The University of Arizona
    For questions, please open a UAService ticket and assign to the Tools Team.
Page tree
Skip to end of metadata
Go to start of metadata

Frequently Asked Questions

Account Access

 Q. How do I create an account?
A step-by-step guide is available on our Account Creation page.
 Q. Why can't I log in?
There are many reasons you may be having issues logging in. A list of possible reasons may include:
  • You haven't created an account yet.
  • Your account isn't sponsored yet.
  • You aren't using two-factor authentication (NetID+).
  • You need to wait 15 minutes. If you just created your account, it takes time before you can log in.
  • You're trying to connect using ssh NetID@login.hpc.arizona.edu. This will not work. Instead, use: ssh NetID@hpc.arizona.edu.
  • You're using NetID@hpc.arizona.edu or NetID@email.arizona.edu as your username in PuTTY. Instead, use only your NetID.
  • You've entered your password incorrectly too many times. After multiple failed password entries, the system will place a 60 minute ban on your account for security reasons.

 Q. Why can't I enter my password in my terminal?
Linux systems do not display character strokes while entering your password which can make it look like the ssh client is frozen. Even though it doesn't appear that anything is happening, the system is still logging your input. To proceed, type your password at the prompt and press enter.
 Q. Why am I seeing "You do not appear to have registered for an HPC account"?
If you have just registered for an HPC account, you need to wait a little while for the request to propagate through the University systems (this can take up to an hour).  Patience (smile)
 Q. Why am I getting "permission denied" when I try to log in?
You need an HPC account - see our Account Creation page for details.  Once you've done that, you'll need to wait a little while to log in. If your PI hasn't already added you to their group, you'll need to wait for that as well.
 Q. Why am I getting the message "incorrect password" when I try to log in?
  • Ensure you are using the correct password. Sometimes typing your password into a plain text file and copying/pasting it into the terminal can help.
  • You need to wait about 15 minutes after your account is approved for the account to be available
  • You must enroll in NetId. Depending on the application you use to log in, you may not get the typical NetID+/DUO menu of options, or an error message indicating this is your problem

 Q. I've forgotten my password, how can I reset it?

HPC uses the same NetID login credentials as all UA services. If you need to reset your NetID password you can do so using the NetID portal: https://netid-portal.iam.arizona.edu/

 Q. How do I add members to my HPC research group?

Faculty members who manage their own HPC groups can follow the instructions in our Research and Class Groups page.

 Q. I'm leaving the university/not affiliated with the university, can I maintain/receive access to HPC?

Yes, if you are a former university affiliate or campus collaborator participating in research, you may register as a Designated Campus Colleague (DCC). Once your DCC status has been approved, you will receive a NetID+ which you may use to create an HPC Account. If you already have an HPC Account, no further action is required.

General Computing

 Q. Why aren't common commands working?
Perhaps your shell is not set to Bash. If you already had another account before joining HPC, that profile will carry over, while a brand new account will always default to bash. If your shell is not set to Bash, contact our consultants so that they can reset it for you.
 Q. Why is my terminal glitching (e.g. CTRL+A puts me in my command prompt)?

When you log into HPC, the variable $COMMAND_PROMPT is set to your current cluster (e.g.: (puma)). Sometimes this can cause formatting problems. If you'd prefer to modify your $PS1, you can add the following to your ~/.bashrc:

if [ -n "${PROMPT_COMMAND}" -a -r /usr/local/bin/slurm-selector.sh ]; then
  SavePS1=${PS1}
  Cur_Cluster=$(eval ${PROMPT_COMMAND} 2>/dev/null)
  PS1="${Cur_Cluster}${SavePS1}"
  unset PROMPT_COMMAND
  for c in puma ocelote elgato; do
     alias ${c}="PS1=\"(${c}) ${SavePS1}\"; . /usr/local/bin/slurm-selector.sh ${c}; unset PROMPT_COMMAND"
  done
  unset Cur_Cluster SavePS1
fi
 Q. Why is my job producing core.xxxx files?

These files are called core dumps and may be created when a program terminates abnormally. Core dumps contain the system's memory at the time of the fault event as well as additional information that can be used with a debugger (e.g. gdb) to track down the source of the error.

One drawback to core dump files is they can be quite large. If you're working with limited space (e.g., your home directory or a nearly-full /groups or /xdisk) or are running many jobs, you may consider disabling them. To do this, include the following line in your batch script before your program's execution:

ulimit -c 0


Jobs and Scheduling

 Q. Why isn't my job running?

There are a few reasons your job may not be running, check below for some ideas on diagnosing the issue:

  • Run squeue --job <jobid> and see if there is anything listed under "(REASON)". This may give an idea why your job is stuck in queue. We have a table in our SLURM documentation that describes what each Reason code means.

  • Due to the number of HPC users, it may not always be possible to run a submitted job immediately. If there are insufficient resources available, your job will be queued and it may take up to a few hours for it to begin executing.

  • Your group may have run out of standard hours. You can check your allocation using the command va.

  • Your group/job has reached a resource usage limit (e.g., number of GPUs that may be used concurrently by a group, or a job has requested more than the 10 day max walltime). Try running job-limits <group_name> to see what limits you're subject to and if there are any problem jobs listed.

  • You may be requesting a rare resource (e.g., 4 GPUs on a single node on Puma or a high memory node).
    • If you are requesting a single GPU on Puma and are frustrated with the wait times, you might consider checking if Ocelote will work for your analyses. There are more GPU nodes available on that cluster with shorter wait times.
    • If you are trying to run a job on a standard node and have been waiting for a very long time, try checking its status using job-history <jobid>. If you see Allocated RAM/CPU above 5gb on Puma or above 6gb on Ocelote, then you are queued for the high memory node which can have very long wait times. To queue for a standard node, cancel your job and check that your script has the correct ratios.

 Q. Why do my jobs keep getting interrupted?
If your jobs keep stopping and restarting, it's likely because you are using Windfall. Windfall is considered lower priority and is subject to preemption by higher priority jobs. Before submitting a job to Windfall, consider using your group's allotted monthly hours first. Jobs using Standard hours will queue for a shorter period of time and will not be interrupted. You can check your group's remaining hours using the command va. To see more information on your allotted hours and the different job queues, see: Allocation and Limits.
 Q. Can I run programs on the login nodes?
No. Software to run applications is not available on the login nodes. To run/test your code interactively, start an interactive session on one of the system's compute nodes. Processes running on the head node are subject to being terminated if we think they are affecting other users. Think of these as 'submit' nodes where you prepare and submit job scripts.
 Q. Can I get root access to my compute nodes?
Unfortunately, that is not possible. The compute nodes get their image from the head node and have to remain the same. If you need to install software that needs root access, for example, you can install the software locally in your account. See this example.
 Q. Can I ssh to compute nodes?
SLURM will let you ssh to nodes that are assigned to your job, but not to others.

Specific Errors

 Q. Why does my Desktop session fail with "Could not connect to session bus: failed to connect to socket /tmp/dbus-"?

This is most commonly seen with users who have Anaconda or Miniconda initialized in their accounts. For a permanent solution, you can run the following command from an interactive terminal session:

conda config --set auto_activate_base false

This will prevent conda from auto-activating when you first log in and allow you to have more control over your environment. When you'd like to activate anaconda, run conda activate. See this example for information running anaconda workflows in batch with auto-activation disabled.

 Q. Why am I getting "/bin/bash^M: bad interpreter: No such file or directory"?

Scripts created in a Windows environment and transferred to HPC retain hidden carriage returns (^M). You can convert your Windows file to Unix format with:

$ dos2unix <filename>
 Q. What does "Bad UID for job execution" mean?

This happens most frequently for new users. It takes a while to propagate new accounts to all the right places. Come back after a coffee break. However, this can occur in other circumstances. Open a support ticket with hpc-consult.

Software and Modules

 Q. Are any software modules loaded by default?

Yes, when you start an interactive terminal session or submit a batch script, the modules ohpc, gnu8, openmpi3, and cmake are automatically loaded. If your code uses Intel compilers, you will want to manually unload gnu8 and openmpi3 to prevent conflicts.

The exception: If you are working in a terminal in an Open OnDemand interactive desktop session, nothing is loaded by default and you will need to manually load any necessary modules.

 Q. How do I install this R package/Why can't I install this R package?
R installations can sometimes be frustrating. We have instructions for how to set up a usable R environment, how to diagnose and troubleshoot problems, and steps to help with known troublesome packages documented in in our Using and Customizing R Packages section. 
 Q. How do I install Python packages?
You can install python packages locally using either a virtual environment or a local conda environment. See our documentation on using Python for instructions on how to set these up.
 Q. I've been using an older version of Singularity, why isn't available anymore?
The current version of Singularity is 3.7.4.  Prior versions have been removed, only the latest one is considered secure.  Notify the consultants if you need help with transition to the current version. Singularity is installed on the operating systems of all compute nodes so does not need to be loaded with a module.
 Q. What executables are available when I load a module?

Load the module, find the path to the executable by checking the $PATH variable, then list the contents.  For example:

module load lammps
echo $PATH
ls /opt/ohpc/pub/apps/lammps/3Mar20/bin
lmp_mpi
 Q. Why am I getting "command: module not found"?

There are a few different possibilities:

  • You are not in an interactive session. Modules are not available on the login nodes. You may request an interactive session by using the command interactive
  • Your shell is not set to bash. If this is the case, contact our consultants so that they can reset it for you.
  • You have modified or deleted your ~/.bashrc. If this is the case, open (if the file exists) or create and open (if the file is missing) the file .bashrc in your home directory and add the lines:

    if [ -f /etc/bashrc ]; then
            . /etc/bashrc
    fi
 Q. How can I maximize my software performance on Puma?

If you are able to compile your software you can take advantage of most of the AMD Zen architecture.

CompilerArch-SpecificArch-Favorable
GCC 9-march=znver2-mtune=znver2
LLVM 9-march=znver2-mtune=znver2

Neither of these compiler versions (GCC 9 or LLVM 9) is available on Puma so you will have to build that first.  If you use GCC 8.3 you can set znver1 instead.

 Q. I have an application that runs on Windows and uses GPUs, where can I run it?

Windows applications can't be run on HPC, however, AWS has been used successfully for Windows software with GPU needs. It’s easy to set up, cost effective, and very scalable. Amazon also has a cloud credit for research program available
https://aws.amazon.com/government-education/research-and-technical-computing/cloud-credit-for-research/ [aws.amazon.com]

 Q. Is the Intel compiler faster than GCC on Puma?

Intel compilers are optimized for Intel processors. There is some debate around the concept of unfair CPU dispatching in Intel compilers. By default, software on the HPC clusters is built with GCC (on Puma it is GCC 8.3).  This is in keeping with our preference for community software.

 Q. How do I access Gaussian or Gaussview?

You need to belong to a special group called g03.  You can request to be added by submitting a help ticket. This is a constraint in Gaussian that other modules do not have.

 Q. How do I take advantage of the Distributed capability of Ansys?

Ansys has the Distributed capability built in to increase performance. Ansys uses the Intel compiler and so uses Intel MPI.  By default, we load OpenMPI, so you will need to do this: 

module unload gnu8 openmpi3
module load intel
module load ansys
 Q. How do I access custom Python packages from an OOD Jupyter session?

Instructions on accessing custom packages are under Accessing Custom Packages from a Jupyter Session in our documentation on Using and Installing Python.

Data Storage and Transfer

 Q. Do you allow users to NFS mount their own storage onto the compute nodes?
No. We NFS mount storage across all compute nodes so that data is available independent of which compute nodes are used.  See this section for how to transfer data.
 Q. I can't transfer my data to HPC with an active account. What's wrong?

After creating your HPC Account, your home directory will not be created until you log in for the first time. Without your home directory, you will not be able to transfer your data to HPC. If you are struggling and receiving errors, sign into your account either using the CLI through the bastion or logging into OnDemand and then try again.

If you are using something like SCP and are receiving errors, make sure your hostname is set to filexfer.hpc.arizona.edu (not hpc.arizona.edu).


 Q. I accidentally deleted files, can I get them back?

Unfortunately, no. Backups are not made and anything deleted is permanently erased. It is impossible for us to recover it. To ensure your data are safe, we recommend:

  • Make frequent backups, ideally in three places and two formats. Helpful information on making backups can be found on our page Transferring Data.
  • Use rm and rm -r with caution as these commands cannot be undone! Consider using rm -i when removing files/directories. The -i flag will prompt you to manually confirm file removals to make really sure they can be deleted.
  • You can open a support ticket to request assistance.  Files that are deleted may not have been removed from the storage array immediately (though this is not guaranteed), don't wait more than a few days.
 Q. What are some common Globus errors to look out for?

Endpoint too busy: This is most commonly seen when users are transferring directories to Google Drive. This is because Google has user limits restricting the number of files that can be transferred per unit time. When many files are being transferred at once, that limit may be exceeded. Globus will automatically hold the transfer until the limit is reset at which point it will continue. One way to avoid this is to archive your work prior to the transfer (e.g. in .tar.gz form). Additionally, archiving will also speed up your transfers considerably, sometimes by orders of magnitude.

Fatal FTP Response, PATH_EXISTS: Globus is finicky about the destination endpoint. If you get this error, check to see whether duplicate files/directories exist at the destination. This can happen frequently with Google Drive as multiple files/directories can exist in the same location with the same name. If duplicates exist, try moving, removing, or renaming them and reinitiate the transfer.

 Q. Why am I getting “Authentication failed” errors when performing file transfers?

In our last maintenance update on July 20th, one of the changes was to ensure HIPAA compliance on the Data Transfer Nodes (DTNs). This change included the insertion of required text:

Authorized uses only. All activity may be monitored and reported.

This change breaks SCP activity. Not in all cases but frequently with WinSCP, Filezilla and from a terminal. Terminal activity will likely still work from Linux or MacOS.

The solution is to not use SCP (SCP is considered outdated, inflexible, and not readily fixed) and to use a more modern protocol like SFTP and rsync. Info on using SFTP:

  • Putty supports SFTP with the “PSFTP” command
  • For FileZilla, in the Toolbar, click on Edit and Settings, then click on SFTP
  • For Cyberduck, choose SFTP in the dropdown for protocols.

xdisk

 Q. Who owns our group's /xdisk?

A group's PI owns the /xdisk allocation. By default, your PI has exclusive read/write/execute privileges for the root folder /xdisk/PI.


 Q. Can a PI make their /xdisk accessible to their whole group?

If they so choose, a PI may allow their group members access to their /xdisk by running one of the following commands:

CommandResult

$ chmod g+r /xdisk/PI

Group members can see the contents of the directory with ls, but may not access it or make modifications (e.g. add, delete, or edit files/directories)

$ chmod g+rx /xdisk/PI

Group members can access the directory and see files but cannot make modifications (e.g. add, delete, or edit files/directories)

$ chmod g+rwx /xdisk/PI

Group members are granted full read/write/execute privileges.
 Q. Where can group members store their files?

When an /xdisk allocation is created, a subdirectory is automatically generated for and owned by each individual group member. If the directory /xdisk/PI does not have group privileges, group members may not access the root directory, but may access their individual spaces by:

$ cd /xdisk/PI/netid

If a user joins the group after the xdisk was created and /xdisk/PI is not writeable for group members, contact our consultants and they can create one.

 Q. A group member's directory isn't in our /xdisk, how can we add it?

Typically when an /xdisk allocation is created, it will automatically generate a directory for each group member. In the unlikely event that it doesn't or, more commonly, a group member is added after the allocation has been created, either the PI may manually create a directory or, if the root directory is group writable, the user may create one themselves. If the group's /xdisk does not have full group permissions, the PI may run:

$ mkdir /xdisk/PI/netid

then can reach out to our hpc consultants to request an ownership change.

 Q. Do we need to request an individual allocation within the /xdisk for each user in our group?

No, the full /xdisk allocation is available for every member of the group. It's up to group members to communicate with one another on how they want to utilize the space.


 Q. Who owns our group's /xdisk?

A group's PI owns the /xdisk allocation. By default, your PI has exclusive read/write/execute privileges for the root folder /xdisk/PI.


 Q. Why am I getting xdisk emails?
xdisk is a temporary storage space available to your research group. When it's close to its expiration date, notifications will be sent to all members of your group. For detailed information on xdisk allocations, see: Storage
 Q. Why am I getting "/xdisk allocations can only be authorized by principal investigators"?
xdisks are managed by your group's PI by default. This means if you want to request an xdisk or modify an existing allocation (e.g., extending the time limit or increasing the storage quota), you will need to consult your PI. Your PI may either perform these actions directly or, if they want to delegate xdisk management to a group member, they may do so by following the instructions under Delegating xdisk Management Rights.
 Q. How can we modify our xdisk allocation?
To modify your allocation's time limit or storage quota, your PI can either do so through the Web Portal under the Storage tab, or via the command line. If your PI would like to delegate management rights to a group member, they may follow the instructions under Delegating xdisk Management Rights. Once a group member has received management rights, they may manage the allocation through our web portal.
 Q. Why am I getting "xdisk: command not found"?

If you're getting errors using xdisk commands in a terminal session, check that you are on a login node. If you are on the bastion host (hostname: gatekeeper), are in an interactive session, or are on the filexfer node, you won't be able to check or modify your xdisk. When you are on a login node, your terminal prompt should show the hostname junonia or wentletrap. You can also check your hostname using the command:

$ hostname
 Q. Why am I getting errors when trying to extend my allocation?

If you're trying to extend your group's allocation but are seeing something like:

(puma) [netid@junonia ~]$ xdisk -c expire -d 1
invalid request_days: 1

for every value you enter, your xdisk has likely reached its maximum time limit. To check, go to portal.hpc.arizona.edu, click Manage XDISK, and look at the box next to Duration. If you see 300, your allocation cannot be extended further.

If your allocation is at it's limit, you will need to back up your data to external storage (e.g., a local machine, lab server, or cloud service). Once your xdisk has expired (either by expiring or through manual deletion), you can immediately create a new allocation and restore your data. Detailed xdisk information can be found on our Storage page. You may also want to look at our page on Transferring Data

 Q. Can we keep our xdisk allocation for more than 300 days?

No, once an xdisk has reached its time limit it will expire. It's a good idea to start preparing for this early by making frequent backups and paying attention to xdisk expiration emails. 

 Q. What happens when our xdisk allocation expires?

Once an xdisk expires, all the associated data are deleted. Deleted data are non-retrievable since HPC is not backed up. It's advised to keep frequent backups of your data on different platforms, for example a local hard drive or a cloud-based service like Google Drive, or (even better) both!

  • No labels