Robin-hpc
From Robin
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| 2 cores/4 vCPU | | 2 cores/4 vCPU | ||
| 16GB<br /> | | 16GB<br /> | ||
- | | | + | | RHEL9 |
|- | |- | ||
| worker node | | worker node | ||
| 120 cores/240 vCPU | | 120 cores/240 vCPU | ||
| 460GB | | 460GB | ||
- | | | + | | RHEL9 |
|} | |} | ||
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Now, <code>ssh hpc-robin</code> should directly establish a connection to the server (commands like <code>scp</code> should also work in the same way). | Now, <code>ssh hpc-robin</code> should directly establish a connection to the server (commands like <code>scp</code> should also work in the same way). | ||
- | == Access == | + | == Access == |
- | + | All you need to do is to <code> ssh <your_username>@hpc.robin.uiocloud.no</code> from a UiO network. | |
== SLURM == | == SLURM == | ||
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== Software == | == Software == | ||
- | === Matlab === | + | <!-- === Matlab === |
- | + | ||
'''Setting up the SLURM job script''' | '''Setting up the SLURM job script''' | ||
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end | end | ||
</pre> | </pre> | ||
+ | ---> | ||
=== Anaconda === | === Anaconda === | ||
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The output is written to <code>"log.txt"</code> and can be traced via <code>"tail -f log.txt"</code>. | The output is written to <code>"log.txt"</code> and can be traced via <code>"tail -f log.txt"</code>. | ||
- | === | + | === Running containers === |
- | + | <code>apptainer</code> is installed on <code>robin-hpc</code>. Read more about apptainer/singularity on https://sylabs.io/guides/3.0/user-guide/index.html . | |
+ | |||
+ | == Acknowledge use of <code>robin-hpc</code> == | ||
+ | |||
+ | The <code>robin-hpc</code> is run on NREC. Please acknoladge useage of their services using the following statment: | ||
+ | |||
+ | The computations were performed on the Norwegian Research and Education | ||
+ | Cloud (NREC), using resources provided by the University of | ||
+ | Bergen and the University of Oslo. http://www.nrec.no/ | ||
+ | |||
+ | Ref https://docs.nrec.no/faq.html#how-to-acknowledge-the-use-of-nrec |
Current revision as of 09:31, 7 May 2024
Contents |
Hardware and network configuration
The robin-hpc
is a shared resource for robins researchers and Master students. The strength of the machine is the amount of CPU cores and RAM. Unforunatly, there's no GPU available in this service.
Specs
CPU | RAM | OS | |
---|---|---|---|
login node | 2 cores/4 vCPU | 16GB | RHEL9 |
worker node | 120 cores/240 vCPU | 460GB | RHEL9 |
Storage
The storage on the nodes consists of one 1TB disk where 100GB is reserved for software and 900GB is reserved for the users of the node. However, each user has a soft limit of 20 GB and a hard limit of 100 GB with a grace period of 14 days.
It's important to note that there is no backup of the disk, so do not use the robin-hpc
as a cloud storage service. We suggest using rsync
/scp
to your home area on login.ifi.uio.no
.
E.g.
rsync --progress <file>.tar.gz <username>@login.ifi.uio.no:~/<path>/<to>/<wherever>
It is also a possibility to mount your UiO home directory to the robin-hpc
.
Network
For security reasons, the robin-hpc
is only accessable from ifis-networks. If you use a desktop machine at ifi, you can access the robin-hpc
directly. However, from your own laptop you are required to login to ifi's login cluster, namely login.ifi.uio.no
, before you can access hpc.robin.uiocloud.no
.
URL for the robin-hpc
login node is: hpc.robin.uiocloud.no
.
SSH from outside UiOs networks
To access the machine from outside UiOs networks, see Configure SSH. To make SSH slightly more pleasant to work with we can create a configuration file at ~/.ssh/config
which can contain additional information about remote machines. The following is a possible configuration for the Robin-hpc (see here for more info). Indiviual key paths can be added with IdentityFile ~/.ssh/<key_on_jump_host>
.
Host uio-login User <my-username> Hostname <my-uio-hostname>
Host hpc-robin HostName hpc.robin.uiocloud.no ProxyJump uio-login User <my-username>
Now, ssh hpc-robin
should directly establish a connection to the server (commands like scp
should also work in the same way).
Access
All you need to do is to ssh <your_username>@hpc.robin.uiocloud.no
from a UiO network.
SLURM
Ropin-hpc uses slurm for job scheduling.
To start a job on robin-hpc you will need to use a job script specifying the resources you want to use. The job is started with the following command:
sbatch nameofthejobscript.sh
(Note: Please do not run your program on the login node, test your implementation before copying the files to robin-hpc. You can easily copy the files needed to run your program to your home area on robin-hpc with scp.)
Below you will find a template for the job script, followed by some convenient commands.
For more information about slurm please visit https://slurm.schedmd.com/quickstart.html.
SLURM job script template
#!/bin/bash # This is a template for a slurm job script. # To start a job on robin-hpc please use the command "sbatch nameofthisscript.sh". # Job name #SBATCH --job-name=nameofmyjob # Wall clock time limit (hh:mm:ss). # (Note: The program will be killed when the time limit is reached.) #SBATCH --time=01:00:00 # Number of tasks to start in parallel from this script. # (i.e. myprogram.py below will be started ntasks times) #SBATCH --ntasks=1 # CPUs allocated per task #SBATCH --cpus-per-task=16 # Memory allocated per cpu #SBATCH --mem-per-cpu=1G # Set exit on errors set -o errexit set -o nounset # Load your environment source myenv/bin/activate # Run your program with "srun yourcommand" # stdout and stderr will be written to a file "slurm-jobid.out". # (warning: all tasks will write to the same slurm.out file) srun python3 myprogram.py
Additional options
To run multiple tasks in sequence you can also use the --array option of the sbatch command. You can add the following to the script. You can then get the job array number with SLURM_ARRAY_TASK_ID. The following example would run 900 jobs:
#SBATCH --array=0-899
Convenient commands
View the status of all jobs:
squeue
View the status of your own jobs:
squeue -u yourusername
Cancel all your jobs:
scancel -u yourusername
Cancel all jobs with name "job_name":
scancel -n job_name
Software
Anaconda
After initializing Anaconda (see Deep Learning Workstations), it is possible to start a job on robin-hpc by using the command above and the following template:
SLURM Anaconda template
#!/usr/bin/bash #SBATCH --job-name=<test_name> #SBATCH --output=log.txt #SBATCH --ntasks=1 #SBATCH --time=01:00:00 #SBATCH --mem-per-cpu=100 # load anaconda and your environment source ~/.bashrc conda activate <your_environment> # Run your program with "srun your_command" srun python3 <script_name>.py
The output is written to "log.txt"
and can be traced via "tail -f log.txt"
.
Running containers
apptainer
is installed on robin-hpc
. Read more about apptainer/singularity on https://sylabs.io/guides/3.0/user-guide/index.html .
Acknowledge use of robin-hpc
The robin-hpc
is run on NREC. Please acknoladge useage of their services using the following statment:
The computations were performed on the Norwegian Research and Education Cloud (NREC), using resources provided by the University of Bergen and the University of Oslo. http://www.nrec.no/
Ref https://docs.nrec.no/faq.html#how-to-acknowledge-the-use-of-nrec