I have a question, how can I submit multiple individual batch jobs in the IFB cluster like ( run more than one.sh files). But, If I will submit a job with the same node, the job will be pending. Please, let me know which node configartion should I use to submit more than one job
Thank you
Hello,
You can submit multiple jobs with a simple sbatch (just lauch the job for each one.sh file) or a job array (SLURM advanced guide - IFB Core Cluster Documentation). The workload manager will manage this jobs and select the nodes.
Please, have a look at the documentation: IFB Core Cluster Documentation
Best regards,
I tired to submit a job using the array command but it doesn't work my job gets killed eventually. Please, could you look into this matter and let me know what should I do?
Thanking you in advance
Here is my script
#!/bin/bash
#SBATCH --partition=gpu
#SBATCH --gres=gpu:7g.40gb:1
#SBATCH --cpus-per-task=10
#SBATCH --mem=50G
#SBATCH --account=ancest_or_
#SBATCH --time 36:00:00
module load alphafold/2.1.1
mkdir -p /tmp/$USER_alphafold
INPUTS=(SfruOR51.fa,SfruOR52.fa,SfruOR58.fa,SfruOR60.fa,SfruOR61.fa,SfruOR62.fa,SfruOR63.fa,SfruOR64.fa,SfruOR65.fa,SfruOR67.fa,SfruOR68.fa,SfruOR69.fa,SfruOR11.fa)
${INPUTS[$SLURM_ARRAY_--fasta_paths=/shared/projects/ancest_or_/SfruOR51.fa,SfruOR52.fa,SfruOR58.fa,SfruOR60.fa,SfruOR61.fa,SfruOR62.fa,SfruOR63.fa,SfruOR64.fa,SfruOR65.fa,SfruOR67.fa,SfruOR68.fa,SfruOR69.fa,SfruOR11.fa}}
srun /path/to/fasta run_alphafold.sh
--output_dir=/shared/projects/ancest_or_
--model_preset=monomer
--db_preset=full_dbs
--data_dir=/shared/bank/alphafold2/current/2.3/2023-04-28
--uniref90_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/uniref90/uniref90.fasta
--mgnify_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/mgnify/mgy_clusters_2018_12.fa
--pdb70_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/pdb70/pdb70
--template_mmcif_dir=/shared/bank/alphafold2/current/2.3/2023-04-28/pdb_mmcif/mmcif_files
--max_template_date=2020-05-14
--obsolete_pdbs_path=/shared/bank/alphafold2/current/2.3/2023-04-28/pdb_mmcif/obsolete.dat
--bfd_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
--uniclust30_database_path=/shared/bank/alphafold2/2022-09-21/uniclust30/uniclust30_2018_08/uniclust30_2018_08
The error
/var/spool/slurm/slurmd/job33229360/slurm_script: line 16: ${INPUTS[$SLURM_ARRAY_--fasta_paths=/shared/projects/ancest_or_/SfruOR48.fa,SfruOR49.fa,SfruOR51.fa,SfruOR52.fa,SfruOR58.fa,SfruOR60.fa,SfruOR61.fa,SfruOR62.fa,SfruOR63.fa,SfruOR69.fa,SfruOR11.fa}} : bad substitution
/var/spool/slurm/slurmd/job33229360/slurm_script: line 18: --output_dir=/shared/projects/ancest_or_: No such file or directory