Application specific Information FAQs
Current list of software
You may check the current list of software under modules by:
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application | actual application name | slurm command to run | Comments |
|---|---|---|---|
matlab | matlab | srun ... matlab | graphics interface |
maple | xmaple | srun ... xmaple | graphics interface |
maple | maple | srun ... maple | text interface |
mathematica | mathematica | srun ... mathematica | graphics interface |
mathematica | math | srun ... math | text interface |
comsol | comsol | srun ... comsol | graphics interface |
xstata | xstata-se | srun ... xstata-se | graphics interface to SE version |
stata | stata-se | srun ... stata-se | text interface to SE version |
xstata | xstata | srun ... xstata | graphics interface to IC version |
stata | stata | srun ... stata | text interface to IC version |
ansys | launcher121 | srun ... launcher121 | graphics interface |
ansys workbench | runwb2 | srun ... runwb2 -mesa | WorkBench interface(Note:you may or may not need the -mesa option depending on your OpenGL support and version of Workbench. Version 13 doesn't need it. |
fluent | fluent | srun ... fluent | graphics interface to 2D and 3D programs |
fluent icepak | icepak | srun ... icepak | graphics interface to Icepak |
R | R | srun ... R | graphics delivery enabled |
abaqus | abq6141 | srun ... abq6141 | command line interface |
abaqus cae | abq6141 cae | srun ... abq6141 cae -mesa | CAE interface |
abaqus 6.9-EF2 | abq69ef2.exe | srun ... abq69ef2.exe | command line interface |
weka | weka.jar | srun ... java -jar /opt/shared/weka/weka-3-6-10/weka.jar | graphics interface |
tecplot | tec360 | srun ... tec360 -mesa | graphics interface |
Cluster scaling considerations
The use of commercial packages like Matlab, Ansys, Mathematica, etc., often have usage scenarios for which one solution does not fit all situations. For example:
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If you are uncertain of a suitable approach, please contact cluster-support@tufts.edu for assistance.
Ansys and Fluent related:
Now that Ansys purchased Fluent, how does one access Fluent functionality?
Most Fluent functionality is incorporated into Ansys WorkBench.
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-bash-3.2$ module load ansys
-bash-3.2$ srun ... icepak
Abaqus related:
How do I run Abaqus?
There are several ways to run jobs. Most will find the following useful for checking syntax,etc..:
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-bash-3.2$ module load abaqus -bash-3.2$ srun ... abq682.exe doc |
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Comsol related:
How do I run Comsol as an interactive threaded job?
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This may solve display issues you might have do to your xserver.
GAMESS related:
-bash-3.2$ module load gamess
-bash-3.2$ srun ...options... rungms exam02
Imagemagick related:
Where do I find information on Imagemagick graphic tools?
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-bash-3.2$ module load ImageMagick How to display a picture using Imagemagick's display command without running the interface |
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Matlab related:
- How do I get matlab command line options?*
-bash-3.2$ srun ... matlab -help
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At this point you can issue commands and demos. Check the website for documentation.
Mathematica related:
Where can I find more Mathematica documentation?
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For MacOSx desktops you need to either install Mathematica or the Mathematica Player and then point to the installed fonts. For example if you have Mathematica installed, to use it's fonts, open a terminal window(shell) and type:
> xset fp+ /Applications/Mathematica.app/SystemFiles/Fonts/Type1/
> xset fp rehash
Assuming that is the path to the fonts.
Then connect to the cluster and start Mathematica normally.
NCAR related:
How do I start NCAR?
NCAR has lots of separate programs. These are all available to you after you setup the environment.
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Please consult the NCAR website for user documentation and examples.
Python related:
How can I verify if a particular Python package is installed?
Add-on tools such as numpy and scipy are installed. Others would be under the install tree located at:
/opt/shared/python/
in the version specific site-packages directory. Another approach uses pip.
| > module load python/2.7.6 > pip list |
|---|
PetSc related.
How do I install PetSc?
PetSc has a complex build environment that allows one to include various applications. We encourage interested users to build the suite of interest in their home directory. Installation instructions for a particular set of applications can be found here.
Perl related:
How can I verify if a particular Perl package is installed?
Suppose you wanted to see if package GD is installed:
-bash-3.2$ rpm -q perl-GD gd
PDF related:
How do I view pdf files on the cluster?
Use the X11 based program evince. It is already in your PATH.
R related:
How do I run a long running R job as a batch job and I require lots of ram?
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Check the R documentation for additional options. Note, you home directory quota is limited to 5 gig.
Stata related:
How to choose between SE, IC and MP editions?
Most users will likely only need IC. All versions have the same statistical functionality but differ in the size of their data structures.
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| > srun --pty --x11=first -p interactive stata -help |
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SAS related:
To run interactively:
> module load SAS > srun --pty --x11=first sas_u8 |
|---|
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You will get yourprogram.log and yourprogram.lst output files dumped to your current directory.
Tecplot related:
On the cluster Tecplot's help button doesn't work, where do I find TecPlot documentation?
Html docs can be found on the vendor's website
PDF versions are an option as well.
Are there any Tecplot tutorials?
See this tutorial link.
Standalone HPC math libraries:
The following libraries are installed. To check to see if there is an environment module associated with these, try:
-bash-3.2$ module avail
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For example:
> gcc mycode.c -o mycode -L /opt/shared/SuperLU_4.0/lib -libsuperlu.a
Bioinformatic programs:
How do I access Blast programs on the cluster?
-bash-3.2$ module load blast
-bash-3.2$ srun ... blastx ...
And likewise for other commands. Also consider what queue is best at meeting your compute needs.
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