Frequently Asked Questions

In this section, we’ll discuss some tips for solving problems with Stanage and Bessemer. It is suggested that you work through some of the ideas here before contacting the IT Services Helpdesk for assistance.

Strange things are happening with my terminal or my terminal seems broken

Symptoms include many of the commands not working and just bash-4.1$ or sh-4.2$ being displayed instead of your username at the bash prompt.

This may be because you’ve deleted your .bashrc and .bash_profile files - these are ‘hidden’ files which live in your home directory and are used to correctly set up your shell environment. If you hit this problem you can run the command resetenv which will restore the default files, then you should logout and log back in.

Note

If the command restenv is not working (possibly removed from $PATH), you can run the resetenv command directly:

/opt/site/bin/resetenv

I can no longer log in

If you are confident that you have no password entry issues, have already requested and been granted a HPC account and are connected to the VPN but you still can not log onto a cluster, you may have inadvertently corrupted your shell environment if you have been installing software or making changes in your .bashrc file. Please attempt to resolve this first by resetting your environment with the following command, replacing the variables appropriately: ssh -t $USER@$CLUSTER.shef.ac.uk 'resetenv -f'

Alternatively, you may be having problems due to exceeding your cluster filestore quota. If you exceed your filestore quota in your $HOME area it is sometimes possible that crucial files in your home directory get truncated which effect or prevent the login process.

If the resetenv -f command does not resolve your issue and you suspect your $HOME area is full , you should contact research-it@sheffield.ac.uk and ask to be unfrozen providing your username and a list files or folders which can be removed or temporarily moved to your /mnt/parscratch area on Stanage or /fastdata area on Bessemer.

I can not log into a cluster via the MyApps applications portal

Most of the time such problems arise due to Java version issues. As Java updates are released regularly, these problems are usually caused by the changes to the Java plug-in for the browser.

Most users can swap to using the HTML5 client to resolve these problems via the “Client Options” link at the bottom right of the login window and then clicking the “To use the HTML5 Client login” link.

It can also help to try a different browser to see if it makes any difference. All failing, you may have to fall back to one of the non-browser access methods.

How do I find out more about the commands available on the clusters with man pages?

Man pages (manuals) are installed by default alongside commands/software on unix-like operating systems such as those found on the clusters.

To view the man page (official manual) for a command, you can use the command:

man <command_name>

You can navigate man pages using (the same keyboard shorcuts as less):

  • Space to advance one page

  • d to advance half a page

  • b to go back one page

  • u to go back half a page

  • / starts search mode, after which you enter a search term

Whilst in search mode press n for next occurrence and N for previous occurrence.

You can also press h when viewing man pages to show help.

Documentation for less is available on the system using the command:

man less

If you don’t know the specific command name then you can use apropos which searches all names of man pages and their one line descriptions:

apropos <search_term>

To list all avaiable command man pages:

apropos .

I cannot see my folders in /shared

Some directories such as /shared/<your project>/ are only made available on-demand:. For example, if your shared area is named my_shared_area and you look in /shared straight after logging in, you may not see /shared/my_shared_area in your terminal or MobaXterm file browser.

The directory is there, it has just not been made available (via a process called mounting) to you automatically yet.

When you attempt to do something with the directory such as ls /shared/my_shared_area or cd /shared/my_shared_area in the terminal, the directory will be mounted automatically and will appear to you.

If you are in MobaXterm, you should attempt to navigate to the folder with using the file browser path entry / display box, then hit the refresh button.

Warning

Directories will be automatically unmounted after a period of inactivity.

Note

On Stanage shared areas are only accessible from a login node and not from a worker node.

I’ve loaded software but it isn’t working

This usually means that you are on a login node. You will need to start an interactive session after which you will be able to load cluster software.

srun --pty bash -i

My batch job terminates without any messages or warnings

When a batch job is initiated by using the sbatch commands, it gets allocated specific amount of real memory and run time that you request, or small default values. If a job exceeds either the real memory or time limits it gets terminated immediately and usually without any warning messages.

It is therefore important to estimate the amount of memory and time that is needed to run your job to completion and specify it at the time of submitting the job to the batch queue.

Please refer to our Choosing appropriate compute resources page for information on how to assess sensible resource amounts and avoid these problems.

Tip

If you are confident that the scheduler is not terminating your job, but your job is prematurely stopping, please check if you have attempted to exceed your disk space quota, instructions for this are seen below.

I’ve submitted a job but it’s not running

I submitted a job and after several days it is still waiting in the queue. How can I resolve this? There are a multitude of factors which could be causing your job to queue for a long time or to not run at all. Occasionally parts of the system may be in a maintenance period or may be utlised to capacity. A few things to consider which would cause your job to not run at all:

  • Did you request an acceptable amount of memory for a given node? (e.g. on Bessemer, 192GB or less.)

  • Did you request too much time? (e.g for Stanage, more than 96 hours or on Bessemer, more than 168 hrs.)

Following are ways to fix too much time requested:

The maximum run time for Bessemer is 168 hours.

You can get an estimate for when your job will run on Bessemer using:

squeue --start -j <jobid>

You can reduce the runtime using:

scontrol update jobid=<job_id> TimeLimit=<new_timelimit>

then to verify the time change type:

squeue -j <jobid> --long

Alternatively, delete the job using scancel and re-submit with the new max runtime

“No space left on device”, “Disk quota exceeded” errors and jobs prematurely stopping

Each user of the system has a fixed amount of disk space available in their home directory. If you see an error in your job’s logs indicating “No space left on device” or “Disk quota exceeded” it is likely that your quota has ran out.

If you attempt to exceed this quota, various problems can emerge such as an inability to launch applications or run jobs, the inability to login or abruptly terminated jobs as programs or executables are now unable to write to your /home folder. To see if you are attempting to exceed your disk space quota, run the quota command:

[te1st@login1 [stanage] ~]$ quota -u -s
    Filesystem   space   quota   limit   grace   files   quota   limit   grace
storage:/export/users
                 3289M  51200M  76800M            321k*   300k    350k   none

In the above, you can see that the ‘soft’ space quota is 50 gigabytes and a small portion of this is currently in use. However, the files ‘soft’ quota is 300k which has been exceeded, additionally the grace period indicates the grace period for exceeding the soft quota has expired. Any jobs submitted by this user will likely result in an Eqw status. The recommended action is for the user to delete enough files, or move enough files to another filestore to allow normal work to continue.

To assess what is using up your quota within a given directory, you can make use of the ncdu module on Stanage or the ncdu module on Bessemer . The ncdu utility will give you an interactive display of which files or folders are taking up storage in a given directory tree.

Sometimes, it is not possible to log in to the system because of a full quota. In this situation you should contact research-it@sheffield.ac.uk to ask for assistance, providing your username and a list files or folders which can be removed or temporarily moved to your /mnt/parscratch area on Stanage or /fastdata area on Bessemer.

I am getting warning messages and warning emails from my batch jobs about insufficient memory

If a job exceeds its real memory resource it gets terminated.

These errors on Stanage and Bessemer will be noted in the job record or sent via email and will resemble:

Slurm Job_id=12345678 Name=job.sh Failed, Run time 00:11:06, OUT_OF_MEMORY

To query if your job has been killed due to insufficient memory please see the cluster specific “Investigating finished jobs” sections on our Job Submission and Control page.

To request more memory and for information on how to assess sensible resource amounts please refer to our Choosing appropriate compute resources page.

Insufficient memory in an interactive session

By default, an interactive session on Stanage provides you with 4016 MB of memory or on Bessemer with 2 GB (2048 MB) of memory.

You can request more than this when running your srun command.

$ srun --mem=8G --pty bash -i

This asks for 8 Gigabytes of RAM (real memory).

Hint

You cannot request more memory than a single node possesses and the larger the memory request, the less likely the interactive session request is to succeed. Please see the cluster specific “Interactive jobs” sections on our Job Submission and Control page.

‘Illegal Instruction’ errors

If attempts to run a binary executable program fail with an Illegal Instruction error then your executable program (or a dynamically-linked library) may have been compiled so as to make more optimal use of the instruction set of a particular CPU architecture (an optimised binary), but you’re running the executable on CPU(s) that use a slightly different instruction set.

For example, you may have a executable program optimised for the Intel Icelake CPU instruction set but you find it fails to run on AMD Milan CPUs, or you might be trying to run a binary optimised for a very new Intel CPU architecture on an older model of Intel CPU.

Important

For the above reasons we recommend that you avoid copying binary executables on to the HPC systems and instead (re)compile programs and libraries on the HPC systems instead where possible.

This has the added benefits of ensuring that:

  • Programs/libraries are compiled against the versions of dependencies provided on the HPC systems.

  • Programs/libraries are more likely to make use of the more advanced features of the CPU models in the HPC systems, which could result in better performance/efficiency.

sbatch: error: Batch script contains DOS line breaks (rn) errors

If you prepare text files such as your job submission script on a Windows machine, you may find that they do not work as intended on the HPC systems.

The reason for this behaviour is that Windows and Unix machines have different conventions for specifying ‘end of line’ in text files. Windows uses the control characters for ‘carriage return’ followed by ‘linefeed’, \r\n, whereas Unix uses just ‘linefeed’ \n.

This means a script prepared in Windows using Notepad which looks like this:

#!/bin/bash
echo 'hello world'

will look like the following to programs on a Unix system:

#!/bin/bash\r\n
echo 'hello world'\r\n

For example, if you uploaded a submission script (test.sh) with windows line endings to the cluster, then tried to submit the script using sbatch, you would see the following:

[te1st@bessemer-login1 ~]$ sbatch test.sh
sbatch: error: Batch script contains DOS line breaks (\r\n)
sbatch: error: instead of expected UNIX line breaks (\n).

If you have seen this error or suspect that this is affecting your jobs, run the following command on the file at the terminal

$ dos2unix your_files_filename

You should set your text editor to use Linux endings to avoid this issue.

error: no DISPLAY variable found with interactive job

If you receive the error message:

error: no DISPLAY variable found with interactive job

the most likely cause is that you forgot the -X switch when you logged into the cluster. That is, you might have typed:

ssh username@clustername.shef.ac.uk

instead of:

ssh -X username@clustername.shef.ac.uk

macOS users might also encounter this issue if their XQuartz is not up to date.

macOS users should also try -Y if -X is not working:

ssh -Y username@clustername.shef.ac.uk

Problems connecting with WinSCP

Some users have reported issues while connecting to the system using WinSCP, usually when working from home with a poor connection and when accessing folders with large numbers of files.

In these instances, turning off Optimize Connection Buffer Size in WinSCP can help:

  • In WinSCP, goto the settings for the site (ie. from the menu Session->Sites->SiteManager)

  • From the Site Manager dialog click on the selected session and click edit button

  • Click the advanced button

  • The Advanced Site Settings dialog opens.

  • Click on connection

  • Untick the box which says Optimize Connection Buffer Size

Problems connecting with Filezilla due to MFA

Due to the change to the use of MFA (multi-factor authentication) two simple changes are needed to connect using Filezilla to the HPC clusters.

  • Change the logon type to interactive login.

  • Limit the number of simultaneous connections to 1.

Detailed instructions are contained in the following link: https://unm-student.custhelp.com/app/answers/detail/a_id/7857/~/filezilla-ftp-configuration-for-duo-mfa-protected-linux-servers

Strange fonts or errors re missing fonts when trying to start a graphical application

Certain programs require esoteric fonts to be installed on the machine running the X server (i.e. your local machine). Example of such programs are qmon, a graphical interface to the Grid Engine scheduling software, and the ANSYS software. If you try to run qmon or ANSYS software on a Linux machine and see strange symbols instead of the Latin alphabet or get an error message that includes:

X Error of failed request: BadName (named color or font does not exist)

Then you should try running the following on your own machine:

for i in 75dpi 100dpi; do
    sudo apt-get install xfonts-75dpi
    pushd /usr/share/fonts/X11/$i/
    sudo mkfontdir
    popd
    xset fp+ /usr/share/fonts/X11/$i
done

Warning

Note that these instructions are Ubuntu/Debian-specific; on other systems package names, paths and commands may differ.

Next, try connecting to a cluster using ssh -X clustername.shef.ac.uk, start a graphical session then try running qmon or ANSYS software again.

If you can now run qmon or ANSYS software without problems then you need to add two lines to the .xinitrc file in your home directory on your own machine so this solution will continue to work following a reboot of your machine:

FontPath /usr/share/fonts/X11/100dpi
FontPath /usr/share/fonts/X11/75dpi

Login node SSH RSA/ECDSA/ED25519 host key fingerprints

The RSA, ECDSA and ED25519 fingerprints for Stanage’s login nodes are:

SHA256:mFfJmZHH0SUogoUhTtlatoZLEacfGAlj0cTrnInO5z0 (RSA)
SHA256:4HdvK3C1KDm+JG1TzxQKxezMz5ojEORynHUqF9tQfoI (ECDSA)
SHA256:aaTv+0TEc0nj7WR2ZuBYWFDD+QqzOKJpMjEFKBx6pQU (ED25519)

The RSA, ECDSA and ED25519 fingerprints for Bessemer’s login nodes are:

SHA256:AqxYHUlW3r+vrmwS0g0Eru9u4ZujcFCRJajkTRdcAfA (RSA)
SHA256:eG/eFhOXyKS77WCsMmkDwZSV4t7y/D8zBFHt1mFP280 (ECDSA)
SHA256:TVzevzGC2uz8r1Z16MB9C9xEQpm7DAJC4tcSvYSD36k (ED25519)

I have a new account, how do I transfer data from my old account

Please note that the below guide assumes that both accounts are still be active. If you have lost access to the old account in the last few weeks then get in touch with us via research-it@sheffield.ac.uk and we may be able to help transfer files across.

To transfer data between your old account and your new account you could make use of either SCP or rsync. We encourage users to use rsync as it preserves timestamps and permisions. Follow the following workflow to carry out the transfer.

  • Log into your new username in the cluster you want to copy to and create a folder named “OldUserAccount”.

mkdir OldUserAccount

  • Log into your old account and run the rsync command. Here we show two examples.

  1. You want to copy the files to the new account on the same cluster node(e.g old account on Bessemer to new account on Bessemer), here we are only going to use the “avP” options as we dont need to compress the data.

rsync -avP /Path/To/File_Or_Directory $Your_New_UserName@$HOSTNAME:/home/$Your_New_UserName/OldUserAccount

  1. You want to copy your files to the new account on a different cluster node (e.g old account on Bessemer to new account on Stanage), here we are going to use the option avzP as we are going to transfer data over the JANET link (Bessemer) and private leased link (Stanage), and it will be faster if it is compressed.

rsync -avzP /Path/To/File_Or_Directory $Your_New_UserName@$clustername.shef.ac.uk:/home/$Your_New_UserName/OldUserAccount

Issue when running multiple MPI jobs in sequence

If you have multiple mpirun commands in a single batch job submission script, you may find that one or more of these may fail after complaining about not being able to communicate with the orted daemon on other nodes. This appears to be something to do with multiple mpirun commands being called quickly in succession, and connections not being pulled down and new connections established quickly enough.

Putting a sleep of e.g. 5s between mpirun commands seems to help here. i.e.

mpirun program1
sleep 5s
mpirun program2

Using ‘sudo’ to install software on the clusters

HPC users do not have sufficient access privileges to use sudo to install software (in /usr/local) and permission to use sudo will not be granted to non-system administrators. Users can however install applications in their /home directory, /mnt/parscratch area on Stanage or /fastdata area on Bessemer.

The webpage Installing Applications on Stanage and Bessemer provides guidance on how to do this.

Is data encrypted at rest on HPC storage areas?

At present, no HPC storage areas on any of our clusters encrypt data at rest.

Are the HPC clusters certified to standards such as Cyber Essentials, Cyber Essentials Plus or ISO 27001?

Due to the complexity of the multi-user High Performance Computing service, the service is not currently certified as being compliant with the Cyber Essentials, Cyber Essentials Plus or ISO 27001 schemes/standards. This is unlikely to change in future.

Can I use VSCode on the HPC clusters?

Usage restrictions

Caution

The usage of VSCode on the Sheffield HPC clusters is partially restricted. Usage of the Visual Studio Code Remote - SSH and Visual Studio Code Remote Explorer extensions to run VSCode on the HPC clusters is not permitted.

The Visual Studio Code Remote - SSH and Visual Studio Code Remote Explorer extensions use SSH to download a copy of VSCode to the cluster then start VSCode on the login nodes and forward back the interface to you. This means the VSCode and all dependent processes you run in the terminal are run on the login nodes. Not only does this tend to spawn lots of processes (which might hit our 100 processes per user limit on the login nodes which will lock you out of the cluster) it also fails to clean up processes correctly when the SSH connection is eventually terminated. This results in orphaned processes using high CPU, wasting resources. Furthermore, some users also try to use large amounts of CPU by running code / debugging on the login nodes which unfairly impacts other users as well.

Hint

As documented elsewhere in this site, if you are doing anything that will require a lot of CPU or memory you should use a worker node.

Permitted alternative methods for running VSCode are detailed below in the ideal order of preference

In the first instance, we recommend a workflow where version control with Github (or similar) is used alongside VSCode where scripts/code are synchronised between machines (e.g. your local machine and the HPC cluster) using conventional Git sync commands. Users are free to use the VSCode terminal on the local machine to SSH to the clusters and execute commands where necessary.

If this is not possible then VSCode can be ran on a worker node and forwarded back to your local machine in a web browser via our VSCode Remote HPC script, (from Github). Details for its use are included on the linked Github page.

If neither of these options are feasible, then running VSCode on a local machine in concert with an SSHFS mount of the desired folders from the HPC clusters to the local filesystem is possible but discouraged due to the likelihood of poor performance from machines remote from the clusters. By mounting the folder from the HPC cluster to a local filesystem folder, users can edit files on the cluster with VSCode as if they were normal local machine files.

Launching MPI tasks with srun versus mpirun or mpiexec

Documentation found elsewhere may recommend launching MPI tasks from batch jobs using the mpirun (or mpiexec) program that comes with the MPI implementation you are using.

On Bessemer and Stanage we recommend launching MPI tasks from batch jobs using Slurm’s srun command. This only works if the MPI implmentation you are using is built against a version of the PMI2 or PMI-X library that is compatible with the PMI2 or PMI-X library used by the Slurm job scheduler. This is the case for the administrator-provided versions of OpenMPI and Intel MPI on Bessemer and Stanage; no extra configuration is required by the end user.

On Bessemer and Stanage in batch scripts you should use the --export=ALL option with the srun command, which tells Slurm to export all of the current shell environment variables to the job environment.

srun --export=ALL my_program

This is important because many applications and libraries rely on environment variables to locate their dependencies, such as shared libraries.

Take, for instance, if we were to submit this OpenMPI non-interactive hello world job without the --export=ALL option, i.e:

 #!/bin/bash
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
 module load OpenMPI/4.1.4-GCC-12.2.0
 srun hello

On the Stanage cluster, we would encounter an error message containing:

[node140.pri.stanage.alces.network:12429] PMIX ERROR: NOT-FOUND in file client/pmix_client.c at line 562

While loading the OpenMPI module will set the variable SLURM_MPI_TYPE=pmix_v4, when srun is initiated it creates a new environment. Since we haven’t instructed it to export the environment variables to this new environment, it will not be able to locate SLURM_MPI_TYPE, even if it’s available in the current shell environment.

For those more familiar with the use of mpirun and mpiexec: srun can here be thought to be functionally equivalent to mpirun and mpiexec, although it takes different arguments and can also be used for starting interactive sessions on Slurm clusters.

Are there any license restrictions for ANSYS?

ANSYS users are subject to a per user limit of 400 concurrent cores via a maximum check out limit of 400 ANSYS multi-core licenses. There are no limitations on the number of ANSYS applications users can open however:

  • Multi-core licenses are checked out per application;

  • when more than 4 cores are used concurrently;

  • with the number required equal to the number of cores in use greater than 4.

This restriction applies on an individual user basis across all applications and devices concurrently, including personal machines, managed desktop machines and the HPC clusters.

As a result of the above anyone on HPC, personal PCs or managed PCs using more than 4 cores per application open will require a number of ANSYS multi-core licenses equivalent to the number of cores they are using minus 4, but cannot use more than 400 at once.

Example of license usage by a user

User using ANSYS

Multi-core licenses in use

On a desktop open using 4 cores

4 - 4 = 0

On another desktop using 6 cores

6 - 4 = 2

A job on Bessemer using 12 cores

12 - 4 = 8

A job on Stanage using 20 cores

20 - 4 = 16

Another job on Stanage using 30 cores

30 - 4 = 26

Total

52