Purdue University

Can you remove me from the Gilbreth mailing list?

Your subscription in the Gilbreth mailing list is tied to your account on Gilbreth. If you are no longer using your account on Gilbreth, 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 mailing list subscription will be removed overnight. Be sure to make a copy of any data you wish to keep first.

How is Gilbreth different than other Community Clusters?

Gilbreth differs from the previous Community Clusters in many significant aspects:

• Each Gilbreth compute nodes are equipped with a variety of Nvidia Tesla GPU accelerator cards which can significantly improve performance of compute-intensive workloads.
• Each Gilbreth front-end contains one Nvidia Tesla A30 accelerator card. This makes GPU code development and testing much simpler.
• GPU-enabled applications have both non-gpu and gpu-enabled versions installed. Typically, gpu-enabled versions are tagged with gpu in their module name, e.g., lammps/31Mar17_gpu is the GPU-enabled version of LAMMPS, while lammps/31Mar17 is the non-gpu version of LAMMPS.
• An exception to the above rule is that for licensed softwares like Abaqus, Ansys, and Matlab, a single module contains both non-gpu and gpu-enabled versions.
• 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 Gilbreth?

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

Errors

Common errors and solutions/work-arounds for them.

Account creation failed

An email came into rcac-help from the automated account checker that an account creation failed. There are a few scenarios that can cause this. There are a few things to check.

Link to section 'Account not created' of 'Account creation failed' Account not created

First check what resource they were added to and the corresponding role status from the User Search page.

Take the following steps for these scenarios:

Link to section 'No Role' of 'Account creation failed' No Role

This means either our website failed and didn't add the role (rare, but there is a known bug where when a faculty requests Radon/Hathi for themselves it fails) or IAMO rejected the role.

You can try manually adding the role through the tool and see if it rejects it again, or ask IAMO about the status and if the role can be added (see below).

Link to section 'Role Pending' of 'Account creation failed' Role Pending

This means two things: IAMO's overnight process failed or the account was added just past the cutoff for the overnight process, but before the account check run.

In the former scenario, something went wrong on IAMO's side. Usually Ben is on top of things and gets things sorted quickly when he gets in the morning, but if it's afternoon and it's still not there ask IAMO about it.

For the latter scenario, there is a very narrow window when users can be added and trigger a false alarm (something like ~4-5am). It's rare, but it happens from time to time when we have a night owl/early bird faculty (or traveling abroad).

Link to section 'Role Ready' of 'Account creation failed' Role Ready

The are two scenarios here: IAMO's overnight process failed and has already been fixed or the transd is broken on our end.

In the first scenario, there probably isn't anything to do. You can verify their account with ldapsearch -x uid=USERNAME | grep host and see if the have the proper host entry. If they do, they should be able to log in.

In the second scenario, the next step would be to investigate the transd. The transd translates packets from IAMO into accounts on our systems. Log into xenon.rcac and look at /var/log/transd_log. Is there recent activity at the end of log? If the end of the log is stale, something is probably stuck, like a full disk or some such. In this case, assign ticket to systems and ask them to look at it. If it has recent activity, you should be able to grep the log for the username and look for account entries for them. If the transd is running further investigation is probably needed.

Link to section 'Asking IAMO' of 'Account creation failed' Asking IAMO

The Footprints queue for IAMO is ITAP_IDENTITY_MANAGEMENT. Ben Lewis and Scott Morris are familiar with our web app, and should be familiar with seeing this "account failed" emails. If they come back and say the account is expired/graduated/etc contact the faculty separately with this information (see below). Otherwise Ben should be able to push accounts or unjam the logjam.

Link to section 'Login Shell /opt/acmaint-3.10/etc/disable is invalid.' of 'Account creation failed' Login Shell /opt/acmaint-3.10/etc/disable is invalid.

This means the user account is no longer valid, ie, they graduated. Remove the account from the Manage User page, and inform the faculty separately (don't use the FP ticket) that added them that we were unable to create an account for the user. Good to verify with PI about student's graudation status (usually that'll ring some bells with the faculty). They will need to have an Request for Privileges (R4P) filed, and then they can re-add the account once complete. If the faculty thinks the student should be valid, ask IAMO about the status. They may have been very recently added back, or had some other issue.

/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.

ncdu command is a convenient interactive tool to examine disk usage. Consider running ncdu $HOME to analyze where the bulk of the usage is. With this knowledge, you could then archive your data elsewhere (e.g. your research group's Data Depot space, or Fortress tape archive), or delete files you no longer need.

There are several common locations that tend to grow large over time and are merely cached downloads.  The following are safe to delete if you see them in the output of ncdu $HOME:

/home/myusername/.local/share/Trash
/home/myusername/.cache/pip
/home/myusername/.conda/pkgs
/home/myusername/.singularity/cache

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-end login nodes. 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 login node 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 support specifying the name of the server where your console is hung.

Thinlinc session frozen

Link to section 'Problem' of 'Thinlinc session frozen' Problem

Your Thinlinc session is frozen and you can not launch any commands or close the session.

Link to section 'Solution' of 'Thinlinc session frozen' Solution

This can happen due to various reasons. The most common reason is that you ran something memory-intensive inside that Thinlinc session on a front-end, so parts of the Thinlinc session got killed by Cgroups, and the entire session got stuck.

• If you are using a web-version Thinlinc remote desktop (inside the browser):

  The web version does not have the capability to kill the existing session, only the standalone client does. Please install the standalone client and follow the steps below:

  ThinLinc

• If you are using a Thinlinc client:

  Close the ThinLinc client, reopen the client login popup, and select End existing session.

  

Thinlinc session unreachable

Link to section 'Problem' of 'Thinlinc session unreachable' Problem

When trying to login to Thinlinc and re-connect to your existing session, you receive an error "Your Thinlinc session is currently unreachable".

Link to section 'Solution' of 'Thinlinc session unreachable' Solution

This can happen if the specific login node your existing remote desktop session was residing on is currently offline or down, so Thinlinc can not reconnect to your existing session.  Most often the session is non-recoverable at this point, so the solution is to terminate your existing Thinlinc desktop session and start a new one.

• If you are using a web-version Thinlinc remote desktop (inside the browser):

  The web version does not have the capability to kill the existing session, only the standalone client does. Please install the standalone client and follow the steps below:

  ThinLinc

• If you are using a Thinlinc client:

  Close the ThinLinc client, reopen the client login popup, and select End existing session.

  

How to disable Thinlinc screensaver

Link to section 'Problem' of 'How to disable Thinlinc screensaver' Problem

Your ThinLinc desktop is locked after being idle for a while, and it asks for a password to refresh it. It means the "screensaver" and "lock screen" functions are turned on, but you want to disable these functions.

Link to section 'Solution' of 'How to disable Thinlinc screensaver' Solution

If your screen is locked, close the ThinLinc client, reopen the client login popup, and select End existing session.

To permanently avoid screen lock issue, right click desktop and select Applications, then settings, and select Screensaver.

Under Screensaver, turn off the Enable Screensaver, then under Lock Screen, turn off the Enable Lock Screen, and close the window.

Questions

Frequently asked questions about logging in & accounts.

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

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

Access to all 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 Request for Privileges (R4P). If you need to continue your collaboration with your Purdue PI, the PI will have 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 RCAC 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 RCAC 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.

Can I manage my Login Activity in Box?

In Box under your account settings, click the "Security" tab. You can review and remove sessions.

Errors

Common errors and potential solutions/workarounds for them.

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).
   • Solution: Try using a client software like Thinlinc or MobaXterm as described in the SSH X11 Forwarding guide.

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.

Jupyter: database is locked / can not load notebook format

Link to section 'Problem' of 'Jupyter: database is locked / can not load notebook format' Problem

You receive the following message after trying to load existing Jupyter notebooks inside your JupyterHub session:

Error loading notebook

An unknown error occurred while loading this notebook.  This version can load notebook formats or earlier. See the server log for details.

Alternatively, the notebook may open but present an error when creating or saving a notebook:

Autosave Failed!

Unexpected error while saving file:  MyNotebookName.ipynb database is locked

Link to section 'Solution' of 'Jupyter: database is locked / can not load notebook format' Solution

When Jupyter notebooks are opened, the server keeps track of their state in an internal database (located inside ~/.local/share/jupyter/ folder in your home directory). If a Jupyter process gets terminated abruptly (e.g. due to an out-of-memory error or a host reboot), the database lock is not cleared properly, and future instances of Jupyter detect the lock and complain.

Please follow these steps to resolve:

1. Fully exit from your existing Jupyter session (close all notebooks, terminate Jupyter, log out from JupyterHub or JupyterLab, terminate OnDemand gateway's Jupyter app, etc).
2. In a terminal window (SSH, Thinlinc or OnDemand gateway's terminal app) use the following command to clean up stale database locks:

   $ unlock-jupyter

3. Start a new Jupyter session as usual.

Questions

Frequently asked questions about jobs.

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

• You can learn about processor layout on Gilbreth nodes using the following command:

  gilbreth-a003:~$ lstopo-no-graphics

• For detailed IO connectivity:

  gilbreth-a003:~$ 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.

Why cannot I use --mem=0 when submitting jobs?

Link to section 'Question' of 'Why cannot I use --mem=0 when submitting jobs?' Question

Why can't I specify --mem=0 for my job?

Link to section 'Answer' of 'Why cannot I use --mem=0 when submitting jobs?' Answer

We no longer support requesting unlimited memory (--mem=0) as it has an adverse effect on the way scheduler allocates job, and could lead to large amount of nodes being blocked from usage.

Most often we suggest relying on default memory allocation (cluster-specific). But if you have to request custom amounts of memory, you can do it explicitly. For example --mem=20G.

If you want to use the entire node's memory, you can submit the job with the --exclusive option.

Can I extend the walltime on a job?

In some circumstances, yes. Walltime extensions must be requested of and completed by staff. Walltime extension requests will be considered on named (your advisor or research lab) queues. Standby or debug queue jobs cannot be extended.

Extension requests are at the discretion of staff based on factors such as any upcoming maintenance or resource availability. Extensions can be made past the normal maximum walltime on named queues but these jobs are subject to early termination should a conflicting maintenance downtime be scheduled.

Please be mindful of time remaining on your job when making requests and make requests at least 24 hours before the end of your job AND during business hours. We cannot guarantee jobs will be extended in time with less than 24 hours notice, after-hours, during weekends, or on a holiday.

We ask that you make accurate walltime requests during job submissions. Accurate walltimes will allow the job scheduler to efficiently and quickly schedule jobs on the cluster. Please consider that extensions can impact scheduling efficiency for all users of the cluster.

Requests can be made by contacting support. We ask that you:

• Provide numerical job IDs, cluster name, and your desired extension amount.
• Provide at least 24 hours notice before job will end (more if request is made on a weekend or holiday).
• Consider making requests during business hours. We may not be able to respond in time to requests made after-hours, on a weekend, or on a holiday.

How is my Data Secured on Gilbreth?

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

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

Gilbreth supports research at the L1 fundamental and L2 sensitive levels. Gilbreth is not approved for storing data at the L3 restricted (covered by HIPAA) or L4 Export Controlled (ITAR), or any Controlled Unclassified 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 Gilbreth?' 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:

• https://docs.globus.org/how-to/share-files/

Can I access Fortress from Gilbreth?

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

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

Julia package installation

Users do not have write permission to the default julia package installation destination. However, users can install packages into home directory under ~/.julia.

Users can side step this by explicitly defining where to put julia packages:

$ export JULIA_DEPOT_PATH=$HOME/.julia
$ julia -e 'using Pkg; Pkg.add("PackageName")'

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 has Geddes, a Community Composable Platform optimized for composable, cloud-like workflows that are complementary to the batch applications run on Community Clusters. Funded by the National Science Foundation under grant OAC-2018926, Geddes consists of Dell Compute nodes with two 64-core AMD Epyc 'Rome' processors (128 cores per node).

To purchase access to Geddes today, go to the Cluster Access Purchase page. Please subscribe to our Community Cluster Program Mailing List to stay informed on the latest purchasing developments or contact us (rcac-cluster-purchase@lists.purdue.edu) if you have any questions.