Adding first applications

# gekko-scripts

## Getting started

To make it easy for you to get started with GitLab, here's a list of recommended next steps.

Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!

## Add your files

- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files

- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:

```

cd existing_repo

git remote add origin https://storage.bsc.es/gitlab/hpc/gekko-scripts.git

git branch -M main

git push -uf origin main

```

## Integrate with your tools

- [ ] [Set up project integrations](https://storage.bsc.es/gitlab/hpc/gekko-scripts/-/settings/integrations)

## Collaborate with your team

- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)

- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)

- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)

- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)

- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)

## Test and Deploy

Use the built-in continuous integration in GitLab.

- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)

- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)

- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)

- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)

- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)

***

# Editing this README

When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.

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This repository contains examples scripts to run various HPC applications. Refer to the README for each app for details.

#!/bin/bash

JOBOUTDIR=$1

# SETUP

WORKDIR=/beegfs/home/m.vef/run/job_tmp/${SLURM_JOB_ID}

mkdir -p $WORKDIR

SLURM_HOSTS=$(squeue -j $SLURM_JOB_ID -o "%N" | tail -n +2)

scontrol show hostname $SLURM_HOSTS | sort -u > $WORKDIR/hostfile_mpi

# dont ask

cat $WORKDIR/hostfile_mpi | while read line

do

    #echo "Running $line"

    ssh -o StrictHostKeychecking=no $line 'hostname' 2>&1 > /dev/null &

done

wait

# RUN

echo "cleaning old dir"

RUNDIR=/beegfs/home/m.vef/admire/turbPipe/run_beegfs/run

#rm -rf $RUNDIR/*

echo "copying input..."

cp /beegfs/home/m.vef/admire/turbPipe/run_beegfs/input/* /beegfs/home/m.vef/admire/turbPipe/run_beegfs/run

# psssht don't ask

cd /beegfs/home/m.vef/admire/turbPipe/run_beegfs

NODE_NUM=$(wc -l $WORKDIR/hostfile_mpi | awk '{print $1}')

PROC_NUM=$(( $NODE_NUM*16 ))

#JOBOUTDIR="/beegfs/home/m.vef/run/job_out/nek_${SLURM_JOB_ID}_${NODE_NUM}n_${PROC_NUM}p"

#mkdir -p $JOBOUTDIR

JOBOUTFILE=$JOBOUTDIR/nek.out

echo "Starting Nek5000 on $NODE_NUM nodes (16 processes each $PROC_NUM total) on Beegfs ..."

echo "Check $JOBOUTFILE for progress"

start_time=$(date +%s.%N)  # Get seconds since epoch with nanoseconds

time mpiexec -np $PROC_NUM --oversubscribe --map-by node --hostfile $WORKDIR/hostfile_mpi ./nek5000 > $JOBOUTFILE

end_time=$(date +%s.%N)

elapsed_time=$(echo "$end_time - $start_time" | bc)

echo "Elapsed time: $elapsed_time seconds"

# cleanup 

#rm -rf $RUNDIR/*

rm -rf $WORKDIR

#!/bin/bash

SCRIPTDIR=$1

SLURM_HOSTS=$(squeue -j $SLURM_JOB_ID -o "%N" | tail -n +2)

NODE_NUM=$(scontrol show hostname $SLURM_HOSTS | wc -l)

PROC_NUM=$(( $NODE_NUM*16 ))

JOBOUTDIR="/beegfs/home/m.vef/run/job_out/beegfs/nek_${NODE_NUM}n_${PROC_NUM}p_${SLURM_JOB_ID}"

mkdir -p $JOBOUTDIR

#execute

$SCRIPTDIR/run_beegfs.sh $JOBOUTDIR >> "${JOBOUTDIR}/slurm.out"

#!/bin/bash

JOBOUTDIR=$1

# SETUP

WORKDIR=/beegfs/home/m.vef/run/job_tmp/${SLURM_JOB_ID}

mkdir -p $WORKDIR

SLURM_HOSTS=$(squeue -j $SLURM_JOB_ID -o "%N" | tail -n +2)

scontrol show hostname $SLURM_HOSTS | sort -u > $WORKDIR/hostfile_mpi

# dont ask

cat $WORKDIR/hostfile_mpi | while read line

do

    #echo "Running $line"

    ssh -o StrictHostKeychecking=no $line 'hostname' 2>&1 > /dev/null &

done

wait

# RUN

~/gekkofs/scripts/run/gkfs -c ~/run/gkfs_sockets.conf -v start 

source ~/run/gkfs_sockets.conf

srun mkdir -p /dev/shm/vef_gkfs_mountdir

echo "copying input..."

export LIBGKFS_HOSTS_FILE=$LIBGKFS_HOSTS_FILE

LD_PRELOAD=${PRELOAD_LIB} cp /beegfs/home/m.vef/admire/turbPipe/run_gkfs/input/* /dev/shm/vef_gkfs_mountdir/

cd /beegfs/home/m.vef/admire/turbPipe/run_gkfs

NODE_NUM=$(wc -l $WORKDIR/hostfile_mpi | awk '{print $1}')

PROC_NUM=$(( $NODE_NUM*16 ))

#JOBOUTDIR="/beegfs/home/m.vef/run/job_out/nek_${SLURM_JOB_ID}_${NODE_NUM}n_${PROC_NUM}p"

#mkdir -p $JOBOUTDIR

JOBOUTFILE=$JOBOUTDIR/nek.out

echo "Starting Nek5000 on $NODE_NUM nodes (16 processes each $PROC_NUM total) on GekkoFS ..."

echo "Check $JOBOUTFILE for progress"

start_time=$(date +%s.%N)  # Get seconds since epoch with nanoseconds

time mpiexec -np $PROC_NUM --oversubscribe --map-by node --hostfile $WORKDIR/hostfile_mpi -x LIBGKFS_HOSTS_FILE=${LIBGKFS_HOSTS_FILE} -x LD_PRELOAD=${PRELOAD_LIB} -x  LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./nek5000 > $JOBOUTFILE

end_time=$(date +%s.%N)

elapsed_time=$(echo "$end_time - $start_time" | bc)

echo "Elapsed time: $elapsed_time seconds"

# cleanup 

~/gekkofs/scripts/run/gkfs -c ~/run/gkfs_sockets.conf stop

rm -rf $WORKDIR

#!/bin/bash

SCRIPTDIR=$1

SLURM_HOSTS=$(squeue -j $SLURM_JOB_ID -o "%N" | tail -n +2)

NODE_NUM=$(scontrol show hostname $SLURM_HOSTS | wc -l)

PROC_NUM=$(( $NODE_NUM*16 ))

JOBOUTDIR="/beegfs/home/m.vef/run/job_out/nek_${NODE_NUM}n_${PROC_NUM}p_${SLURM_JOB_ID}"

mkdir -p $JOBOUTDIR

#execute

$SCRIPTDIR/run_gkfs.sh $JOBOUTDIR >> "${JOBOUTDIR}/slurm.out"