Cyfronet

Cyfronet

Applying for grant and access to Cluster

Sign up at https://portal.plgrid.pl/
Apply for grant and activate it at https://portal.plgrid.pl/services
- Note: Access to the Ares cluster at the Cyfronet centre [grant required]

Login to Ares

$ ssh <login>@ares.cyfronet.pl

<login> = username starting with “plg”

Add infor about ssh key

Storages

$HOME
$SCRATCH
$PLG_GROUPS_STORAGE (starts with “plgg”)

Add how to share files

Install libraries/packages using module

$ module avail

Lists all available libraries/packages

$ module list

Lists loaded libraries/packages

$ module load <package>

Loads specified package

$ module spider <keyword>

Searches available packages with the keyword

$ module purge

Purges the environment

System utilities

$ hpc-grants

Shows available grants, resource allocations, consumed resourced

$ hpc-fs

Shows available storage

$ hpc-jobs

Shows currently pending/running jobs

$ hpc-jobs-history

: Shows information about past jobs

Install Herwig7

Load necessary modules:

    module load python/2.7.18-gcccore-11.2.0
    module load libtool
    module load emacs
    module load gcc/11.2.0
    module load gcccore/11.2.0
    module load cmake/3.22.1-gcccore-11.2.0
    module load gsl/2.7-gcc-11.2.0

Move to $SCRATCH or $PLG_GROUPS_STORAGE (preferred):
```
 $ cd $PLG_GROUPS_STORAGE/<groupname> 
```

Download bootstrap script and make it executable:

 $ wget https://herwig.hepforge.org/downloads/herwig-bootstrap
 $ chmod +x herwig-bootstrap

Start an interactive node session (Easier to debug if installation fails):
```
 $ srun -p plgrid-now -t 5:00:00 --mem=5GB -A <grantname-cpu> --pty /bin/bash 
```
Note: Only one interactive plgrid-now session can be run at a time. Adjust the session duration and memory allocation as required. The above specified parameters should suffice in general.
Run bootstrap and exit session when completed:
```
[ares][username@ac0787 ~]$ ./herwig-bootstrap -j4 $PWD/Herwig
[ares][username@ac0787 ~]$ exit 
```
Note: The login01 node changes to ac0xxx when in a computing node.
More options for running bootstrap can be found with
```
 $ ./herwig-bootstrap --help 
```
Activate Herwig environment :
```
 $ source Herwig/bin/activate 
```

A sample run script (and common slurm commands)

Run script (run.sh) :

     #!/bin/bash
     #SBATCH --job-name=Sample_Run
     #SBATCH --nodes=1
     #SBATCH --ntasks-per-node=1
     #SBATCH --cpus-per-task=1
     #SBATCH --mem-per-cpu=1GB
     # set wall time to 1 day
     #SBATCH --time=1-00:00:00
     ## Name of partition
     #SBATCH -p plgrid
     cd <Run directory>
     source <path/to/>Herwig/bin/activate
     export HW=Herwig
     ${HW} run *.run --seed=$seed -N 1000000 > /dev/null &
     HWPID="$!"
     wait "${HWPID}"

Run commands from CLI

Submit parallel jobs:
```
$ sbatch --array=0-5 -A <grantname-suffix> run.sh
```
- Suffix = cpu, cpu-bigmem, gpu
sprio: show status of pending jobs
sshare: show usage of available grants

Run interactive bash session:

$ srun -p plgrid-now -t 1:00:00 --mem=1GB -A <grantname-cpu> --pty /bin/bash

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