Frequently asked questions

Job status and submission

Why are my jobs waiting in the queue with reason AssocGrpMemRunMinutes/AssocGrpCPURunMinutes or such?

Accounts are limited in how much the can run at a time, in order to prevent a single or a few users from hogging the entire cluster with long-running jobs if it happens to be idle (e.g. after a service break). The limit is such that it limits the maximum remaining runtime of all the jobs of a user. So the way to run more jobs concurrently is to run shorter and/or smaller (less CPU’s, less memory) jobs. For an in-depth explanation see and for a graphical simulator you can play around with: . You can see the exact limits of your account with

sacctmgr -s show user $USER format=user,account,grptresrunmins%70
Why are my jobs in state "launch failed requeued held"?

Slurm is configured such that if a job fails due to some outside reason (e.g. the node where it’s running fails rather than the job itself crashing due to a bug in the job) the job is requeued in a held state. If you’re sure that everything is ok again you can release the job for scheduling with “scontrol release JOBID”. If you don’t want this behavior (i.e. you’d prefer that such failed jobs would just disappear) then you can prevent the requeuing with

#SBATCH --no-requeue
How can I find out the remaining runtime of my job/allocation?

You can find out the remaining time of any job that is running with

squeue -h -j  -o %L

Inside a job script or sinteractive session you can use the environment variable SLURM_JOB_ID to refer to the current job ID.

There seems to be running a lot of jobs in the short queue that has gone for longer than 4 hours. Should that be possible?

SLURM kills jobs based on the partition’s TimeLimit + OverTimeLimit parameter. The later in our case is 60 minutes. If for instance queue time limit is 4 hours, SLURM will allow to run on it 4 hours, plus 1 hour, thus no longer than 5 hours. Though OverTimeLimit may vary, don’t rely on it. Partition’s (aka queue’s) TimeLimit is the one that end user should take into account when submit his/her job. Time limits per partiton one can check with slurm p command.

For setting up exact time frame after which you want your job to be killed anyway, set --time parameter when submitting the job. When the time limit is reached, each task in each job step is sent SIGTERM followed by SIGKILL. If you run a parallel job, set --time with srun as well. See ‘man srun' and ‘man sbatch’ for details.

#SBATCH --time=1:00:00

srun --time=1:00:00 ...
``srun: error: Unable to allocate resources: Requested node configuration is not available``

You have requested some Slurm options which do not include any nodes (for example, asking for a GPU with --gres=gpu and a partition without GPUs). Figure out what the problem is and adjust your Slurm options.

``srun: Required node not available (down, drained or reserved)``

This error usually occurs when a requested node is down, drained or reserved which can happen if the cluster is undergoing some work - and might happen if there are very few default nodes that Slurm chooses from. If this error occurs then the shell will usually hang after the job has been submitted if the job is still waiting for allocation. To find which nodes are available for us to run jobs we can use sinfo and under the STATE column you will see for each partition the states of the nodes.

To fix this we can either wait for the node to be available or choose a different partition with the --partition= command, using one of the partitions from sinfo which has free and available (idle) nodes.

Accounts and Access to triton

How can I access my Triton files from outside?

Remote mounting

The scratch filesystem can be mounted from inside the Aalto networks by using smb:// For example, from Nautilus (the file manager) on Ubuntu, use “File” -> “Connect to server”. Outside Aalto networks, use the Aalto VPN. If it is not an Aalto computer, you may need to us AALTO\username as the username, and your Aalto password.

Or you can use sshfs – filesystem client based on SSH. Most Linux workstations have it installed by default, if not, install it or ask your local IT support to do it for you. For setting up your SSHFS mount from your local workstation: create a local directory and mount remote directory with sshfs

$ mkdir /LOCALDIR/triton
$ sshfs /LOCALDIR/triton

Replace user1 with your real username and /LOCALDIR with a real directory on your local drive. After successful mount, use you /LOCALDIR /triton directory as it would be local. To unmount it, run fusermount -u /LOCALDIR/triton.

PHYS users example, assuming that Triton and PHYS accounts are the same:

$ mkdir /localwrk/$USER/triton
$ sshfs$USER  /localwrk/$USER/triton
$ cd /localwrk/$USER/triton
... (do what you need, and then unmount when there is no need any more)
$ fusermount -u /localwrk/$USER/triton

Easy access with Nautilus

The SSHFS method described above works from any console. Though in case of Linux desktops, when one has a GUI like Gnome or Unity (read all Ubuntu users) one may use Nautilus – default file manager – to mount remote SSH directory. Click File -> Connect to Server choose SSH, input as a server and directory /triton/PATH/TO/DIR you’d like to mount, type your name. Leave password field empty if you use SSH key. As soon as Nautilus will establish connection it will appear on the left-hand side below Network header. Now you may access it as it would be your local directory. To keep it as a bookmark click on the mount point and press Ctrl+D, it will appear below Bookmark header on the same menu.

Copying files

If your workstatios has no NFS mounts from Triton (CS and NBE have, consult with your local admins for exact paths), you may always use SSH. Either copy your files from triton to a local directory on your workstation, like:

$ sftp* .
I need to connect to some server on a node

Let’s say you have some server (e.g. debugging server, notebook server, …) running on a node. As usual, you can do this with ssh using port forwarding. It is the same principle as in several of the above questions.

For example, you want to connect from your own computer to port AAAA on node nnnNNN. You run this command:


Then, when you connect to port BBBB on your own computer (localhost, it gets forwarded straight to port AAAA on node nnnNNN. Thus only one ssh connection gets us to any node. It is possible for BBBB to be the same as AAAA. By the way, this works with any type of connection. The node has to be listening on any interface, not just the local interface. To connect to localhost:AAAA on a node, you need to repeat the above steps twice to forward from workstation->login and login->node, with the second nnnNNN being localhost.

Graphical programs don't work (X11, -X)

In order for graphical programs on Linux to work, a file ~/.Xauthority has to be written. If your home directory quota (check with quota) is exceeded, then this can’t be written and graphical programs can’t open. If your quota is exceeded, clean up some files, close connections, and log in again. You can find where most of your space goes with du -h $HOME | sort -hr | less.

This is often the case if you get X11 connection rejected because of wrong authentication.

Storage, file transfer and quota

``Disk quota exceeded`` error but I have plenty of space

Main article: Triton Quotas

Everyone should have a group quota, but no user quota. All files need to be in a proper group (either a shared group with quota, or your “user private group”). First of all, use the ‘quota’ command to make sure that neither disk space nor number of files are exceeded. Also, make sure that you use $WRKDIR for data and not $HOME. If you actually need more quota, ask us.

Solution: add to your main directory and all your subdirectories to the right group, and make sure all directories have the group s-bit set, (SETGID bit, see man chmod). This means “any files created within this directory get the directory’s group”. Since your default group is “domain users” which has no quota, if the s-bit is not set, you get an immediate quota exceeded by default.

# Fix everything
#  (only for $WRKDIR or group directories, still in testing):
/share/apps/bin/quotafix -sg --fix /path/to/dir/

# Manual fixing:
# Fix sticky bit:
lfs find $WRKDIR -type d --print0 | xargs -0 chmod g+s
# Fix group:
lfs find /path/to/dir  ! --group $GROUP -print0 | xargs -0 chgrp $GROUP

Why this happens: $WRKDIR directory is owned by the user and user’s group that has the same name and GID as UID. Quota is set per group, not per user. That is how it was implemented since 2011 when we got Lustre in use. Since spring 2015 Triton is using Aalto AD for the authentication which sets everyone a default group ID to ‘domain users’. If you copy anything to $WRKDIR/subdirectory that has no +s bit you copy as a ‘domain users’ member and file system refuses to do so due to no quota available. If g+s bit is set, all your directories/files copied/created will get the directory’s group ownership instead of that default group ‘domain users’. There can be very confusing interactions between this and user/shared directories.

While copying to $WRKDIR with rsync or cp I'm getting 'Disk quota exceeded' error, though my quota is fine.

It is related to the above mentioned issue, something like rsync -a … or cp -p … are trying to save original group ownership attribute, which will not work. Try this instead:

## mainly one should avoid -g (as well as -a) that preserves group attributes
$ rsync -urlptDxv --chmod=Dg+s somefile

## avoid '-p' with cp, or if you want to keep timestapms, mode etc, then use '--preserve='
$ cp -r --preserve=mode,timestamps  somefile /path/to/mounted/triton/work/directory
My $WRKDIR is not visible on my department computer

Most likely your Kerberos ticket has expired. If you log in with a password or use ‘kinit’, you can get an another ticket. See page on data storage and remote data for more information.

How can I copy Triton files from outside of Aalto?

It is an extension of the previous question. In case you are outside of Aalto and has neither direct access to Triton nor access to NFS mounted directories on your directory servers. Say you want to copy your Triton files to your home workstation. It could be done by setting up an SSH tunnel to your department SSH server. A few steps to be done: set tunnel to your local department server, then from your department server to Triton, and then run any rsync/sftp/ssh command you want from your client using that tunnel. The tunnel should be up during whole session.

client: ssh -L9509:localhost:9509 department.ssh.server
department server: ssh -L9509:localhost:22
client: sftp -P 9509 localhost:/triton/own/dir/* /local/dir

Note that port 9509 is taken for example only. One can use any other available port. Alaternatively, if you have a Linux or Mac OS X machine, you can setup a “proxy command”, so you don’t have to do the steps above manually everytime. On your home machine/laptop, in the file ~/.ssh/config put the lines

Host triton
    ProxyCommand /usr/bin/ssh DEPARTMENTUSERNAME@department.ssh.server "/usr/bin/nc -w 10 22"

This creates a host alias “triton” that is proxied via the department server. So you can copy a file from your home machine/laptop to triton with a command like:

rsync filename triton:remote_filename
I can't save anything to my ``$HOME`` directory, get some fsync error.

Most probably your quota has exceeded, check it out with quota command.

quota is a wrapper at /usr/local/bin/quota on front end which merges output from classic quota utility that supports NFS and Lustre’s lfs quota. NFS $HOME directory is limited to 10GB for everyone and intended for initialization files mainly. Grace period is set to 7 days and “hard” quota is set to 11GB, which means you may exceed your 10GB quota by 1GB and have 7 days to go below 10GB again. However none can exceed 11GB limit.

Note: Lustre mounted under /triton is the right place for your simulation files. It is fast and has large quotas.

Can you recovery some files from my ``$HOME`` or ``$WRKDIR`` directory?

Short answer: yes for $HOME directory and no for $WRKDIR.

$HOME is slow NFS with small quota mounted through Ethernet. Intended mainly for user initialization files and for some plain configs. We make regular backups from $HOME.
$WRKDIR (aka /triton) is fast Lustre, has large quota, mounted through InfiniBand. Though no backups made from /triton, the DDN storage system as such is secure and safe place for your data, though you can always loose your data deleting them by mistake. Every user must take care about his work files himself. We provide as much diskspace to every user, as one needs and the amount of data is growing rapidly. That is the reason why the user should manage his important data himself. Consider backups of your valuable data on DVDs/ USB drives or other resources outside of Triton.

Command line interface

Can I change zsh to bash?

Yes. Change shell to your Aalto account and re-login to Triton to get your newly changed shell to work. For Aalto account changes one can login to, run kinit first and then run chsh, then type /bin/bash. To find out what is your current shell, run echo $SHELL

For the record: your default shell is not set by Triton environment but by your Aalto account.

Modules and environment settings

Job fails due to missed module environment variables.

You have included ‘module load module/name’ but job still fails due to missing shared libraries or that it can not find some binary etc. That is a known ZSH related issue. In your sbatch script please use -l option (aka --login) which forces bash to read all the initialization files at /etc/profile.

#!/bin/bash -l

Alternatively, one can change shell from ZSH to BASH to avoid this hacks, see the post above.

Can I use a more up-to-date version of git on triton?

Indeed the default git with Triton OS system (CentOS) is quite old (v 1.8.x). To get a more modern git you can run module load git (version 2.28.0 when this is being written).

Coding and Compiling cannot open shared object file: No such file or directory

You are trying to run a GPU program (using CUDA) on a node without a GPU (and thus, no Remember to specify that you need GPUs

The cluster has a few compiler sets. Which one am I suppose to use? What are the limits for commercial compilers?

Currently there are two different sets of compilers: (i) GNU compilers, native for Linux, installed by default, (ii) Intel compilers plus MKL, a commercial suite, often the fastest compiler on Xeons.

FGI provides all FGI sites with 7 Intel licenses, thus only 7 users can compile/link with Intel at once.

Code is compiled with shared libraries and it stops with an error message: ``error while loading shared libraries: cannot open shared object file: No such file or directory``

That means your program can’t find libraries which has been used at linking/compiling time. You may always check shared library dependencies:

$ ldd YOUR_PROGRAM # print the list of libraries required by program
If some of libraries is marked as not found, then you should first (i) find the exact path to that lib (suppose it is installed), then second (ii) explicitly add it to your environment variable $LD_LIBRARY_PATH.
For instance, if your code has been previously compiled with the but on SL6.2 it reports an error like error while loading shared libraries: try to locate the library:
$ locate

and the add it to your $LD_LIBRARY_PATH

export LD_LIBRARY_PATH=/usr/lib64/compat-openmpi/lib:$LD_LIBARY_PATH # export the lib in BASH environment

or, as in case of we have ready module config, just run

module load compat-openmpi-x86_64

In case your code is missing some specific libs, not installed on Triton (say you got a binary compiled from somewhere else), you have a few choices: (i) get statically linked program or (ii) find/download missing libs (for instance from developers’ site). For the second, copy libs to your $WRKDIR and add paths to $LD_LIBRARY_PATH, in the same maner as described above.

See also:

ldconfig -p # print the list of system-wide available shared libraries
While compiling should I use static or shared version of some library?

One can use both, though for shared libs all your linked libs must be either in your $WRKDIR in /shared/apps or must be installed by default on all the compute nodes like vast majority of GCC and other default Linux libs.

I've got a binary file, may I find out somehow whether it is 32-bit or 64-bit compiled?

Use file utility:

# file /usr/bin/gcc
/usr/bin/gcc: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV),
for GNU/Linux 2.4.0, dynamically linked (uses shared libs), not stripped

it displays the type of an executable or object file.

Other issues

How can I print my text file to a local department printer?

We don’t have local department printers configured anywhere on Triton. But one can use SSH magic to send a file or command output to a remote printer. Run from your local workstation, insert the target printer name:

... printing text file
$ ssh "cat file.txt" | enscript -P printer_name
... printing a PostScript file
$ ssh "cat" | lp -d printer_name -
... printing a man page
$ ssh "man -t sbatch" | lp -d printer_name -
How do I subscribe to triton-users maillist?

Having a user account on Triton also means being on the triton-users at mailist. That is where support team sends all the Triton related announcements. All the Triton users MUST be subscibed to the list. It is automatically kept up to date these days, but just in case you are not yet there, please send an email to your local team member and ask to add your email.

How to unsubscribe? You will be removed from the maillist as soon as your Triton account is deleted from the system. Otherwise no way, since we can’t notify about urgent things that affect data integrity or other issues.

What node names like cn[01-224] mean?

All the hardware delivered by the vendor has been labeled with some short name. In particular every single compute node has a label like Cn01 or GPU001 etc. we used this notation to name compute nodes, that is cn01 is just a hostname for Cn01, gpu001 is a hostname for GPU001 etc. Shorthands like cn[01-224] mean all the hostnames in the range cn01, cn02, cn03 .. cn224. Same for gpu[001-008], tb[003-008], fn[01-02]. Similar notations can be used with SLURM commands like:

$ scontrol show node cn[01-12]
Can't run graphical applications on nodes and "Warning: untrusted X11 forwarding setup failed: xauth key data not generated"

Check your .bashrc and other startup files. Some modules bring in so many dependencies that it can interfere with standard operating system functions: in this case, SSH setting up X11 forwarding for graphical applications.