Frequently Asked Questions

Some common questions, errors, and problems are categorized below. Click the Expand Topics link in the upper right to see all entries at once. You can also use the search box above to search the user guide for any issues you are seeing.

Link to section 'About Scholar' of 'About Scholar' About Scholar

Can you remove me from the Scholar mailing list?

Your subscription in the Scholar mailing list is tied to your account on Scholar. If you are no longer using your account on Scholar, your account can be deleted from the My Accounts page. Hover over the resource you wish to remove yourself from and click the red 'X' button. Your account and mailinglist subscription will be removed overnight. Be sure to make a copy of any data you wish to keep first.

How is Scholar different than other Community Clusters?

  • Scholar differs from the previous Community Clusters in many significant aspects:
  • Scholar is a hybrid cluster for teaching courses that require high-performance computing.
  • A subset of Scholar front-ends contain Nvidia Tesla V100 accelerator cards. You can access these front ends by logging in to gpu.scholar.rcac.purdue.edu.
  • A subset of Scholar compute nodes contain Nvidia Tesla V100 accelerator cards which can significantly improve performance of compute-intensive workloads. These can be utilized by submitting jobs to the gpu queue (add -A gpu to your job submission command).
  • A selection of GPU-enabled application containers from the Nvidia GPU Cloud (NGC) collection is installed.

Do I need to do anything to my firewall to access Scholar?

No firewall changes are needed to access Scholar. However, to access data through Network Drives (i.e., CIFS, "Z: Drive"), you must be on a Purdue campus network or connected through VPN.

Does Scholar have the same home directory as other clusters?

The Scholar home directory and its contents are exclusive to Scholar cluster front-end hosts and compute nodes. This home directory is not available on other ITaP research computing machines but Scholar. There is no automatic copying or synchronization between home directories.

At your discretion you can manually copy all or parts of your main research computing home to Scholar using one of the suggested methods.

If you plan to use hsi or htar commands to access Fortress tape archive from Scholar, please see also the keytab generation question for a temporary workaround to a potential caveat, while a permanent mitigation is being developed.

Link to section 'Logging In & Accounts' of 'Logging In & Accounts' Logging In & Accounts

Link to section 'Errors' of 'Errors' Errors

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

Link to section 'Problem' of '/usr/bin/xauth: error in locking authority file' Problem

I receive this message when logging in:

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

Link to section 'Solution' of '/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.

My SSH connection hangs

Link to section 'Problem' of 'My SSH connection hangs' Problem

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

Link to section 'Solution' of 'My SSH connection hangs' 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.

Link to section 'Questions' of 'Questions' Questions

I worked on Scholar after I graduated/left Purdue, but can not access it anymore

Link to section 'Problem' of 'I worked on Scholar after I graduated/left Purdue, but can not access it anymore' Problem

You have graduated or left Purdue but continue collaboration with your Purdue colleagues. You find that your access to Purdue resources has suddenly stopped and your password is no longer accepted.

Link to section 'Solution' of 'I worked on Scholar after I graduated/left Purdue, but can not access it anymore' Solution

Access to all Research Computing resources depends on having a valid Purdue Career Account. Expired Career Accounts are removed twice a year, during Spring and October breaks (more details at the official page). If your Career Account was purged due to expiration, you will not be be able to access the resources.

To provide remote collaborators with valid Purdue credentials, the University provides a special procedure called R4P ("request for privileges") (see details under 'Data/Access' tab). If you need to continue your collaboration with your Purdue PI, the PI will have to work with their departmental Business Office to submit or renew an R4P request on your behalf.

After your R4P is completed and Career Account is restored, please note two additional necessary steps:

  • Access: Restored Career Accounts by default do not have any Research Computing resources enabled for them. Your PI will have to login to the Manage Users tool and explicitly re-enable your access by un-checking and then ticking back checkboxes for desired queues/Unix groups resources.

  • Email: Restored Career Accounts by default do not have their @purdue.edu email service enabled. While this does not preclude you from using Research Computing resources, any email messages (be that generated on the clusters, or any service announcements) would not be delivered - which may cause inconvenience or loss of compute jobs. To avoid this, we recommend setting your restored @purdue.edu email service to "Forward" (to an actual address you read). The easiest way to ensure it is to go through the Account Setup process.

Link to section 'Jobs' of 'Jobs' Jobs

Link to section 'Errors' of 'Errors' Errors

cannot connect to X server / cannot open display

Link to section 'Problem' of 'cannot connect to X server / cannot open display' Problem

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

cannot connect to X server cannot open display

Link to section 'Solution' of 'cannot connect to X server / cannot open display' Solution

This can happen due to multiple reasons:

  1. Reason: Your SSH client software does not support graphical display by itself (e.g. SecureCRT or PuTTY).
  2. Reason: 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

  3. Reason: If you are trying to open a graphical window within an interactive PBS 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 in the Interactive Jobs guide.
  4. Reason: If none of the above apply, make sure that you are within quota of your home directory.

bash: command not found

Link to section 'Problem' of 'bash: command not found' Problem

You receive the following message after typing a command

bash: command not found

Link to section 'Solution' of '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.

bash: module command not found

Link to section 'Problem' of '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

Link to section 'Solution' of '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

close Firefox / Firefox is already running but not responding

Link to section 'Problem' of 'close Firefox / Firefox is already running but not responding' Problem

You receive the following message after trying to launch Firefox browser inside your graphics desktop:

Close Firefox

Firefox is already running, but not responding.  To open a new window,
you  must first close the existing Firefox process, or restart your system.

Link to section 'Solution' of 'close Firefox / Firefox is already running but not responding' Solution

When Firefox runs, it creates several lock files in the Firefox profile directory (inside ~/.mozilla/firefox/ folder in your home directory). If a newly-started Firefox instance detects the presence of these lock files, it complains.

This error can happen due to multiple reasons:

  1. Reason: You had a single Firefox process running, but it terminated abruptly without a chance to clean its lock files (e.g. the job got terminated, session ended, node crashed or rebooted, etc).
    • Solution: If you are certain you do not have any other Firefox processes running elsewhere, please use the following command in a terminal window to detect and remove the lock files:
      $ unlock-firefox
  2. Reason: You may indeed have another Firefox process (in another Thinlinc or Gateway session on this or other cluster, another front-end or compute node). With many clusters sharing common home directory, a running Firefox instance on one can affect another.
    • Solution: Try finding and closing running Firefox process(es) on other nodes and clusters.
    • Solution: If you must have multiple Firefoxes running simultaneously, you may be able to create separate Firefox profiles and select which one to use for each instance.

Link to section 'Questions' of 'Questions' Questions

How do I know Non-uniform Memory Access (NUMA) layout on Scholar?

  • You can learn about processor layout on Scholar nodes using the following command:
    scholar-a000:~$ lstopo-no-graphics
  • For detailed IO connectivity:
    scholar-a000:~$ lstopo-no-graphics --physical --whole-io
  • Please note that NUMA information is useful for advanced MPI/OpenMP/GPU optimizations. For most users, using default NUMA settings in MPI or OpenMP would give you the best performance.

Link to section 'Data' of 'Data' Data

How is my Data Secured on Scholar?

Scholar is operated in line with policies, standards, and best practices as described within Secure Purdue, and specific to Research Computing Resources.

Security controls for Scholar are based on ones defined in NIST cybersecurity standards.

Scholar supports research at the L1 fundamental and L2 sensitive levels. Scholar is not approved for storing data at the L3 restricted (covered by HIPAA) or L4 Export Controlled (ITAR), or any Controlled Unclassfied Information (CUI).

For resources designed to support research with heightened security requirements, please look for resources within the REED+ Ecosystem.

Link to section 'For additional information' of 'How is my Data Secured on Scholar?' For additional information

Log in with your Purdue Career Account.

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 institutions. See the Globus documentation on how to share data:

Does Scholar have the same home directory as other clusters?

The Scholar home directory and its contents are exclusive to Scholar cluster front-end hosts and compute nodes. This home directory is not available on other ITaP research computing machines but Scholar. There is no automatic copying or synchronization between home directories.

At your discretion you can manually copy all or parts of your main research computing home to Scholar using one of the suggested methods.

If you plan to use hsi or htar commands to access Fortress tape archive from Scholar, please see also the keytab generation question for a temporary workaround to a potential caveat, while a permanent mitigation is being developed.

HSI/HTAR: Unable to authenticate user with remote gateway (error 2 or 9)

There could be a variety of such errors, with wordings along the lines of

Could not initialize keytab on remote server.
result = -2, errno = 2rver connection
*** hpssex_OpenConnection: Unable to authenticate user with remote gateway at 128.211.138.40.1217result = -2, errno = 9
Unable to setup communication to HPSS...
ERROR (main) unable to open remote gateway server connection
HTAR: HTAR FAILED

and

*** hpssex_OpenConnection: Unable to authenticate user with remote gateway at 128.211.138.40.1217result = -11000, errno = 9
Unable to setup communication to HPSS...
*** HSI: error opening logging
Error - authentication/initialization failed

The root cause for these errors is an expired or non-existent Kerberos keytab file (a special authentication token stored in your home directory). These keytabs are valid for 90 days and on most RCAC resources they are usually automatically checked and regenerated when you execute hsi or htar commands. However, if the keytab is invalid, or fails to generate, Fortress may be unable to authenticate you and you would see the above errors. This is especially common on those RCAC clusters that have their own dedicated home directories (such as Bell), or on standalone installations (such as if you downloaded and installed HSI and HTAR on your non-RCAC computer).

This is a temporary problem and a permanent system-wide solution is being developed. In the interim, the recommended workaround is to generate a new valid Kerberos keytab file in your main research computing home directory, and then copy it to your home directory on Scholar. The fortresskey command is used to generate the keytab and can be executed on another cluster or a dedicated data management host data.rcac.purdue.edu:

$ ssh myusername@data.rcac.purdue.edu fortresskey
$ scp -pr myusername@data.rcac.purdue.edu:~/.private $HOME

With a valid keytab in place, you should then be able to use hsi and htar commands to access Fortress from Scholar. Note that only one keytab can be valid at any given time (i.e. if you regenerated it, you may have to copy the new keytab to all systems that you intend to use hsi or htar from if they do not share the main research computing home directory).

Can I access Fortress from Scholar?

Yes. While Fortress directories are not directly mounted on Scholar for performance and archival protection reasons, they can be accessed fromScholar front-ends and nodes using any of the recommended methods of HSI, HTAR or Globus.

Link to section 'Software' of 'Software' Software

Cannot use pip after loading ml-toolkit modules

Link to section 'Question' of 'Cannot use pip after loading ml-toolkit modules' Question

Pip throws an error after loading the machine learning modules. How can I fix it?

Link to section 'Answer' of 'Cannot use pip after loading ml-toolkit modules' Answer

Machine learning modules (tensorflow, pytorch, opencv etc.) include a version of pip that is newer than the one installed with Anaconda. As a result it will throw an error when you try to use it.

$ pip --version
Traceback (most recent call last):
  File "/apps/cent7/anaconda/5.1.0-py36/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name 'main'

The preferred way to use pip with the machine learning modules is to invoke it via Python as shown below.

$ python -m pip --version

How can I get access to Sentaurus software?

Link to section 'Question' of 'How can I get access to Sentaurus software?' Question

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

Link to section 'Answer' of 'How can I get access to Sentaurus software?' 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

Link to section 'About Research Computing' of 'About Research Computing' About Research Computing

Can I get a private server from RCAC?

Link to section 'Question' of 'Can I get a private server from RCAC?' Question

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

Link to section 'Answer' of 'Can I get a private 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.

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