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If you are uncertain of a suitable approach, please contact cluster-support@tufts.edu for assistance.
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PetSc related
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How do I run Abaqus?
There are several ways to run jobs. Most will find the following useful for checking syntax,etc..:
-bash-3.2$ module load abaqus -bash-3.2$ srun ... abq682.exe job=mydesign datacheck interactive input=./design.inp |
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To actually run the code, remove the option datacheck and interactive.
This will run your abaqus input file called design.inp as a serial job and if successful will create about 14 files in the directory you are working in. One such file is the .odb Abaqus database file. All the files are created with the job name "mydesign" and differ in the filename extensions and type of file.
Note, normally there are several versions of Abaqus available. Therefore one needs to note which one reflects what was set up with Modules. For example, the command abq682.exe is version specific.
How do I run a parallel Abaqus job?
| -bash-3.2$ srun ... abq682.exe job=design_4cpus cpus=4 mp_mode=mpi input=./design.inp |
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Note different Abaqus products may invoke different solvers. Check the documentation for options.
How can I find the abaqus command line options?
Suppose you are using the default version of abaqus.
> module load abaqus >srun --pty --x11=first -p interactive abq6112.exe -help This will produce a several page list of command line options. |
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How can find out what abaqus licenses are available?
> module load abaqus > srun --pty --x11=first -p interactive abq6112.exe licensing lmstat -a -c |
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How do I run Abaqus version 6.9.2 CAE gui?
| -bash-3.2$ srun ... abq692.exe cae |
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Why is OpenGl not working with CAE?
Add the -mesa option to the start of abaqus as mentioned above.
How do I read Abaqus documentation?
If you have X11 forwarding in place you will get a webpage with documentation.
-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?
| > module load comsol/5.0 > salloc -N 1 -c 8 -p interactive > srun --pty --x11=first comsol |
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How do I run Comsol as a mpi parallel job?
Start Comsol as above, but add the command line options as follows:
| -bash-3.2$ srun ... comsol -np 8 -mpmode owner |
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Then in the gui setup for Solver parameters, change the default Solver to the Parallel Direct Solver(Pardiso) and rerun your model.
To do the same task but on an node with exclusive access use the --exclusive option, but note that the request may take some time to be granted depending of loads.
The comsol help button doesn't work, how do I find the documentation?
The compute nodes do not have browsers installed. Firefox is available on the headnode of the cluster instead. The install tree for Comsol contains html docs and some pdfs as well.
$ ls /opt/comsol35a/doc/
aco browser chem multiphysics plain sme
For example to view the html chem docs:
$ firefox file:///opt/comsol35a/doc/chem/index.htm
Sometimes you may find that your comsol efforts no longer work as they may have in the past; resulting in java errors of several types. These errors will be noted in your log file. What can one do to get around this?
Close any open Comsol sessions, and remove your .comsol directory located in your home directory. Make a backup and then delete everything in .comsol directory. > mv .comsol .comsol.backup > mkdir .comsol > ln -s /cluster/shared/your_utln/.comsol ./.comsol |
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This soft link will redirect comsol temp structures to your dir. in /cluster/shared/ . There is no disk quota on this filesystem.
Restart comsol and a new set of structures will be created. If you have requested Research Storage, you may use that for a longer term solution.
Note: You only need to do this once.
How do I run comsol in batch mode?
> module load comsol To run Comsol's tube1b.mph example: > sbatch ...options.... --wrap="comsol batch -inputfile tube1b.mph -outputfile tube1b-output.mph" |
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The solution will update a new version of the .mph file as output. You can read the output file into Comsol later for further post processing. There will be 3 output files and a directory created with name tube1b_files containing graphics and other files produced from the batch job.
Note, you may then log off while your job runs. YOu will be notified by email when the job is done.
How do I run comsol gui interface with software rendering?
Use the Comsol commandline option: -3drend sw
| > srun --pty --x11=first -p interactive comsol -3drend sw |
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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?
Imagemagick home, usage info and scripting links. Also local man pages on individual commands is available. Note Imagemagick is not a command. It is a suite of programs.
For example to use the convert program:
-bash-3.2$ module load ImageMagick How to display a picture using Imagemagick's display command without running the interface |
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NCAR related:
How do I start NCAR?
NCAR has lots of separate programs. These are all available to you after you setup the environment.
-bash-3.2$ module load NCAR
These executables are located at: /opt/shared/NCAR/5.2.1/bin
To submit a job, for example:
-bash-3.2$ sbatch ...options..... --wrap="ng4ex gsun01n.ncl"
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 |
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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?
You may send your R script to the slurm batch partition requesting access to a 32gig ram node, as an example:
| -bash-3.2$ sbatch --mem=32g -p batch --wrap="R CMD BATCH your-inputfile.r outputfilename" |
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For example, for the most part, option -p batch will place the job on nodes with 128gig memory allocations. Default units of memory is megabytes:
--mem= 30000 will request 30gig of ram. Use of the largemem partition should be considered when more total ram is required.
Where is the R documentation?
Extensive user documentation and tutorials are available on the R web site. There are many texts as well, here is nice example
And if you are an Spss or SAS user check this out.
And another source for comparative statistical package example usage can be found at UCLA
Where can I find command line R documentation?
> module load R
> srun ... R CMD INSTALL --help
Or use the man pages available at the linux shell prompt.
-bash-3.2$ man R
Also of note is the following online CodeSchool tutorial
Additional info on R can be found in the admin guide
How can I install an R package that is only available as a tar file?
Download the tar file and from within R try the following. Make changes to the utln and path to reflect the location. For example:
| > install.packages("/cluster/shared/utln/your_R_package.tar", repos = NULL) You may also install a package into another location: -bash-4.1$ srun ... R CMD INSTALL --library=/cluster/shared/utln /cluster/shared/utln/someRpackage.tar.gz Change the utln to your login name and adjust the filesystem path. |
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You will need to add the location to R search path for libraries.
Within R type:
> .libPaths() This is the default library system wide. Now to add the new additional location: > .libPaths(/cluster/shared/utln/) > .libPaths() |
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How can I install an R package from the CRAN repository?
From within R issue the commands:
> options(CRAN="http://cran.us.r-project.org/") Note that R package names are case sensitive. Alternatively, try: |
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Edit the utln to reflect your Tufts username and directory locations. Locations may be home directory or optional storage locations.
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.
How does one send a Stata batch job to the cluster compute nodes?
Make a stata do file with stata commands. To send:
| > sbatch --wrap="stata -b your_filename.do" |
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How to run stata interactively:
bash-4.1$ srun --pty --x11=first bash bash-4.1$ module load stata/13 bash-4.1$ xstata |
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What are the command line arguments to Stata?
To find out:
| > 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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For batch use:
> module load SAS >sbatch -p batch sas_u8 yourprogram.sas |
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You will get yourprogram.log and yourprogram.lst output files dumped to your current directoryinstall 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.
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.
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What is required to run Solar?
This program requires a user specific ID key. Send a request to cluster-support@tufts.edu requesting one. This can take up to 24 hours for the vendor to respond. This is a one time registration event. Once you have received your key:
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This example is straight forward. However enhancements to bsub options and to QIIME python functions will vary as will data sources locations.