From d898e395a296a86da87cc03ff8843e9e595d1c22 Mon Sep 17 00:00:00 2001 From: Coos Baakman Date: Thu, 5 Aug 2021 10:25:54 +0200 Subject: [PATCH] add a command to docker-compose --- docker-compose-preprocess.yml | 3 ++- scripts/preprocess_bioprodict.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/docker-compose-preprocess.yml b/docker-compose-preprocess.yml index 58d5181..c4ef7f2 100644 --- a/docker-compose-preprocess.yml +++ b/docker-compose-preprocess.yml @@ -9,7 +9,8 @@ services: - "/home/cbaakman/deeprank-datasets:/datasets" - "/home/cbaakman/pdb:/pdb" - "/home/cbaakman/pssm-gen:/pssm-gen" - working_dir: /runs/run-mp + working_dir: /runs/run2 + command: mpiexec -n 10 --allow-run-as-root /usr/src/app/scripts/preprocess_bioprodict.py /datasets/54e500aa7123e7f2f6ca4062db0e4fa4_efro_t96_25052021.parq /datasets/GPCR_variantsv2_increased_coverage.hdf5 /pdb /pssm-gen variants.hdf5 environment: - MASTER_ADDR=0.0.0.0 - MASTER_PORT=1088 diff --git a/scripts/preprocess_bioprodict.py b/scripts/preprocess_bioprodict.py index 3fc2002..0a65c1c 100755 --- a/scripts/preprocess_bioprodict.py +++ b/scripts/preprocess_bioprodict.py @@ -38,7 +38,7 @@ arg_parser.add_argument("pdb_root", help="the path to the pdb root directory") arg_parser.add_argument("pssm_root", help="the path to the pssm root directory, containing files generated with PSSMgen") arg_parser.add_argument("out_path", help="the path to the output hdf5 file") -arg_parser.add_argument("-A", "--data-augmentation", help="the number of data augmentations", type=int, default=0) +arg_parser.add_argument("-A", "--data-augmentation", help="the number of data augmentations", type=int, default=5) arg_parser.add_argument("-p", "--grid-points", help="the number of points per edge of the 3d grid", type=int, default=20) arg_parser.add_argument("-S", "--grid-size", help="the length in Angstroms of each edge of the 3d grid", type=float, default=20)