This repository has been archived by the owner on Mar 16, 2023. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 14
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
105 changed files
with
5,645 additions
and
710 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,327 @@ | ||
| { | ||
| "workflow": { | ||
| "header": { | ||
| "version": "1.9.0", | ||
| "workflow_id": "Full PMX workflow - rbfe", | ||
| "description": "PMX full map calculation with parallel GPU sims.", | ||
| "environment": { | ||
| "export": [ | ||
| { | ||
| "key": "GMX_GPU_DD_COMMS", | ||
| "value": "true" | ||
| }, | ||
| { | ||
| "key": "GMX_GPU_PME_PP_COMMS", | ||
| "value": "true" | ||
| }, | ||
| { | ||
| "key": "GMX_FORCE_UPDATE_DEFAULT_GPU", | ||
| "value": "true" | ||
| }, | ||
| { | ||
| "key": "PMX_PYTHON", | ||
| "value": "${CONDA}/envs/pmx/bin/python" | ||
| }, | ||
| { | ||
| "key": "PMX", | ||
| "value": "/home/kmzp800/miniconda3/envs/pmx/bin/pmx" | ||
| }, | ||
| { | ||
| "key": "GMXLIB", | ||
| "value": "/projects/cc/mai/pmx/src/pmx/data/mutff/" | ||
| } | ||
| ] | ||
| }, | ||
| "global_variables": { | ||
| "file_path": "{package_dir}/../IcolosData/pmx", | ||
| "output_dir": "{work_dir}/tests/junk/pmx/protein_pmx" | ||
| }, | ||
| "global_settings": { | ||
| "single_directory": true, | ||
| "remove_temporary_files": false | ||
| } | ||
| }, | ||
| "steps": [ | ||
|
|
||
| { | ||
| "step_id": "01_pmx_mutate", | ||
| "type": "pmx_mutate", | ||
| "execution": { | ||
| "prefix_execution": "module load GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2", | ||
|
|
||
| "parallelization": { | ||
| "jobs": 24 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": { | ||
| "water": "tip3p", | ||
| "forcefield": "amber14sbmut" | ||
| } | ||
| }, | ||
| "input": { | ||
| "generic": [ | ||
| { | ||
| "source": "{file_path}/mutate/2flu.pdb", | ||
| "extension": "pdb" | ||
| }, | ||
| { | ||
| "source": "{file_path}/mutate/mutations.mut", | ||
| "extension": "mut" | ||
| }, | ||
| { | ||
| "source": "{file_path}/run_simulations/input/mdp/", | ||
| "extension": "mdp" | ||
| } | ||
| ], | ||
| "work_dir": "{output_dir}" | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "02_pmx_gentop", | ||
| "type": "pmx_gentop", | ||
| "execution": { | ||
| "parallelization": { | ||
| "jobs": 24 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": { | ||
|
|
||
| } | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "05_box_water_ions", | ||
| "type": "pmx_box_water_ions", | ||
| "execution": { | ||
| "prefix_execution": "module load GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2", | ||
| "parallelization": { | ||
| "jobs": 24 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": {} | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "06_prepare_simulations", | ||
| "type": "pmx_prepare_simulations", | ||
| "execution": { | ||
| "prefix_execution": "module load GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2", | ||
| "parallelization": { | ||
| "jobs": 8 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": { | ||
| "sim_type": "em" | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "06b_run_simulations", | ||
| "type": "pmx_run_simulations", | ||
| "execution": { | ||
| "platform": "slurm", | ||
| "resources": { | ||
| "cores": "8", | ||
| "partition": "gpu", | ||
| "gres": "gpu:1", | ||
| "modules": [ | ||
| "GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2" | ||
| ] | ||
| }, | ||
| "parallelization": { | ||
| "jobs": 1 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": { | ||
| "sim_type": "em" | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "06c_prepare_simulations_nvt", | ||
| "type": "pmx_prepare_simulations", | ||
| "execution": { | ||
| "prefix_execution": "module load GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2", | ||
| "parallelization": { | ||
| "jobs": 24 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": { | ||
| "sim_type": "nvt" | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "06d_run_simulations", | ||
| "type": "pmx_run_simulations", | ||
| "execution": { | ||
| "platform": "slurm", | ||
| "resources": { | ||
| "partition": "core", | ||
| "cores": 16, | ||
| "mem": "8g", | ||
| "modules": [ | ||
| "GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2" | ||
| ] | ||
| }, | ||
| "parallelization": { | ||
| "jobs": 1 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": { | ||
| "-ntomp": 16, | ||
| "-ntmpi": 1 | ||
| } | ||
| }, | ||
| "additional": { | ||
| "sim_type": "nvt" | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "07_prepare_simulations", | ||
| "type": "pmx_prepare_simulations", | ||
| "execution": { | ||
| "prefix_execution": "module load GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2", | ||
| "parallelization": { | ||
| "jobs": 24 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": { | ||
| "sim_type": "eq" | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "07b_run_simulations", | ||
| "type": "pmx_run_simulations", | ||
| "execution": { | ||
| "platform": "slurm", | ||
| "resources": { | ||
| "partition": "gpu", | ||
| "gres": "gpu:1", | ||
| "modules": [ | ||
| "GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2" | ||
| ] | ||
| }, | ||
| "parallelization": { | ||
| "jobs": 1 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": { | ||
| "sim_type": "eq" | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "08_prep_transitions", | ||
| "type": "pmx_prepare_transitions", | ||
| "execution": { | ||
| "prefix_execution": "module load GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2", | ||
| "parallelization": { | ||
| "jobs": 24 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": { | ||
| "sim_type": "transitions" | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "09_run_transitions", | ||
| "type": "pmx_run_simulations", | ||
| "execution": { | ||
| "platform": "slurm", | ||
| "resources": { | ||
| "partition": "core", | ||
| "cores": 16, | ||
| "mem": "8g", | ||
| "time": "48:00:00", | ||
| "modules": [ | ||
| "GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2" | ||
| ] | ||
| }, | ||
| "parallelization": { | ||
| "jobs": 1 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": { | ||
| "sim_type": "transitions" | ||
| } | ||
| }, | ||
| "input": { | ||
| "generic": [] | ||
| } | ||
| }, | ||
| { | ||
| "step_id": "pmx_analyse", | ||
| "type": "pmx_run_analysis", | ||
| "execution": { | ||
| "parallelization": { | ||
| "jobs": 24 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": {} | ||
| }, | ||
| "additional": {} | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -51,7 +51,7 @@ | |
| "settings": { | ||
| "arguments": { | ||
| "parameters": { | ||
| "-num-procs": 24 | ||
| "-num-procs": 1 | ||
| } | ||
| } | ||
| }, | ||
|
|
||
Oops, something went wrong.