Bonjour,
Je voudrais faire tourner AlphaFold à partir du script ci-dessous:
#!/bin/bash
#SBATCH -p gpu
#SBATCH --gres=gpu:7g.40gb:1
#SBATCH --cpus-per-task=10
#SBATCH --mem=50G
module purge
module load alphafold/2.2.3
mkdir -p /tmp/$USER_alphafold
if [[ "${mode}" == "monomer" ]]; then
param='--pdb70_database_path=/shared/bank/alphafold2/2022-09-21/pdb70/pdb70'
elif [[ "${mode}" == "multimer" ]]; then
param='--uniprot_database_path=/shared/bank/alphafold2/2022-09-21/uniprot/uniprot.fasta --pdb_seqres_database_path=/shared/bank/alphafold2/2022-09-21/pdb_seqres/pdb_seqres.txt'
else
param='--pdb70_database_path=/shared/bank/alphafold2/2022-09-21/pdb70/pdb70'
fi
srun run_alphafold.sh --fasta_paths="${path}/${query_file}" \
--output_dir="${path}/${out_dir}" \
--model_preset="${mode}" \
--use_gpu_relax=True \
--db_preset=full_dbs \
--data_dir=/shared/bank/alphafold2/2022-09-21/ \
--uniref90_database_path=/shared/bank/alphafold2/2022-09-21//uniref90/uniref90.fasta \
--mgnify_database_path=/shared/bank/alphafold2/2022-09-21/mgnify/mgy_clusters_2018_12.fa \
--template_mmcif_dir=/shared/bank/alphafold2/2022-09-21/pdb_mmcif/mmcif_files \
--max_template_date=2020-05-14 \
--use_precomputed_msas=True \
--obsolete_pdbs_path=/shared/bank/alphafold2/2022-09-21/pdb_mmcif/obsolete.dat \
--bfd_database_path=/shared/bank/alphafold2/2022-09-21/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 \
${param}
mais j'obtiens l'erreur suivante en faisant tourner avec cette ligne
sbatch script_af223.sh -mode monomer -path /shared/projects/molsco -query_file /protein_sequences/scep1.fasta -out_dir work
sbatch: error: Batch job submission failed: Requested node configuration is not available. J'avais cru comprendre à partir de ce fil de discussion qu'il fallait utiliser --gres=gpu:7g.40gb:1, est-ce toujours d'actualité ?
Merci beaucoup et bonne journée,
Marion