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pub:forge [2019/02/01 22:02]
brrgdw [Modules] 		pub:forge [2022/05/06 20:15] (current)
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 ===== System Information ===== ===== System Information =====
 ==== Software ==== ==== Software ====
-The Forge was built with rocks 6.1.1 which is built on top of CentOS 6.5. With the Forge we made the conversion from using PBS/Maui to using SLURM as our scheduler and resource manager. +The Forge was built with rocks 6.1.1 which is built on top of CentOS 6.8. With the Forge we made the conversion from using PBS/Maui to using SLURM as our scheduler and resource manager. 
  
 ==== Hardware ==== ==== Hardware ====
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 ==Scratch Directories== ==Scratch Directories==
  
-Each user will get a scratch directory created for them at /mnt/stor/scratch/$USER. As with all storage scratch space is not backed up, and even more to the fact of data impermanence in this location it is actively cleaned in an attempt to prevent the storage from filling up. The intent for this storage is for your programs to create temporary files which you may need to keep after the calculation completes for a short time only. The volume is a high speed network attached scratch space, there currently are no quotas placed on the directories in this scratch space, however if the 20TB volume filling up becomes a problem we will have to implement quotas. +Each user will get a scratch directory created for them at /mnt/stor/scratch/$USER an alias of `cdsc` has also been made for users to cd directly to this location. As with all storage scratch space is not backed up, and even more to the fact of data impermanence in this location it is actively cleaned in an attempt to prevent the storage from filling up. The intent for this storage is for your programs to create temporary files which you may need to keep after the calculation completes for a short time only. The volume is a high speed network attached scratch space, there currently are no quotas placed on the directories in this scratch space, however if the 20TB volume filling up becomes a problem we will have to implement quotas. 
  
 Along with the networked scratch space, there is always local scratch on each compute node for use during calculations in /tmp. There is no quota placed on this space, and it is cleaned regularly as well, but things stored in this space will only be available to processes executing on the node in which they were created. Meaning if you create it in /tmp in a job, you won't be able to see it on the login node, and other processes won't be able to see it if they are on a different node than the process which created the file.  Along with the networked scratch space, there is always local scratch on each compute node for use during calculations in /tmp. There is no quota placed on this space, and it is cleaned regularly as well, but things stored in this space will only be available to processes executing on the node in which they were created. Meaning if you create it in /tmp in a job, you won't be able to see it on the login node, and other processes won't be able to see it if they are on a different node than the process which created the file. 
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 ==== Abaqus ==== ==== Abaqus ====
   * Default Vesion = 6.12.3   * Default Vesion = 6.12.3
-  * Other versions available: 6.11.2, 6.14.1, 2016, 2018+  * Other versions available: 2019, 2018, 2016, 6.14.1, 6.11.2 
 +<code> 
 +module load abaqus/2019 
 +module load abaqus/2018 
 +module load abaqus/2016 
 +module load abaqus/6.14-1 
 +module load abaqus/6.12-3 
 +</code>
  
 This example is for 6.12 This example is for 6.12
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 ==== Abaqus 2016 ==== ==== Abaqus 2016 ====
  
 +<code>
 module load abaqus/2016 module load abaqus/2016
 +</code>
  
 <file bash abaqus2016.sbatch> <file bash abaqus2016.sbatch>
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 rlm_roam rlm_roam
 </code> </code>
 +
 +====Comsol====
 +
 +===Licensing===
 +
 +The licensing scheme for Comsol is seat based, which means if you only have 1 license, and you have it installed on your workstation and the Forge you can only use one or the other at the same point in time. If your workstation has the license checked out when your Forge job starts, your job will fail to get a license and will fail to run. 
 +
 +This problem only gets compounded when you are also working with other users inside a group with a handful of shared seats. You will need to coordinate with them when you and they will run so that you don't run into license problems when trying to run. 
 +
 +
 +===Running Batch===
 +
 +Running Comsol with the Forge as your solver is fairly straight forward, first you load your module (module names for comsol differ by which license pool you are using). 
 +    module load comsol/5.4_$pool
 +    
 +then create your batch file for submission.
 +
 +<file bash comsol.sbatch>
 +#SBATCH --job-name=comsol_test
 +#SBATCH --nodes=1
 +#SBATCH --ntasks=20
 +#SBATCH --mem=20000
 +#SBATCH --time=60:00:00
 +#SBATCH --export=ALL
 +
 +comsol -np 20 batch -inputfile multilayer.mph -outputfile laminate_out.mph
 +
 +</file>
 +
 +Please note that comsol is a memory intensive application, you will likely have to adjust the values for mem and ntasks to suit what your simulation will need. 
 +
 +We also advise creating the input file on a windows workstation and using the Forge for simulation solving, however running interactively should be possible inside an interactive job with X forwarding enabled. 
  
 ====CST==== ====CST====
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 This contains the output of the finished job.\\ This contains the output of the finished job.\\
 ==== Matlab ==== ==== Matlab ====
 +
 +**IMPORTANT NOTE**
 +Currently campus has 100 Matlab seat licenses to be shared between the Forge and research desktops.  There are certain times of the year where Matlab usage is quite high.  License check out is on a first come, first served basis.  If you are not able to get a Matlab license, you might consider using GNU Octave.  This is available on the Forge and will do much of what Matlab will do.
  
 Matlab is available to run in batch form or interactively on the cluster. Matlab is available to run in batch form or interactively on the cluster.
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 ===Python 3=== ===Python 3===
 There are many modules available for Python 3. However, unlike Python 2.7, all of the python modules are installed in the python directory rather than being separate modules. Currently, the newest Python 3 version available on the Forge is Python 3.6.4. To see a current list of available python versions, run the command <code>module avail python</code> To see a list of all available Python modules available for a particular Python version, load that Python version and run <code>pip list</code> Users are welcome to install additional modules on their account using <code>pip install --user <package name></code> There are many modules available for Python 3. However, unlike Python 2.7, all of the python modules are installed in the python directory rather than being separate modules. Currently, the newest Python 3 version available on the Forge is Python 3.6.4. To see a current list of available python versions, run the command <code>module avail python</code> To see a list of all available Python modules available for a particular Python version, load that Python version and run <code>pip list</code> Users are welcome to install additional modules on their account using <code>pip install --user <package name></code>
 +
 +***NOTE***
 +The default versions of Python on the Forge do ***NOT*** have pip installed.  You will have to load a Python module to get pip functionality.
 ====QMCPack==== ====QMCPack====
  
pub/forge.1549058532.txt.gz · Last modified: 2022/05/06 20:15 (external edit)

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