initial implementation of lammps support

mdbenchmark/generate.py

@@ -33,7 +33,11 @@
     "Parameter paths must be absolute. Only crude file checks are performed! "
     "If you use the {} option make sure you use the GPU compatible NAMD module!"
 )
-
+LAMMPS_WARNING = (
+    "LAMMPS support is experimental."
+    "All input files must be in the same directory and have the same base name!"
+    "We hope you know what you're doing..."
+)
 
 def validate_name(ctx, param, name=None):
     """Validate that we are given a name argument."""
@@ -222,9 +226,11 @@ def generate(
     # click does the validation for us
     template = utils.retrieve_host_template(host)
 
-    # Warn the user that NAMD support is still experimental.
+    # Warn the user that NAMD and LAMMPS support is still experimental.
     if any(["namd" in m for m in module]):
         console.warn(NAMD_WARNING, "--gpu")
+    if any(["lammps" in m for m in module]):
+        console.warn(LAMMPS_WARNING)
 
     module = mdengines.normalize_modules(module, skip_validation)
 

mdbenchmark/mdengines/__init__.py

@@ -22,10 +22,10 @@
 
 import six
 
-from . import gromacs, namd
+from . import gromacs, namd, lammps
 from .. import console
 
-SUPPORTED_ENGINES = {"gromacs": gromacs, "namd": namd}
+SUPPORTED_ENGINES = {"gromacs": gromacs, "namd": namd, "lammps": lammps}
 
 
 def detect_md_engine(modulename):
@@ -63,6 +63,7 @@ def prepare_module_name(module, skip_validation=False):
                 "--skip-validation",
                 "gromacs/dummy",
                 "namd/dummy",
+                "lammps/dummy"
             )
         console.error("We were not able to determine the module name.")
 
@@ -120,7 +121,7 @@ def normalize_modules(modules, skip_validation):
         if detect_md_engine(engine_name) is None:
             console.error(
                 "There is currently no support for '{}'. "
-                "Supported MD engines are: gromacs, namd.",
+                "Supported MD engines are: gromacs, namd, lammps.",
                 engine_name,
             )
 

mdbenchmark/mdengines/lammps.py

@@ -0,0 +1,64 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
+#
+# MDBenchmark
+# Copyright (c) 2017 Max Linke & Michael Gecht and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# MDBenchmark is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# MDBenchmark is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
+import os
+import re
+from glob import glob
+from shutil import copyfile
+
+import mdsynthesis as mds
+import numpy as np
+
+from .. import console
+
+NAME = "lammps"
+
+
+def prepare_benchmark(name, *args, **kwargs):
+    sim = kwargs["sim"]
+
+    full_filename = name + ".in"
+    if name.endswith(".in"):
+        full_filename = name
+        name = name[:-3]
+
+    input_file_list = glob("{}*".format(name))
+    for fn in input_file_list:
+        copyfile(full_filename, sim[fn].relpath)
+
+    return name
+
+
+def check_input_file_exists(name):
+    """Check and append the correct file extensions for the LAMMPS module."""
+    # Check whether the needed files are there.
+    fn = name
+    if fn.endswith(".in"):
+        fn = name[:-4]
+
+    infile = fn + ".in"
+    if not os.path.exists(infile):
+        console.error(
+            "File {} does not exist, but is needed for LAMMPS benchmarks.", infile
+        )
+
+    input_files = glob("{}*".format(fn))
+    console.info("The following files will be used to generate the benchmarks:\n {}", ", ".join(input_files))
+
+    return True

mdbenchmark/mdengines/namd.py

@@ -77,6 +77,7 @@ def analyze_namd_file(fh):
 def check_input_file_exists(name):
     """Check and append the correct file extensions for the NAMD module."""
     # Check whether the needed files are there.
+    input_files = []
     for extension in ["namd", "psf", "pdb"]:
         if name.endswith(".{}".format(extension)):
             name = name[: -2 + len(extension)]
@@ -86,5 +87,8 @@ def check_input_file_exists(name):
             console.error(
                 "File {} does not exist, but is needed for NAMD benchmarks.", fn
             )
+        input_files.append(fn)
+
+    console.info("The following files will be used to generate the benchmarks: {}", ", ".join(input_files))
 
     return True

mdbenchmark/mdengines/utils.py

@@ -31,6 +31,7 @@
 FILES_TO_KEEP = {
     "gromacs": [".*/bench\.job", ".*\.tpr", ".*\.mdp"],
     "namd": [".*/bench\.job", ".*\.namd", ".*\.psf", ".*\.pdb"],
+    "lammps": [".*/bench\.job", ".*\.in"],
 }
 
 PARSE_ENGINE = {
@@ -48,6 +49,13 @@
         "ncores_return": lambda line: int(line.split()[3]),
         "analyze": "*out*",
     },
+    "lammps": {
+        "performance": "Performance",
+        "performance_return": lambda line: 1 / float(line.split()[1]),
+        "ncores": "Loop",
+        "ncores_return": lambda line: int(line.split()[5]),
+        "analyze": "*log*",
+    }
 }
 
 

mdbenchmark/templates/cobra

@@ -40,4 +40,6 @@ module load {{ module }}
 srun gmx_mpi mdrun -v -maxh {{ time / 60 }} -deffnm {{ name }}
 {%- elif mdengine == "namd" %}
 srun namd2 {{ name }}.namd
+{%- elif mdengine == "lammps" %}
+srun lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
 {%- endif %}

mdbenchmark/templates/draco

@@ -37,4 +37,6 @@ module load {{ module }}
 srun gmx_mpi mdrun -v -maxh {{ time / 60 }} -deffnm {{ name }}
 {%- elif mdengine == "namd" %}
 srun namd2 {{ name }}.namd
+{%- elif mdengine == "lammps" %}
+srun lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
 {%- endif %}

mdbenchmark/templates/hydra

@@ -23,4 +23,6 @@ module load cuda
 poe gmx_mpi mdrun -deffnm {{ name }} -maxh {{ time / 60 }}
 {%- elif mdengine == "namd" %}
 poe namd2 {{ name }}.namd
+{%- elif mdengine == "lammps" %}
+poe lmp_mpi -v f tmp.out -l my.log -sc none -i {{ name }}.in
 {%- endif %}

mdbenchmark/tests/data/analyze-files-lammps/1/Sim.d9427a82-789d-4789-9186-83e390455fee.json

@@ -0,0 +1 @@
+{"mdsynthesis": {}, "categories": {"module": "lammps/2016", "gpu": false, "nodes": 1, "host": "draco", "time": 15, "name": "bulk", "started": false}, "tags": []}

mdbenchmark/tests/data/analyze-files-lammps/1/bench.job

@@ -0,0 +1,25 @@
+#!/bin/bash -l
+# Standard output and error:
+#SBATCH -o ./bulk.out.%j
+#SBATCH -e ./bulk.err.%j
+# Initial working directory:
+#SBATCH -D ./
+# Job Name:
+#SBATCH -J bulk
+#
+# Queue (Partition):
+#SBATCH --partition=express
+#
+# Number of nodes and MPI tasks per node:
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=32
+# Wall clock limit:
+#SBATCH --time=00:20:00
+
+module purge
+module load impi
+module load cuda
+module load lammps/2016
+
+# Run lammps/2016 for 15 minutes
+srun lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy

mdbenchmark/tests/data/analyze-files-lammps/1/bulk.in

@@ -0,0 +1,90 @@
+# LAMMPS input script for standardized atomistic simulations
+# Created by emc_setup.pl v2.2.12, July 28, 2017 as part of EMC
+# on Mon Mar  5 16:29:28 CET 2018
+
+# Variable definitions
+
+variable	project		index	"bulk"	# project name
+variable	source		index	.	# data directory
+variable	params		index	.	# parameter directory
+variable	temperature	index	300		# system temperature
+variable	tdamp		index	100.0		# temperature damping
+variable	dielectric	index	1		# medium dielectric
+variable	kappa		index	4		# electrostatics kappa
+variable	cutoff		index	9.5		# standard cutoff
+variable	charge_cutoff	index	9.5		# charge cutoff
+variable	precision	index	0.001		# kspace precision
+variable	lseed		index	723853		# langevin seed
+variable	vseed		index	1486234		# velocity init seed
+variable	tequil		index	1000		# equilibration time
+variable	trun		index	5000  		# run time
+variable	frestart	index	0		# 0: equil, 1: restart
+variable	dtrestart	index	100000		# delta restart time
+variable	dtdump		index	100		# delta dump time
+variable	dtthermo	index	1000		# delta thermo time
+variable	timestep	index	1		# integration time step
+variable	tfreq		index	10		# profile sampling freq
+variable	nsample		index	1000		# profile conf sampling
+variable	dtime		equal	${tfreq}*${nsample}	# profile dtime
+variable	restart		index	${params}/${project}.restart
+
+if "${frestart} != 0" then &
+"variable	data		index	${restart}" &
+else &
+"variable	data		index	${params}/${project}.data" &
+
+# LAMMPS atomistic input script
+
+echo		screen
+units		real
+atom_style	full
+
+# Interaction potential definition
+
+pair_style	lj/class2/coul/long ${cutoff} ${charge_cutoff}
+bond_style	harmonic
+special_bonds	lj/coul 0 0 1
+if "${frestart} != 0" then "read_restart ${data}" else "read_data ${data}"
+include		${params}/${project}.params
+
+# Integration conditions (check)
+
+timestep	${timestep}
+kspace_style	pppm/cg ${precision}
+dielectric	${dielectric}
+fix		mom all momentum 100 linear 1 1 1 angular
+
+# Equilibration
+
+thermo		${dtthermo}
+if "${frestart} != 0" then "jump SELF simulate"
+velocity	all create ${temperature} ${vseed} &
+		dist gaussian rot yes mom yes sum yes
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve/limit 0.1
+run		${tequil}
+unfix		temp
+unfix		int
+write_restart	${project}.restart2
+
+# Simulation
+
+label		simulate
+fix		temp all langevin ${temperature} ${temperature} ${tdamp} &
+		${lseed}
+fix		int all nve
+
+# System sampling: pressure
+
+fix		press all ave/time ${tfreq} ${nsample} ${dtime} &
+		c_thermo_temp &
+		c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+		c_thermo_press[4] c_thermo_press[5] c_thermo_press[6] &
+		file ${project}.pressure
+
+# Run conditions
+
+restart		${dtrestart} ${project}.restart1 ${project}.restart2
+dump		1 all custom ${dtdump} ${project}.dump id type x y z
+run		${trun}