def grompp_mdruns(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
return
pers = cpc.dataflow.Persistence(
os.path.join(inp.getPersistentDir(), "persistent.dat"))
grompp_inputs = ['mdp', 'top', 'conf', 'ndx', 'settings', 'include']
mdrun_inputs = ['priority', 'cmdline_options', 'resources']
inputs = grompp_inputs + mdrun_inputs
grompp_outputs = ['tpr']
mdrun_outputs = ['conf', 'xtc', 'trr', 'edr', 'log']
outputs = grompp_outputs + mdrun_outputs
running = 0
if (pers.get("running")):
running = pers.get("running")
it = iterate.iterations(inp, inputs, outputs, pers)
out = inp.getFunctionOutput()
for i in xrange(running, it.getN()):
gromppInstName = "grompp_%d" % i
mdrunInstName = "mdrun_%d" % i
out.addInstance(gromppInstName, "grompp")
out.addInstance(mdrunInstName, "mdrun")
out.addConnection('%s:out.tpr' % gromppInstName,
'%s:in.tpr' % mdrunInstName)
it.connectOnly(grompp_inputs, grompp_outputs, out, i, gromppInstName)
it.connectOnly(mdrun_inputs, mdrun_outputs, out, i, mdrunInstName)
running += 1
pers.set("running", running)
pers.write()
return out
def runGmxCheckGap(fileTypeFlag, checkFile):
cmdnames = cmds.GromacsCommands()
cmd = cmdnames.gmxcheck.split() + [fileTypeFlag, checkFile]
proc = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
#noMatchLine=re.compile(r'Timesteps at.*don\'t match.*\(([0-9.]+),\s([0-9.]+)\)')
stdExpected = None
for line in proc.stdout:
#m = noMatchLine.match(line)
#if m:
if 'Timesteps at t=' in line:
log.debug("%s, %s", checkFile, line)
parts = line.split()
thisExpected = float(parts[5][1:-1])
thisActual = float(parts[6][:-1])
if stdExpected == None:
stdExpected = thisExpected
if thisActual > stdExpected:
log.debug("Discarding %s due to a gap in the file" % checkFile)
return False
return True
def __init__(self, persDir):
self.persDir = persDir
lastfound = True
self.trajlist = []
self.lastcpt = None
lastrundir = None
i = 0
while lastfound:
i += 1
currundir = os.path.join(persDir, "run_%03d" % i)
lastfound = False
try:
st = os.stat(currundir)
if st.st_mode & stat.S_IFDIR:
lastfound = True
lastrundir = currundir
trajl = self.checkResults(lastrundir)
self.trajlist.append(trajl)
except OSError:
pass
self.lastDirNr = i
self.lastDir = lastrundir
self.newRunDir = currundir
self.lastTrajNr = self._extractLastTrajNr()
self.cmdnames = cmds.GromacsCommands()
def mdruns(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjcat)
cpc.util.plugin.testCommand("%s -version" % cmdnames.eneconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
return
pers = cpc.dataflow.Persistence(
os.path.join(inp.getPersistentDir(), "persistent.dat"))
inputs = ['tpr', 'priority', 'cmdline_options', 'resources']
outputs = ['conf', 'xtc', 'trr', 'edr', 'log']
running = 0
if (pers.get("running")):
running = pers.get("running")
it = iterate.iterations(inp, inputs, outputs, pers)
out = inp.getFunctionOutput()
for i in xrange(running, it.getN()):
instName = "mdrun_%d" % i
out.addInstance(instName, "mdrun")
it.connect(out, i, instName)
running += 1
pers.set("running", running)
pers.write()
return out
def grompps(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
return
pers = cpc.dataflow.Persistence(
os.path.join(inp.getPersistentDir(), "persistent.dat"))
inputs = ['mdp', 'top', 'conf', 'ndx', 'settings', 'include']
outputs = ['tpr']
running = 0
if (pers.get("running")):
running = pers.get("running")
it = iterate.iterations(inp, inputs, outputs, pers)
out = inp.getFunctionOutput()
for i in xrange(running, it.getN()):
instName = "grompp_%d" % i
out.addInstance(instName, "grompp")
it.connect(out, i, instName)
out.addConnection("%s:out.tpr" % instName, "self:ext_out.tpr[%d]" % i)
running += 1
pers.set("running", running)
pers.write()
return out
def tune_fn(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
#cpc.util.plugin.testCommand("grompp -version")
#cpc.util.plugin.testCommand("mdrun -version")
return
fo = inp.getFunctionOutput()
persDir = inp.getPersistentDir()
mdpfile = procSettings(inp, inp.getOutputDir())
# copy the topology and include files
topfile = os.path.join(inp.getOutputDir(), 'topol.top')
shutil.copy(inp.getInput('top'), topfile)
incl = inp.getInput('include')
if incl is not None and len(incl) > 0:
for i in range(len(incl)):
filename = inp.getInput('include[%d]' % i)
if filename is not None:
# same name, but in one directory.
nname = os.path.join(inp.getOutputDir(),
os.path.split(filename)[1])
shutil.copy(filename, nname)
# and execute grompp
cmdlist = cmdnames.grompp.split()
cmdlist += [
"-f",
mdpfile,
"-quiet",
"-c",
inp.getInput('conf'),
"-p",
'topol.top', # we made sure it's there
"-o",
"topol.tpr"
]
if inp.hasInput('ndx'):
cmdlist.append('-n')
cmdlist.append(inp.getInput('ndx'))
proc = subprocess.Popen(cmdlist,
stdin=None,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
cwd=inp.getOutputDir())
(stdo, stde) = proc.communicate(None)
if proc.returncode != 0:
#raise GromacsError("Error running grompp: %s"%
# (open(stdoutfn,'r').read()))
fo.setError("Error running grompp: %s, %s" % (stdo, stde))
return fo
rsrc = Resources()
tune.tune(rsrc, inp.getInput('conf'),
os.path.join(inp.getOutputDir(), 'topol.tpr'), persDir)
fo.setOut('mdp', FileValue(mdpfile))
fo.setOut('resources', rsrc.setOutputValue())
return fo
def extractConf(tprFile, confFile):
"""Extract a configuration to confFile from tprFile."""
cmdnames = cmds.GromacsCommands()
cmdlist = cmdnames.editconf.split() + ['-f', tprFile, '-o', confFile]
proc = subprocess.Popen(cmdlist,
stdin=None,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
cwd=os.path.split(confFile)[0])
proc.communicate(None)
if proc.returncode != 0:
raise GromacsError("Error running editconf: %s" % proc.stdout)
def g_energy(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.g_energy)
return
edrfile=inp.getInput('edr')
item=inp.getInput('item')
outDir=inp.getOutputDir()
xvgoutname=os.path.join(outDir, "energy.xvg")
cmdlist = cmdnames.g_energy.split() + ["-f", edrfile, "-o", xvgoutname]
proc=subprocess.Popen(cmdlist,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
cwd=inp.getOutputDir(),
close_fds=True)
(stdout, stderr)=proc.communicate(item)
if proc.returncode != 0:
raise GromacsError("ERROR: g_energy returned %s"%(stdout))
regitem=re.compile(r'^%s'%(item))
regsplit=re.compile(r'---------------')
splitmatch=False
for line in iter(stdout.splitlines()):
if not splitmatch:
if regsplit.match(line):
splitmatch=True
else:
if regitem.match(line):
foundmatch=True
sp=line.split()
av=float(sp[1])
err=float(sp[2])
rmsd=float(sp[3])
drift=float(sp[4])
unit=sp[5]
break
if not foundmatch:
raise GromacsError("ERROR: couldn't find match for energy item %s in output."%
item)
fo=inp.getFunctionOutput()
fo.setOut('xvg', FileValue(xvgoutname))
fo.setOut('average', FloatValue(av))
fo.setOut('error', FloatValue(err))
fo.setOut('rmsd', FloatValue(rmsd))
fo.setOut('drift', FloatValue(drift))
fo.setOut('unit', StringValue(unit))
return fo
def tryRun(tprFile, runDir, Ncores):
"""Try to run mdrun with Ncores cores."""
cmdnames = cmds.GromacsCommands()
cmdlist = cmdnames.mdrun.split()
cmdlist += [
"-nt",
"%d" % Ncores, "-s", tprFile, "-rcon", "0.7", "-maxh", "0.0005"
]
proc = subprocess.Popen(cmdlist,
stdin=None,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
cwd=runDir)
(stdo, stde) = proc.communicate(None)
if proc.returncode != 0:
return (False, stdo)
return (True, stdo)
def pdb2gmx(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.pdb2gmx)
return
input_choices=inp.getInput('input_choices')
if input_choices is None:
input_choices=''
pdbfile=inp.getInput('conf')
#pdbfile=os.path.join(inp.getOutputDir(),inp.getInput('conf'))
#shutil.copy(inp.getInput('conf'),pdbfile)
forcefield=inp.getInput('ff')
watermodel=inp.getInput('water')
skip_hydrogens=True #default to ignh
if inp.getInput('cmdline_options') is not None:
cmdlineOpts=shlex.split(inp.getInput('cmdline_options'))
else:
cmdlineOpts=[]
cmdline = cmdnames.pdb2gmx
cmdline += ["-f", pdbfile, "-ff", forcefield, "-water", watermodel]
if skip_hydrogens:
cmdline.extend(["-ignh"])
cmdline.extend(cmdlineOpts)
proc=subprocess.Popen(cmdline,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
cwd=inp.getOutputDir(),
close_fds=True)
(stdout, stderr)=proc.communicate(input_choices)
if proc.returncode != 0:
raise GromacsError("ERROR: pdb2gmx returned %s"%(stdout))
fo=inp.getFunctionOutput()
fo.setOut('conf', FileValue(os.path.join(inp.getOutputDir(),'conf.gro')))
fo.setOut('top', FileValue(os.path.join(inp.getOutputDir(),'topol.top')))
#how do we handle itp output files?
itpfiles=glob.glob(os.path.join(inp.getOutputDir(),'*.itp'))
fo.setOut('include',itpfiles)
for i in xrange(len(itpfiles)):
fo.setOut('include[%d]'%(i),itpfiles[i])
return fo
def _eneconv(inp, fo):
"""Internal implementation of eneconv"""
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.eneconv)
return
pers=cpc.dataflow.Persistence(os.path.join(inp.getPersistentDir(),
"persistent.dat"))
if pers.get('init') is None:
init=True
pers.set('init', 1)
else:
inpItems=[ 'edr_files', 'scalefac', 'dt', 'offset', 'cmdline_options' ]
if not checkUpdated(inp, inpItems):
return
init=False
writeStdin=StringIO()
edrFilesList=inp.getInput('edr_files')
outDir=inp.getOutputDir()
edrOutname=os.path.join(outDir, "fixed.edr")
#cmdline=["eneconv", '-f', edrFiles, '-o', edrOutname]
cmdline = cmdnames.eneconv.split() + ['-f']
for i in xrange(len(edrFilesList)):
cmdline.append(inp.getInput('edr_files[%d]' % i))
cmdline.extend(['-o', edrOutname])
first_frame_ps=inp.getInput('first_frame_ps')
if first_frame_ps is not None:
cmdline.extend(['-b', "%g"%first_frame_ps] )
last_frame_ps=inp.getInput('last_frame_ps')
if last_frame_ps is not None:
cmdline.extend(['-e', "%g"%last_frame_ps] )
dt=inp.getInput('dt')
if dt is not None:
cmdline.extend(['-dt', "%g"%dt] )
offset=inp.getInput('offset')
if offset is not None:
cmdline.extend(['-offset', "%g"%offset] )
scaleF=inp.getInput('scalefac')
if scaleF is not None:
cmdline.extend(['-scalefac', "%g"%scaleF] )
if inp.getInput('cmdline_options') is not None:
cmdlineOpts=shlex.split(inp.getInput('cmdline_options'))
else:
cmdlineOpts=[]
cmdline.extend(cmdlineOpts)
log.debug(cmdline)
proc=subprocess.Popen(cmdline,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
cwd=inp.getOutputDir(),
close_fds=True)
(stdout, stderr)=proc.communicate(writeStdin.getvalue())
if proc.returncode != 0:
raise GromacsError("ERROR: eneconv returned %s"%(stdout))
fo.setOut('edr', FileValue(edrOutname))
pers.write()
def _trjconv(inp, fo, split):
"""Internal implementation of trjconv and trjconv_split"""
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
return
pers=cpc.dataflow.Persistence(os.path.join(inp.getPersistentDir(),
"persistent.dat"))
if pers.get('init') is None:
init=True
pers.set('init', 1)
else:
inpItems=[ 'traj', 'tpr', 'ndx', 'dt', 'skip', 'dump', 'pbc', 'ur',
'center', 'fit', 'fit_type', 'cmdline_options' ]
if not checkUpdated(inp, inpItems):
return
init=False
writeStdin=StringIO()
trajfile=inp.getInput('traj')
tprfile=inp.getInput('tpr')
#item=inp.getInput('item')
outDir=inp.getOutputDir()
xtcoutname=os.path.join(outDir, "trajout.xtc")
grooutname=os.path.join(outDir, "out.gro")
cmdline = cmdnames.trjconv.split() + ['-s', tprfile, '-f', trajfile]
if not split:
cmdline.extend(['-o', xtcoutname])
else:
cmdline.extend(['-sep', '-o', grooutname])
ndxfile=inp.getInput('ndx')
if ndxfile is not None:
cmdline.extend(['-n', ndxfile] )
first_frame_ps=inp.getInput('first_frame_ps')
if first_frame_ps is not None:
cmdline.extend(['-b', "%g"%first_frame_ps] )
last_frame_ps=inp.getInput('last_frame_ps')
if last_frame_ps is not None:
cmdline.extend(['-b', "%g"%last_frame_ps] )
dt=inp.getInput('dt')
if dt is not None:
cmdline.extend(['-dt', "%g"%dt] )
skip=inp.getInput('skip')
if skip is not None:
cmdline.extend(['-skip', "%d"%skip] )
dump=inp.getInput('dump')
if dump is not None:
cmdline.extend(['-dump', "%g"%dump] )
pbc=inp.getInput('pbc')
if pbc is not None:
cmdline.extend(['-pbc', pbc] )
ur=inp.getInput('ur')
if ur is not None:
cmdline.extend(['-ur', ur] )
center=inp.getInput('center')
if center is not None:
cmdline.extend(['-center'])
writeStdin.write("%s\n"%center)
fit=inp.getInput('fit')
fit_type=inp.getInput('fit_type')
if fit is not None:
if center is not None:
raise GromacsError('Both fit and center set')
if fit_type is None:
fit_type='rot+trans'
cmdline.extend(['-fit', fit_type])
writeStdin.write("%s\n"%fit)
if inp.getInput('cmdline_options') is not None:
cmdlineOpts=shlex.split(inp.getInput('cmdline_options'))
else:
cmdlineOpts=[]
cmdline.extend(cmdlineOpts)
log.debug(cmdline)
outputGroup=inp.getInput('output_group')
if outputGroup is not None:
writeStdin.write("%s\n"%outputGroup)
else:
writeStdin.write("System\n")
proc=subprocess.Popen(cmdline,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
cwd=inp.getOutputDir(),
close_fds=True)
(stdout, stderr)=proc.communicate(writeStdin.getvalue())
if proc.returncode != 0:
raise GromacsError("ERROR: trjconv returned %s"%(stdout))
if not split:
fo.setOut('xtc', FileValue(xtcoutname))
else:
i=0
# iterate as long as there are files with anme 'out%d.gro' for
# increasing i
while True:
filename=os.path.join(outDir, 'out%d.gro'%i)
if not os.path.exists(filename):
break
fo.setOut('confs[%d]'%i, FileValue(filename))
i+=1
pers.write()
def mdrun(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjcat)
cpc.util.plugin.testCommand("%s -version" % cmdnames.eneconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
return
persDir = inp.getPersistentDir()
outDir = inp.getOutputDir()
fo = inp.getFunctionOutput()
rsrc = Resources(inp.getInputValue("resources"))
rsrcFilename = os.path.join(persDir, 'rsrc.dat')
# check whether we need to reinit
pers = cpc.dataflow.Persistence(os.path.join(persDir, "persistent.dat"))
init = False
lasttpr = pers.get('lasttpr')
newtpr = inp.getInput('tpr')
#if inp.getInputValue('tpr').isUpdated():
if newtpr != lasttpr:
lasttpr = newtpr
# there was no previous command.
# purge the persistent directory, by moving the confout files to a
# backup directory
log.debug("(Re)initializing mdrun")
confout = glob.glob(os.path.join(persDir, "run_???"))
if len(confout) > 0:
backupDir = os.path.join(persDir, "backup")
try:
os.mkdir(backupDir)
except OSError:
pass
for conf in confout:
try:
os.rename(conf,
os.path.join(backupDir,
os.path.split(conf)[-1]))
except OSError:
pass
init = True
pers.set('lasttpr', lasttpr)
elif inp.cmd is None:
return fo
if init:
if rsrc.max.get('cores') is None:
confFile = os.path.join(persDir, 'conf.gro')
extractConf(newtpr, confFile)
tune.tune(rsrc, confFile, newtpr, persDir)
if inp.cmd is not None:
log.debug("Canceling commands")
fo.cancelPrevCommands()
pers.set('initialized', True)
else:
if rsrc.max.get('cores') is None:
rsrc.load(rsrcFilename)
if inp.cmd is not None:
log.debug("Return code was %s" % str(inp.cmd.getReturncode()))
# try to find out whether the run has already finished
confout = glob.glob(os.path.join(persDir, "run_???", "confout.*gro"))
if len(confout) > 0:
confoutDir = os.path.dirname(confout[0])
hasFinalData = checkConfoutDir(confoutDir)
if hasFinalData:
log.debug("Extracting data. ")
# confout exists. we're finished. Concatenate all the runs if
# we need to, but first create the output dict
extractData(confout, outDir, persDir, fo)
return fo
tfc = TrajFileCollection(persDir)
lastDir = tfc.getLastDir()
# first check whether we got an error code back
if (inp.cmd is not None) and inp.cmd.getReturncode() != 0:
# there was a problem. Check the log
if lastDir:
stde = os.path.join(lastDir, "stderr")
if checkErr(stde, rsrc, newtpr, persDir):
if os.path.exists(stde):
stdef = open(stde, 'r')
errmsg = unicode(stdef.read(), errors='ignore')
stdef.close()
raise MdrunError("Error running mdrun: %s" % errmsg)
else:
log.debug("An error has occured, but no lastDir was found.")
# now check whether any of the last 4 iterations produced
# trajectories
trajlist = tfc.getTrajList()
if len(trajlist) > 4:
ret = False
for j in range(4):
haveTraj = (len(trajlist[-j - 1]) > 0)
ret = ret or haveTraj #prevtraj[-j-1]
if not ret:
if lastDir:
stde = os.path.join(lastDir, "stderr")
if os.path.exists(stde):
stdef = open(stde, 'r')
errmsg = unicode(stdef.read(), errors='ignore')
stdef.close()
else:
errmsg = ""
raise MdrunError(
"Error running mdrun. No trajectories: %s" % errmsg)
else:
raise MdrunError(
"Error running mdrun. No trajectories and no lastDir was found."
)
# Make a new directory with the continuation of this run
#newdirname=currundir #"run_%03d"%(i+1)
newdirname = tfc.getNewRunDir()
log.debug("Making a new directory for this run: %s" % newdirname)
try:
os.mkdir(newdirname)
except OSError:
log.debug("Directory already exists.")
pass
tpr = newtpr
src = os.path.join(inp.getBaseDir(), tpr)
dst = os.path.join(newdirname, "topol.tpr")
shutil.copy(src, dst)
# handle command line inputs
if inp.getInput('cmdline_options') is not None:
cmdlineOpts = shlex.split(inp.getInput('cmdline_options'))
else:
cmdlineOpts = []
if inp.getInput('priority') is not None:
prio = inp.getInput('priority')
else:
prio = 0
lastcpt = tfc.getLastCpt()
# copy the checkpoint to the new cmd dir
if lastcpt is not None:
shutil.copy(lastcpt, os.path.join(newdirname, "state.cpt"))
log.debug("Continuing from checkpoint")
# now add to the priority if this run has already been started
completed = tfc.getFractionCompleted(tpr)
if completed > 0:
log.debug("Fraction completed: %s" % completed)
# Already finished, but no confout.gro?
if completed >= 1:
log.debug(
"Iteration finished, but the final coordinates were not written."
)
if tfc.trajlist[-1].get('edr') or tfc.trajlist[-1].get(
'xtc') or tfc.trajlist[-1].get('trr'):
log.debug(
"Last run produced output files without gaps (but no confout.gro). Generating coordinates from checkpoint."
)
confout = tfc.checkpointToConfout()
if confout:
log.debug("Extracting data.")
extractData([confout], outDir, persDir, fo)
return fo
else:
log.debug(
"Last run did not produce any output files. Cannot generate coordinates from checkpoint."
)
# now the priority ranges from 1 to 4, depending on how
# far along the simulation is.
prio += 1 + int(3 * (completed))
log.debug("Setting new priority to %d because it's in progress" % prio)
# we can always add state.cpt, even if it doesn't exist.
args = [
"-quiet", "-s", "topol.tpr", "-noappend", "-cpi", "state.cpt", "-rcon",
"0.7"
]
args.extend(cmdlineOpts)
# for the new neighbor search scheme in Gromacs 4.6, set this env
# variable
# any expected output files.
newFileNr = tfc.getLastTrajNr() + 1
outputFiles = [
"traj.part%04d.xtc" % newFileNr,
"traj.part%04d.trr" % newFileNr,
"confout.part%04d.gro" % newFileNr,
"ener.part%04d.edr" % newFileNr,
"dhdl.part%04d.xvg" % newFileNr,
"pullx.part%04d.xvg" % newFileNr,
"pullf.part%04d.xvg" % newFileNr,
"md.part%04d.log" % newFileNr, "state.cpt", "state_prev.cpt"
]
log.debug("Expected output files: %s" % outputFiles)
cmd = cpc.command.Command(newdirname,
"gromacs/mdrun",
args,
minVersion=cpc.command.Version("4.5"),
addPriority=prio,
outputFiles=outputFiles)
if inp.hasInput("resources") and inp.getInput("resources") is not None:
#log.debug("resources is %s"%(inp.getInput("resources")))
#rsrc=Resources(inp.getInputValue("resources"))
rsrc.updateCmd(cmd)
log.debug("Adding command")
fo.addCommand(cmd)
if inp.getInputValue('tpr').isUpdated() and inp.cmd is not None:
log.debug("Canceling commands")
fo.cancelPrevCommands()
# and save for further invocations
rsrc.save(rsrcFilename)
pers.write()
return fo
def extractData(confout, outDir, persDir, fo):
"""Concatenate all output data from the partial runs into the end results"""
cmdnames = cmds.GromacsCommands()
#outputs=dict()
# Concatenate stuff
confoutPath = os.path.join(outDir, "confout.gro")
shutil.copy(confout[0], confoutPath)
#outputs['conf'] = Value(confoutPath,
# inp.function.getOutput('conf').getType())
fo.setOut('conf', FileValue(confoutPath))
# fix the xtc files
xtcso = sorted(glob.glob(os.path.join(persDir, "run_???", "traj.*xtc")))
# cull empty files and duplicate trajectory names
xtcs = []
xtcbase = []
try:
for file in xtcso:
st = os.stat(file)
base = os.path.split(file)[1]
if st.st_size > 0:
if base not in xtcbase:
xtcs.append(file)
xtcbase.append(base)
else:
# there already was a file with this name. Overwrite
# it because mdrun wasn't aware of it when writing.
ind = xtcbase.index(base)
xtcs[ind] = file
except OSError:
pass
# concatenate them
xtcoutname = os.path.join(outDir, "traj.xtc")
if len(xtcs) > 0:
cmd = cmdnames.trjcat.split() + ["-f"]
cmd.extend(xtcs)
cmd.extend(["-o", xtcoutname])
stdo = open(os.path.join(persDir, "trjcat_xtc.out"), "w")
sp = subprocess.Popen(cmd, stdout=stdo, stderr=subprocess.STDOUT)
sp.communicate(None)
stdo.close()
fo.setOut('xtc', FileValue(xtcoutname))
# do the trrs
trrso = sorted(glob.glob(os.path.join(persDir, "run_???", "traj.*trr")))
# cull empty files and duplicate trajectory names
trrs = []
trrbase = []
try:
for file in trrso:
st = os.stat(file)
base = os.path.split(file)[1]
if st.st_size > 0:
if base not in trrbase:
trrs.append(file)
trrbase.append(base)
else:
# there already was a file with this name. Overwrite
# it because mdrun wasn't aware of it when writing.
ind = trrbase.index(base)
trrs[ind] = file
except OSError:
pass
# concatenate them
trroutname = os.path.join(outDir, "traj.trr")
if len(trrs) > 0:
cmd = cmdnames.trjcat.split() + ["-f"]
cmd.extend(trrs)
cmd.extend(["-o", trroutname])
stdo = open(os.path.join(persDir, "trjcat_trr.out"), "w")
sp = subprocess.Popen(cmd, stdout=stdo, stderr=subprocess.STDOUT)
sp.communicate(None)
stdo.close()
fo.setOut('trr', FileValue(trroutname))
# and the edrs
edrso = glob.glob(os.path.join(persDir, "run_???", "ener.*edr"))
# cull empty files and duplicate trajectory names
edrs = []
edrbase = []
try:
for file in edrso:
st = os.stat(file)
base = os.path.split(file)[1]
if st.st_size > 0:
if base not in edrbase:
edrs.append(file)
edrbase.append(base)
else:
# there already was a file with this name. Overwrite
# it because mdrun wasn't aware of it when writing.
ind = edrbase.index(base)
log.debug("Overwriting existing edr file %s with %s" %
(edrs[ind], file))
edrs[ind] = file
except OSError:
pass
edroutname = os.path.join(outDir, "ener.edr")
if len(edrs) > 1:
log.debug("Concatenating edr files: %s" % edrs)
# concatenate them
if len(edrs) > 0:
cmd = cmdnames.eneconv.split() + ["-f"]
cmd.extend(edrs)
cmd.extend(["-o", edroutname])
stdo = open(os.path.join(persDir, "eneconv.out"), "w")
sp = subprocess.Popen(cmd, stdout=stdo, stderr=subprocess.STDOUT)
sp.communicate(None)
stdo.close()
log.debug("Setting edr output to %s" % edroutname)
fo.setOut('edr', FileValue(edroutname))
# do the stdout
stdouto = glob.glob(os.path.join(persDir, "run_???", "stdout"))
stdoutname = os.path.join(outDir, "stdout")
outf = open(stdoutname, "w")
for infile in stdouto:
inf = open(infile, "r")
outf.write(inf.read())
inf.close()
outf.write("%s\n" % time.strftime("%a, %d %b %Y %H:%M:%S"))
outf.write("%f\n" % time.time())
outf.close()
fo.setOut('stdout', FileValue(stdoutname))
# do the stderr
stderro = glob.glob(os.path.join(persDir, "run_???", "stderr"))
stderrname = os.path.join(outDir, "stderr")
outf = open(stderrname, "w")
for infile in stderro:
inf = open(infile, "r")
outf.write(inf.read())
inf.close()
outf.close()
fo.setOut('stderr', FileValue(stderrname))
# and do md.log
logo = glob.glob(os.path.join(persDir, "run_???", "md.*log"))
logname = os.path.join(outDir, "md.log")
outf = open(logname, "w")
for infile in logo:
inf = open(infile, "r")
outf.write(inf.read())
inf.close()
outf.close()
fo.setOut('log', FileValue(logname))
log.debug("Returning without command.")
log.debug("fo.cmds=%s" % str(fo.cmds))
def grompp(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing whether the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
return
#log.debug("base dir=%s"%inp.getBaseDir())
#log.debug("output dir=%s"%inp.getOutputDir())
#log.debug("persistent dir=%s"%inp.getPersistentDir())
pers = cpc.dataflow.Persistence(
os.path.join(inp.getPersistentDir(), "persistent.dat"))
fo = inp.getFunctionOutput()
if not (inp.getInputValue('conf').isUpdated()
or inp.getInputValue('top').isUpdated()
or inp.getInputValue('include').isUpdated()
or inp.getInputValue('settings').isUpdated()
or inp.getInputValue('ndx').isUpdated()):
if pers.get('init') is not None:
return fo
if pers.get('init') is not None:
log.debug("conf: %s" % (inp.getInputValue('conf').isUpdated()))
log.debug("top: %s" % (inp.getInputValue('top').isUpdated()))
log.debug("include: %s" % (inp.getInputValue('include').isUpdated()))
log.debug("settings: %s" % (inp.getInputValue('settings').isUpdated()))
log.debug("ndx: %s" % (inp.getInputValue('ndx').isUpdated()))
pers.set('init', 1)
mdpfile = procSettings(inp, inp.getOutputDir())
# copy the topology and include files
topfile = os.path.join(inp.getOutputDir(), 'topol.top')
shutil.copy(inp.getInput('top'), topfile)
incl = inp.getInput('include')
if incl is not None and len(incl) > 0:
for i in range(len(incl)):
filename = inp.getInput('include[%d]' % i)
if filename is not None:
# same name, but in one directory.
nname = os.path.join(inp.getOutputDir(),
os.path.split(filename)[1])
shutil.copy(filename, nname)
# and execute grompp
cmdlist = cmdnames.grompp.split() + [
"-f",
mdpfile,
"-quiet",
"-c",
inp.getInput('conf'),
"-p",
'topol.top',
# we made sure it's there
"-o",
"topol.tpr"
]
if inp.hasInput('ndx'):
cmdlist.append('-n')
cmdlist.append(inp.getInput('ndx'))
# TODO: symlink all the auxiliary files into the run dir
stdoutfn = os.path.join(inp.getOutputDir(), "stdout")
stdoutf = open(stdoutfn, "w")
stdoutf.write("%s\n" % time.strftime("%a, %d %b %Y %H:%M:%S"))
stdoutf.write("%f\n" % time.time())
#stdoutf=open(os.path.join(inp.getOutputDir(), "stderr"),"w")
proc = subprocess.Popen(cmdlist,
stdin=None,
stdout=stdoutf,
stderr=subprocess.STDOUT,
cwd=inp.getOutputDir())
proc.communicate(None)
stdoutf.close()
if proc.returncode != 0:
raise GromacsError("Error running grompp: %s" %
(open(stdoutfn, 'r').read()))
fo.setOut('stdout', FileValue(stdoutfn))
fo.setOut('tpr', FileValue(os.path.join(inp.getOutputDir(), "topol.tpr")))
pers.write()
return fo
