#!/usr/bin/env python3
"""Module containing the MDrun class and the command line interface."""
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_gromacs.gromacs.common import get_gromacs_version
[docs]
class Mdrun(BiobbObject):
"""
| biobb_gromacs Mdrun
| Wrapper of the `GROMACS mdrun <http://manual.gromacs.org/current/onlinehelp/gmx-mdrun.html>`_ module.
| MDRun is the main computational chemistry engine within GROMACS. It performs Molecular Dynamics simulations, but it can also perform Stochastic Dynamics, Energy Minimization, test particle insertion or (re)calculation of energies.
Args:
input_tpr_path (str): Path to the portable binary run input file TPR. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/mdrun.tpr>`_. Accepted formats: tpr (edam:format_2333).
output_gro_path (str): Path to the output GROMACS structure GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_mdrun.gro>`_. Accepted formats: gro (edam:format_2033).
output_edr_path (str): Path to the output GROMACS portable energy file EDR. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_mdrun.edr>`_. Accepted formats: edr (edam:format_2330).
output_log_path (str): Path to the output GROMACS trajectory log file LOG. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_mdrun.log>`_. Accepted formats: log (edam:format_2330).
output_trr_path (str) (Optional): Path to the GROMACS uncompressed raw trajectory file TRR. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_mdrun.trr>`_. Accepted formats: trr (edam:format_3910).
input_cpt_path (str) (Optional): Path to the input GROMACS checkpoint file CPT. File type: input. Accepted formats: cpt (edam:format_2333).
output_xtc_path (str) (Optional): Path to the GROMACS compressed trajectory file XTC. File type: output. Accepted formats: xtc (edam:format_3875).
output_cpt_path (str) (Optional): Path to the output GROMACS checkpoint file CPT. File type: output. Accepted formats: cpt (edam:format_2333).
output_dhdl_path (str) (Optional): Path to the output dhdl.xvg file only used when free energy calculation is turned on. File type: output. Accepted formats: xvg (edam:format_2033).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **mpi_bin** (*str*) - (None) Path to the MPI runner. Usually "mpirun" or "srun".
* **mpi_np** (*int*) - (0) [0~1000|1] Number of MPI processes. Usually an integer bigger than 1.
* **mpi_flags** (*str*) - (None) Path to the MPI hostlist file.
* **checkpoint_time** (*int*) - (15) [0~1000|1] Checkpoint writing interval in minutes. Only enabled if an output_cpt_path is provided.
* **noappend** (*bool*) - (False) Include the noappend flag to open new output files and add the simulation part number to all output file names
* **num_threads** (*int*) - (0) [0~1000|1] Let GROMACS guess. The number of threads that are going to be used.
* **num_threads_mpi** (*int*) - (0) [0~1000|1] Let GROMACS guess. The number of GROMACS MPI threads that are going to be used.
* **num_threads_omp** (*int*) - (0) [0~1000|1] Let GROMACS guess. The number of GROMACS OPENMP threads that are going to be used.
* **num_threads_omp_pme** (*int*) - (0) [0~1000|1] Let GROMACS guess. The number of GROMACS OPENMP_PME threads that are going to be used.
* **use_gpu** (*bool*) - (False) Use settings appropriate for GPU. Adds: -nb gpu -pme gpu
* **gpu_id** (*str*) - (None) list of unique GPU device IDs available to use.
* **gpu_tasks** (*str*) - (None) list of GPU device IDs, mapping each PP task on each node to a device.
* **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
* **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
* **container_path** (*str*) - (None) Path to the binary executable of your container.
* **container_image** (*str*) - (None) Container Image identifier.
* **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
* **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
* **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
* **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
Examples:
This is a use example of how to use the building block from Python::
from biobb_gromacs.gromacs.mdrun import mdrun
prop = { 'num_threads': 0,
'binary_path': 'gmx' }
mdrun(input_tpr_path='/path/to/myPortableBinaryRunInputFile.tpr',
output_trr_path='/path/to/newTrajectory.trr',
output_gro_path='/path/to/newStructure.gro',
output_edr_path='/path/to/newEnergy.edr',
output_log_path='/path/to/newSimulationLog.log',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS Mdrun
* version: 2025.2
* license: LGPL 2.1
* multinode: mpi
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_tpr_path: str, output_gro_path: str, output_edr_path: str,
output_log_path: str, output_trr_path: Optional[str] = None, input_cpt_path: Optional[str] = None,
output_xtc_path: Optional[str] = None, output_cpt_path: Optional[str] = None,
output_dhdl_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {"input_tpr_path": input_tpr_path, "input_cpt_path": input_cpt_path},
"out": {"output_trr_path": output_trr_path, "output_gro_path": output_gro_path,
"output_edr_path": output_edr_path, "output_log_path": output_log_path,
"output_xtc_path": output_xtc_path, "output_cpt_path": output_cpt_path,
"output_dhdl_path": output_dhdl_path}
}
# Properties specific for BB
# general mpi properties
self.mpi_bin = properties.get('mpi_bin')
self.mpi_np = properties.get('mpi_np')
self.mpi_flags = properties.get('mpi_flags')
# gromacs cpu mpi/openmp properties
self.num_threads = str(properties.get('num_threads', ''))
self.num_threads_mpi = str(properties.get('num_threads_mpi', ''))
self.num_threads_omp = str(properties.get('num_threads_omp', ''))
self.num_threads_omp_pme = str(
properties.get('num_threads_omp_pme', ''))
# gromacs gpus
self.use_gpu = properties.get(
'use_gpu', False) # Adds: -nb gpu -pme gpu
self.gpu_id = str(properties.get('gpu_id', ''))
self.gpu_tasks = str(properties.get('gpu_tasks', ''))
# gromacs
self.checkpoint_time = properties.get('checkpoint_time')
self.noappend = properties.get('noappend', False)
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.binary_path: str = properties.get('binary_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.binary_path += ' -nobackup'
if self.gmx_nocopyright:
self.binary_path += ' -nocopyright'
if (not self.mpi_bin) and (not self.container_path):
self.gmx_version = get_gromacs_version(self.binary_path)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Mdrun <gromacs.mdrun.Mdrun>` object."""
# Setup Biobb
if self.check_restart():
return 0
# Optional output files (if not added mrun will create them using a generic name)
if not self.stage_io_dict["out"].get("output_trr_path"):
self.stage_io_dict["out"]["output_trr_path"] = fu.create_name(
prefix=self.prefix, step=self.step, name='trajectory.trr')
self.tmp_files.append(self.stage_io_dict["out"]["output_trr_path"])
self.stage_files()
self.cmd = [self.binary_path, 'mdrun',
'-o', self.stage_io_dict["out"]["output_trr_path"],
'-s', self.stage_io_dict["in"]["input_tpr_path"],
'-c', self.stage_io_dict["out"]["output_gro_path"],
'-e', self.stage_io_dict["out"]["output_edr_path"],
'-g', self.stage_io_dict["out"]["output_log_path"]]
if self.stage_io_dict["in"].get("input_cpt_path"):
self.cmd.append('-cpi')
self.cmd.append(self.stage_io_dict["in"]["input_cpt_path"])
if self.stage_io_dict["out"].get("output_xtc_path"):
self.cmd.append('-x')
self.cmd.append(self.stage_io_dict["out"]["output_xtc_path"])
else:
self.tmp_files.append('traj_comp.xtc')
if self.stage_io_dict["out"].get("output_cpt_path"):
self.cmd.append('-cpo')
self.cmd.append(self.stage_io_dict["out"]["output_cpt_path"])
if self.checkpoint_time:
self.cmd.append('-cpt')
self.cmd.append(str(self.checkpoint_time))
if self.stage_io_dict["out"].get("output_dhdl_path"):
self.cmd.append('-dhdl')
self.cmd.append(self.stage_io_dict["out"]["output_dhdl_path"])
# general mpi properties
if self.mpi_bin:
mpi_cmd = [self.mpi_bin]
if self.mpi_np:
mpi_cmd.append('-n')
mpi_cmd.append(str(self.mpi_np))
if self.mpi_flags:
mpi_cmd.extend(self.mpi_flags)
self.cmd = mpi_cmd + self.cmd
# gromacs cpu mpi/openmp properties
if self.num_threads:
fu.log(
f'User added number of gmx threads: {self.num_threads}', self.out_log)
self.cmd.append('-nt')
self.cmd.append(self.num_threads)
if self.num_threads_mpi:
fu.log(
f'User added number of gmx mpi threads: {self.num_threads_mpi}', self.out_log)
self.cmd.append('-ntmpi')
self.cmd.append(self.num_threads_mpi)
if self.num_threads_omp:
fu.log(
f'User added number of gmx omp threads: {self.num_threads_omp}', self.out_log)
self.cmd.append('-ntomp')
self.cmd.append(self.num_threads_omp)
if self.num_threads_omp_pme:
fu.log(
f'User added number of gmx omp_pme threads: {self.num_threads_omp_pme}', self.out_log)
self.cmd.append('-ntomp_pme')
self.cmd.append(self.num_threads_omp_pme)
# GMX gpu properties
if self.use_gpu:
fu.log('Adding GPU specific settings adds: -nb gpu -pme gpu', self.out_log)
self.cmd += ["-nb", "gpu", "-pme", "gpu"]
if self.gpu_id:
fu.log(
f'list of unique GPU device IDs available to use: {self.gpu_id}', self.out_log)
self.cmd.append('-gpu_id')
self.cmd.append(self.gpu_id)
if self.gpu_tasks:
fu.log(
f'list of GPU device IDs, mapping each PP task on each node to a device: {self.gpu_tasks}', self.out_log)
self.cmd.append('-gputasks')
self.cmd.append(self.gpu_tasks)
if self.noappend:
self.cmd.append('-noappend')
if self.gmx_lib:
self.env_vars_dict['GMXLIB'] = self.gmx_lib
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def copy_to_host(self):
"""
Updates the path to the original output files in the sandbox,
to catch changes due to noappend restart.
GROMACS mdrun will change the output file names from md.gro to md.part0001.gro
if the noappend flag is used.
"""
import pathlib
def capture_part_pattern(filename):
"""
Captures the 'part' pattern followed by digits from a string.
"""
import re
pattern = r'part\d+'
match = re.search(pattern, filename)
if match:
return match.group(0)
else:
return None
if self.noappend:
# List files in the staging directory
staging_path = self.stage_io_dict["unique_dir"]
files_in_staging = list(pathlib.Path(staging_path).glob('*'))
# Find the part000x pattern in the output files
for file in files_in_staging:
part_pattern = capture_part_pattern(file.name)
if part_pattern:
break
# Update expected output files
for file_ref, stage_file_path in self.stage_io_dict["out"].items():
if stage_file_path:
# Find the parent and the file name in the sandbox
parent_path = pathlib.Path(stage_file_path).parent
file_stem = pathlib.Path(stage_file_path).stem
file_suffix = pathlib.Path(stage_file_path).suffix
# Rename all output files except checkpoint files
if file_suffix != '.cpt':
# Create the new file name with the part pattern
if part_pattern:
new_file_name = f"{file_stem}.{part_pattern}{file_suffix}"
new_file_path = parent_path / new_file_name
# Update the stage_io_dict with the new file path
self.stage_io_dict["out"][file_ref] = str(
new_file_path)
return super().copy_to_host()
[docs]
def mdrun(input_tpr_path: str, output_gro_path: str, output_edr_path: str,
output_log_path: str, output_trr_path: Optional[str] = None, input_cpt_path: Optional[str] = None,
output_xtc_path: Optional[str] = None, output_cpt_path: Optional[str] = None,
output_dhdl_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
"""Create :class:`Mdrun <gromacs.mdrun.Mdrun>` class and
execute the :meth:`launch() <gromacs.mdrun.Mdrun.launch>` method."""
return Mdrun(**dict(locals())).launch()
mdrun.__doc__ = Mdrun.__doc__
main = Mdrun.get_main(mdrun, "Wrapper for the GROMACS mdrun module.")
if __name__ == '__main__':
main()