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pub:foundry [2022/02/02 18:47]
jonesjosh adding starccm to the wiki 		pub:foundry [2023/08/22 15:15] (current)
lantzer
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 Missouri S&T users can mount their web volumes and S Drives with the <code>mountdfs</code> command. This will mount your user directories to the login machine under /mnt/dfs/$USER. The data can be copied over with command line tools to your home directory, **your data will not be accessible from the compute nodes so do not submit jobs from these directories.** Aliases "cds" and "cdwww" have been created to allow you to cd into your s drive and web volume quickly and easily.  Missouri S&T users can mount their web volumes and S Drives with the <code>mountdfs</code> command. This will mount your user directories to the login machine under /mnt/dfs/$USER. The data can be copied over with command line tools to your home directory, **your data will not be accessible from the compute nodes so do not submit jobs from these directories.** Aliases "cds" and "cdwww" have been created to allow you to cd into your s drive and web volume quickly and easily. 
 +
 +You can un-mount your user directories with the <code>umountdfs</code> command. If you have trouble accessing these resources, you may be able to get it working again by un-mounting the directories and then mount the directory again. When the file servers reboot for monthly patching or other scheduled maintenance, the mount might not reconnect automatically.
  
 === Windows === === Windows ===
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 ===== Applications ===== ===== Applications =====
 ** The applications portion of this wiki is currently a Work in progress, not all applications are currently here, nor will they ever be as the applications we support continually grows. ** ** The applications portion of this wiki is currently a Work in progress, not all applications are currently here, nor will they ever be as the applications we support continually grows. **
 +
 +==== Abaqus ====
 +
 +  * Default Version = 2022
 +  * Other versions available: 2020
 +
 +
 +=== Using Abaqus ===
 +
 +Abaqus should not be operated on the login node at all.
 +\\
 +Be sure you are connected to the Foundry with X forwarding enabled, and running inside an interactive job using command 
 +    sinteractive
 +Before you attempt to run Abaqus. Running sinteractive without any switches will give you 1 cpu for 10 minutes, if you need more time or resources you may request it. See [[pub:foundry#interactive_jobs|Interactive Jobs]] for more information.
 +\\
 +Once inside an interactive job you need to load the Abaqus module.
 +    module load abaqus
 +Now you may run abaqus.
 +    ABQLauncher cae -mesa
 +
 +
 +
 ====Anaconda==== ====Anaconda====
 If you would like to install python modules via conda, you may load the anaconda module to get access to conda for this purpose. After loading the module you will need to initialize conda to work with your shell. If you would like to install python modules via conda, you may load the anaconda module to get access to conda for this purpose. After loading the module you will need to initialize conda to work with your shell.
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 #SBATCH --mail-user=username@mst.edu #SBATCH --mail-user=username@mst.edu
  
-module load starccm/10.04+module load starccm/2021.2
  
 time starccm+ -batch -np 12 /path/to/your/starccm/simulation/example.sim time starccm+ -batch -np 12 /path/to/your/starccm/simulation/example.sim
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 Breakdown of the script:\\ Breakdown of the script:\\
-This job will use **1** node, asking for **12** processors, 40,000 MB of memory for a total wall time of **12 hours** and will email you when the job starts, finishes or fails.+This job will use **1** node, asking for **12** processors, **40,000 MB** of memory for a total wall time of **12 hours** and will email you when the job starts, finishes or fails.
  
 The StarCCM commands:\\ The StarCCM commands:\\
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 |/path/to/your/starccm/simulation/example.sim| use the true path to your .sim file in your cluster home directory| |/path/to/your/starccm/simulation/example.sim| use the true path to your .sim file in your cluster home directory|
  
 +
 +====TensorFlow with GPU support====
 +
 +https://www.tensorflow.org/
 +
 +We have been able to get TensorFlow to work with GPU support if we install it within an anacoda environment. Other methods do not seem to work as smoothly (if they even work at all).
 +
 +First use [[#Anaconda|Anaconda]] to create and activate a new environment (e.g. tensorflow-gpu). Then use anaconda to install TensorFlow with GPU support:
 +
 +conda install tensorflow-gpu
 +
 +At this point you should be able to activate that anaconda environment and run TensorFlow with GPU support.
 +
 +Job Submission Information
 +
 +Copy your python script to the cluster. Once copied, create your job file.
 +
 +Example job file:
 +
 +<file bash tensorflow-gpu.sub>
 +#!/bin/bash
 +#SBATCH --job-name=tensorflow_gpu_test
 +#SBATCH --nodes=1
 +#SBATCH --ntasks=1
 +#SBATCH --partition=cuda
 +#SBATCH --time=01:00:00
 +#SBATCH --gres=gpu:1
 +#SBATCH --mail-type=BEGIN
 +#SBATCH --mail-type=FAIL
 +#SBATCH --mail-type=END
 +#SBATCH --mail-user=username@mst.edu
 +
 +module load anaconda/2020.7
 +conda activate tensorflow
 +python tensorflow_script_name.py
 +</file>
 +
 +==== Thermo-Calc ====
 +
 +  * Default Version = 2021a
 +  * Other versions available: none yet
 +
 +=== Accessing Thermo-Calc ===
 +
 +Thermo-Calc is a restricted software. If you need access please email nic-cluster-admins@mst.edu for more info.
 +
 +=== Using Thermo-Calc ===
 +
 +Thermo-Calc will not operate on the login node at all.
 +\\
 +Be sure you are connected to the Foundry with X forwarding enabled, and running inside an interactive job using command 
 +    sinteractive
 +before you attempt to run Thermo-Calc. Running sinteractive without any switches will give you 1 cpu for 10 minutes, if you need more time or resources you may request it. See [[pub:foundry#interactive_jobs|Interactive Jobs]] for more information.
 +\\
 +Once inside an interactive job you need to load the Thermo-Calc module.
 +    module load thermo-calc
 +Now you may run thermo-calc.
 +    Thermo-Calc.sh
 +
 +====Vasp====
 +
 +To use our site installation of Vasp you must first prove that you have a license to use it by emailing your vasp license confirmation to <nic-cluster-admins@mst.edu>.
 +
 +Once you have been granted access to using vasp you may load the vasp module <code>module load vasp</code> (you might need to select the version that you are licensed for).
 +
 +and create a vasp job file, in the directory that your input files are, that will look similar to the one below.
 +
 +<file bash vasp.sub>
 +#!/bin/bash
 +
 +#SBATCH -J Vasp
 +#SBATCH -o Foundry-%j.out
 +#SBATCH --time=1:00:00
 +#SBATCH --ntasks=8
 +
 +module load vasp
 +module load libfabric
 +
 +srun vasp
 +
 +</file>
 +
 +This example will run the standard vasp compilation on 8 cpus for 1 hour. \\
 +
 +If you need the gamma only version of vasp use <code> srun vasp_gam </code> in your submission file. \\
 +
 +If you need the non-colinear version of vasp use <code> srun vasp_ncl </code> in your submission file.\\
 +
 +It might work to launch vasp with "mpirun vasp", but running "srun vasp" should automatically configure the MPI job parameters based on the configured slurm job parameters and should run more cleanly than mpirun.\\\
 +
 +There are some globally available Psudopoetentials available, the module sets the environment variable $POTENDIR to the global directory.
  
  
pub/foundry.1643827629.txt.gz ยท Last modified: 2022/05/06 20:15 (external edit)

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