Science Software, CLI version
octave5.2.0module load octaveInstalled on all compute nodes, start with 'octave'. Mathematics-oriented syntax with built-in 2D/3D plotting and visualization 
OpenFOAMv2206module load OpenFOAM/v2206Computational fluid dynamics.
openmpi4.1.5a1module load openmpi/gcc/64/4.1.5a1OpenMPI Compiler (provided by Nvidia/Mellanox)
Quantum Espresso7.2module load QE/7.2Quantum Espresso
R3.6.3module load R/3.6.3Programming Language
R4.3.1module load R/4.3.1Programming Language
samtools1.19module load samtools/1.19Suite of programs for interacting with high-throughput sequencing data

ScaLAPACK 

2.2.0module load scalapack/2.2.0Scalable Linear Algebra PACKage
Schrodinger2024-1module load schrodinger/2024-1Modeling, analysis and computational tasks

SeaDAS

8.4.1module 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.

Singularity3.7.1module load singularity/3.7.1

Run Docker-like containers

Stata18

module load stata/18

General-purpose statistical software
stopos0.93module load stoposCreate and manage computing tasks
tesseract5.3.1module load tesseractOCR
VCFTools0.1.17module load vcftools/0.1.17A set of tools written in Perl and C++ for working with VCF files
vim9.1module load vim/9.1vi improved test editor

Visual Studio Code Server


Not a moduleA server side Integrated Development Environment hosted on Ginsburg compute nodes
WIEN2kWIEN2k_21.1module load WIEN2k_21.1Perform electronic structure calculations of solids using density functional theory.
workbench1.5.0module load workbench/1.5.0Visualization and Discovery tool used to map neuro-imaging data 

Quantum Espresso Notes

  • The –with-hdf5 yes  and –enable-parallel options were specified with cmake.
  • openmpi/gcc/64/4.1.5a1, netcdf-fortran/4.5.3 & fftw3/openmpi/gcc/64/3.3.10 are pre-loaded. 
  •  In an interactive job with srun specify 4 nodes, i.e., --nodes=4. Note, using 2 nodes does not appear to be enough.
  • In order for the examples, e.g., in the PP or PW directories, the following values in  environment_variables need updating (replace <my-uni> accordingly):
    • BIN_DIR=/burg/opt/QE/7.2/bin
      PSEUDO_DIR=/burg/home/<my-uni>/qe-7.2/pseudo
      TMP_DIR=/local
      PARA_PREFIX="mpirun -np 4"
    • Around line 119 I changed the wget option to:
      WGET="wget -k -o"

Running LBPM in a Singularity container from Nvidia's NGC Catalog

LBPM (Lattice Boltzmann Methods for Porous Media) is an open source software framework designed to model flow processes based on digital rock physics, and is freely available through the Open Porous Media project. Digital rock physics refers to a growing class of methods that leverage microscopic data sources to obtain insight into the physical behavior of fluids in rock and other porous materials. LBPM simulation protocols are based on two-fluid lattice Boltzmann methods, focusing in particular on wetting phenomena. The Department of Earth and Environmental Engineering and the Kelly Lab are the main users

Some modifications are needed to get the water-flooding simulation to work correct. You can start with an interactive session via Slurm's srun command and request a GPU as well as requesting at least 10 GB of memory.

srun --pty --mem=10gb -t 0-10:00 --gres=gpu:1  -A <your-account> /bin/bash

Update the wget commands as below:

export BENCHMARK_DIR=$PWD
wget https://gitlab.com/NVHPC/ngc-examples/-/raw/master/LBPM/2020.10/single-node/input.db
wget https://gitlab.com/NVHPC/ngc-examples/-/raw/master/LBPM/2020.10/single-node/run.sh
wget https://gitlab.com/NVHPC/ngc-examples/-/raw/master/LBPM/2020.10/single-node/mask_water_flooded_water_and_oil.raw.morphdrain.raw
chmod +x run.sh

Ginsburg has Singularity version 3.7.1 available. The run.sh file defaults the compute capable option as GPU_ARCH="sm70" which works on nodes with the V100 and RTX 8000. Note you can update this option to sm80 if you use a GPU node with the A40 or A100 The file also runs the mpirun command so remember to load OpenMPI as well as CUDA toolkit.

module load singularity/3.7.1 openmpi/gcc/64/4.0.3rc4 cuda11.7/toolkit/11.7.1
cd $BENCHMARK_DIR
singularity run --nv -B $BENCHMARK_DIR:/benchmark --pwd /benchmark docker://nvcr.io/hpc/lbpm:2020.10 ./run.sh

If you see errors such as:

Primary job  terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID ##### on node g### exited on signal 11 (Segmentation fault).

Make sure you are on a node with a GPU and have loaded OpenMPI and/or CUDA toolkit, e.g., openmpi/gcc/64/4.0.3rc4 cuda11.7/toolkit/11.7.1

Running LBPM multi-node with Slurm and Singularity

Modify the instructions and sample Slurm batch file as follows:

wget https://gitlab.com/NVHPC/ngc-examples/-/raw/master/LBPM/2020.10/multi-node/slurm/run.sh

Update the run.sh filename, which you may want to rename to differ from the previous run.sh file:

#!/bin/bash
#SBATCH --job-name=lbpm      # Job name
#SBATCH --account=<accuont_name>    # Replace <account_name> accordingly    
#SBATCH --nodes=1                   # Use one node
#SBATCH --ntasks=1                  # Run a single task
#SBATCH --mem-per-cpu=10gb           # Memory per processor
#SBATCH --gres=gpu:1
module load singularity/3.7.1
module load cuda11.7/toolkit
module load openmpi/gcc/64/4.0.3rc4  
module load gcc/10.2.0
# Build SIF, if it doesn't exist
if [[ ! -f "lbpm.sif" ]]; then
    singularity build lbpm.sif docker://nvcr.io/hpc/LBPM:2020.10
fi
export BENCHMARK_DIR=$PWD
export GPU_ARCH="sm70" # Valid options are: sm60, sm70, sm75, sm80
singularity run -B $BENCHMARK_DIR:/host_pwd --nv lbpm.sif  bash -c 'cp -r /usr/local/LBPM_$GPU_ARCH/example/Sph1896/ /host_pwd/'
srun --mpi=pmi2 --ntasks-per-node=1 singularity run -B $BENCHMARK_DIR:/host_pwd --nv lbpm.sif  bash -c 'cd /host_pwd/Sph1896 && /usr/local/LBPM_$GPU_ARCH/bin/GenerateSphereTest input.db'
srun --mpi=pmi2 --ntasks-per-node=1 singularity run -B $BENCHMARK_DIR:/host_pwd --nv lbpm.sif  bash -c 'cd /host_pwd/Sph1896 && /usr/local/LBPM_$GPU_ARCH/bin/lbpm_color_simulator input.db'

Run the  script with sbatch:

sbatch run.sh

An output file will be created and should contain similar results:

********************************************************
Running Sphere Packing pre-processor for LBPM-WIA    
********************************************************
voxel length = 0.003125 micron 
Reading the sphere packing 
Reading the packing file...
Number of spheres extracted is: 1896
Domain set.
Sauter Mean Diameter (computed from sphere packing) = 34.151490 
Media porosity = 0.359970 
MorphOpen: Initializing with saturation 0.500000 
Media Porosity: 0.366707 
Maximum pore size: 14.075796 
Performing morphological opening with target saturation 0.500000 
Final saturation=0.503602
Final critical radius=4.793676
level=info msg="legacy OFED driver set: 4.9-0.1.7.0"
********************************************************
Running Color LBM    
********************************************************
MPI rank=0 will use GPU ID 0 / 1 
voxel length = 0.003125 micron 
voxel length = 0.003125 micron 
Read input media... 
Initialize from segmented data: solid=0, NWP=1, WP=2 
Media porosity = 0.359970 
Initialized solid phase -- Converting to Signed Distance function 
Domain set.
Create ScaLBL_Communicator 
Set up memory efficient layout, 11795503 | 11795520 | 33386248 
Allocating distributions 
Setting up device map and neighbor list 
Component labels: 1 
   label=0, affinity=-1.000000, volume fraction==0.652189
Initializing distributions 
Initializing phase field 
********************************************************
No. of timesteps: 3000 
Affinities - rank 0:
Main: 0
-------------------------------------------------------------------
********************************************************
CPU time = 0.046325 
Lattice update rate (per core)= 254.623329 MLUPS 
Lattice update rate (total)= 254.623329 MLUPS 
********************************************************

Running FSL in a Singularity container; notes for Mac OS X & XQuartz

Recent versions of FSL are available in a Singularity container at the Max Planck Institute for Human Development Git repo. Follow the instructions to build the container. Using Windows, MobaXterm will work best. For Macs, XQuartz is needed. If FSLEyes crashes with errors such as "The program 'fsleyes' received an X Window System error" follow the tips at Running FSLeyes remotely with special attention to XQuartz - FSLeyes doesn’t start, and just shows an error.  If you still get errors running FSL or FSLEyes, run Apple's Software Update and reboot. 

For multiple monitors on a Mac FSL and FSLEyes will start in a very stretched view and unable to see any menu options. We have a PKL file that you can place in your  $HOME/.config/fsleyes/ directory. It is located in the RCS 'files' directory.

Mathematica

The first time you launch Mathematica you will need to provide the host details of the MathLM (license) server. Using the Activating Mathematica guide, click 'Other ways to activate' then choose 'Connect to a Network License Server' and enter the IP address, 128.59.30.140

OpenMPI Settings 

The default OpenMPI on Ginsburg is  openmpi-4.1.5a1, which is provided by Nvidia Mellanox and optimized for the MOFED stack. You will receive the following warnings when using mpirun/mpiexec:

WARNING: There was an error initializing an OpenFabrics device.

  Local host:   g###
  Local device: mlx5_0

Default device parameters will be used, which may result in lower performance. You can edit any of the files specified by the
btl_openib_device_param_files MCA parameter to set values for your device.

NOTE: You can turn off this warning by setting the MCA parameter btl_open ib_warn_no_device_params_found to 0.

You can pass the following option, which will use ucx which is default as of version 3.x:

--mca pml ucx --mca btl '^openib' 

To help with the following warning:

Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

You can also add:

--mca orte_base_help_aggregate 0

If you choose to use the openmpi/gcc/64/4.1.1_cuda_11.0.3_aware module, this version expects a GPU and will throw the following warning on non-GPU nodes:

The library attempted to open the following supporting CUDA libraries, but each of them failed. CUDA-aware support is disabled.
libcuda.so.1: cannot open shared object file: No such file or directory
libcuda.dylib: cannot open shared object file: No such file or directory
/usr/lib64/libcuda.so.1: cannot open shared object file: No such file or directory
/usr/lib64/libcuda.dylib: cannot open shared object file: No such file or directory

If you are not interested in CUDA-aware support, then run with --mca opal_warn_on_missing_libcuda 0 to suppress this message. If you are interested in CUDA-aware support, then try setting LD_LIBRARY_PATH to the location of libcuda.so.1 to get passed this issue.

You can pass this option:

--mca opal_warn_on_missing_libcuda 0

RStudio in a Singularity container

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".

srun -X -A <GROUP> --pty -t 0-01:00 -X /bin/bash

Load the Singularity module:

module load singularity

This next step will take a few minutes and will only need to be done the first time you launch this application. On subsequent sessions you skip this step as the container is downloaded:

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:

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.

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.



Now open another Terminal and start the RStudio rserver session using Port Forwarding to connect a local port on your computer to a remote one on Ginsburg.

ssh -Nf -L 8787:10.197.16.39:8787 [email protected]  


NOTE FOR WINDOWS USERS:

If you are using Windows Subsystem for Linux (WSL/WSL2), then the above line work fine, BUT remember to forward the WSL session ports to the Windows browser. Set the System Browser as the WSL default and open 






The above Port Forwarding line works on Linux/Unix/MacOS, or any virtual machine running Linux. For Windows, we are assuming you are using PuTTY and the above line would be accomplished using the alternative steps below:

I.    Launch PuTTY

II.   In the "Session" category (the default screen when you open PuTTY), enter burg.rcs.columbia.edu in the "Host Name (or IP address)" field. 

III.   Ensure the "Port" field is set to 22, which is the default SSH port.       Optionally, you can enter a name in the "Saved Sessions" field and click "Save" to save these settings for future re-use

IV.   In the "Category" pane on the left, expand the "SSH" category by clicking the + sign next to it.

V.    Click on "Tunnels" under the "SSH" category.

VI.   In the "Source port" field, enter 8787.

VII.   In the "Destination" field, enter 10.197.16.39:8787.    (Remember,  10.197.16.39 is only an example IP, your actual one may be different)

VIII.   Click the "Add" button. You should see the forwarded port appear in the list box as L8787 10.197.16.39:8787.

IX.     Optional but recommended,   To save this configuration for future use, go back to the "Session" category, and enter a name for the session in the "Saved Sessions" field (e.g., <myuni>@burg.rcs.columbia.edu) and click the "Save" button.

X.      Click the "Open" button at the bottom of the PuTTY window and connect to burg.rcs.columbia.edu



Next, use a web browser to connect to to your locally forwarded port.

In any browser, e.g., Google Chrome, enter localhost:8787. The login screen for RStudio will appear and you enter your UNI (without the @columbia.edu) and whatever password you put from the above example (where it says CHANGME). If you need a session that last longer than an hour you can add --auth-timeout-minutes=0 --auth-stay-signed-in-days=30 to the end of the above singularity. command. A sample Slurm bash script is available at Rocker Project's Singularity page. If you run into an error such as [rserver] ERROR system error 98 (Address already in use), you can specify the port number as an additional option, e.g.,  --www-port 8788. The new command could look like this:

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 --www-port 8788 --auth-none=0 --auth-pam-helper-path=pam-helper --server-user=$USER

***IMPORTANT NOTE***

When you are finished with RStudio remember to stop the Singularity session via ctl-c, and you can kill the SSH forwarding session by finding the process ID (PID) with the following command, noting that the PID is the second column:

ps -ef | grep 8787
  503 82438     1   0 10:56AM ??         0:00.31 ssh -Nf -L 8787:10.197.16.39:8787 [email protected]
kill -9 82438

Visual Studio Code Server

A pre-existing Github account is now required to use the below instructions.


Visual Studio Code is an Integrated Development Environment that some like to use on their laptops. If you are familiar with that, the HPC has a server-side version hosted on the compute nodes (NOT the login nodes) for users to connect their local VS Code application on their laptop to Ginsburg and open files from their Ginsburg folder directly.  To use it, do the following:

After logging into Ginsburg, start an srun session to a CPU or GPU node of your choice:

srun --pty -t 0-01:00  -A <ACCOUNT> /bin/bash

     OR, if you need a GPU

srun --pty -t 0-01:00 --gres=gpu:1 -A <ACCOUNT> /bin/bash


Then type

$ code tunnel

You will get a message like the one below:

* Visual Studio Code Server

*

* By using the software, you agree to

* the Visual Studio Code Server License Terms (https://aka.ms/vscode-server-license) and

* the Microsoft Privacy Statement (https://privacy.microsoft.com/en-US/privacystatement).

*

[2024-04-05 16:12:16] info Using Github for authentication, run `code tunnel user login --provider <provider>` option to change this.

To grant access to the server, please log into https://github.com/login/device and use code <###-###>


When you use the device login url, you will first get a page asking you to use your GitHub credentials to login.

After using your GitHub login, then you will get a page asking you to input the device code  given you above (represented as <###-###> here)

Next you will see a page requesting you to authorize VS Code studio's access permissions.

After that, when you use your local VS Code application on your computer, you will see a running ssh tunnel listed. Double click to connect to it. This can take a moment to finish.

Once done, you will be able to open files in your Ginsburg folder the same as you do ones on your local computer.