FAQ

How do I connect to Beocat

Connection Settings
Hostname	headnode.beocat.ksu.edu
Port	22
Username	eID
Password	eID Password

Supported Connection Software (Latest Versions of Each)
Shell
	Putty
	ssh from openssh
File Transfer Utilities
	Filezilla
	WinSCP
	scp and sftp from openssh
Combination
	MobaXterm

Duo

If you're account is Duo Enabled, you will be asked to approve each connection through Duo's push system to your smart device by default for any non-interactive protocols. If you don't have a smart device, or your smart device is not currently able to be contacted by Duo, there are options.

Automating Duo Method

You would need to configure your connection client to send an Environment variable called DUO_PASSCODE. Its value could be the currently valid passcode from Duo, push or it could be set to phone. push will push the prompt to your smart device. phone will have duo call your phone number to approve.

With OpenSSH (Linux or Mac command-line), to automatically set the Duo method to "push", use the command

DUO_PASSCODE=push ssh -o SendEnv=DUO_PASSCODE headnode.beocat.ksu.edu

In PuTTY to automatically set the Duo method to "push", expand "Connection" (if it isn't already), then click "Data". Under Environment variables, enter DUO_PASSCODE beside Variable and push beside Value. Click the "Add" button and it will show up underneath. Be sure to go back to "Session" to save this change for PuTTY to remember this change.

There doesn't seem to be a way to send an environment variable in MobaXTerm, so you won't be able to set DUO_PASSCODE to an actual valid temporary key. To get MobaXterm to push automatically, you can edit your SSH session and on the "Advanced SSH Settings" tab, change the "Execute command" to

DUO_PASSCODE=push bash

Common issues

MobaXTerm has excessive prompts for managing files.

MobaXTerm has a sidebar browser for managing your files. Unfortunately, that sidebar browser initiates another SSH connection for every file transfer, which triggers a Duo push that you need to approve. MobaXTerm's dedicated SFTP Session doesn't have this same issue, it initiates a connection, keeps it open and re-uses it as needed, so you will have much fewer Duo approvals to respond to. If you choose to use the dedicated SFTP Session, you might consider disabling the sidebar file browser. "Advanced SSH settings" -> "SSH-browser type" -> "None"

Duo Pushes sometimes don't show up in a timely manner.

If you open the Duo MFA application on your smart device when you're expecting an authentication challenge, the prompts seem to show up faster.

How do I compile my programs?

Serial programs

Fortran

ifort or gfortran

C/C++

icc, gcc and g++

Parallel programs

Fortran

mpif77 or mpif90

C/C++

mpicc or mpic++

Do Beocat jobs have a maximum Time Limit

Yes, there is a time limit, the scheduler will reject jobs longer than 28 days. The other side of that is that we reserve the right to a maintenance period every 14 days. Unless it is an emergency, we will give at least 2 weeks notice before these maintenance periods actually occur. Jobs 14 days or less that have started when we announce a maintenance period should be able to complete before it begins.

With that being said, there is no guarantee that any physical piece of hardware and the software that runs on it will behave for any significant length of time. Memory, processors, disk drives can all fail with little to no warning. Software may have bugs. We have had issues with the shared filesystem that resulted in several nodes losing connectivity and forced reboots. If you can, we always recommend that you write your jobs so that they can be resumed if they get interrupted.

The 28 day limit can be overridden on a temporary and per-user basis provided there is enough justification

How are the filesystems on Beocat set up?

Mountpoint	Local / Shared	Size	Filesystem	Advice
/bulk	Shared	3.1PB shared with /homes and /scratch	cephfs	Slower than /homes; costs $45/TB/year
/homes	Shared	3.1PB shared with /bulk and /scratch	cephfs	Good enough for most jobs; limited to 1TB per home directory
/scratch	Shared	3.1PB shared with /bulk and /homes	cephfs	Fast shared tmp space; files not used in 30 days are automatically culled
/fastscratch	Shared	280TB	nfs on top of ZFS	Faster than /scratch, built with all NVME disks; files not used in 30 days are automatically culled.
/tmp	Local	>100GB (varies per node)	XFS	Good for I/O intensive jobs. Unique per job, culled with the job finishes.

Usage Advice

For most jobs you shouldn't need to worry, your default working directory is your homedir and it will be fast enough for most tasks. I/O intensive work should use /tmp, but you will need to remember to copy your files to and from this partition as part of your job script. This is made easier through the $TMPDIR environment variable in your jobs.

Example usage of $TMPDIR in a job script

#!/bin/bash

#copy our input file to $TMPDIR to make processing faster
cp ~/experiments/input.data $TMPDIR

#use the input file we copied over to the local system
#generate the output file in $TMPDIR as well
~/bin/my_program --input-file=$TMPDIR/input.data --output-file=$TMPDIR/output.data

#copy the results back from $TMPDIR
cp $TMPDIR/output.data ~/experiments/results.$SLURM_JOB_ID

You need to remember to copy over your data from $TMPDIR as part of your job. That directory and its contents are deleted when the job is complete.

What is "killable:1" or "killable:0"

On Beocat, some of the machines have been purchased by specific users and/or groups. These users and/or groups get guaranteed access to their machines at any point in time. Often, these machines are sitting idle because the owners have no need for it at the time. This would be a significant waste of computational power if there were no other way to make use of the computing cycles.

If you're wondering why a job may have the exit status of PREEMPTED from kstat or sacct, this is the reason.

Enter the "killable" resource

Killable (--gres=killable:1) jobs are jobs that can be scheduled to these "owned" machines by users outside of the true group of owners. If a "killable" job starts on one of these owned machines and the owner of said machine comes along and submits a job, the "killable" job will be returned to the queue, (killed off as it were), and restarted at some future point in time. The job will still complete at some future point, and if the job makes use of a checkpointing algorithm it may complete even faster. The trade off between marking a job "killable" and not, is that sometimes applications need a significant amount of runtime, and cannot resume running from a partial output, meaning that it may get restarted over and over again, never reaching the finish line. As such, we only auto-enable "killable" for relatively short jobs (<=168:00:00). Some users still feel this is a hindrance, so we created a way to tell us not to automatically mark short jobs "killable"

Disabling killable

Specifying --gres=killable:0 will tell us to not mark your job as killable.

The trade-off

If a job is marked killable, there are a non-trivial amount of additional nodes that the job can run on. If your job checkpoints itself, or is relatively short, there should be no downside to marking the job killable, as the job will probably start sooner. If your job is long-running and doesn't checkpoint (save its state to restart a previous session) itself, it could cause your job to take longer to complete.

Help! When I submit my jobs I get "Warning To stay compliant with standard unix behavior, there should be a valid #! line in your script i.e. #!/bin/tcsh"

Job submission scripts are supposed to have a line similar to '#!/bin/bash' in them to start. We have had problems with people submitting jobs with invalid #! lines, so we enforce that rule. When this happens the job fails and we have to manually clean it up. The warning message is there just to inform you that the job script should have a line in it, in most cases #!/bin/tcsh or #!/bin/bash, to indicate what program should be used to run the script. When the line is missing from a script, by default your default shell is used to execute the script (in your case /usr/local/bin/tcsh). This works in most cases, but may not be what you are wanting.

Help! When I submit my jobs I get "A #! line exists, but it is not pointing to an executable. Please fix. Job not submitted."

Like the above, error says you need a #!/bin/bash or similar line in your job script. This error says that while the line exists, the #! line isn't mentioning an executable file, thus the script will not be able to run. Most likely you wanted #!/bin/bash instead of something else.

Help! My jobs keep dying after 1 hour and I don't know why

Beocat has default runtime limit of 1 hour. If you need more than that, or need more than 1 GB of memory per core, you'll want to look at the documentation here to see how to request it.

In short, when you run sbatch for your job, you'll want to put something along the lines of '--time=0-10:00:00' before the job script if you want your job to run for 10 hours.

Help my error file has "Warning: no access to tty"

The warning message "Warning: no access to tty (Bad file descriptor)" is safe to ignore. It typically happens with the tcsh shell.

Help! My job isn't going to finish in the time I specified. Can I change the time requirement?

Generally speaking, no.

Jobs are scheduled based on execution times (among other things). If it were easy to change your time requirement, one could submit a job with a 15-minute run-time, get it scheduled quickly, and then say "whoops - I meant 15 weeks", effectively gaming the job scheduler. In extreme circumstances and depending on the job requirements, we may be able to manually intervene. This process prevents other users from using the node(s) you are currently using, so are not routinely approved. Contact Beocat support (below) if you feel your circumstances warrant special consideration.

Help! My perl job runs fine on the head node, but only runs for a few seconds and then quits when submitted to the queue.

Take a look at our documentation on Perl

Help! When using mpi I get 'CMA: no RDMA devices found' or 'A high-performance Open MPI point-to-point messaging module was unable to find any relevant network interfaces'

This message simply means that some but not all nodes the job is running on have infiniband cards. The job will still run, but will not use the fastest interconnect we have available. This may or may not be an issue, depending on how message heavy your job is. If you would like to not see this warning, you may request infiniband as a resource when submitting your job. --gres=fabric:ib:1

Help! when I use sbatch I get an error about line breaks

Beocat is a Linux system. Operating Systems use certain patterns of characters to indicate line breaks in their files. Linux and operating systems like it use '\n' as their line break character. Windows uses '\r\n' for their line breaks.

If you're getting an error that looks like this:

sbatch: error: Batch script contains DOS line breaks (\r\n)
sbatch: error: instead of expected UNIX line breaks (\n).

It means that your script is using the windows line endings. You can convert it with the dos2unix command

dos2unix myscript.sh

It would probably be beneficial for your editor to save the files with UNIX line breaks in the future.

• Visual Studio Code -- “Text Editor” > “Files” > “Eol”
• Notepad++ -- "Edit" > "EOL Conversion"

Common Storage For Projects

Sometimes it is useful for groups of people to have a common storage area.

If you do not have a project, send a request via email to beocat@cs.ksu.edu. Note that these projects are generally reserved for tenure-track faculty and with a single project per eID.

If you already have a project you can do the following:

Note: The $group_name variable in the commands below needs to be replaced with the lower case name of your project. Membership of the projects can be done using our Group Management application.

• Create a directory in one of the home directories of someone in your group, ideally the project owner's.
  • mkdir $directory
• Set the default permissions for new files and directories created in the directory:
  • setfacl -d -m g:$group_name:rX -R $directory
• Set the permissions for the existing files and directories:
  • setfacl -m g:$group_name:rX -R $directory

This will give people in your group the ability to read files in the 'share' directory. If you also want them to be able to write or modify files in that directory then use change the ':rX' to ':rwX' instead. e.g. 'setfacl -d -m g:$group_name:rwX -R $directory' for both setfacl commands.

How do I get more help?

There are many sources of help for most Linux systems.

Unix man pages

Linux provides man pages (short for manual pages). These are simple enough to call, for example: if you need information on submitting jobs to Beocat, you can type 'man sbatch'. This will bring up the manual for sbatch.

GNU info system

Not all applications have "man pages." Most of the rest have what they call info pages. For example, if you needed information on finding a file you could use 'info find'.

This documentation

This documentation is very thoroughly researched, and has been painstakingly assembled for your benefit. Please use it.

Contact support

Support can be contacted here. Please include detailed information about your problem, including the job number, applications you are trying to run, and the current directory that you are in.