def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=False,
rundir=None, print_git_status=False, nohup=False, nice=None):
"""
Run the Fortran version of Clawpack using executable xclawcmd, which is
typically set to 'xclaw', 'xamr', etc.
If it is not set by the call, get it from the environment variable
CLAW_EXE. Default to 'xclaw' if that's not set.
If rundir is None, all *.data is copied from current directory, if a path
is given, data files are copied from there instead.
If print_git_status is True, print a summary of the git status of all
clawpack repositories in the file claw_git_status.txt in outdir.
If nohup is True, run the xclawcmd in nohup mode: runs in background and
output goes into nohup.out file in the directory specified by outdir,
rather than all output going to the screen. The job keeps running if user
logs off. Useful for scripts starting long jobs in batch mode.
If type(nice) is int, runs the code using "nice -n "
with this nice value so it doesn't hog computer resources.
"""
import os,glob,shutil,time
verbose = True
xclawout = None
xclawerr = None
try:
nice = int(nice)
except:
nice = None
# convert strings passed in from Makefile to boolean:
if type(overwrite) is str:
overwrite = (overwrite.lower() in ['true','t'])
if type(restart) is str:
restart = (restart.lower() in ['true','t'])
if type(print_git_status) is str:
print_git_status = (print_git_status.lower() in ['true','t'])
if type(nohup) is str:
nohup = (nohup.lower() in ['true','t'])
if xclawcmd is None:
# Determine what executable to use from environment variable CLAW_EXE
# Default to 'xclaw' if it's not set:
xclawcmd = os.environ.get('CLAW_EXE', 'xclaw')
if outdir is None:
outdir = '.'
if rundir is None:
rundir = os.getcwd()
rundir = os.path.abspath(rundir)
print "==> runclaw: Will take data from ", rundir
# directory for fort.* files:
outdir = os.path.abspath(outdir)
print '==> runclaw: Will write output to ',outdir
#returncode = clawjob.runxclaw()
if 1:
startdir = os.getcwd()
xdir = os.path.abspath(startdir)
outdir = os.path.abspath(outdir)
rundir = os.path.abspath(rundir)
xclawcmd = os.path.join(xdir,xclawcmd)
try:
os.chdir(xdir)
except:
raise Exception( "==> runclaw: Cannot change to directory xdir = %s" %xdir)
return
if os.path.isfile(outdir):
print "==> runclaw: Error: outdir specified is a file"
return
if (os.path.isdir(outdir) & (not overwrite)):
# copy the old outdir before possibly overwriting
tm = time.localtime(os.path.getmtime(outdir))
year = str(tm[0]).zfill(4)
month = str(tm[1]).zfill(2)
day = str(tm[2]).zfill(2)
hour = str(tm[3]).zfill(2)
minute = str(tm[4]).zfill(2)
second = str(tm[5]).zfill(2)
outdir_backup = outdir + '_%s-%s-%s-%s%s%s' \
% (year,month,day,hour,minute,second)
if verbose:
print "==> runclaw: Directory already exists: ",os.path.split(outdir)[1]
if restart:
print "==> runclaw: Copying directory to: ",os.path.split(outdir_backup)[1]
else:
print "==> runclaw: Moving directory to: ",os.path.split(outdir_backup)[1]
time.sleep(1)
try:
shutil.move(outdir,outdir_backup)
if restart:
shutil.copytree(outdir_backup,outdir)
except:
print "==> runclaw: Could not move directory... copy already exists?"
if (not os.path.isdir(outdir)):
try:
os.mkdir(outdir)
except:
print "Cannot make directory ",outdir
return
try:
os.chdir(outdir)
except:
print '==> runclaw: *** Error in runxclaw: cannot move to outdir = ',\
outdir
raise
return
if print_git_status not in [False,'False']:
make_git_status_file()
fortfiles = glob.glob(os.path.join(outdir,'fort.*'))
if (overwrite and (not restart)):
# remove any old versions:
if verbose:
print "==> runclaw: Removing all old fort files in ", outdir
for file in fortfiles:
os.remove(file)
elif restart:
if verbose:
print "==> runclaw: Restart: leaving original fort files in ", outdir
else:
if len(fortfiles) > 1:
print "==> runclaw: *** Remove fort.* and try again,"
print " or use overwrite=True in call to runxclaw"
print " e.g., by setting CLAW_OVERWRITE = True in Makefile"
return
try:
os.chdir(rundir)
except:
raise Exception("Cannot change to directory %s" % rundir)
return
datafiles = glob.glob('*.data')
if datafiles == ():
print "==> runclaw: Warning: no data files found in directory ",rundir
else:
if rundir != outdir:
for file in datafiles:
shutil.copy(file,os.path.join(outdir,file))
if xclawout:
xclawout = open(xclawout,'wb')
if xclawerr:
xclawerr = open(xclawerr,'wb')
os.chdir(outdir)
#print "\nIn directory outdir = ",outdir,"\n"
# execute command to run fortran program:
try:
#print "\nExecuting ",xclawcmd, " ... "
#pclaw = subprocess.Popen(xclawcmd,stdout=xclawout,stderr=xclawerr)
#print '+++ pclaw started'
#pclaw.wait() # wait for code to run
#returncode = pclaw.returncode
#print '+++ pclaw done'
if nohup:
# run in nohup mode:
print "\n==> Running in nohup mode, output will be sent to:"
print " %s/nohup.out" % outdir
if type(nice) is int:
cmd = "nohup time nice -n %s %s " % (nice,xclawcmd)
else:
cmd = "nohup time %s " % xclawcmd
print "\n==> Running with command:\n ", cmd
returncode = os.system(cmd)
else:
if type(nice) is int:
cmd = "nice -n %s %s " % (nice,xclawcmd)
else:
cmd = xclawcmd
print "\n==> Running with command:\n ", cmd
returncode = os.system(cmd)
if returncode == 0:
print "\n==> runclaw: Finished executing\n"
else:
print "\n ==> runclaw: *** Runtime error: return code = %s\n "\
% returncode
print '==> runclaw: Done executing %s via clawutil.runclaw.py' %\
xclawcmd
print '==> runclaw: Output is in ', outdir
except:
raise Exception("Could not execute command %s" % xclawcmd)
os.chdir(startdir)
if returncode != 0:
print '==> runclaw: *** fortran returncode = ', returncode, ' aborting'
def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=False,
rundir=None, print_git_status=False):
"""
Run the Fortran version of Clawpack using executable xclawcmd, which is
typically set to 'xclaw', 'xamr', etc.
If it is not set by the call, get it from the environment variable
CLAW_EXE. Default to 'xclaw' if that's not set.
If rundir is None, all *.data is copied from current directory, if a path
is given, data files are copied from there instead.
"""
import os,glob,shutil,time
verbose = True
xclawout = None
xclawerr = None
if type(overwrite) is str:
# convert to boolean
overwrite = (overwrite.lower() in ['true','t'])
if type(restart) is str:
# convert to boolean
restart = (restart.lower() in ['true','t'])
if xclawcmd is None:
# Determine what executable to use from environment variable CLAW_EXE
# Default to 'xclaw' if it's not set:
xclawcmd = os.environ.get('CLAW_EXE', 'xclaw')
if outdir is None:
outdir = '.'
if rundir is None:
rundir = os.getcwd()
rundir = os.path.abspath(rundir)
print "==> runclaw: Will take data from ", rundir
# directory for fort.* files:
outdir = os.path.abspath(outdir)
print '==> runclaw: Will write output to ',outdir
#returncode = clawjob.runxclaw()
if 1:
startdir = os.getcwd()
xdir = os.path.abspath(startdir)
outdir = os.path.abspath(outdir)
rundir = os.path.abspath(rundir)
xclawcmd = os.path.join(xdir,xclawcmd)
try:
os.chdir(xdir)
except:
raise Exception( "==> runclaw: Cannot change to directory xdir = %s" %xdir)
return
if os.path.isfile(outdir):
print "==> runclaw: Error: outdir specified is a file"
return
if (os.path.isdir(outdir) & (not overwrite)):
# copy the old outdir before possibly overwriting
tm = time.localtime(os.path.getmtime(outdir))
year = str(tm[0]).zfill(4)
month = str(tm[1]).zfill(2)
day = str(tm[2]).zfill(2)
hour = str(tm[3]).zfill(2)
minute = str(tm[4]).zfill(2)
second = str(tm[5]).zfill(2)
outdir_backup = outdir + '_%s-%s-%s-%s%s%s' \
% (year,month,day,hour,minute,second)
if verbose:
print "==> runclaw: Directory already exists: ",os.path.split(outdir)[1]
if restart:
print "==> runclaw: Copying directory to: ",os.path.split(outdir_backup)[1]
else:
print "==> runclaw: Moving directory to: ",os.path.split(outdir_backup)[1]
time.sleep(1)
try:
shutil.move(outdir,outdir_backup)
if restart:
shutil.copytree(outdir_backup,outdir)
except:
print "==> runclaw: Could not move directory... copy already exists?"
if (not os.path.isdir(outdir)):
try:
os.mkdir(outdir)
except:
print "Cannot make directory ",outdir
return
try:
os.chdir(outdir)
except:
print '==> runclaw: *** Error in runxclaw: cannot move to outdir = ',\
outdir
raise
return
if print_git_status not in [False,'False']:
make_git_status_file()
fortfiles = glob.glob(os.path.join(outdir,'fort.*'))
if (overwrite and (not restart)):
# remove any old versions:
if verbose:
print "==> runclaw: Removing all old fort files in ", outdir
for file in fortfiles:
os.remove(file)
elif restart:
if verbose:
print "==> runclaw: Restart: leaving original fort files in ", outdir
else:
if len(fortfiles) > 1:
print "==> runclaw: *** Remove fort.* and try again,"
print " or use overwrite=True in call to runxclaw"
print " e.g., by setting CLAW_OVERWRITE = True in Makefile"
return
try:
os.chdir(rundir)
except:
raise Exception("Cannot change to directory %s" % rundir)
return
datafiles = glob.glob('*.data')
if datafiles == ():
print "==> runclaw: Warning: no data files found in directory ",rundir
else:
if rundir != outdir:
for file in datafiles:
shutil.copy(file,os.path.join(outdir,file))
if xclawout:
xclawout = open(xclawout,'wb')
if xclawerr:
xclawerr = open(xclawerr,'wb')
os.chdir(outdir)
#print "\nIn directory outdir = ",outdir,"\n"
# execute command to run fortran program:
try:
#print "\nExecuting ",xclawcmd, " ... "
#pclaw = subprocess.Popen(xclawcmd,stdout=xclawout,stderr=xclawerr)
#print '+++ pclaw started'
#pclaw.wait() # wait for code to run
#returncode = pclaw.returncode
#print '+++ pclaw done'
returncode = os.system(xclawcmd)
if returncode == 0:
print "\n==> runclaw: Finished executing\n"
else:
print "\n ==> runclaw: *** Runtime error: return code = %s\n " % returncode
except:
raise Exception("Could not execute command %s" % xclawcmd)
os.chdir(startdir)
if returncode != 0:
print '==> runclaw: *** fortran returncode = ', returncode, ' aborting'
print '==> runclaw: Done executing %s via clawutil.runclaw.py' % xclawcmd
print '==> runclaw: Output is in ', outdir
def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=None,
rundir=None, print_git_status=False, nohup=False, nice=None):
"""
Run the Fortran version of Clawpack using executable xclawcmd, which is
typically set to 'xclaw', 'xamr', etc.
If it is not set by the call, get it from the environment variable
CLAW_EXE. Default to 'xclaw' if that's not set.
If overwrite is True, it's ok to zap current contents of the outdir.
If overwrite is False, move the outdir (or copy in the case of a restart)
to a backup directory with a unique name based on time executed.
If restart is None, determine whether this is a restart from claw.data
(as set in setrun.py). Can remove setting RESTART in Makefiles.
If rundir is None, all *.data is copied from current directory, if a path
is given, data files are copied from there instead.
If print_git_status is True, print a summary of the git status of all
clawpack repositories in the file claw_git_status.txt in outdir.
If nohup is True, run the xclawcmd in nohup mode: runs in background and
output goes into nohup.out file in the directory specified by outdir,
rather than all output going to the screen. The job keeps running if user
logs off. Useful for scripts starting long jobs in batch mode.
If type(nice) is int, runs the code using "nice -n "
with this nice value so it doesn't hog computer resources.
"""
from clawpack.clawutil.data import ClawData
import os,glob,shutil,time
verbose = True
xclawout = None
xclawerr = None
try:
nice = int(nice)
except:
nice = None
# convert strings passed in from Makefile to boolean:
if type(overwrite) is str:
overwrite = (overwrite.lower() in ['true','t'])
if type(restart) is str:
if restart == 'None':
restart = None
else:
restart = (restart.lower() in ['true','t'])
if type(print_git_status) is str:
print_git_status = (print_git_status.lower() in ['true','t'])
if type(nohup) is str:
nohup = (nohup.lower() in ['true','t'])
if xclawcmd is None:
# Determine what executable to use from environment variable CLAW_EXE
# Default to 'xclaw' if it's not set:
xclawcmd = os.environ.get('CLAW_EXE', 'xclaw')
if outdir is None:
outdir = '.'
if rundir is None:
rundir = os.getcwd()
rundir = os.path.abspath(rundir)
print "==> runclaw: Will take data from ", rundir
# directory for fort.* files:
outdir = os.path.abspath(outdir)
print '==> runclaw: Will write output to ',outdir
if restart is None:
# Added option to determine restart from claw.data (i.e. setrun.py)
clawdata = ClawData()
clawdata.read(os.path.join(rundir,'claw.data'), force=True)
restart = clawdata.restart
#print '+++ From claw.data determined restart = %s' % restart
#returncode = clawjob.runxclaw()
if 1:
startdir = os.getcwd()
xdir = os.path.abspath(startdir)
outdir = os.path.abspath(outdir)
rundir = os.path.abspath(rundir)
xclawcmd = os.path.join(xdir,xclawcmd)
try:
os.chdir(xdir)
except:
raise Exception( "==> runclaw: Cannot change to directory xdir = %s" %xdir)
return
if os.path.isfile(outdir):
print "==> runclaw: Error: outdir specified is a file"
return
if (os.path.isdir(outdir) & (not overwrite)):
# copy the old outdir before possibly overwriting
tm = time.localtime(os.path.getmtime(outdir))
year = str(tm[0]).zfill(4)
month = str(tm[1]).zfill(2)
day = str(tm[2]).zfill(2)
hour = str(tm[3]).zfill(2)
minute = str(tm[4]).zfill(2)
second = str(tm[5]).zfill(2)
outdir_backup = outdir + '_%s-%s-%s-%s%s%s' \
% (year,month,day,hour,minute,second)
if verbose:
print "==> runclaw: Directory already exists: ",os.path.split(outdir)[1]
if restart:
print "==> runclaw: Copying directory to: ",os.path.split(outdir_backup)[1]
else:
print "==> runclaw: Moving directory to: ",os.path.split(outdir_backup)[1]
time.sleep(1)
try:
shutil.move(outdir,outdir_backup)
if restart:
shutil.copytree(outdir_backup,outdir)
except:
print "==> runclaw: Could not move directory... copy already exists?"
if (not os.path.isdir(outdir)):
try:
os.mkdir(outdir)
except:
print "Cannot make directory ",outdir
return
try:
os.chdir(outdir)
except:
print '==> runclaw: *** Error in runxclaw: cannot move to outdir = ',\
outdir
raise
return
if print_git_status not in [False,'False']:
make_git_status_file()
fortfiles = glob.glob(os.path.join(outdir,'fort.*'))
if (overwrite and (not restart)):
# remove any old versions:
if verbose:
print "==> runclaw: Removing all old fort files in ", outdir
for file in fortfiles:
os.remove(file)
elif restart:
if verbose:
print "==> runclaw: Restart: leaving original fort files in ", outdir
else:
if len(fortfiles) > 1:
print "==> runclaw: *** Remove fort.* and try again,"
print " or use overwrite=True in call to runxclaw"
print " e.g., by setting CLAW_OVERWRITE = True in Makefile"
return
try:
os.chdir(rundir)
except:
raise Exception("Cannot change to directory %s" % rundir)
return
datafiles = glob.glob('*.data')
if datafiles == ():
print "==> runclaw: Warning: no data files found in directory ",rundir
else:
if rundir != outdir:
for file in datafiles:
shutil.copy(file,os.path.join(outdir,file))
if xclawout:
xclawout = open(xclawout,'wb')
if xclawerr:
xclawerr = open(xclawerr,'wb')
os.chdir(outdir)
#print "\nIn directory outdir = ",outdir,"\n"
# execute command to run fortran program:
try:
#print "\nExecuting ",xclawcmd, " ... "
#pclaw = subprocess.Popen(xclawcmd,stdout=xclawout,stderr=xclawerr)
#print '+++ pclaw started'
#pclaw.wait() # wait for code to run
#returncode = pclaw.returncode
#print '+++ pclaw done'
if nohup:
# run in nohup mode:
print "\n==> Running in nohup mode, output will be sent to:"
print " %s/nohup.out" % outdir
if type(nice) is int:
cmd = "nohup time nice -n %s %s " % (nice,xclawcmd)
else:
cmd = "nohup time %s " % xclawcmd
print "\n==> Running with command:\n ", cmd
returncode = os.system(cmd)
else:
if type(nice) is int:
cmd = "nice -n %s %s " % (nice,xclawcmd)
else:
cmd = xclawcmd
print "\n==> Running with command:\n ", cmd
returncode = os.system(cmd)
if returncode == 0:
print "\n==> runclaw: Finished executing\n"
else:
print "\n ==> runclaw: *** Runtime error: return code = %s\n "\
% returncode
print '==> runclaw: Done executing %s via clawutil.runclaw.py' %\
xclawcmd
print '==> runclaw: Output is in ', outdir
except:
raise Exception("Could not execute command %s" % xclawcmd)
os.chdir(startdir)
if returncode != 0:
print '==> runclaw: *** fortran returncode = ', returncode, ' aborting'