Getting started

Welcome to MetaCentrum

MetaCentrum provides free computing resources to Czech academic institutions through distributed compute clusters.

Before getting started you need an active MetaCentrum account (see Account guide).

Getting started: Logging in

Once you have an activated account, connect to MetaCentrum using SSH with your username. Here we are using the tarkil.metacentrum.cz login server (frontend). You can use any frontend, but we recommend choosing the one closest to your physical location to minimize network latency.

ssh your_username@tarkil.metacentrum.cz

For the full list of frontends, their locations, and detailed login instructions (including Windows/PuTTY), see the Log in guide.

Understanding the architecture

MetaCentrum distributed ecosystem consists of compute clusters (or “compute nodes”, where the high performance computing itself is done), storage servers (a space for user data where users’ home directories are) and frontends (nodes dedicated for logging in).

The operating system used within MetaCentrum is Debian Linux. The system you will interact with for scheduling jobs is Portable Batch System (PBS).

Each frontend has a native home directory on a storage server. After logging in, you can access any storage from a given frontend. Every compute node has a fast local disk usually referred to as scratch.

Frontends are shared by all users and are not intended for heavy computing. Use them only for data preparation, job management, or light compiling.

For detailed infrastructure information see Frontend & Storage guide.

Running your first job

This tutorial will guide you through the process of running a simple Python script on a compute node.

Make sure to replace myuser with your username. In the bash commands, the $ sign is used to indicate the command prompt, while the > sign is used to indicate the output of the command.

user123@home_PC:~$ scp myfile.txt myuser@tarkil.metacentrum.cz:~
> myuser@tarkil.metacentrum.cz's password:
> myfile.txt          100%     10     2.9KB/s    00:00

user123@home_PC:~$ ssh myuser@tarkil.metacentrum.cz
> myuser@tarkil.metacentrum.cz's password:

import sys

infile = sys.argv[1]
outfile = sys.argv[2]

with open(infile, "r", encoding="utf-8") as f:
    line_count = sum(1 for _ in f)
with open(outfile, "w", encoding="utf-8") as f:
    f.write(str(line_count))

#!/bin/bash

# run the job max 30 minutes
#PBS -l walltime=0:30:00

# reserve 1 CPU, 1 GB disc space and 1 GB RAM
#PBS -l select=1:ncpus=1:mem=1gb:scratch_local=1gb  

# name of the job (not necessary)
#PBS -N my_counter

# name a job info file
infofile=job_info.${PBS_JOBID}

# load the python module
module load python

# copy the files to the scratch directory
cp ${PBS_O_WORKDIR}/myfile.txt $SCRATCHDIR
cp ${PBS_O_WORKDIR}/counter.py} $SCRATCHDIR

# go to the scratchdir 
cd ${SCRATCHDIR}

# create the job info file
touch ${infofile}

# save a basic info about the job 
echo -e "Hello world at `date` from user ${USER}!\n" >> ${infofile}
echo -e "$PBS_JOBID is running on node `hostname -f` in a scratch directory $SCRATCHDIR\n" >> ${infofile}

python counter.py myfile.txt out_count.txt

# copy the outputs back to where qsub was called
cp ${infofile} ${PBS_O_WORKDIR}/
cp out_count.txt ${PBS_O_WORKDIR}/

# apply a scratch automatic cleanup utility
clean_scratch

myuser@tarkil:~$ qsub test.sh
> 18411451.pbs-m1.metacentrum.cz
myuser@tarkil:~$ qstat -xu myuser
> Job ID          Name      User    S
  -----------  ----------  ------   -
  18411451...  my_counter  myuser   R

myuser@tarkil:~$ ls
> 18411451.pbs-m1.metacentrum.cz  counter.py  my_counter.o18411451  my_counter.e18411451  out_count.txt  test.sh

myuser@tarkil:~$ cat out_count.txt
> 11

myuser@tarkil:~$ qsub -I -l walltime=00:30:00 -l select=1:ncpus=1:mem=1gb:scratch_local=1gb

> qsub: waiting for job 18359645.pbs-m1.metacentrum.cz to start
> qsub: job 18359645.pbs-m1.metacentrum.cz ready

myuser@tarkil16:~$ hostname
> tarkil16.grid.cesnet.cz
myuser@tarkil16:~$ echo $SCRATCHDIR
> /scratch/myuser/job_18359645.pbs-m1
myuser@tarkil16:~$ pwd
> /storage/praha1/home/myuser

myuser@tarkil16:~$ module load python
myuser@tarkil16:~$ cp ${PBS_O_WORKDIR}/counter.py $SCRATCHDIR
myuser@tarkil16:~$ cp ${PBS_O_WORKDIR}/myfile.txt $SCRATCHDIR
myuser@tarkil16:~$ cd $SCRATCHDIR

myuser@tarkil16:~$ python counter.py myfile.txt out_count.txt
myuser@tarkil16:~$ cat out_count.txt
> 11

myuser@tarkil16:~$ cp out_count.txt ${PBS_O_WORKDIR}/
myuser@tarkil16:~$ clean_scratch

Account maintenance

Renewal: Accounts expire February 2nd. You’ll be notified by email.

Security: Use a strong password and never share credentials. For password changes and complete security rules, see Account page and Terms and conditions.

Software modules

Software in MetaCentrum is installed in so-called modules. To be able to use a software, you have to load it first by module add.

module avail amber/       # list existing versions of "amber" module
module add amber          # load default version of amber
module list               # show loaded modules

Next steps

Now that you understand the basics, you can:

• See a visual tool for assembling qsub commands, the Qsub assembler
• Learn advanced job configuration and troubleshooting
• Explore available software
• Read about parallel computing
• Check GPU resources
• Try usegalaxy.cz web interface – an alternative way to run jobs in a web-based platform with workflow support.

Troubleshooting basics

If your job fails:

1. Check the error file (*.e<jobID>).
2. Verify your input files exist and have correct permissions.
3. Check if software modules are loaded correctly.
4. Ensure you requested adequate resources (memory, walltime, scratch).

For more advanced troubleshooting, see the Advanced guide.

Acknowledgements

Publications created with MetaCentrum support must be submitted to the publications system and acknowledged.

See Terms and conditions for an up-to-date acknowledgement wording.