initial implementation of lammps support

mdbenchmark/generate.py

@@ -31,7 +31,11 @@
     "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."""
@@ -215,9 +219,11 @@ def generate(name, cpu, gpu, module, host, min_nodes, max_nodes, time, skip_vali
     # 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 +1,83 @@
+# -*- 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]
+
+    copyfile(full_filename, sim[full_filename].relpath)
+
+    return name
+
+
+def analyze_lammps_file(fh):
+    """ Check whether the LAMMPS config file has any relative imports or variables
+    """
+    lines = fh.readlines()
+
+    for line in lines:
+        # Continue if we do not need to do anything with the current line
+        if (
+            ("parameters" not in line)
+            and ("coordinates" not in line)
+            and ("structure" not in line)
+        ):
+            continue
+
+        path = line.split()[1]
+        if "$" in path:
+            console.error("Variable Substitutions are not allowed in NAMD files!")
+        if ".." in path:
+            console.error("Relative file paths are not allowed in NAMD files!")
+        if "/" not in path or ("/" in path and not path.startswith("/")):
+            console.error("No absolute path detected in NAMD file!")
+
+
+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
+        )
+
+
+    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 %}