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.

Ansys and Fluent related:

Now that Ansys purchased Fluent, how does one access Fluent functionality?
Most Fluent functionality is incorporated into Ansys WorkBench.

How do I run Ansys WorkBench interface?

-bash-3.2$ module load ansys
-bash-3.2$ srun ... runwb2

How can I read Ansys/Fluent/WorkBench and other docs while on the cluster?
You may run the Ansys Help application after you set up the module by:

Documents are version specific.

How do I run ansys in batch mode without using the Launcher if I already have an Ansys .dat file prepared?

Where can I find example ansys files?  Various directories for different versions are available.

/opt/shared/ansys_inc/v130/ansys/data/models/

The following Fluent related info may no longer work due to Ansys incorporation of Fluent into WorkBench.

How do I run a Fluent 2D parallel job?
Define the number of cpus(up to 8) within the bsub and fluent command line. The -n and -t arguments is the location to change the number of cpus.

-bash-3.2$ sbatch  ....sbatch_options  --wrap="fluent 2d -g -t8 -pib -mpi=intel  -i yourfluent.script"
Note: replace 2d with the appropriate fluent product, such as 3d and so on...

• What is a useful Fluent resource?*
  CDF-Online

How can I view the Fluent docs?
> module load fluent
> firefox file:///opt/Fluent.Inc/fluent6.3.26/help/index.htm

How do I get fluent command line options?
-bash-3.2$ srun ... fluent -help

How do I run the 2D or 3D fluent without asking the questions interactively?
-bash-3.2$ srun ... fluent 3d

How do I run Icepak?
Icepak is available from within Ansys WorkBench interface and as a command line standalone application. Start WorkBench in the normal fashion, as above. Icepak will be a choice on the Components Pane, click on it and then click setup. To run just the Icepak interface try:

-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..:

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?

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.

How can find out what abaqus licenses are available?

How do I run Abaqus version 6.9.2 CAE gui?

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.

Comsol related:

How do I run Comsol as an interactive  threaded job?

How do I run Comsol as a mpi parallel job?
Start Comsol as above, but add the command line options as follows:

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?

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?

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

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:

Matlab related:

• How do I get matlab command line options?*
  -bash-3.2$ srun ... matlab -help

How do I run a matlab batch job?

This will submit your code to the slurm partition you choose in the sbatch options. Matlab has several ways to direct output and results by use of matlab commands such as: diary, print and several other commands.

How do I speed up my Matlab calculations?
By default Matlab on the cluster has multi-thread parallelism enabled. Many Matlab functions will automatically use the threaded libraries. The number of threads obtained is equal to the number of cores on the node your job is placed on. Currently it is either 8 or 12. You no longer need to request exclusive node access via bsub.

How do I access the Parallel capability of Matlab?
Matlab can make use of MPI parallelism if you modify your code accordingly(see Parallel computing documentation within Matlab) and setup your session to instruct Matlab to use slurm. Currently Distributed Computing Engine Toolbox is licensed for 32 cores. It is strongly recommended to initially use 4, 8 or 16 cores while you explore how your code scales. Depending on what you are doing, execution times may not benefit from additional cores. To setup this feature, import a working configuration found at:

----Currently this has not been tested with slurm. Matlab R2015b, expected Fall 2015 will have slurm support -----

To view an older lsf based config file:

/cluster/shared/dmarshal/ISO/matlab-R2012-lsfconfig16.settings

Use Matlab's Cluster Profile Manager Tool to import the settings. Choose the menu options Parallel -> Import Cluster Profile and browse to the config file.

To test this out, you may run the Validation tests by choosing Start Validation. This will take several minutes and should result in five passed tests.

I want to run hundreds of matlab jobs using my matlab scripts. What do I need to know?
Your jobs will end up on a partition with a limit of 512 concurrent jobs/cores/user. 

Is Matlab MCR available to run compiled jobs?
Yes. You will need to load the MCR version corresponding to the Matlab version you used to compile your standalone executable. The Matlab example called magicsquare in the documentation can be used as an example. Once compiled the named executable, magicsquare, can be run without loading Matlab nor checking out licenses. Such an example is available below. Note, be sure to quote any needed command line arguments to your named executable.

How do I access the public domain Matlab toolbox EDGE?

EDGE has been installed into cluster directory /opt/shared/EDGE/1.02. To use it you'll need to launch MATLAB then change into the /opt/shared/EDGE/1.0/Matlab directory by issuing the following command at the Matlab prompt:

cd /opt/shared/EDGE/1.0/Matlab

Or better yet, add this path to your Matlab path within Matlab. Choose File -> Set Path and Add with subfolders.

To launch the Importer tool from within Matlab type on the command line:

semiauto

See the EDGE website for additional documentation.

How do I access the public domain Matlab toolbox WaveLab?
Load the corresponding module:
> module load Wavelab
> module load matlab

In Matlab choose File -> Set Path and then Add with Subfolders. Add the following: /opt/shared/Wavelab/Wavelab850

Then issue the command startup at the Matlab command line.

At this point you can issue commands and demos. Check the website for documentation.

Mathematica related:

Where can I find more Mathematica documentation?

The vendor's website and the online help in the application. In addition look at the broadcast section on the vendor site to view various movies on how to do many tasks in Mathematica. Also check out some paper based options.

My Mathematica notebook file doesn't work like it did before, what is up?
The following explanation is a good starting point to explore this issue.

How does one submit a mathematica batch job?
Suppose you have a text file called my_mathematica.m created with a text editor with the following tasks:

I get an error about Mathematica missing fonts,etc... What does this mean?

The cluster does not provide a Font Server supporting Mathematica font sets. Whereas a local install of Mathematica on your desktop includes this font set. Remote users need to provide access to the fonts locally.

For linux desktops, the easy way is to obtain the Mathematica helper program called, Mathematica Player. You may download this from the vendor website. Before you start Mathematica on the cluster for display on your computer, start the helper program locally. This will provide the font support.

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.

-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.

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:

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:

You will need to add the location to R search path for libraries.
Within R type:

How can I install an R package from the CRAN repository?
From within R issue the commands:

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:

How to run stata interactively:

What are the command line arguments to Stata?
To find out:

SAS related:

To run interactively:

For batch use:

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

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"

...