50 recent changes in Main Web retrieved at 08:53 (GMT)

CUDA
CUDA is a parallel computing platform and programming model developed by NVIDIA for general purpose computing on GPU devices. CUDA application can dramatically sp...
Anaconda-EnvironmentReportsCorruptedMetadataWhenYouTryToInstallPackages
If a conda environment reports errors like a "corrupted manifest" file or "package manifest can't be found" then you can perform this command to scrub all package...
WebHome
Welcome to the Research Computing Support Group at UTSA! The Research Computing Support Group at UTSA provides computing, storage and visualization resources to s...
R-CorruptedRLibrariesWhenUsingBioconductor
If the user uses bioconductor for biology projects in R and their R library becomes corrupted you can do this command in the R prompt. BiocManager::valid() At t...
Abaqus
Abaqus Abaqus is used for both the modeling and analysis of mechanical components and assemblies (pre processing) and visualizing the finite element analysis resu...
UsingTACCSResources
https://portal.tacc.utexas.edu/user guides To use TACC's Corral system you must request via TACC's User Portal for access: https://portal.tacc.utexas.edu/user gu...
GNUParallel
GNU Parallel is a shell tool for executing many sequential tasks at the same time on one or more nodes. It is useful for running a large number of sequential task...
UseSlurmOnShamu
Slurm (Simple Linux Utility for Resource Management) is a highly configurable workload manager and job scheduler for an HPC cluster. It is an open source software...
ModuleEnvironments
Module Environments Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the enviro...
QueueDefinitions
Partition Definitions There are eight (8) Slurm partitions on Shamu that users are able to utilize. Below are their definitions. * defq This is the main queu...
UsingTheOnDemandPortal
Shamu OnDemand Portal We recently introduced the OnDemand Portal which allows you as a user to connect to Shamu via a web browser instead of an SSH client. The On...
UsingTheGPUResources
The GPU resources on Shamu have been configured as a "consumable resource". This means you can request individual GPU cards, nodes, etc... We have two types of GP...
Slurm-NewJobSchedulingSystem
Main.AdminUser 01 Jul 2020 On July 13, 2020, the job scheduler Sun Grid Engine (SGE) on Shamu will be switched to Slurm, a new job scheduling system. Existing SGE...
SampleSlurmSubmitScripts
The page has been moved to UseSlurmOnShamu
ApplicationCheckpointAndRestart
Checkpoint and Restart Checkpointing is the action of saving the state of a running process to a checkpoint image file. Restart is the actions to resume the check...
RestartScriptGenerationExample
Here's a simple example of a checkpointing program being run with a slurm job script that will automatically generate a restart script for when you need to restar...
FAQ
Frequently Asked Questions Who can use Shamu? The Shamu research cluster is available at no charge to all University of Texas at San Antonio students, faculty an...
CheckpointAndRestartSequentialAndMulti-threadingApplicationsInteractively(nonBatch)
To checkpoint and restart an interactive job, follow the steps below: log onto a compute node from the login node. srun pty bash Load the dmtcp module module...
Checkpoint-and-RestartForDeepLearningModelsWithTensorflow
By using the checkpoint feature, model progress can be saved during training. The model can resume training where it left off and avoid starting from scratch if s...
ShamuFairUsePolicy
Shamu Fair Use Policy Effective July 13, 2020 Active Jobs Compute nodes will no longer be shared among multiple users. Instead, when a user grabs a compute nod...
SimpleCheckpoingAndRestartForPythonUsingAClass
This is a simple example of a program that checkpoints using python and the pickle class. It will run for 15 minutes. The script checks for a file called "countin...
CProgrammingWithSelf-DefinedCheckpoint-and-Restart
Checkpoint and restart with DMTCP can create large disk images, and the checkpoint details are controlled by the third party system. To avoid the problems, the pr...
EmbedDMTCPCheckpointAndRestartInCCode
In the previous examples, the checkpoint action is controlled by the coordinator, either by i number_of_second option or by manually type in 'c' in the coordinat...
CheckpointAndRestartSequentialAndMulti-threadingBatchJobs
Here is a Slurm job script for submit a job with checkpoint feature: #!/bin/bash# Put your SLURM options here#SBATCH partition=defq # change to proper pa...
OtherTools
Checkpoint and Restart Checkpointing is the action of saving the state of a running process to a checkpoint image file. Restart is the actions to resume the check...
CheckpointAndRestart
Checkpointing is the action of saving the state of a running process to a checkpoint image file. Restart is the actions to resume the checkpointed application fro...
TensorFlow
We have the GPU version of TensorFlow installed on the GPU nodes with the Python 3.6.1 module install (native Python 2.7 version is currently not working). This d...
SetupWindowsSubsystemForLinux(Advanced)
Windows Subsystem for Linux After the Windows 10 Fall Creators Update (FCU) released on October 17th 2017 Microsoft started to officially support on Windows OS th...
Cuda
Cuda Cuda is a GPU programming language developed by NVIDIA. Currently Shamu contains two (4) very high end GPU nodes consisting of eight (8) Telsa K80 GPU comput...
Matlab
Using Matlab Interactively (GUI mode) You can run Matlab with the srun command: abc123@login01 ~ $ srun pty bash abc123@compute003 ~ $ module load matlab...
MonitoringYourJobs
Monitoring your jobs Using the squeue Command Check the status of all jobs on Shamu using the squeue command: $ squeue JOBID PARTITION NAME USER ST TIME NODES N...
GettingStarted
Getting Started with Shamu Shamu is the Research Support Groups premier cluster consisting of many compute cores and GPU cores. Connecting from Windows environme...
QuickStartGuide
Quick Start Guide The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support research that has specialized or...
AboutShamuCluster
About Shamu cluster Shamu is UTSA's primary high performance (HPC) resource; heavily utilized by researchers, students, faculty and staff from a broad range of di...
GettingHelp
Getting Help Shamu Office Hours Shamu Office hours are held in the Tech Cafe Monday through Friday 8am to 5pm. No appointment necessary, just drop by. Email UTS...
SubmittingYourBatchJob
How to submit your batch job Using the Slurm sample script located here, you will be able to submit your job with this command but first you need to load the "slu...
RunningYourInteractiveJobsThroughBatch
How to run interactive jobs If you want to use a GUI or have a short program you want to test or debug, we suggest using the "srun" command. This will automatical...
SoftwareAndApplications
Software Installed on Shamu Below is the list of software that is currently installed on Shamu. If you need additional software, please email your request to rcsg...
GPU
Sample GPU submit script using the Caffe training network Using the Tesla K80 cards: #SBATCH partition="gpu" #SBATCH nodes=1 #SBATCH gres=gpu:k80:1 . /etc/prof...
TransferringFilesWithFilezilla
How to connect to shamu with filezilla to transfer files. This was done with filezilla 3.47.2.1 The quickconnect button When you open the program, there is a 'qu...
Gamess
Gamess How to run Gamess on Shamu Run test job from the command line$ cd ~$ mkdir gamess $ mkdir /local/ insert your abc123 $ cp p /apps/gamess/tests/standard/ex...
Mathematica
Sample submit script for non gui mode. You can copy/paste this script below to your Shamu directory, call it math.qsub. Submit the job on Shamu with qsub math.qsu...
CellRanger
Cell Ranger Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA seq output to align reads, generate gene cell matrices and perfo...
Hoomd
HOOMD blue is a general purpose particle simulation toolkit. It performs hard particle Monte Carlo simulations of a variety of shape classes, and molecular dynami...
R
R How to add packages to your local repository Depending on the packages you want installed, you can do one of two things within R. First we load the R module an...
GridEngineJobSubmission
Grid Engine Job Submission In order to use the Grid Engine commands you first need to load the "sge" module: abc123@login 0 0 abc123 $ module load sge You can su...
PerilNotebookExample
Main.AdminUser 26 Sep 2019 When you log into notebooks.azure.com go to your My Projects page. Click on Upload Github Repo and a form will come up. To upload the r...
NotebooksOnAzureCloud
Main.AdminUser 25 Sep 2019 You can make a free jupyter notebook on notebooks.azure.com by logging in to your microsoft account. After logging in if you go to 'My ...
LAMMPS
LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soli...
Fluent
Fluent When running Fluent v16 or above in parallel batch mode, additional parameters need to be added to the Fluent command line. Fluent supports integration wit...
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Topic revision: r1 - 03 May 2016, UnknownUser
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