Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing,
communications and data analytics.

SVDetect

 

SVdetect is a tool to detect structural variations from paired-end and mate-pair sequencing data.

 

Installed on blacklight

 

Other resources that may be helpful

Websites: http://svdetect.sourceforge.net/Site/Home.html and http://svdetect.sourceforge.net/Site/Manual.html

 

Running SVDetect

1. Create a batch job which

    1. Sets up the use of the module command in a batch job

    2. Loads the SVDetect module

              module load SVDetect

    3. Includes other commands to run SVDetect

2. Submit the batch job with the qsub command

 

Cushaw

 

Cushaw is an open-source, parallelized, sensitive and accurate short-read aligner.

 

Installed on blacklight

 

Other resources that may be helpful include

Website: cushaw3.sourceforge.net/homepage.htm

 

Running Cushaw

1. Create a batch job which

      1. Sets up the use of the module command in a batch job

      2. Loads the cushaw module

        module load cushaw

      3. Includes the other commands to run cushaw

2. Submit the batch job with the qsub command

To see the usage of the various cushaw commands issue the commands

    cushaw3 index cushaw3 align
    cushaw3 calign

 

 

FLUENT example files

Note: you will probably need to edit the job script for it to run succesfully.  Some things that may need to change:  your file names may be different;  your files may be stored in a different directory structure;  your job might need more time to complete; your job may require more or fewer cpus.  There may be others.

Be sure to tailor the script to suit your situation before submitting a job.  If you don't,  you may use up some of your allocation on a job that fails. If you have any questions, please contact remarks@psc.edu.

 

Files include:

fluent.pbs, PBS job script View  
pipe.cas, input case file    
pipe.in, input file View  
fluent.out, standard output and error from job View  

ANSYS example files

Note: you will probably need to edit the job script for it to run succesfully.  Some things that may need to change:  your file names may be different;  your files may be stored in a different directory structure;  your job might need more time to complete; your job may require more or fewer cpus.  There may be others.

Be sure to tailor the script to suit your situation before submitting a job.  If you don't,  you may use up some of your allocation on a job that fails. If you have any questions, please contact remarks@psc.edu.

 

Files include:

ansys.pbs, PBS job script View  
bm-8.dat, input data file View  
ansys.out, standard output and error from job View  

FFTW example files

Note: you will probably need to edit the job script for it to run succesfully.  Some things that may need to change:  your file names may be different;  your files may be stored in a different directory structure;  your job might need more time to complete; your job may require more or fewer cpus.  There may be others.

Be sure to tailor the script to suit your situation before submitting a job.  If you don't,  you may use up some of your allocation on a job that fails. If you have any questions, please contact remarks@psc.edu.

 

Files include:

fftw3.job, PBS job script View  
f77_test.F, Fortran source code View  
fftw3.out, standard output and error from job View