2. FAQ: HPC Basic Usage#

2.1. How can I connect to Hydra?#

  1. Connecting to Hydra requires an active VSC account. If you are eligible, you can already create your account.

  2. Once you have your VSC account, you need a client software in your computer to connect to Hydra. We provide instructions for Windows, macOS, and Linux to setup your connection.

2.2. Issues connecting to Hydra#

If you cannot connect after following the instructions in How to Connect, here is a list of things you can check:

  1. Changes in your VSC account can take up to an hour to become active in the HPC clusters

    This includes the approval of your account, new uploaded public keys, as well as memberships to user groups and Virtual Organizations.

  2. Are you trying to connect from outside Belgium?

    Make sure to first register your IP in the HPC firewall, see the instructions in Connecting from outside Belgium.

  3. Check the location of your private SSH key

    Verify that the file of your private key corresponds to the same key that was generated together with the public key that you uploaded to your VSC account page.

    If you can’t find the correct private key, you can create a new key pair and upload the new public key to your VSC account page. Please check VSCdocReset your SSH keys if you need to start over.

    The location of your private key in your computer must be known to your SSH client:

    • Windows (PuTTY or MobaXterm): select the path to your private key in the SSH settings

    • Linux, macOS: the recommended path is ~/.ssh/id_rsa_vsc. Make sure to configure SSH to use the key in this path whenever you use your VSC-id by following the instructions in VSCdoclink your key and VSC-id.

      Alternatively, you can manually specify a custom location of your key to SSH with the following command:

      # replace <path_to_private_key> with the full path of your key
# replace vsc1xxxx with your VSC account ID
ssh -i <path_to_private_key> vsc1xxxx@login.hpc.vub.be

  4. Check the file permissions of your private SSH key

    The file of your private key must only have read permission for your user (the owner) and no permissions for group or other.

    Command for Linux and macOS users to set the correct permissions#
      chmod 400 <path_to_private_key>

  5. Check the format of your private SSH key

    • MobaXterm: both OpenSSH and PuTTY (.ppk) formats are supported.

    • PuTTY: only PuTTY format is supported.

    • Linux, macOS: only OpenSSH format is supported.

    On Windows computers, keys can be converted between PuTTY and OpenSSH formats with MobaXterm or PuTTYgen (bundled with PuTTY). Follow the instructions in VSCdocconvert to OpenSSH format.

  6. Check the passphrase of your SSH key

    Upon login you will be asked to re-enter the passphrase that you entered during generation of your SSH key pair. If you forgot this passphrase, you will have to reset your keys following the instructions in VSCdocReset your SSH keys. Note that it can take up to 1 hour before you will be able to use your new SSH key. Note also that passphrase is not the same as password. If the system asks for your password, something else is wrong.

  7. Double check for spelling mistakes

    Common mistakes are the hostname of the login server (e.g. login.hpc.vub.be) or your VSC account ID (vsc1xxxx: ‘vsc’ followed by 5 digits).

  8. You previously connected to Hydra from a different computer than the one you are currently using?

    There are two solutions:

    • copy your existing private key to the new computer in the correct location

    • create a new SSH key pair and upload this new public key as your second key to your VSC account page

  9. Check software updates on your computer

    Software updates can be critical on Windows, as older versions of PuTTY or MobaXterm may not support some required (security-related) features.

Helpdesk If you still cannot connect with the above suggestions, we can assist you in the login process. Linux/macOS users, please provide the full output of the command:

# replace <path_to_private_key> with the full path of your key
# replace vsc1xxxx with your VSC account ID
ssh -vvv -i <path_to_private_key> vsc1xxxx@login.hpc.vub.be

2.3. How can I simplify my login to the HPC?#

On Windows, once your connection to any VSC cluster is properly configured in the SSH client software of your choice (i.e. PuTTY or MobaXterm), the login process becomes a click in the respective connection icon. The SSH client will automatically use your VSC ID and pick your SSH key.

On Linux and MacOS, it is possible to create a shortcut in SSH for your connections to the VSC clusters as well. You can configure all the details of your connection in the file ~/.ssh/config as follows:

Note

Create the file ~/.ssh/config if it does not exist.

1Host login.hpc.vub.be login.hpc.uantwerpen.be login.hpc.ugent.be login.hpc.kuleuven.be login1-tier1.hpc.kuleuven.be login2-tier1.hpc.kuleuven.be
2    User vsc10xxx
3    IdentityFile ~/.ssh/your_vsc_key_file
4Host vubhpc
5    Hostname login.hpc.vub.be
6Host ugenthpc
7    Hostname login.hpc.ugent.be
8Host breniac
9    Hostname login1-tier1.hpc.kuleuven.be login2-tier1.hpc.kuleuven.be

  • Host login.hpc…: this first block defines the connection settings for all existing VSC login nodes

    • User: replace vsc10xxx with your VSC ID

    • IdentityFile: replace ~/.ssh/your_vsc_key_file with the path to your SSH key

  • Host vubhpc: this block creates a shortcut that is specific for login.hpc.vub.be

Once these settings are added to ~/.ssh/config, you will be able to connect to Hydra with the command

ssh vubhpc

Or to the Tier-1 Breniac cluster in KU Leuven with

ssh breniac

More information and advanced options are available in VSCdocSSH config

2.4. What can I do in the login node?#

The login node is your main interface with the compute nodes. This is where you can access your data, write the scripts and input files for your calculations and submit them to the job scheduler of Hydra. It is also possible to run small scripts in the login nodes, for instance to process the resulting data from your calculations or to test your scripts before submission to the scheduler. However, the login node is not the place to run your calculations and hence, the following restrictions apply:

  • Any single user can use a maximum of 12GB of memory in the login node.

  • The amount of CPU time that can be used is always fairly divided over all users. A single user cannot occupy all CPU cores.

  • The allowed network connections to the outside are limited to SSH, FTP, HTTP and HTTPS.

Lightweight graphical applications can be launched through X11 forwarding. For more complex programs and visualization tools, a graphical desktop environment is available through a VNC. More information in the Software section: Graphical applications

Jobs submitted to the scheduler are preprocessed before placement in the queues to ensure that their requirements of resources are correct. For instance, the system automatically assigns memory limits to your job if you didn’t specify it manually. Detailed information can be found in the section Job Submission.

Users compiling their own software should check Installing additional software

2.5. What software is available?#

Software in Hydra is provided with modules that can be dynamically loaded by the users. Please, read our documentation on the Module System.

2.6. How can I check my disk quota?#

Your VSC account page shows up to date information (updated every 15 min) about data usage and the quota of your $HOME ($VSC_HOME), $VSC_DATA and $VSC_SCRATCH, as well as your Virtual Organization ($VSC_DATA_VO and $VSC_SCRATCH_VO). You can get more up to date information about the scratch storage with the command myquota (updated every 5 min).

You will receive a warning notification by email whenever you reach 90% of your quota in any of the partitions in Hydra.

To prevent your account from becoming unusable, you should regularly check your disk quota and cleanup any files that are no longer necessary for your active projects.

For more information, please check our documentation on HPC Data Storage and VSCdocDisk space usage

2.7. How can I check my resource usage?#

Making an efficient use of the HPC cluster is important for you and your colleagues. Requesting too many resources is detrimental in several ways:

  1. Your jobs will stay more time in queue: the larger the pool of requested resources, the more difficult is it for the resource manager to free them

  2. The bigger the job the larger impact it will have on the queue and big enough jobs can cause a general slow down of the speed of the queue

  3. Any computational resources not used are a waste of energy, which directly translate to carbon emissions

2.7.1. slurm_jobinfo#

The command slurm_jobinfo <jobID> shows the resource usage of a given job, where <jobID> has to be replaced by the 8-digit number that identifies your job.

Example output of slurm_jobinfo#
 Name                : my-job01
 User                : vscXXXXX
 Partition           : skylake
 Nodes               : node300
 Cores               : 1
 State               : COMPLETED
 Submit              : 2023-09-26T11:01:12
 Start               : 2023-09-26T11:01:14
 End                 : 2023-09-26T11:07:45
 Reserved walltime   : 00:10:00
 Used walltime       : 00:06:31
 Used CPU time       : 00:05:29
 % User (Computation): 83.81%
 % System (I/O)      : 16.19%
 Mem reserved        : 4500M
 Max Mem used        : 171.21M (node300)
 Max Disk Write      : 75.88M (node300)
 Max Disk Read       : 555.45M (node300)
 Working directory   : /theia/scratch/brussel/XXX/vscXXXXX

The 3 main resources to keep an eye on are:

time limit (Reserved walltime, Used walltime)

Maximum is 5 days. Always set a time limit that is close to the duration of your job (with some margin). Longer time limits cause longer wait times in queue as it is more difficult for the scheduler to find a window in the schedule for your job.

memory (Max Mem used, Mem reserved)

Jobs get ~4 GB per core by default. Always set a slightly higher (10%) amount of memory than needed by your job. Requesting excessive memory will not make your job any faster but it will make it wait longer in queue.

core activity (Used CPU time)

Amount of time spent by the job using its CPU cores. Very efficient jobs should have a Used CPUTime close to Used walltime multiplied by the number of cores requested by the job. Keep in mind that not all software can exploit any arbitrary number of cores. For instance, Python and R are limited to 1 core by default and any additional cores will be ignored (see How to run Python in parallel? and How can I run R in parallel? for more information).

The command mysacct also shows the resource usage of recently finished jobs, including individual job steps (advanced usage).

2.8. How can I get more storage?#

The storage provided in the individual partitions $HOME, $VSC_DATA or $VSC_SCRATCH is relatively limited on purpose. Users needing a larger storage space are expected to be part of a Virtual Organization (VO) and use the shared storage in it.

2.9. How can I use GPUs in my jobs?#

The available GPUs in Hydra are listed in VSCdocHydra hardware

To use GPUs with Slurm have a look at Jobs for GPUs.

2.10. Where can I find public datasets and databases?#

We provide storage for datasets and databases that are public and free to use in the shared directory /databases. The data in there is accessible by all users of the HPC cluster. Users who need public data to run their calculations should always check first if it is already available in /databases.

Helpdesk We can add new databases to the HPC cluster upon request.

Tip

The PDB database can be found in /databases/bio/PDB and is automatically updated on a weekly basis.

2.11. Can I run containers on Hydra?#

We support Singularity containers in Hydra. Singularity allows any user to run a container without root privileges. You can either use any of the containers already installed in Hydra that are located in /apps/brussel/singularity/, use your own container or request the installation of a container to VUB-HPC Support.

Users can create their own Singularity image in their personal computer (with root privileges) either manually or by importing an existing Docker image. Then the resulting container can then be transferred to Hydra and run with your VSC user account. We recommend using Singularity containers to use software with very specific and complex requirements (dependencies, installation, …) and for quickly testing any software.

See also

The documentation by Sylabs, the developers of Singularity.

Note

The Module System is still the preferred method to run software in Hydra. Singularity containers are usually not optimized for the different CPU architectures present in the cluster and put more network pressure on the system.

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