Installed Applications

Software packages maintained by SaM are installed using Environment Modules. While there may be several versions of each package installed on Frank, they all fall into one of the following categories. To see the full list of packages in each category, use module avail <category>. To see the full list of versions for each package use module avail <package>.

Compilers
gcc
intel
pgi
gcc
Scripting
perl
python

Matlab

Matlab 2012a has been installed on Frank, but the following licensing restrictions apply:

  • All students enrolled at the Oakland campus may use Matlab free of charge.

  • A per-user fee of $100 is required for Faculty, Staff, and postdoctoral researchers. A license must be purchased for each user.

  • Faculty, Staff, and postdoctoral researchers in the Swanson School of Engineering may use Matlab free of charge because the school has purchased the licenses.

If one of the above criteria has been met, please submit a ticket to request access.

See the example job script for information about how to run Matlab on Frank.

Gaussian

Gaussian 09 has been installed on Frank. The license permits access to students, faculty and staff of the Oakland campus. Please submit a ticket to request access.

VASP

VASP has been installed on Frank. In order to use VASP a license must be purchased. Once a license has been purchased the licensee must submit a ticket with the PittIDs of the users who are allowed to run VASP.

Turbomole

Turbomole 6 has been installed on Frank. Any group with a valid license should submit a ticket to request access.

Installing perl module ?

Hi, there,

My name is Charles and I am from Pitt biostatistics department Dr. George Tseng's group. Our lab needs to use a tool called "HLAminer" for human leukocyte antigen calling which needs the perl module called "Bio::SearchIO" (part of Bioperl, so bioperl is definitely needed). However, it seems the installation of perl modules would need sudo authorization which I do not have on Frank.

Since we need to use the TCGA raw data (bam files) from PGRR so we cannot copy the data to other servers. So we have to run the tool on Frank, which will need those modules to be installed.

Thanks so much and any help would be greatly appreciated.

Best, Charles