Application specific Information FAQs

Current list of software

You may check the current list of software under modules by:

-bash-3.2$ module available

When in doubt, always be version explicit in the named module you load.

The following table lists the new submission format for interactive sessions. In some cases the program name may have a version specific name. This in not an exhaustive list. For specific examples see the slurm page on this wiki.

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:

If you are uncertain of a suitable approach, please contact cluster-support@tufts.edu for assistance.

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.

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

BLACS
BLAS
Lapack
Scalapack
SuperLU
gsl
UMFPack

Corresponding installation locations are found at:

SuperLU: /opt/shared/SuperLU_4.0/lib
Scalapack: /opt/shared/scalapack-1.8.0/
Lapack: /opt/shared/lapack-3.2.1/
BLAS: /opt/shared/BLAS/
BLACS: /opt/shared/BLACS/LIB/
UMFPACK: /opt/shared/UMFPACK/5.5.1
Cula: /opt/shared/cula/

Installed library files for gsl, atlas and many others are located in /usr/lib64/.

Linkage to specific library file(s) can be found in their respective install location at /opt/shared/. Note, you need to specify which libary file, since in general there may be more than one. For example:

> ls /opt/shared/BLACS/LIB/*.a
/opt/shared/BLACS/LIB/blacsCinit_MPI-LINUX-0.a /opt/shared/BLACS/LIB/blacsF77init_MPI-LINUX-0.a /opt/shared/BLACS/LIB/blacs_MPI-LINUX-0.a

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.

Where are the blast commands located?
/opt/shared/ncbi-blast/bin

How do I start the serial version of MrBayes in interactive mode?
-bash-3.2$ module load mrbayes
-bash-3.2$ srun ... mb

How do I start the parallel version of MrBayes in interactive mode?
-bash-3.2$ module load mrbayes
-bash-3.2$ module load openmpi
-bash-3.2$ srun ... mb -openmpi

A similar solution is available for mpi using mvapich2.

How do I start Haploview?
-bash-3.2$ module load java
-bash-3.2$ module load haploview
-bash-3.2$ srun ... java -jar /opt/CTSA/Haploview4.1/Haploview.jar

How do I start plink?
plink requires the presence of two file with .ped and .med extensions. These correspond to the expected input format and corresponding data information. As an example copy the test.ped and test.med files from the installation directory to your home directory.
-bash-3.2$ cp /opt/CTSA/plink-1.06-x86_64/test* .
-bash-3.2$ module load plink
-bash-3.2$ srun ... plink --file test --noweb

How do I access online help for plink?
Command line help can be seen by:
-bash-3.2$ plink --help

Also check the plink site for additional up to date information.

HOw do I start velvet?
-bash-3.2$ module load velvet

Velvet has two versions: velvetg and velveth
To run one of these:
-bash-3.2$ srun ... velvetg (velvet arguments)
Without arguments velvet returns some command line options.

Where is velvet installed?
/opt/shared/velvet-1.0.02/

How do I start Merlin?
-bash-3.2$ module load merlin
-bash-3.2$ srun ... merlin

How do I start Pedcheck?
-bash-3.2$ module load pedcheck
For interactive command line use:
-bash-3.2$ srun ... pedcheck

Submitting as a batch job:
-bash-3.2$ srun ... pedcheck -p myfile.ped -d myfile.dat
where -p <pedigree file> and -d <locus file> are your input files.

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:

Key for username abcde01 is: 3gakiuxe
To register, log in with the specified username, run SOLAR, and use the
`register` command, for example:

solar> register 3gakiuxe

This will create a file named .solar_reg in the home directory.

How do I start Solar?
-bash-3.2$ module load solar
For interactive command line use:
-bash-3.2$ srun ... solar

Note, to follow the Readme file suggestions, run the .tcl scripts this way:
solar> makemibd
solar> doanalysis

How do I run Bowtie?
The install directory is /opt/shared/bowtie/bowtie-0.12.7/ where you will find sample indexes and reads in subdirectories of the same name. As an example, to run bowtie against ecoli indexes with a sample reads file:
-bash-3.2$ module load bowtie
-bash-3.2$ cp /opt/shared/bowtie/bowtie-0.12.7/indexes/e_coli.* .
-bash-3.2$ cp /opt/shared/bowtie/bowtie-0.12.7/reads/e_coli_1000.fq .
-bash-3.2$ srun ... bowtie e_coli e_coli_1000.fq > my_ecoli.outputfile

This will run an interactive job and dump the output to a text file, called my_ecoli.outputfile

How do I run Cufflinks?
The installed version has 3 binaries: cuffcompare cuffdiff cufflinks

Load the Cufflinks module to access them.
-bash-3.2$ module load cufflinks

To test it out, download the test data file from the cufflinks website or grab a copy from:
-bash-3.2$ cp /cluster/shared/dmarshal/cufflinks-test_data.txt .
To run an interactive job:
-bash-3.2$ srun ... cufflinks cufflinks-test_data.txt

How to run Tophat?
All tophat binaries are located at:
/opt/shared/tophat/1.0.14/bin/

To access them and the bowtie dependices:
-bash-3.2$ module load tophat
-bash-3.2$ module load bowtie

To test it out, download the test data set from the tophat site or grab the tar file from:
-bash-3.2$ cp /cluster/shared/dmarshal/ISO/tophat_test_data.tar .
-bash-3.2$ tar xvf tophat_test_data.tar
-bash-3.2$ cd test_data/

-bash-3.2$ srun ... tophat -r 20 test_ref reads_1.fq reads_2.fq

How to run IMa2?
-bash-3.2$ module load ima2/8.27.12

Refer to module output for explicit versions:
-bash-3.2$ module available

How to list command line arguments for IMa2?
-bash-3.2$ srun ... IMa2

How to run a typical IMa2 example?
-bash-3.2$ srun ... IMa2 -iyour_input_data -oyour_output_file_name -q2 -m1 -t3 -b10000 -l100 -s123
Note those commandline options are only for illustration, yours may be very different.

Documentation may be found on the IMa website.

How to get started with bioPerl?
Check the corresponding BioPerl wiki

How to start Structure and the interfaces?
Check the public Structure website for the manual. A parameter file is needed in both cases of usage below.

For the graphical interface:
-bash-4.1$ module load structure-java/2.3.4
-bash-4.1$ srun ... java -jar /opt/shared/structure/2.3.4/class/Structure.jar

For the command line text version:

-bash-4.1$ module load structure
-bash-4.1$ srun ... structure

How to start Desmond?

-bash-4.1$ module load Schrodinger

To see command line arguments for desmond, type:

-bash-4.1$ srun ... desmond

Several arguments are need to specify a proper desmond run.
Check the manual on the Desmond website for details.

Where do I find the PolyPhred programs and how do I access them?
The program binaries are in /opt/shared/phred/. You must load the phred module for access.

-bash-3.2$ module load phred

How does one work with diyabc on the cluster?
The cluster version is simply two linux executables, diyabc_sim and diyabc_cat. The first is for simulation generation and the second is for combining output reference table files. Unlike the Windows version, these are command line tools without a gui user interface. The manual pdf available on the diyabc website details usage. The following is how to run the example from the manual.
-bash-3.2$ module load diyabc
Copy the two input files to your local directory:
-bash-3.2$ cp /opt/shared/diyabc/ga_* .
-bash-3.2$ sbatch ....options.... --wrap="diyabc.output diyabc_sim ga_001 1 1000 4"

Output files can be combined for transfer back to you your PC version for post processing and display.

How is QIIME started?
This functionality is built upon python modules and codes. The environment to support it has many dependencies that are satisfied by loading the QIIME module.

-bash-3.2$ module load QIIME

To submit a job from the QIIME tutorial:
-bash-3.2$ sbatch ....options....   --wrap="check_id_map.py -m Fasting_Map.txt -o mapping_output"

This example is straight forward. However enhancements to bsub options and to QIIME python functions will vary as will data sources locations.