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Run_on_Cheaha.md

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Analysis on Cheaha

  • Open the local directory in terminal.
  • Copy all the files from local directory to Cheaha:
scp -r . [email protected]:/home/ashovon/newaumri/matfiles/TemporalBrainPH/
  • Open an SSH connection to Cheaha:
ssh [email protected]
  • Change directory to the desired directory:
cd newaumri/matfiles/TemporalBrainPH/
  • Create a virtual environment to one directory up. So, we can pull the current directory to local machine again without the venv files.
python3 -m venv ../venv
  • Activate the environment:
source ../venv/bin/activate
  • Upgrade pip:
pip install --upgrade pip
  • Install the requirements:
pip install -r requirements.txt
  • Upload a file from local machine to Cheaha:
scp README.md [email protected]:/home/ashovon/newaumri/matfiles/TemporalBrainPH/
scp run_bg.sh [email protected]:/home/ashovon/newaumri/matfiles/TemporalBrainPH/
scp distance_calculation.py [email protected]:/home/ashovon/newaumri/matfiles/TemporalBrainPH/
scp cluster_calculation.py [email protected]:/home/ashovon/newaumri/matfiles/TemporalBrainPH/
  • Upload all files from a local directory to Cheaha recursively:
scp -r . [email protected]:/home/ashovon/newaumri/matfiles/analysis/dfc_1400_subjects_distance_matrix/
scp -r . [email protected]:/home/ashovon/newaumri/matfiles/analysis/dfc_1400_subjects_mds/
scp -r . [email protected]:/home/ashovon/newaumri/matfiles/analysis/dfc_2500_subjects_mds/
scp -r [email protected]:/home/ashovon/newaumri/matfiles/analysis/clusters_kmeans/ .
  • Download single file from Cheaha to local machine:
scp [email protected]:/home/ashovon/newaumri/matfiles/dfc_645_subjects_mds/subject_1.json .
scp [email protected]:/home/ashovon/newaumri/matfiles/dfc_645_down_subjects_mds_ws/subject_1.json .
scp [email protected]:/home/ashovon/newaumri/matfiles/dfc_2500_subjects_mds/subject_1.json .

scp [email protected]:/home/ashovon/newaumri/matfiles/TemporalBrainPH/clusters_bn.csv .
scp [email protected]:/home/ashovon/newaumri/matfiles/dfc_645_normal_nonan/normalize_dfc_645_subject_1_time_1.txt .
scp [email protected]:/home/ashovon/newaumri/matfiles/dfc_645_normal_nonan/normalize_dfc_645_subject_2_time_4.txt .
scp [email protected]:/home/ashovon/newaumri/matfiles/normalize_645.m .
scp [email protected]:/home/ashovon/newaumri/matfiles/normalize_1400.m .
scp [email protected]:/home/ashovon/newaumri/matfiles/normalize_2500.m .

scp [email protected]:/home/ashovon/newaumri/matfiles/TemporalBrainPH/clusteringresult_job_ws.out .
scp [email protected]:/home/ashovon/newaumri/matfiles/TemporalBrainPH/clusteringresult_job_bn.out .
  • Download all files from a Cheaha directory to local machine:
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_2500_normal_original .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_1400_normal_original .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_645_normal_original .

scp -r [email protected]:/home/ashovon/newaumri/matfiles/clusters_kmeans_direct_clustering .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/clusters_kmeans/ .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/clusters_kmeans_non_tda/ .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_2500_subjects_mds_ws/ .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_1400_subjects_mds_ws/ .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_645_subjects_mds_ws/ .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_2500_normal/ .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/clusters_kmeans_bn/ .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_2500_subjects_mds_bn/ .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_1400_subjects_mds_bn/ .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_645_subjects_mds_bn/ .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/New_formula_generated_nontda/ .
  • Download all files from a Cheaha directory to local machine which has a specific pattern:
scp -r [email protected]:/home/ashovon/newaumri/matfiles/dfc_645_normal/normalize_dfc_645_subject_1_time_\*.txt .
scp -r [email protected]:/home/ashovon/newaumri/matfiles/TemporalBrainPH/dfc\*.job .
  • Create a batch job:
#!/bin/bash
#
#SBATCH --job-name=dfc645
#SBATCH --output=dfc645_job.out
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --partition=amd-hdr100
#SBATCH --time=10:00:00
#SBATCH --mem-per-cpu=4069

# load your Anaconda module here and activate your virtual environment (if needed)
set -e
source /home/ashovon/newaumri/matfiles/venv/bin/activate


# execute your python scripts (change it to whatever it needs to be for you).
python -u /home/ashovon/newaumri/matfiles/TemporalBrainPH/distance_calculation.py
  • Run the Job in Cheaha (job should run from root directory, not scripts directory):
sbatch dfc645.job
sbatch dfc1400.job
sbatch dfc2500.job
sbatch dfc645_nontda.job
sbatch dfc1400_nontda.job
sbatch dfc2500_nontda.job
sbatch clusteringresult.job
  • To kill a Slurm job
scancel <jobid>

You can find your jobid with the following command:

squeue -u $USER
  • See the users in a partition:
squeue -p amd-hdr100
  • See the command history:
history | cut -c 8-
  • See last 5 lines for a pattern of files:
tail -n 5 dfc645_*_job.out
tail -n 2 dfc645_*.job
  • Check details of a job, (13626634 is the job id):
squeue -j 13626634 -o "%all"
  • Check job history for a user within a specific start and end time:
sacct --accounts ashovon  --format=jobname,elapsed,ncpus,state --starttime 2023-02-20 --endtime 2023-02-22
  • See the running scripts for the user:
ps aux | grep ashovon
  • Get a medium instance:
srun --ntasks=1 --cpus-per-task=6 --mem-per-cpu=8192 --time=50:00:00 --partition=medium --job-name=fmri --pty /bin/bash
srun --ntasks=4 --cpus-per-task=6 --mem-per-cpu=8192 --time=50:00:00 --partition=medium --job-name=fmri_1400 --pty /bin/bash