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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 12:46 (GMT)
SettingUpPasswordlessLogin
To set up passwordless login you'll need to have set up an RSA key pair on your local machine for SSH. On linux and Mac OS. To generate an RSA keypair, just do t...
r2 - 16 Sep 2021 - 23:25 by AdminUser
BrentTesting
BrentTesting
NEW - 01 Aug 2021 - 23:36 by RegistrationAgent
WikiUsers
List of UTSA Research Support Group users Below is a list of users with accounts. If you want to edit topics or see protected areas of the site then you can get a...
r7 - 01 Aug 2021 - 23:36 by AdminUser
SarahOrtega
SarahOrtega
NEW - 20 Jul 2021 - 19:33 by RegistrationAgent
JeremyMann
JeremyMann
NEW - 20 Jul 2021 - 17:52 by RegistrationAgent
MonitoringYourJobs
Monitoring your jobs Using the squeue Command Check the status of all jobs on Shamu using the squeue command (this is just an example compute names may be differ...
r4 - 14 Jul 2021 - 19:12 by AdminUser
AnsysLumerical
Use Lumerical You can skip steps 1 10 on Shamu and ARC. You can skip steps 1 10 on Stampede2 if Lumerical executable path is provided. Please follow the instructi...
r7 - 30 Jun 2021 - 14:49 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...
r32 - 03 Jun 2021 - 20:48 by AdminUser
ParallelProgrammingInR
R parallelization with mclapply mclapply is a parallelized version of lapply if provided mc.cores 1. For mc.cores == 1, it simply calls lapply​. By default, the m...
r4 - 14 May 2021 - 17:17 by AdminUser
IntelOneAPI
Intel oneAPI is an open, unified programming model built on standards to simplify the development and deployment of data centric workloads across CPUs, GPUs, FPGA...
NEW - 06 Apr 2021 - 20:00 by AdminUser
REnvironments
Create local R library Repo As Python packages, we suggest that users maintain their R library repoes in the home directory. Install R libraries using 'install.p...
NEW - 02 Apr 2021 - 20:48 by AdminUser
REvnironmentsInAnaconda
Create local R library Repo As Python packages, we suggest that users maintain an R library repo in the home directory. Install R libraries using 'install.packag...
r3 - 02 Apr 2021 - 20:47 by AdminUser
MFIX
MFiX is an open source multiphase flow solve. The detailed information can be found at https://mfix.netl.doe.gov/. The software is installed as a global shared Py...
r2 - 25 Mar 2021 - 19:53 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...
r9 - 23 Mar 2021 - 16:55 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...
r2 - 25 Feb 2021 - 19:14 by AdminUser
PythonEnvs-SavingAndImportingInAPackageList
It's handy to make a package list from your conda virtual environment in case you install something that breaks it or you want to replicate the packages exactly o...
NEW - 09 Feb 2021 - 02:00 by AdminUser
DeepLearningModel
TensorFlow CPU Version First, grab a compute node with srun and start a Python Virtualenv environment: abc123@login 0 0 ~ $ srun n 80 N 1 time=48:00:00 pty b...
r5 - 18 Jan 2021 - 04:18 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...
r3 - 14 Jan 2021 - 23:10 by AdminUser
R-ERRORC++14StandardRequestedButCXX14IsNotDefined
If you get the error: C 14 standard requested but CXX14 is not defined You need to create some environment variables that R can use to compile the code. If it do...
NEW - 14 Jan 2021 - 18:48 by AdminUser
OpenSees
OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. We have ...
r2 - 04 Jan 2021 - 21:51 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,...
r6 - 18 Dec 2020 - 16:15 by AdminUser
AbaqusUsageOnSHAMU
Main.AdminUser 02 Nov 2020 ABAQUS at UTSA Introduction ABAQUS is a software suite from Dassault Systems. It can be used for finite element analysis and computer ...
r3 - 03 Nov 2020 - 18:13 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...
r18 - 02 Nov 2020 - 22:41 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...
r3 - 29 Oct 2020 - 22:04 by AdminUser
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
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
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
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
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
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
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