UIT Research Computing Resources

Note: The following information is temporary and meant to support the new replacement research cluster. A new site will replace this in a couple of months.

The following communication was sent to cluster users introducing the upcoming changes:
On September 15, 2008, University Information Technology (UIT) will be upgrading its high-performance computing research cluster to accommodate growing research demands on all Tufts campuses. We would like to inform you of some of the new features you can expect:

Over the past few months researchers in various Tufts departments have helped UIT test the new research cluster. This beta testing program helped us confirm that the new environment allows for operations and results similar to the old cluster. We would like to take this opportunity to thank them in the name of UIT and the Tufts research community for their help.

For additional information, please contact Lionel Zupan, Associate Director for Research Computing, at x74933 or via email Lionel.Zupan@Tufts.edu.

Tufts UIT Research computing options

1. Tufts High-performance computing research cluster

What is a Cluster?

Cluster computing is the result of connecting many local computers (nodes) together via a high speed connection to provide a single shared resource. Its distributed processing system allows complex computations to run in parallel as the tasks are shared among the individual processors and memory. Applications that are capable of utilizing cluster systems break down the large computational tasks into smaller components that can run in serial or parallel across the cluster systems, enabling a dramatic improvement in the time required to process large problems and complex tasks.

Tufts Linux Research Cluster

The Tufts Linux Research Cluster is comprised of 40 identical IBM Linux systems (compute nodes) interconnected via an Infiniband network. Each cluster node has eight  2.8Ghz Intel Xeon CPUs and 16 or 32 gigabytes of memory for a total of 320 compute cores. The Linux operating system on each node is RedHat 5 configured identically across every machine. In addition there is a login node and a management node supporting the compute node array. Client/user workstations access the cluster via the Tufts LAN or remotely with ssh. The user/login node has an additional network interface  that connects to the compute nodes using private non-routable IP addressing via the Infiniband hardware. This scheme allows the compute nodes to be a "virtualized" resource managed by the queueing software LSF, and abstracted away behind the user node. This approach also allows the cluster to scale to a large number of nodes and provides the structure for future growth.

The login node of the cluster is reserved for the use of compilers, running shell tools, and launching and submitting programs to compute nodes. The login node is not for running long running programs, etc... for computing purpose, please use the compute nodes and various queues.

Account Information

UIT Support Center (UITSC) provides account management assistance. Access to the cluster requires a Research Cluster account. Faculty, other staff, and students are required to fill out a UIT Research Computer Account Application form. For all campuses, contact the UITSC at x7-3376 or by email at uitsc@tufts.edu for further assistance.

Alternatively, you can download a copy of the UIT Research Computer Account Application:

Click here to download a copy in Microsoft Word format.

Click here to download a copy in Adobe PDF format.

Note: Students must have their application form signed by a faculty member or advisor.

All completed applications should be returned to the UITSC, either by fax to 617-627-3205 or interoffice or US mail to:
169 Holland Ave., Room 301
Somerville, MA 02144

How to connect to the cluster?

What is the name of the cluster?


What is the Tufts responsible use policy?

Find it here.

How do I login to the cluster?

Use your Tufts UTLN and LDAP password associated with your Tufts email.

What is a Tufts UTLN?

This is your Tufts username issued for purposes of Tufts email.

I have forgotten my password, how do I change my UTLN password?

If you have forgotten your Trumpeter email password and need assistance
resetting it, please contact one of the following:

A&S Students: Student E-Mail Support <student-email@ase.tufts.edu> or

A&S Faculty & Staff: ITS Help Desk <helpdesk@ase.tufts.edu> or 617-627-5898

Or visit Trumpeter email website to assist yourself.

How to connect to the cluster with a PC?

UIT research servers require an ssh connection to a host providing shell access. Use of Cygin ssh, SecureCRT, Putty, etc... will work. Other forms of connection such as XDM, rsh, rlogin, telnet are not supported.

What connection protocols are supported on the cluster?

ssh, ssh2, sftp, scp

How to connect to the cluster with a Mac?

Open an xterm window and use ssh.

> ssh -Y cluster.uit.tufts.edu

Provide your username and password (same as your email).

How to connect to the cluster under Linux?

Open a local shell window or xterm and connect with:

> ssh -Y cluster.uit.tufts.edu

Provide your username and password (same as your email).

Can I connect to the cluster from home or while I am traveling?

Yes, use an ssh based login solution such as ssh, SecureCrt, etc...

Do I need SecureCRT to connect to a host?

No, if you use Cygwin you do not need SecureCRT. If you choose to use it, you will likely need a windows based X server such as Exceed or Xwin32 or similar if you expect to display graphics.

Contribute your own nodes to the new research cluster

Researchers that need their own high-performance computing (HPC) resources (and are applying for external grant funding to do so) may wish to consider contributing additional nodes to the research cluster rather than to develop and support their own HPC infrastructure. The research cluster has been designed to allow for this kind of compute node expansion. The obvious advantage to a researcher is that one does not have to support a separate computing resource, obtain additional licensing, etc.

In order to participate, additional nodes need to be of a certain kind, consistent with the current cluster design. In addition, a special LSF queue will be structured to allow one or more designated researchers priority access to the contributed nodes. In return, when those nodes are unused, they will become part of the larger pool of LSF managed compute node resources available to the Tufts research community.

For additional information, please contact Lionel Zupan, Associate Director for Research Computing, at x74933 or via email Lionel.Zupan@Tufts.edu.

Software request policy

Please send your request via email to cluster-support@tufts.edu and address the following questions:

Cluster and Storage Options

All cluster accounts are created with a fixed 200 MB home directory disk quota.

In addition, a directory is automatically created in filesystem /scratch on the head node and each compute node. The directory is named with your Tufts UTLN; such as /scratch/utln/. There is no quota and no backup for files located there. Typically ~100+ gig is available. In addition this file system is subject to automated cleaning based on a moving window of 28 days. You may use this for temporary storage supporting your research computing needs. Note: this storage is not available to your desktop as a mounted file system, but you can access it via your ssh login or through a file transfer program such as WinScp.

For additional temporary storage beyond what is offered in /scratch, Tufts UIT provides a 2TB file system called /cluster/shared/. Access to this storage is by request and with suitable application requirement/justification. The naming convention is the same as /scratch/ and thus /cluster/shared/utln/. Please work out of your named directory.

Finally, another available file system is /tmp. This file system is used by applications and the operating system for temporary storage. Please note that it is under the same 28 day cleaning rule as /scratch.

Research Storage Solution

Tufts UIT provides a networked storage solution to faculty researchers who request it based on their identified needs. This solution is often used in support of grant based projects that produce large size of data sets, and these data sets need both to be accessed by multiple users and to be backed up. Such networked storage solution usually supports a small lab where multiple persons may interact with research data from computers at different locations. Another possibility is to request that the storage be made available to one or more accounts on the research cluster.

For additional information, please contact Lionel Zupan, Associate Director for Research Computing, at x74933 or via email Lionel.Zupan@Tufts.edu.

To request storage

Storage User guide

Research database (HPCdb) node

Cluster users may request access to mySQL database for supporting their research computing needs. Requests are treated like software requests. Please reference the Software Request Policy statement in this document.

Network Concurrent Software Licenses

Network concurrent licenses are a class of licenses that grants access to a network attached software client installed on remote hardward. However, not all cluster software is of this type. Concurrent network licenses are chosen to allow flexible use by a larger user-base than the number of licenses offered. As a result, most of the licensed software on the cluster is "shared" within Tufts. In effect, access is possible for Tufts owned workstations found in various computer labs and faculty desktops.

The following software license count is as follows:


Concurrent seat count














1 user - 16 cpus






32 core license - default license 8 cores per user


2 user - 8 cpus



Portland Compilers




Software on the research cluster is supported by a 3-head redundant FlexLM license server. This makes possible uninterrupted 24x7 license service requests by software clients. Setup and additional information can be found here or here.
NOTE: Authenticated access is restricted to the Tufts network domain.

Mathematica Faculty Home Use Program

Tufts Mathematica license allows for Tufts' participation in the vendor's Home Use Program. Full-time Tufts Faculty may obtain access to a stand-alone copy from the vendor. The version the vendor supplies is a stand alone version(with it's own license). Under this program, this is a transaction between the faculty member and the vendor. The vendor supplied individual password and media expire in conjunction with the Tufts license each year on March 31st. It is up to the requesting faculty member to contact Mathematica to receive an updated password. It is not automatic. If no action is taken, your license expires. In addition, upgrades are free, but you will need to request those as well via the vendor home-use website. Note, the number of faculty that may participate is capped to the size of our concurrent license and is first come first serve. The following license id is needed to register: L2806-0850

Faculty may register here.

Support venue

If you have any questions about cluster related usage, applications, or assistance with software, please contact cluster-support@tufts.edu.

Cluster user software environment

Each cluster shell account has a default bash shell upon login. This should meet the needs of most users. To change to other shells, such as csh, zsh, tcsh, use the chsh command. Additional info on the chsh command is available through the man pages.

Module management for software package user environment

Software environments are managed through the use of the module approach. Many commercial packages and some public domain software require various settings that can often lead to clashes in the user shell environment. In order to use a package on the cluster, you must load that package's module. For example to use matlab:

> module load matlab

before running the command matlab:

> matlab

To see what packages are under module control:

> module avail

To unload a package from your environment:

> module unload matlab

To see loaded packages in your environment:

> module list

To see unload all packages in your environment:

> module purge

Currently there are some packages that are not under module control; such as DEFORM-3d, Materials Studio and maybe others.

Installed Software Applications:

Here is a list of all 64-bit applications currently installed on our research cluster:


Platform Computing, Inc.'s LSF (Load Sharing Facility) software is a distributed load sharing and batch queuing suite of applications that can dispatch user requests to compute nodes in accordance with a Tufts-defined policy. It manages, monitors, and analyzes resources and load on the cluster. Platform LSF is layered in a way that allows it to sits on top of and extend the operating system services, speaking to the competing needs of resource management on the cluster. LSF commands must be used to submit batch jobs and assign interactive jobs to processors. bsub and lsrun are the usual command tools for this. It's important to note that cluster compute nodes are the only targets under LSF control. Jobs are not submitted to computers outside of the cluster. For more information about LSF command usage and job submission, you can read the man pages (example: type man lsrun at the cluster prompt). Most commands begin with the letter 'b' such as: bsub, bkill, lsrun, and bjobs.


Ansys is a suite of finite element based applications that provide real-world simulations of structural, thermal, electromagnetic and fluid-flow behavior of 3-D product. All Ansys products integrate with CAD environments.


Abaqus is a suite of applications used by many in the engineering community for the analysis of multi-body dynamics problems that aid the medical, automotive, aerospace, defense, and manufacturing community.

Fluent is a Computational Fluid Dynamics (CFD) software package commonly used in engineering education for research in fluid mechanics. The Fluent University Program provides universities with special, low-cost access to many of Fluents full-featured general use products. Each package includes a preprocessor, solver, and postprocessor.


MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages, such as C, C++, and Fortran. Extensive documentation and tutorials are provided within Matlab. The following Matlab toolboxes are licensed:

Control System Toolbox
Distributed Computing Toolbox
Financial Toolbox
Fuzzy Logic Toolbox
Image Processing Toolbox
MATLAB Compiler
Neural Network Toolbox
Optimization Toolbox
Partial Differential Equation Toolbox
Real-Time Workshop
Signal Processing Toolbox
Simulink Control Design
Spline Toolbox
Statistics Toolbox
System Identification Toolbox
Virtual Reality Toolbox
Wavelet Toolbox


Comsol is specifically designed to easily couple transport phenomena, including computational fluid dynamics (CFD) as well as mass and energy transport to chemical-reaction kinetics and process-related modeling. Licensed Modules include: MultiPhysics, Chemical Engineering, Acoustics, Structural Mechanics, Script.


Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.


Stata SE is an integrated statistical package for Windows, Macintosh, and Unix platforms. More than just a statistical package, Stata is also a full data-management system with complete statistical and graphical capabilities. It features both X-window and text user interfaces.


DEFORM (Design Environment for FORMing) is an engineering software environment that enables designers to analyze metal forming processes. DEFORM-3D is also a simulation system that is designed to analyze the three-dimensional flow of complex metal forming processes, allowing for a more complex analysis of shapes than 2D models can provide.


R is a widely available object oriented statistical package. The current list of installed packages can be found in directory /usr/lib/R/library/. This represents a base installation suitable for most routine tasks, however not all available packages as found on the web site are installed. If some other R package is needed, please make a software installation request as outlined above. Extensive user documentation and tutorials are available on the web site.

Materials Studio

Materials Studio® is a validated software environment that brings the world's most advanced materials simulation and informatics technology.
It dramatically enhances your ability to mine, analyze, present, and communicate data and information relating to chemicals and materials. Materials Studio's accurate prediction and representation of materials structure, properties, and inter-relationships provides valuable insight. The following Materials Studio products are available: CASTEP, DMol.

Dacapo (available Fall 2008)

Dacapo is a total energy program based on density functional theory. It uses a plane wave basis for the valence electronic states and describes the core-electron interactions with Vanderbilt ultrasoft pseudo-potentials.


Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.


Maple is a well known environment for mathematical problem-solving, exploration, data visualization, and technical authoring. In may ways it is similar to Mathematica and Matlab.

The cluster has a 32 core StarP license. Star-P software is a client-server parallel-computing platform that's been designed to work with multiple Very High Level Language (VHLL) client applications such as MATLAB®, Python, or R, and has built-in tools to expand VHLL computing capability through addition of libraries and hardware-based accelerators.


MCCE (Multi-Conformation Continuum Electrostatics) is a biophysics simulation program combining continuum electrostatics and molecular mechanics.


WPP is a parallel computer program for simulating time-dependent elastic and viscoelastic wave propagation, with some provisions for acoustic wave propagation. WPP solves the governing equations in displacement formulation using a node-based finite difference approach on a Cartesian grid.  WPP implements substantial capabilities for 3-D seismic modeling,

Mathematica and gridMathematica

Mathematica, advertised as a one stop for technical work that integrates a numeric and symbolic computational engine, graphics system, programming language, documentation and advanced connectivity to other applications. Not only does this application have parallel functionality built into it from the ground up. The wolfram.com web site has extensive documentation, including numerous detailed tutorials.


ImageMagick® is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to translate, flip, mirror, rotate, scale, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.


ParaView is a multi-platform visualization application designed to visualize large data sets.

GGobi is an open source visualization program for exploring high-dimensional data. It provides highly dynamic and interactive graphics such as tours, as well as familiar graphics such as the scatterplot, barchart and parallel coordinates plots. Plots are interactive and linked with brushing and identification.


Spice is a general-purpose electric circuit simulation program for nonlinear dc, nonlinear transient and linear ac analysis.

Python Compiler

Installed python modules: matplotlib, numpy, Networkx, Biopython

Perl Compiler

Perl is a stable, cross platform programming language. Perl is extensible. There are over 500 third party modules available from the Comprehensive Perl Archive Network (CPAN).

Portland Compilers

Portland Group compilers are available for use on the cluster. They are not part of the default environment on the head node, but they can be accessed by use of the module command. Fortran, C and C++ compilers and development tools enable use of networked compute nodes of Intel x64 processor-based workstations and servers to tackle serious scientific computing applications. PGI compilers offer world-class performance and features including auto-parallelization for multi-core, OpenMP directive-based parallelization, and support for the PGI Unified Binary™ technology.

The cluster has jdk version 1.6.0_07 for x86_64 hardware installed and under module control.
For command line options:
-bash-3.2$ java -h
Local documentation via man pages:
-bash-3.2$ man java
For useful troubleshooting and other Java docs:

GCC (C, C++, Fortran) compilers

The cluster 64-bit login node requires Gnu GCC 64-bit compiler and as a result becomes the default native compiler. No Module setup is required.
Documentation is available at GCC online documentation or from the following man pages:
> man gcc
> man g77

Lisp compiler

Steel Bank Common Lisp (SBCL) is an open source (free software) compiler and runtime system for ANSI Common Lisp. It provides an interactive environment including an integrated native compiler, a debugger, and many extensions.

Intel compilers

Tufts licenses the Intel compilers for use on the cluster. Access is via the following two commands:

ifort - Intel fortran compiler
icc - Intel C compiler

Local Fortran documentation in HTML format can be found at:

>firefox file:////opt/intel/fce/10.1.017/doc/main_for/index.htm

or via manpages depending on what Module is loaded:

> man icc
> man ifc

Fortran quick reference is available by typing:

> man ifort
> ifort -help

Text Editing tools:

emacs, vi, vim, nano, nedit   

FireFox browser:

A web browser is provided to allow viewing of locally installed software product documentation. Access to the internet is restricted.

Frequently Asked Questions - FAQs:

What are some reasons for using the cluster

Parallel programming related information

What is MPI?

MPI stands for Message Passing Interface. The goal of MPI is to develop a widely used standard for writing message-passing programs.

What installed programs provide a parallel solution?

The following provide MPI based solutions:  Abaqus, Ansys, Fluent, gridMathematica, StarP/matlab, StarP/python, paraview, MaterialStudio, Dacapo

The following provide thread based parallelism: comsol, matlab

When does 64bit computing matter?

When there is a need for memory and storage beyond the 32bit barriers.

Is it possible to run linux 32-bit executables on the cluster?

There is a good chance that it will succeed. But there might be other issues preventing it from running. Try it out...

Where can I find additional information about MPI?





What is a good web based tutorial for MPI?


How do I run a compiled mpi based program?

-bash-3.2$ bsub -I -q parallel -a openmpi -n 8 mpirun.lsf yourcode

Note: -bash-3.2$ is the default prompt for your bash shell on the cluster. The command is what follows it.

This will submit yourcode executable to the parallel queue using openmpi and requesting 8 cpus.

What mpi software is available?

Openmpi and Mvapich is offered and under module setup control.

Can you recommend a good text on MPI?
The Tisch Library has:
William Gropp, Ewing Lusk, Anthony Skjellum, Using MPI: Portable Parallel Programming with the Message-Passing Interface, Second Edition, MIT Press, 1999, ISBN: 0262571323.

Account related FAQs:

What is the name of the cluster?


What is the Tufts responsible use policy?

Find it here.

How do I login to the cluster?

Use your Tufts UTLN and LDAP password associated with your Tufts email.

What is a Tufts UTLN?

This is your Tufts username issued for purposes of Tufts email.

I have forgotten my password, how do I change my UTLN password?

If you have forgotten your Trumpeter email password and need assistance
resetting it, please contact one of the following:

A&S Students: Student E-Mail Support <student-email@ase.tufts.edu> or

A&S Faculty & Staff: ITS Help Desk <helpdesk@ase.tufts.edu> or 617-627-5898

Or visit Trumpeter email website to assist yourself.

When I login I see the following -bash-3.2$ , what is it?

This is the default prompt for your bash shell. This is where you issue linux commands.

How to transfer files?

Any file transfer agent program supporting either scp or sftp protocol will work. There are many freeware choices.WinScp for WindowXP is very good.

SecureCRT also provides sftp file transfers. The graphical file transfer program filezilla is available to linux and unix users.

What is my home directory?

This is where you have access to storage that allows you to read, write and delete files. The path to your home directory is: /cluster/home/xx/yy/utln

where xx is the first letter of your first name

where yy is the first letter of your last name

where utln is your Tufts issued username for purposes of email.

What is the disk quota on home directories?

All accounts are created with a 200 megabyte quota.

May I request a disk quota increase to my home directory?

Often the best solution is to use cluster specific temporary storage options in conjunction with your desktop. Programs such as WinScp allow you to drag and drop files between the cluster and your desktop. You may use /scratch/utln for additional short term storage or if you require 100's of gigabytes, consider requesting access to /cluster/shared/ storage.

How do I find out how much total diskspace I have used?

Login to your account and type the following:

-bash-3.2$ du -sk


-bash-3.2$ quota

You may also use WinScp or other such tools to view file summaries.

How do I obtain access to additional temporary storage on file system /cluster/shared/ ?

Please send your request via email to cluster-support@tufts.edu.

What is the local storage automated cleaning policy?

The head node of the cluster and compute nodes provide three areas of temporary storage separate from your home directory. File systems /scratch/utln/, /cluster/shared/utln/ and /tmp are available to support different storage needs. Each is subject to automated cleaning rules. All files older than 28 days are deleted and these file systems are not backed up!

Connecting to the cluster FAQs

How to connect to the cluster with a PC?

UIT research servers require an ssh connection to a host providing shell access. Use of Cygin ssh, SecureCRT, Putty, etc... will work. Other forms of connection such as XDM, rsh, rlogin, telnet are not supported.

What connection protocols are supported on the cluster?

ssh, ssh2, sftp, scp

How to connect to the cluster with a Mac?

Open an xterm window and use ssh.

> ssh -Y cluster.uit.tufts.edu

Provide your username and password.

How to connect to the cluster under Linux?

Open a local shell window or xterm and connect with:

> ssh -Y cluster.uit.tufts.edu

Provide your username and password.

Can I connect to the cluster from home or while I am traveling?

Yes, use an ssh based login solution such as ssh, SecureCrt, etc...

Do I need SecureCRT to connect to a host?

No, if you use Cygwin you do not need SecureCRT. If you choose to use it, you will likely need a windows based X server such as Exceed or Xwin32 or similar if you expect to display graphics.

X based graphics FAQs

What is an X Server:

This is a program that runs on your workstation/desktop OS that 'listens' for X-Window transmissions sent from the cluster and redisplays these on your workstation. These transmissions are generated by an application running on a host that you are connected to. For example, if you intend to use Ansys on the cluster, you need to display the Ansys gui interface locally on your desktop.

What X server is needed for WinXP desktops?

There are many free and commercial X server programs. UIT recommends Cygwin. Commercial options include Exceed, XWin32, and others...

Where do I get Cygwin?

A&S Cygwin installation documentation can be obtained here.

What Cygwin programs do I install?

Install base Cygwin, OpenSSH, and OpenGL at a minimun.

How do I connect to the cluster using Cygin?

Connect with ssh to the head node of the cluster:

> ssh -Y -C yourusername@cluster.uit.tufts.edu

How can I make sure Cygwin is working with the cluster?

To test the cygwin X server,try a simple cluster-side X-window application:

> xclock

A clock should appear on your desktop.

What X server is needed for a Mac?

An X server is either provided with Mac OS X (X11 in newer versions) or when you install the Mac X developement tools (older versions).

What X server is needed for a desktop linux user?

Linux distributions come with Xwindows which provides X server support.

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. 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.

Application specific Information FAQs

How do I run program R interactively?

For interactive use type R-gui . The program will be dispatched on some compute node and any produced graphics will be displayed.

-bash-3.2$ R-gui

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 normal queue, as an example:

-bash-3.2$ bsub -q normal -R bigmem R CMD BATCH your-inputfile.r outputfilename

How do I run an MPI parallel program I compiled for use on 8 cpus?

For example, it the program requires interactive keyboard input, try:

-bash-3.2$ bsub -q express -Ip -n 8 mpirun.lsf ./yourprogram

How do I run Maple?

Maple has two interfaces. One is text based and the other is a graphical gui.

Text based:

-bash-3.2$ maple


-bash-3.2$ xmaple

How do I run gridMathematica?

How do I run StarP and Matlab?
-bash-3.2$ module load starp
-bash-3.2$ starp

StarP access is first come first served subject to load constraints and how many cores are requested. Note, StarP start up time delay on the order of 60+ seconds is normal. You may have to retry if you receive an error. This behavior is due to the LSF load balancing behavior during the job placement task. The default behavior of StarP is to use 8 cores. You may request up to 32 cores. For initial developement purposes please obtain proof of concept success with 8 cores before scaling.

For example, to use 16 cores:
-bash-3.2$ starp -p 16

IMPORTANT: Before running StarP, make sure that Matlab's Multithreading option is disabled. You can check this via Matlab's (File->Preferences->Multithreading) choice.

Where can I find StarP documentation?
You can find it on the cluster or the vendor's website. On the cluster it is located at /opt/starp/2.6.2/doc/Manuals/. Both html and pdfs are available. For html try:

-bash-3.2$ firefox file:///opt/starp/2.6.2/doc/Manuals/doc.html

Where can I find Chimera documentation?
If the gui and Help pull down option fails to open a browser then try:
-bash-3.2$ firefox file:///opt/chimera64/share/chimera/helpdir/index.html

How do I run StarP and Python?

How do I run a ggobi?

-bash-3.2$ module load ggobi

-bash-3.2$ ggobi

How do I run a Matlab?

-bash-3.2$ module load matlab

-bash-3.2$ matlab

How do I run a matlab batch job?

-bash-3.2$ module load matlab

-bash-3.2$ bsub -q long "matlab -nojvm -nodisplay < your-matlab-code.m"

This will submit your code to the long queue. Matlab has several ways to direct output and results by use of commands such as: diary, print and other commands.

How do I speed up my Matlab calculations
By default matlab on the cluster has multithreading parallelism turned off. To enable it within Matlab choose: (File->Preferences->Multithreading). The alternative is to use StarP.

How do I run MaterialStudio?

How do I run Fluent?

-bash-3.2$ module load fluent

-bash-3.2$ fluent

How do I run a Fluent 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$ bsub -I -n8 -a fluent fluent 2d -g -t8 -pib -mpi=intel -lsf -i yourfluent.script
Note: replace 2d with the appropriate fluent product, such as 3d and so on...

How do I run Fluent's Gambit?

-bash-3.2$ module load fluent

-bash-3.2$ Gambit

How do I run Abaqus?

How do I read Abaqus documentation?

-bash-3.2$ module load abaqus

-bash-3.2$ abaqus doc

How do I run Mathematica?

-bash-3.2$ module load mathematica

For the gui interface:

-bash-3.2$ mathematica

For the text command line interface:

-bash-3.2$ math

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.

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 do I run Deform3D?

-bash-3.2$ module load deform

-bash-3.2$ deform3

Where do I find Deform documentation?

Both Html and Pdf manual versions are available at:

Is there a way to read the manuals on the cluster?

-bash-3.2$ firefox file:///opt/deform/3d/v61/MANUALS/HTML/DEFORM-3D.htm

How do I run Comsol?

-bash-3.2$ module load comsol

-bash-3.2$ comsol

How do I run Comsol as a parallel job?
Start Comsol as above, but add the command line options as follows:
-bash-3.2$ comsol -np 8 -mpmode owner

Then in the gui setup for Solver parameters, change the default Solver to the Parallel Direct Solver(Pardiso) and rerun your model.

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.

Linux information FAQs

Where do I find basic unix/linux resources?

There are many web based tutorials and howto's for anything linux oriented. Some sites of interest:

linux-tutorial, Unix info , linux.org

What are some of the basic linux and related commands?

Most usage is centered around a dozen or so commands:

ls, more, less, cat, nano, pwd, cd, man, bsub, bkill, bjobs, ps, scp, ssh, cp, chmod, rm, mkdir, passwd, history, zip, unzip, tar, df, du
See the man pages for complete documentation. Here is a short description of some.

Basic Unix Commands

Action Needed



Display contents of a file


cat filename

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Copy a file


cp [-op] source destination


Change file protection


chmod mode filename or
chmod mode directory_name

Change working directory


cd pathname

Display file (/w pauses)


more filename

Display first page of text


less filename

Display help


man command or
man -k topic

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="507590e1-9e2e-437d-b2e5-8b7bbc5a83f9"><ac:plain-text-body><![CDATA[

Rename a file


mv [-op] filename1 filename2 or
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<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="8a9ad447-3062-4d29-bb2d-55702188e35b"><ac:plain-text-body><![CDATA[mv [-op] filename directory


Compare file


diff file1 file2

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Delete file


rm [-op] filename


Create a directory


mkdir directory_name

Delete a directory /w files in it

rmdir -r

rm -r directory_name

Delete a directory


rmdir directory_name

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Display a list of files


ls [-op] directory_name


Change the password



Display a long list (details)

ls -l

ls -l directory_name

Display current directory



What is a man page?

man pages are linux/unix style text based documentation. To obtain documentation on the command cat:

> man cat

>xman is the command for the x-based interface to man.

> man man is the man documentation.

> man -k graphics finds all related commands concerning graphics.

Are the compute nodes named differently from the old cluster compute nodes?

Yes. You should not hard code the names anywhere. The convention is node01, node02, ...

Some applications required a login to former node compute01, is this still the case?


Why do I have to submit jobs to compute nodes?

The cluster has been configured to allocate work to compute nodes in a manner that provides efficient and fair use of resources. A job queueing system called LSF is provided as the work interface to the compute nodes. Your work is then distributed to queues that provide compute node resources. Login to compute nodes via ssh is not suggested and you will be asked to refrain from using the resouces in that manner; let LSF do it!

My program needs access to more than 16 gig or ram, what are my options?
An lsf resource has been defined to identify those nodes with 32 gig of ram. You access this through a bsub command line option, -R, when you submit your job.

-bash-3.2$ bsub -R bigmem -queue normal ./myprogram

Note: -bash-3.2$ is the default prompt for your bash shell on the cluster. The command is what follows it.

Are the LSF queues different than the old cluster:

No, for the most part. These may change in the future to accommodate needs.

How do I choose between queues:

You may view queue properties with the bqueues command:

-bash-3.2$ bqueues

And extra details by:

-bash-3.2$ bqueues -l |more

What are some of the most common LSF commands:

Action Needed



System verification



Display load levels



Display hosts



Summarize past usage


bacct or
bacct job ID #

Display hosts



View current jobs


bjobs or
bjobs job ID #

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Run LSF batch job


bsub [-op] filename


Kill a job


bkill job id #

Review/select queue


bqueues or
bqueues queue_name

Suspend a job


bstop job ID #

Changes job order (new or pending)


btop job ID | "job_ID"(index_list)"

Resume suspended jobs


bresume job ID #

View job history


bhist job ID #

How can I get notified when my lsf submitted jobs finish:

You need to add the -u option to bsub.
-bash-3.2$ bsub ... -u firstname.lastname@tufts.edu sleep 10

This will cause an e-mail to be sent when the job finishes, containing a summary of the job, the output, CPU & memory utilization, etc.

Compilation FAQs

How do I compile my old 32-bit code under the new 64-bit environment?

You should be able to recompile your code using the same compiler as you did on the old cluster. However, some compiler options may need to be 'tweaked'. For starters try using as few options as possible. For example, remove optimizations, check and debugging options. Investigate possible data alignment issues. If the code worked before, you shouldn't be too far from a solution. For new public domain codes, the task can be a much larger effort.

Where can I find some C++ info?
There are many internet resources. Try the compiler vendors first. Otherwise try:

Miscellaneous FAQs

What email and web services are available on the cluster:

The cluster does not accept incoming mail, nor is a webserver available for public use. These services are provided elsewhere by Tufts.

What is the backup policy:

Your data residing in your home directory is automatically backed up by UIT.  The policy adheres to industry standard best backup practices.  To request a retrivial of data, contact the UIT support center x73376.  You should have available basic info such as the file name(s) and approximately when it existed and what directory.

Is SPSS or SAS available on the cluster:

Neither is available on the cluster. Software packages R and Stata provide that functionality instead.

Where can I find information about PC/Mac based Tufts software licenses:


Can I connect to the license server from home via my ISP to use Matlab on my Tufts laptop:

Programs such as Matlab and others that check out FlexLM based network concurrent licenses can not be used directly over the Internet, as you can while on campus. IP filtering limits license check-outs to the Tufts network domain. You may use the Tufts VPN solution to obtain check-outs.

2. Bioinformatics services

a. Emboss and wEmboss:

Access to Emboss software is available on server http//emboss.uit.tufts.edu, which provides both shell and web access. In both cases you will need an account.

For shell access to command line tools:
> ssh -Y emboss.uit.tufts.edu

For access to the web interface wEmboss.

For access to emboss web documentation.

Former GCG/Seqweb users can find equivalent Emboss functionality

Emboss tutorial

If you have any questions about Emboss related usage, applications, or assistance with software, please contact bio-support@tufts.edu.

Bioinformatic related FAQs

Where are my old seqweb sequences:
Your old seqweb data is at: /nfshome/seqweb/users/your-user-name/

There you will find three directories with your data:
result state work

You may retrieve these with a file transfer program like
WinScp (http://(www.winscp.org) and store locally on your pc/mac. You may then
use a local web browser to look at the old seqweb data. You may also cut and paste sequence data into a wEmboss web session.

If I use the web interface to emboss where is data stored:
wemboss data is written into a directory called wProjects under your shell account. The path will be: /home/your-user-name/wProjects/

Will I have access to my old gcg shell account and data:
Your home directory on the old bioinformatic server is mounted as your directory on the new emboss server. However, access is via a shell login, not with the web interface, wEmboss.

b. Carmaweb server

UIT and the Medical School hosts and supports a web based service known as CarmaWeb. The focus of CarmaWeb is genetic microarray analysis. CARMAweb is a web based tool that allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays. The analysis includes normalization and data preprocessing, detection for differentially expressed genes, cluster analysis and GO analysis. These tools are built upon bioConductor and R software. One may request an account via the website.
Additional information here.

A CARMAweb tutorial is available here

If you have any questions about CarmaWeb related usage, applications, or assistance with software, please contact bio-support@tufts.edu.

3. Tufts Center for Scientific Visualization (or VisWall)

A description may be found here. The user guide is available here.

The research cluster is available to VisWall users for additional computational resources. Current connectivity follows standard practices using ssh and x11 forwarding. Viswall users with a cluster account may forward cluster based application graphic output for display on the VisWall. Future plans to integrate high speed network connectivity between the VisWall and research cluster is in development.

Monthly training classing on the use of the facility can be checked here

4. GIS Center

Several GIS links can be found here.

Tufts Research Cluster indirectly supports GIS spatial statistical computation with the availability of modern spatial statistics programs as found in R. This is a useful resource when faced with either complex estimation tasks, long runtimes or access to more memory than is often available on desktop workstations. R programs such as the following are available:

fields, ramps, spatial, geoR, geoRglm, RandomFields, sp, spatialCovariance, spatialkernel, spatstat, spBayes, splancs,

For additional information please contact cluster-support@tufts.edu.

5. Tufts ICPSR data subscription

The Inter-university Consortium for Political and Social Research (ICPSR) is a unit of the Institute for Social Research at the University of Michigan. ICPSR was established in 1962 to serve social scientists around the world by providing a central repository and dissemination service for computer-readable social science data, training facilities in basic and advanced techniques of quantitative social analysis, and resources that facilitate the use of advanced computer technology by social scientists.

The Tufts community may obtain research data and related web services from the ICPSR while one's computer is in the Tufts network domain. This is required for license authenication purposes. Special case exceptions are possible, but need to be arranged ahead of time. For additional information please contact cluster-support@tufts.edu.