Changes between Version 1 and Version 2 of Ticket #5578, comment 6


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Timestamp:
Nov 17, 2021, 8:38:13 PM (4 years ago)
Author:
Tom Goddard

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  • Ticket #5578, comment 6

    v1 v2  
    1010module load cuda/11.0
    1111
    12 env CUDA_VISIBLE_DEVICES=$GPU_ID NVIDIA_VISIBLE_DEVICES=$GPU_ID TF_FORCE_UNIFIE\
    13 D_MEMORY=1 XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 singularity run --nv -B "/wynton/\
    14 group/databases/alphafold_CASP14_v2.1.1" -B /wynton/group/databases/alphafold_C\
    15 ASP14 -B "/wynton/home/ferrin/goddard/alphafold_singularity" /wynton/home/ferri\
    16 n/goddard/alphafold_singularity/alphafold21.sif --fasta_paths=7e40_ab.fasta --u\
    17 niref90_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/uniref90/\
    18 uniref90.fasta --mgnify_database_path=/wynton/group/databases/alphafold_CASP14_\
    19 v2.1.1/mgnify/mgy_clusters_2018_12.fa --data_dir=/wynton/group/databases/alphaf\
    20 old_CASP14_v2.1.1 --template_mmcif_dir=/wynton/group/databases/alphafold_CASP14\
    21 _v2.1.1/pdb_mmcif/mmcif_files --obsolete_pdbs_path=/wynton/group/databases/alph\
    22 afold_CASP14_v2.1.1/pdb_mmcif/obsolete.dat --uniprot_database_path=/wynton/grou\
    23 p/databases/alphafold_CASP14_v2.1.1/uniprot/uniprot.fasta --pdb_seqres_database\
    24 _path=/wynton/group/databases/alphafold_CASP14_v2.1.1/pdb_seqres/pdb_seqres.txt\
    25  --uniclust30_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/uni\
    26 clust30/uniclust30_2018_08/uniclust30_2018_08 --bfd_database_path=/wynton/group\
    27 /databases/alphafold_CASP14_v2.1.1/bfd/bfd_metaclust_clu_complete_id30_c90_fina\
    28 l_seq.sorted_opt --output_dir=/wynton/home/ferrin/goddard/alphafold_singularity\
    29 /output --max_template_date=2021-11-01 --db_preset=full_dbs --model_preset=mult\
    30 imer --benchmark=False --use_precomputed_msas=False --logtostderr --is_prokaryo\
    31 te_list=false
     12env CUDA_VISIBLE_DEVICES=$GPU_ID NVIDIA_VISIBLE_DEVICES=$GPU_ID TF_FORCE_UNIFIED_MEMORY=1 XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 singularity run --nv -B "/wynton/group/databases/alphafold_CASP14_v2.1.1" -B /wynton/group/databases/alphafold_CASP14 -B "/wynton/home/ferrin/goddard/alphafold_singularity" /wynton/home/ferri\
     13n/goddard/alphafold_singularity/alphafold21.sif --fasta_paths=7e40_ab.fasta --uniref90_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/uniref90/uniref90.fasta --mgnify_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/mgnify/mgy_clusters_2018_12.fa --data_dir=/wynton/group/databases/alphafold_CASP14_v2.1.1 --template_mmcif_dir=/wynton/group/databases/alphafold_CASP14_v2.1.1/pdb_mmcif/mmcif_files --obsolete_pdbs_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/pdb_mmcif/obsolete.dat uniprot_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/uniprot/uniprot.fasta --pdb_seqres_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/pdb_seqres/pdb_seqres.txt --uniclust30_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/uniclust30/uniclust30_2018_08/uniclust30_2018_08 --bfd_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --output_dir=/wynton/home/ferrin/goddard/alphafold_singularity/output --max_template_date=2021-11-01 --db_preset=full_dbs --model_preset=multimer --benchmark=False --use_precomputed_msas=False --logtostderr --is_prokaryote_list=false
    3214}}}