Rossmann User Guide

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    Overview of Rossmann
        Overview of Rossmann

    Common Error Messages
        cannot connect to X server
        E233: cannot open display
        How do I chek my job output while it is running
        bash: command not found
        qdel: Server could not connect to MOM 12345.rice-adm.rcac.purdue.edu
        bash: module command not found
        /usr/bin/xauth: error in locking authority file
        My SSH connection hangs

    Common Questions
        How can my collaborators outside Purdue get access to Rossmann?
        How can I get email alerts about my PBS job status?
        How can I get access to Sentaurus software?
        Can I share data with outside collaborators?
        Can I get a private server from RCAC?

    Biography of Michael Rossmann
        Overview of Michael Rossmann


path breadcrumb divider Overview of Rossmann path breadcrumb divider Overview of Rossmann

Overview of Rossmann

Rossmann was a compute cluster operated by ITaP and was a member of Purdue's Community Cluster Program. Rossmann went into production on September 1, 2010. It consisted of HP (Hewlett Packard) ProLiant DL165 G7 nodes with 64-bit, dual 12-core AMD Opteron 6172 processors (24 cores per node) and 48 GB, 96 GB, or 192 GB of memory. All nodes had 10 Gigabit Ethernet interconnects and a 5-year warranty. Rossmann was decommissioned on November 2nd, 2015.

Detailed Hardware Specification

Sub-Cluster Number of Nodes Processors per Node Cores per Node Memory per Node Interconnect Disk
-A 392 Two 2.1 GHz 12-Core AMD 6172 24 48 GB 10 GigE 250 GB
-B 40 Two 2.1 GHz 12-Core AMD 6172 24 96 GB 10 GigE 250 GB
-C 2 Two 2.1 GHz 12-Core AMD 6172 24 192 GB 10 GigE 1 TB
-D 4 Two 2.1 GHz 12-Core AMD 6172 24 192 GB 10 GigE 2 TB

Rossmann nodes run Red Hat Enterprise Linux 6 (RHEL6) and use Moab Workload Manager 8 and TORQUE Resource Manager 5 as the portable batch system (PBS) for resource and job management. Rossmann also runs jobs for BoilerGrid whenever processor cores in it would otherwise be idle. The application of operating system patches occurs as security needs dictate. All nodes allow for unlimited stack usage, as well as unlimited core dump size (though disk space and server quotas may still be a limiting factor).

path breadcrumb divider Common Error Messages path breadcrumb divider cannot connect to X server

Problem

You receive the following message after entering a command to bring up a graphical window

cannot connect to X server

Solution

This can happen due to multiple reasons:

  • Reason 1: Your SSH client software does not support graphical display by itself (e.g. SecureCRT or PuTTY).
    • Solution: Try using a client software like Thinlinc or MobaXTerm as described here.
  • Reason 2: You did not enable X11 forwarding in your SSH connection.

    • Solution: If you are in a Windows environment, make sure that X11 forwarding is enabled in your connection settings (e.g. in MobaXTerm or PuTTY). If you are in a Linux environment, try

      ssh -Y -l username hostname

  • Reason 3: If you are trying to open a graphical window within an interactive job, make sure you are using the -X option with qsub after following the previous step(s) for connecting to the front-end. Please see the example here.
  • Reason 4: If none of the above apply, make sure that you are within quota of your home directory as described here.

path breadcrumb divider Common Error Messages path breadcrumb divider E233: cannot open display

Problem

You receive the following message after entering a command to bring up a graphical window

E233: cannot open display

Solution

This means you did not enable X11 forwarding which supports remote graphical access to applications. Try

ssh -Y -l username hostname

path breadcrumb divider Common Error Messages path breadcrumb divider How do I chek my job output while it is running

Problem

After submitting your job to the cluster, you want to see the output that it generates.

Solution

There are two simple ways to do this:

  • qpeek: Use the tool qpeek to check the job's output. Syntax of the command is:
    qpeek <jobid>
  • Redirect your output to a file: To do this you need to edit the main command in your jobscript as shown below. Please note the redirection command starting with the greater than (>) sign.
    myapplication ...other arguments... > "${PBS_JOBID}.output"
    On any front-end, go to the working directory of the job and scan the output file.
    tail "<jobid>.output"
    Make sure to replace <jobid> with an appropriate jobid.

path breadcrumb divider Common Error Messages path breadcrumb divider bash: command not found

Problem

You receive the following message after typing a command

bash: command not found

Solution

This means the system doesn't know how to find your command. Typically, you need to load a module to do it.

path breadcrumb divider Common Error Messages path breadcrumb divider qdel: Server could not connect to MOM 12345.rice-adm.rcac.purdue.edu

Problem

You receive the following message after attempting to delete a job with the 'qdel' command

qdel: Server could not connect to MOM 12345.rice-adm.rcac.purdue.edu

Solution

This error usually indicates that at least one node running your job has stopped responding or crashed. Please forward the job ID to rcac-help@purdue.edu, and ITaP Research Computing staff can help remove the job from the queue.

path breadcrumb divider Common Error Messages path breadcrumb divider bash: module command not found

Problem

You receive the following message after typing a command, e.g. module load intel

bash: module command not found

Solution

The system cannot find the module command. You need to source the modules.sh file as below

source /etc/profile.d/modules.sh

or

#!/bin/bash -i

path breadcrumb divider Common Error Messages path breadcrumb divider /usr/bin/xauth: error in locking authority file

Problem

I receive this message when logging in:

/usr/bin/xauth: error in locking authority file

Solution

Your home directory disk quota is full. You may check your quota with myquota.

You will need to free up space in your home directory.

path breadcrumb divider Common Error Messages path breadcrumb divider My SSH connection hangs

Problem

Your console hangs while trying to connect to a RCAC Server.

Solution

This can happen due to various reasons. Most common reasons for hanging SSH terminals are:

  • Network: If you are connected over wifi, make sure that your Internet connection is fine.
  • Busy front-end server: When you connect to a cluster, you SSH to one of the front-ends. Due to transient user loads, one or more of the front-ends may become unresponsive for a short while. To avoid this, try reconnecting to the cluster or wait until the server you have connected to has reduced load.
  • File system issue: If a server has issues with one or more of the file systems (home, scratch, or depot) it may freeze your terminal. To avoid this you can connect to another front-end.

If neither of the suggestions above work, please contact rcac-help@purdue.edu specifying the name of the server where your console is hung.

path breadcrumb divider Common Questions path breadcrumb divider How can my collaborators outside Purdue get access to Rossmann?

How can my collaborators outside Purdue get access to Rossmann?

Your Departmental Business Office can submit a Request for Privileges (R4P) to provide access to collaborators outside Purdue, including recent graduates. Once the R4P process is complete, you will need to add your outside collaborators to Rossmann as you would any for any Purdue collaborator.

path breadcrumb divider Common Questions path breadcrumb divider How can I get email alerts about my PBS job status?

Question

How can I be notified when my PBS job was executed and if it completed successfully?

Answer

Submit your job with the following command line arguments

qsub -M email_address -m bea myjobsubmissionfile

Or, include the following in your job submission file.

#PBS -M email_address                                                  
#PBS -m bae                                                                         

The -m option can have the following letters; "a", "b", and "e":

a - mail is sent when the job is aborted by the batch system.
b - mail is sent when the job begins execution.
e - mail is sent when the job terminates.

path breadcrumb divider Common Questions path breadcrumb divider How can I get access to Sentaurus software?

Question

How can I get access to Sentaurus tools for micro- and nano-electronics design?

Answer

Sentaurus software license requires a signed NDA. Please contact Dr. Mark Johnson, Director of ECE Instructional Laboratories to complete the process.

Once the licensing process is complete and you have been added into a cae2 Unix group, you could use Sentaurus on RCAC community clusters by loading the corresponding environment module:

module load sentaurus

path breadcrumb divider Common Questions path breadcrumb divider Can I share data with outside collaborators?

Yes! Globus allows convenient sharing of data with outside collaborators. Data can be shared with collaborators' personal computers or directly with many other computing resources at other intstitutions. See the Globus documentation on how to share data:

path breadcrumb divider Common Questions path breadcrumb divider Can I get a private server from RCAC?

Question

Can I get a private (virtual or physical) server from RCAC?

Answer

Often, researchers may want a private server to run databases, web servers, or other software. RCAC currently does not offer private servers (formerly known as "Firebox").

For use cases like this, we recommend the Jetstream Cloud (http://jetstream-cloud.org/) an NSF-funded science cloud allocated through the XSEDE project. RCAC staff can help get you access to Jetstream to test, or to help write an allocation proposal for larger projects.

Alternatively, you may consider commercial cloud providers such as Amazon Web Services, Azure, or Digital Ocean. These services are very flexible, but do come with a monetary cost.

path breadcrumb divider Biography of Michael Rossmann path breadcrumb divider Overview of Michael Rossmann

Portrait of Michael Rossmann

Michael Rossmann

Michael Rossmann, Purdue's Hanley Distinguished Professor of Biological Sciences, is a pioneer in using high-performance computing in concert with X-ray crystallography and cryo-electron microscopy to deduce the structure of viruses and their component protein molecules. He began using computers for crystallography while a post-doc in Minnesota where he had to program one of the first commercial computers by writing code in octal. In the 1970s, he used computers to map the atomic structure of plant viruses and in 1979 he and collaborators constructed a 3-D model of the crop-damaging southern bean mosaic virus. Rossmann recalls it as a back-breaking endeavor involving some 50 error-prone magnetic tapes recording the electron density of this virus. He gained worldwide attention in 1985 by determining the structure of human rhinovirus serotype14, HRV-14, one of about 100 known cold virus strains. He is examining viruses ranging from those that cause the common cold; to flaviviruses, such as West Nile and Yellow Fever viruses; to parvovirus in cats and dogs; and to Mimivirus that approaches the size of small bacteria—from things that make us feel bad to things that can kill us or have major economic consequences. The knowledge gained could help lead to improved treatments against dangerous viruses and a better understanding of the body's immune system.

Professor Rossmann was a friend, colleague and next door neighbor of the late Saul Rosen, the Purdue research computing pioneer. Grants awarded Rossmann by the National Science Foundation and other funders helped pay for early large-scale systems for research at Purdue from the 1960s to the 1980s, including Control Data Systems 6000 series and CYBER 205 supercomputers. ITaP has operated a high-performance computing cluster for Rossmann's lab and he used the Hamlet and Lear clusters before becoming one of the investors in the Steele community cluster in 2008. Rossmann began his teaching and research at Purdue in 1964. He was a member of the National Science Board from 2000 to 2006 after being nominated by President Clinton. He is a member of the U.S. National Academy of Sciences and a foreign member of the British Royal Society.

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