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You are here: UTSA Research Support Group>Main Web>WebChanges (03 May 2016, UnknownUser)Edit Attach
50 recent changes in Main Web retrieved at 07:50 (GMT)
UsingJetstream
Jetstream is a level 1 service provider of XSEDE (Extreme Science and Engineering Discovery Environment). It is a user friendly cloud computing environment for re...
r2 - 17 Oct 2020 - 03:19 by AdminUser
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...
r64 - 16 Oct 2020 - 21:27 by AdminUser
DeepLearningModelParallelization
Parallelize Deep Learning Models Across Multiple GPU Devices Deep Learning models written in Tensorflow can automatically take advantage of a GPU device on a comp...
r5 - 16 Oct 2020 - 21:21 by AdminUser
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...
r2 - 12 Oct 2020 - 22:08 by AdminUser
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...
r8 - 23 Sep 2020 - 19:20 by AdminUser
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 par...
r2 - 14 Sep 2020 - 16:47 by AdminUser
MessagePassingInterface(MPI)
MPI Basics MPI is standardized and portable standard which defines the syntax and semantics of library routines for users writing portable parallel programs in C,...
r5 - 08 Sep 2020 - 20:51 by AdminUser
UsingSingularity
Singularity is available on Shamu for users to run container based applications. Users can access the software via the module system, as shown below: abc123@shamu...
r5 - 26 Aug 2020 - 22:49 by AdminUser
PythonVmsInAnaconda
If you need to install your own programs/modules in python you can do it via creating vms. Some programs may need specific versions of modules to work correctly a...
r6 - 13 Aug 2020 - 19:27 by AdminUser
ParallelProgrammingInPython
Single Node Parallelization A program in Python programming language can utilize the power of the multiple CPU/Core on a computer to significantly improve the per...
r2 - 11 Aug 2020 - 22:37 by AdminUser
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...
r5 - 06 Aug 2020 - 02:01 by AdminUser
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...
NEW - 04 Aug 2020 - 20:11 by AdminUser
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...
NEW - 04 Aug 2020 - 19:44 by AdminUser
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...
r7 - 04 Aug 2020 - 19:00 by AdminUser
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...
r8 - 04 Aug 2020 - 14:57 by AdminUser
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...
r7 - 30 Jul 2020 - 20:51 by AdminUser
ModuleEnvironments
Module Environments Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the enviro...
r3 - 24 Jul 2020 - 15:08 by AdminUser
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...
r8 - 24 Jul 2020 - 13:58 by AdminUser
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...
r4 - 20 Jul 2020 - 20:02 by AdminUser
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...
r4 - 14 Jul 2020 - 22:08 by AdminUser
SampleSlurmSubmitScripts
The page has been moved to UseSlurmOnShamu
r6 - 14 Jul 2020 - 21:49 by AdminUser
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...
r9 - 14 Jul 2020 - 14:00 by AdminUser
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...
NEW - 14 Jul 2020 - 13:57 by AdminUser
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...
r4 - 14 Jul 2020 - 12:58 by AdminUser
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...
r2 - 13 Jul 2020 - 20:40 by AdminUser
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...
r2 - 13 Jul 2020 - 15:33 by AdminUser
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...
r4 - 13 Jul 2020 - 15:13 by AdminUser
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...
r2 - 13 Jul 2020 - 04:32 by AdminUser
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...
r2 - 12 Jul 2020 - 22:12 by AdminUser
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...
NEW - 12 Jul 2020 - 16:40 by AdminUser
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...
NEW - 12 Jul 2020 - 16:18 by AdminUser
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...
NEW - 08 Jul 2020 - 22:01 by AdminUser
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...
r15 - 26 Jun 2020 - 21:59 by AdminUser
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...
NEW - 24 Jun 2020 - 22:28 by AdminUser
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...
r2 - 24 Jun 2020 - 21:21 by AdminUser
Matlab
Using Matlab Interactively (GUI mode) You can run Matlab with the srun command: abc123@login01 ~ $ srun pty bash abc123@compute003 ~ $ module load matlab...
r7 - 24 Jun 2020 - 21:18 by AdminUser
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...
r3 - 24 Jun 2020 - 20:16 by AdminUser
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...
r16 - 24 Jun 2020 - 20:06 by AdminUser
QuickStartGuide
Quick Start Guide The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support research that has specialized or...
r17 - 24 Jun 2020 - 19:41 by AdminUser
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...
r5 - 24 Jun 2020 - 19:39 by AdminUser
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...
r6 - 24 Jun 2020 - 19:37 by AdminUser
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...
r5 - 12 Jun 2020 - 16:39 by AdminUser
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...
r7 - 12 Jun 2020 - 16:36 by AdminUser
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...
r29 - 13 May 2020 - 20:13 by AdminUser
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...
r3 - 21 Apr 2020 - 19:08 by AdminUser
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...
NEW - 10 Apr 2020 - 21:26 by AdminUser
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...
r2 - 10 Mar 2020 - 18:08 by AdminUser
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...
r2 - 05 Feb 2020 - 13:56 by AdminUser
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...
r4 - 04 Feb 2020 - 20:51 by AdminUser
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...
r2 - 04 Feb 2020 - 14:40 by AdminUser
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CondaEnvironmentSaysMetadataCorruptedWhenInstalling
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