def runLogic(inp,i):
#Sending a job for a worker to compute
val = inp.getInputValue('integer_inputs')
arr = inp.getInput('integer_inputs')
#1 create command
storageDir = "%s/%s"%(inp.getPersistentDir(),i)
#the command name should match the executable name of the plugin
commandName = "math/double"
args = [arr[i].get()]
cmd =cpc.command.Command(storageDir
,commandName
,args)
#2 define how many cores we want for this job
resources = Resources()
resources.min.set('cores',1)
resources.max.set('cores',1)
resources.updateCmd(cmd)
#2 add the command to the function output --> will be added to the queue
fo = inp.getFunctionOutput()
fo.addCommand(cmd)
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 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 pairmodel(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("pairmodel --help")
return
persDir=inp.getPersistentDir()
outDir=inp.getOutputDir()
fo=inp.getFunctionOutput()
rsrc=Resources(inp.getInputValue("resources"))
rsrcFilename=os.path.join(persDir, 'rsrc.dat')
log.debug("Initializing pairmodel")
seq1=inp.getInput('seq1')
seq2=inp.getInput('seq2')
pdb1=inp.getInput('pdb1')
pdb2=inp.getInput('pdb2')
testseq=inp.getInput('testseq')
#how do we assign suffix name?
suffixname=pdb1.split('_')[-1]
if len(suffixname)>3:
suffixname=suffixname[:-4]
#do we need to copy files to working directory?
if inp.getInput('cmdline_options') is not None:
if has_split:
cmdlineOpts=shutil.split(inp.getInput('cmdline_options'))
else:
cmdlineOpts=inp.getInput('cmdline_options').split()
else:
cmdlineOpts=[]
# now add to the priority if this run has already been started
# we can always add state.cpt, even if it doesn't exist.
args=["--seqfile", testseq, "--template1", seq1, "--template2", seq2,
"--seqname", os.path.basename(testseq)[:-4], "--samples1", pdb1,
"--samples2", pdb2, "--suffix", suffixname ]
args.extend(cmdlineOpts)
cmd=cpc.command.Command(newdirname, "modeltools/pairmodel", args)
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)
# and save for further invocations
rsrc.save(rsrcFilename)
return fo
def runLogic(inp, i):
#Sending a job for a worker to compute
val = inp.getInputValue('integer_inputs')
arr = inp.getInput('integer_inputs')
#1 create command
storageDir = "%s/%s" % (inp.getPersistentDir(), i)
#the command name should match the executable name of the plugin
commandName = "math/double"
args = [arr[i].get()]
cmd = cpc.command.Command(storageDir, commandName, args)
#2 define how many cores we want for this job
resources = Resources()
resources.min.set('cores', 1)
resources.max.set('cores', 1)
resources.updateCmd(cmd)
#2 add the command to the function output --> will be added to the queue
fo = inp.getFunctionOutput()
fo.addCommand(cmd)
def pairmodel(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("pairmodel --help")
return
persDir = inp.getPersistentDir()
outDir = inp.getOutputDir()
fo = inp.getFunctionOutput()
rsrc = Resources(inp.getInputValue("resources"))
rsrcFilename = os.path.join(persDir, 'rsrc.dat')
log.debug("Initializing pairmodel")
seq1 = inp.getInput('seq1')
seq2 = inp.getInput('seq2')
pdb1 = inp.getInput('pdb1')
pdb2 = inp.getInput('pdb2')
testseq = inp.getInput('testseq')
#how do we assign suffix name?
suffixname = pdb1.split('_')[-1]
if len(suffixname) > 3:
suffixname = suffixname[:-4]
#do we need to copy files to working directory?
if inp.getInput('cmdline_options') is not None:
if has_split:
cmdlineOpts = shutil.split(inp.getInput('cmdline_options'))
else:
cmdlineOpts = inp.getInput('cmdline_options').split()
else:
cmdlineOpts = []
# now add to the priority if this run has already been started
# we can always add state.cpt, even if it doesn't exist.
args = [
"--seqfile", testseq, "--template1", seq1, "--template2", seq2,
"--seqname",
os.path.basename(testseq)[:-4], "--samples1", pdb1, "--samples2", pdb2,
"--suffix", suffixname
]
args.extend(cmdlineOpts)
cmd = cpc.command.Command(newdirname, "modeltools/pairmodel", args)
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)
# and save for further invocations
rsrc.save(rsrcFilename)
return fo
def replica(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
# cpc.util.plugin.testCommand("trjcat -version")
# cpc.util.plugin.testCommand("eneconv -version")
# cpc.util.plugin.testCommand("gmxdump -version")
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(inp.getPersistentDir(),
"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:
pass
for conf in confout:
try:
os.rename(conf, os.path.join(backupDir,
os.path.split(conf)[-1]))
except:
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.part*.gro"))
if len(confout) > 0:
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
else:
tfc=TrajFileCollection(persDir)
# 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
stde=os.path.join(tfc.getLastDir(), "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:
# 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:
stde=os.path.join(tfc.getLastDir(), "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)
# Make a new directory with the continuation of this run
#newdirname=currundir #"run_%03d"%(i+1)
newdirname=tfc.getNewRunDir()
try:
os.mkdir(newdirname)
except OSError:
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"))
# now add to the priority if this run has already been started
completed=tfc.getFractionCompleted(tpr)
if completed > 0:
# 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.
# include the plumed file here
args=["-quiet", "-s", "topol.tpr", "-noappend", "-cpi", "state.cpt",
"-rcon", "0.7", "-plumed", "plumed.dat" ]
args.extend(cmdlineOpts)
# for the new neighbor search scheme in Gromacs 4.6, set this env
# variable
if lastcpt is not None:
shutil.copy(lastcpt, os.path.join(newdirname,"state.cpt"))
# 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,
"COLVAR",
"HILLS",
"bias.dat",
"state.cpt", "state_prev.cpt" ]
log.debug("Expected output files: %s"%outputFiles)
cmd=cpc.command.Command(newdirname, "replica/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")
# copy the plumed file to the run dir
plumed_inp=inp.getInput("plumed")
log.debug("Adding the PLUMED file: %s"%plumed_inp)
src=os.path.join(inp.getBaseDir(),plumed_inp)
dst=os.path.join(newdirname,"plumed.dat")
# check if we need to restart metadynamics
if tfc.lastDir is not None:
lasthills=os.path.join(tfc.lastDir,"HILLS")
if os.path.isfile(lasthills):
plumed_dat=open(plumed_inp,'r').read()
log.debug("Adding a RESTART statement to the PLUMED file.")
newplumed=re.sub(r"HILLS","HILLS RESTART",plumed_dat)
open(dst,"w").write(newplumed)
newhills=os.path.join(newdirname,"HILLS")
shutil.copy(lasthills,newhills)
else: shutil.copy(src,dst)
else: shutil.copy(src,dst)
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 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 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