def create_script(self):
''' create the script '''
self.script_name = 'Run.' + self.runid + '.' + str(self.current_job)
fidt = open(self.template, 'r')
lines = fidt.readlines()
fidt.close()
cdir = self.userspace
fid = open(self.script_name, 'w')
for line in lines:
line = line.replace('<NCORES>', str(self.ncores))
line = line.replace('<CASE>', str(self.confcase))
line = line.replace('<JOB>', str(self.current_job))
line = line.replace('<NAMELIST>', str(self.namelist_current))
line = line.replace('<CDIR>', str(cdir))
line = line.replace('<WALLTIME>', str(self.walltime))
line = line.replace('<PROJECTCODE>', str(self.projectcode))
line = line.replace('<QUEUE>', str(self.queue))
fid.write(line)
fid.close()
os_utils.execute('chmod +x ' + self.script_name)
return None
def create_script(self):
''' create the script '''
self.script_name = 'Run.' + self.runid + '.' + str(self.current_job)
fidt = open(self.template,'r')
lines = fidt.readlines()
fidt.close()
cdir = self.userspace
fid = open(self.script_name,'w')
for line in lines:
line = line.replace('<NCORES>',str(self.ncores))
line = line.replace('<CASE>',str(self.confcase))
line = line.replace('<JOB>',str(self.current_job))
line = line.replace('<NAMELIST>',str(self.namelist_current))
line = line.replace('<CDIR>',str(cdir))
line = line.replace('<WALLTIME>',str(self.walltime))
line = line.replace('<PROJECTCODE>',str(self.projectcode))
line = line.replace('<QUEUE>',str(self.queue))
fid.write(line)
fid.close()
os_utils.execute('chmod +x ' + self.script_name)
return None
def run(self,scrpt): # go to run directory command cdcmd = ' cd ' + self.run_opts['output_dir'] # run the script command runcmd = self.sub_opts['subcmd'] + scrpt.script_name # call system : this is where all the magic happens os_utils.execute( cdcmd + ' ; ' + runcmd ) return None
def run(self, scrpt):
# go to run directory command
cdcmd = ' cd ' + self.run_opts['output_dir']
# run the script command
runcmd = self.sub_opts['subcmd'] + scrpt.script_name
# call system : this is where all the magic happens
os_utils.execute(cdcmd + ' ; ' + runcmd)
return None
def _create_script(self):
'''create control script for one run '''
fidr = open( self.rmanager_root + 'user/template/template_script_ctl.py', 'r' )
fidw = open( self.myrmanager + '/' + self.runname + '_ctl.py', 'w' )
for line in fidr.readlines():
fidw.write( line.replace( '<MY_RMANAGER>', self.myrmanager ).replace( '<MY_RUN>', self.runname ) )
fidr.close()
fidw.close()
os_utils.execute('chmod +x ' + self.myrmanager + '/' + self.runname + '_ctl.py' )
return None
def set_value(self, textToSearch, textToReplace):
'''replace <VALUE> by its value '''
fidr = open('namelist.tmp1', 'r')
fidw = open('namelist.tmp2', 'w')
for line in fidr.readlines():
fidw.write(line.replace(textToSearch, textToReplace))
fidr.close()
fidw.close()
os_utils.execute('mv namelist.tmp2 namelist.tmp1')
return None
def set_value(self,textToSearch, textToReplace):
'''replace <VALUE> by its value '''
fidr = open( 'namelist.tmp1', 'r' )
fidw = open( 'namelist.tmp2', 'w' )
for line in fidr.readlines():
fidw.write( line.replace( textToSearch, textToReplace ) )
fidr.close()
fidw.close()
os_utils.execute('mv namelist.tmp2 namelist.tmp1')
return None
def create_hostfile(self):
self.fileout = 'hostfile.' + self.run_opts['runid']
offset = int( self.sub_opts['host_offset'] )
fid = open(self.fileout,'w')
for kp in np.arange(self.nodes_needed):
fid.write('node' + str(int(kp+offset+1)) + ' slots=16 max_slots=16 \n') # 16 harcoded
fid.close()
# move this directly to run directory
rundir = self.run_opts['output_dir']
os_utils.execute('mv ' + self.fileout + ' ' + rundir + '/.')
return None
def archive_rst(self):
'''copy restart in a safe place'''
rstin = self.restart_file
rstout = self.restart_file.replace('.nc','.nc' + '.' + str(self.previous_job))
status = os_utils.execute('rsync -av ' + self.output_dir + '/' + rstin + ' ' + self.rstdir + '/' + rstout)
# tidal filter files
list_filtered = os_utils.get_output('ls ' + self.output_dir + ' | grep ocean_fil*nc')
if len(list_filtered) > 0:
status = os_utils.execute('rsync -av ' + self.output_dir + '/ocean_fil*nc' + ' ' + self.rstdir + '/.')
else:
pass
return None
def create_hostfile(self):
self.fileout = 'hostfile.' + self.run_opts['runid']
offset = int(self.sub_opts['host_offset'])
fid = open(self.fileout, 'w')
for kp in np.arange(self.nodes_needed):
fid.write('node' + str(int(kp + offset + 1)) +
' slots=16 max_slots=16 \n') # 16 harcoded
fid.close()
# move this directly to run directory
rundir = self.run_opts['output_dir']
os_utils.execute('mv ' + self.fileout + ' ' + rundir + '/.')
return None
def rename_file(self):
''' call unix command mv '''
# remove filein from full path
wrk = self.filein.replace('/',' ').split()[0:-1]
# re-create path
path = ''
for part in wrk:
path = path + '/' + part
# rename file only if different
if self.filein == path + '/' + self.fileout:
pass
else:
os_utils.execute('mv ' + self.filein + ' ' + path + '/' + self.fileout)
return None
def _create_build_script(self):
'''create custom build.bash script '''
self.model_dir = ''
while self.model_dir == '':
self.model_dir = raw_input('Where is the ROMS code installed ? \n >>> ')
fidr = open( self.rmanager_root + 'user/template/build.bash.template', 'r' )
fidw = open( self.myrmanager + '/' + self.runname + '/build.bash', 'w' )
for line in fidr.readlines():
fidw.write( line.replace( '<ROMS_APP>', self.roms_app ).replace( '<ROMS_DIR>', self.model_dir ).replace( '<MY_TMPDIR>', self.tmpdir ) )
fidr.close()
fidw.close()
os_utils.execute('chmod +x ' + self.myrmanager + '/' + self.runname + '/build.bash' )
return None
def create_archive_dir(self):
''' check existence of directories for restart and outputs
and create them if needed'''
#--- restarts directory
inq_restart = os_utils.execute('test -d ' + self.rootrst)
if inq_restart == 0:
pass
else:
print '<RMANAGER> creating ' + self.rootrst
status = os_utils.execute('mkdir ' + self.rootrst)
#--- this restart
inq_restart = os_utils.execute('test -d ' + self.rstdir)
if inq_restart == 0:
pass
else:
print '<RMANAGER> creating ' + self.rstdir
status = os_utils.execute('mkdir ' + self.rstdir)
#--- output directory
inq_arch = os_utils.execute('test -d ' + self.sarchive_dir)
if inq_arch == 0:
pass
else:
print '<RMANAGER> creating ' + self.sarchive_dir
status = os_utils.execute('mkdir ' + self.sarchive_dir)
#---- by year
for year in self.list_years:
inq_arch = os_utils.execute('test -d ' + self.sarchive_dir + '/' + str(year))
if inq_arch == 0:
pass
else:
print '<RMANAGER> creating ' + self.sarchive_dir + '/' + str(year)
status = os_utils.execute('mkdir ' + self.sarchive_dir + '/' + str(year))
return None
def rename_file(self):
''' call unix command mv '''
# remove filein from full path
wrk = self.filein.replace('/', ' ').split()[0:-1]
# re-create path
path = ''
for part in wrk:
path = path + '/' + part
# rename file only if different
if self.filein == path + '/' + self.fileout:
pass
else:
os_utils.execute('mv ' + self.filein + ' ' + path + '/' +
self.fileout)
return None
def _create_script(self):
'''create control script for one run '''
fidr = open(
self.rmanager_root + 'user/template/template_script_ctl.py', 'r')
fidw = open(self.myrmanager + '/' + self.runname + '_ctl.py', 'w')
for line in fidr.readlines():
fidw.write(
line.replace('<MY_RMANAGER>',
self.myrmanager).replace('<MY_RUN>',
self.runname))
fidr.close()
fidw.close()
os_utils.execute('chmod +x ' + self.myrmanager + '/' + self.runname +
'_ctl.py')
return None
def write_log_timeline(self):
''' write the current status of run time line in a log file '''
ftimeline = self.sarchive_dir + '/timeline_run'
# if file already exists, load it
check = os_utils.execute('test -f ' + ftimeline)
if check == 0:
f = open(ftimeline, 'r')
lines = f.readlines()
f.close()
list_timeline = []
for line in lines:
list_timeline.append(line.split()[0])
print 'already in timeline_run :', list_timeline
# update timeline
list_timeline.extend(self.list_years)
list_timeline = list(set(list_timeline))
print 'timeline updated :', list_timeline
else:
list_timeline = self.list_years
list_timeline = list(set(list_timeline))
print 'new timeline_run', list_timeline
# overwrite with the new list
f = open(ftimeline, 'w')
for year in list_timeline:
f.write(year + '\n')
f.close()
return None
def archive_output(self):
'''move outputs files'''
list_files = os_utils.get_output('ls ' + self.output_dir + ' | grep :')
for myfile in list_files:
year = myfile.replace(self.confcase,'').replace('_',' ').replace('-',' ').split()[1]
status = os_utils.execute('mv ' + self.output_dir + '/' + myfile + ' ' + self.sarchive_dir + '/' + str(year) + '/.')
return None
def write_log_timeline(self):
''' write the current status of run time line in a log file '''
ftimeline = self.sarchive_dir + '/timeline_run'
# if file already exists, load it
check = os_utils.execute('test -f ' + ftimeline )
if check ==0:
f = open(ftimeline,'r') ; lines = f.readlines() ; f.close()
list_timeline = []
for line in lines:
list_timeline.append(line.split()[0])
print 'already in timeline_run :', list_timeline
# update timeline
list_timeline.extend(self.list_years)
list_timeline = list(set(list_timeline))
print 'timeline updated :', list_timeline
else:
list_timeline = self.list_years
list_timeline = list(set(list_timeline))
print 'new timeline_run', list_timeline
# overwrite with the new list
f = open(ftimeline,'w')
for year in list_timeline:
f.write( year + '\n')
f.close()
return None
def archive_rst(self):
'''copy restart in a safe place'''
rstin = self.restart_file
rstout = self.restart_file.replace(
'.nc', '.nc' + '.' + str(self.previous_job))
status = os_utils.execute('rsync -av ' + self.output_dir + '/' +
rstin + ' ' + self.rstdir + '/' + rstout)
# tidal filter files
list_filtered = os_utils.get_output('ls ' + self.output_dir +
' | grep ocean_fil*nc')
if len(list_filtered) > 0:
status = os_utils.execute('rsync -av ' + self.output_dir +
'/ocean_fil*nc' + ' ' + self.rstdir +
'/.')
else:
pass
return None
def _create_build_script(self):
'''create custom build.bash script '''
self.model_dir = ''
while self.model_dir == '':
self.model_dir = raw_input(
'Where is the ROMS code installed ? \n >>> ')
fidr = open(self.rmanager_root + 'user/template/build.bash.template',
'r')
fidw = open(self.myrmanager + '/' + self.runname + '/build.bash', 'w')
for line in fidr.readlines():
fidw.write(
line.replace('<ROMS_APP>', self.roms_app).replace(
'<ROMS_DIR>',
self.model_dir).replace('<MY_TMPDIR>', self.tmpdir))
fidr.close()
fidw.close()
os_utils.execute('chmod +x ' + self.myrmanager + '/' + self.runname +
'/build.bash')
return None
def archive_output(self):
'''move outputs files'''
list_files = os_utils.get_output('ls ' + self.output_dir + ' | grep :')
for myfile in list_files:
year = myfile.replace(self.confcase,
'').replace('_', ' ').replace('-',
' ').split()[1]
status = os_utils.execute('mv ' + self.output_dir + '/' + myfile +
' ' + self.sarchive_dir + '/' +
str(year) + '/.')
return None
def _create_run_directory(self):
self.tmpdir = self.scratch + '/tmpdir_'+ self.runname
# create the appropriate directories
os_utils.execute('mkdir ' + self.myrmanager + '/' + self.runname)
os_utils.execute('mkdir ' + self.myrmanager + '/' + self.runname + '/src')
os_utils.execute('mkdir ' + self.tmpdir )
return None
def transfer_one_file(self,file,fromdir,todir):
exit_code = 0 # 0 normal, 1 problem
checksum = 0
check = 0
# first check if file already on storage
exist = self.check_existence_file(todir + file)
# verify it is the same file
if exist:
sum_original = self.compute_md5sum(fromdir + file)
sum_copy = self.compute_md5sum(todir + file)
# or copy to a different file
if sum_original != sum_copy:
datenow = dt.datetime.now()
os_utils.execute('mv ' + todir + file + ' ' + todir + file + '.' + datenow.isoformat() )
checksum = 1
self.run_copy(file,fromdir,todir)
if (check != 0) or (checksum != 0):
exit_code = 1
return exit_code
def _create_run_directory(self):
self.tmpdir = self.scratch + '/tmpdir_' + self.runname
# create the appropriate directories
os_utils.execute('mkdir ' + self.myrmanager + '/' + self.runname)
os_utils.execute('mkdir ' + self.myrmanager + '/' + self.runname +
'/src')
os_utils.execute('mkdir ' + self.tmpdir)
return None
def transfer_one_file(self, file, fromdir, todir):
exit_code = 0 # 0 normal, 1 problem
checksum = 0
check = 0
# first check if file already on storage
exist = self.check_existence_file(todir + file)
# verify it is the same file
if exist:
sum_original = self.compute_md5sum(fromdir + file)
sum_copy = self.compute_md5sum(todir + file)
# or copy to a different file
if sum_original != sum_copy:
datenow = dt.datetime.now()
os_utils.execute('mv ' + todir + file + ' ' + todir + file +
'.' + datenow.isoformat())
checksum = 1
self.run_copy(file, fromdir, todir)
if (check != 0) or (checksum != 0):
exit_code = 1
return exit_code
def copy2rundir(self,namlist,scrpt,infiles):
rundir = self.run_opts['output_dir']
# namelist
os_utils.execute('mv ' + namlist.namelist_current + ' ' + rundir +'/.')
# script
os_utils.execute('mv ' + scrpt.script_name + ' ' + rundir +'/.')
# varinfo.dat and all other files ice.in, bio.in,...
for infile in infiles:
os_utils.execute('cp ' + infile + ' ' + rundir )
return None
def copy2rundir(self, namlist, scrpt, infiles):
rundir = self.run_opts['output_dir']
# namelist
os_utils.execute('mv ' + namlist.namelist_current + ' ' + rundir +
'/.')
# script
os_utils.execute('mv ' + scrpt.script_name + ' ' + rundir + '/.')
# varinfo.dat and all other files ice.in, bio.in,...
for infile in infiles:
os_utils.execute('cp ' + infile + ' ' + rundir)
return None
def create_archive_dir(self):
''' check existence of directories for restart and outputs
and create them if needed'''
#--- restarts directory
inq_restart = os_utils.execute('test -d ' + self.rootrst)
if inq_restart == 0:
pass
else:
print '<RMANAGER> creating ' + self.rootrst
status = os_utils.execute('mkdir ' + self.rootrst)
#--- this restart
inq_restart = os_utils.execute('test -d ' + self.rstdir)
if inq_restart == 0:
pass
else:
print '<RMANAGER> creating ' + self.rstdir
status = os_utils.execute('mkdir ' + self.rstdir)
#--- output directory
inq_arch = os_utils.execute('test -d ' + self.sarchive_dir)
if inq_arch == 0:
pass
else:
print '<RMANAGER> creating ' + self.sarchive_dir
status = os_utils.execute('mkdir ' + self.sarchive_dir)
#---- by year
for year in self.list_years:
inq_arch = os_utils.execute('test -d ' + self.sarchive_dir + '/' +
str(year))
if inq_arch == 0:
pass
else:
print '<RMANAGER> creating ' + self.sarchive_dir + '/' + str(
year)
status = os_utils.execute('mkdir ' + self.sarchive_dir + '/' +
str(year))
return None
def copy_skel(self):
'''copy into a tmp file'''
os_utils.execute('cp ' + self.userspace + '/' + self.namelist_skel + ' namelist.tmp1')
return None
def finalize_namelist(self):
'''copy into the final file'''
os_utils.execute('mv namelist.tmp1 ' + self.namelist_current)
return None
def run_copy(self,file,fromdir,todir):
check = os_utils.execute('nice -0 rsync -av ' + fromdir + file + ' ' + todir + file )
return check
def make_dir(self,dir):
os_utils.execute('mkdir ' + dir)
return None
def check_existence_dir(self,mydir):
exist=True
check = os_utils.execute('test -d ' + mydir)
if check != 0:
exist=False
return exist
def check_existence_file(self,myfile):
exist=True
check = os_utils.execute('test -f ' + myfile)
if check != 0:
exist=False
return exist
def finalize_namelist(self):
'''copy into the final file'''
os_utils.execute('mv namelist.tmp1 ' + self.namelist_current)
return None
def _prepare_transfer(self):
''' check presence of directories on workdir '''
check = os_utils.execute('test -d ' + self.run_opts['output_dir'] )
if check != 0:
self._stop('Error : the tmpdir for this run does not exist on the scrath')
check = os_utils.execute('test -d ' + self.myworkdir )
if check != 0:
self._stop('Error : the workdir does not exist or path is wrong')
check = os_utils.execute('test -d ' + self.storagedir )
if check != 0:
os_utils.execute('mkdir '+ self.storagedir )
check = os_utils.execute('test -d ' + self.storagedir + 'outputs' )
if check != 0:
os_utils.execute('mkdir '+ self.storagedir + 'outputs' )
check = os_utils.execute('test -d ' + self.storagedir + 'restarts' )
if check != 0:
os_utils.execute('mkdir '+ self.storagedir + 'restarts' )
return None
def run_copy(self, file, fromdir, todir):
check = os_utils.execute('nice -0 rsync -av ' + fromdir + file + ' ' +
todir + file)
return check
def copy_skel(self):
'''copy into a tmp file'''
os_utils.execute('cp ' + self.userspace + '/' + self.namelist_skel +
' namelist.tmp1')
return None
def _prepare_transfer(self):
''' check presence of directories on workdir '''
check = os_utils.execute('test -d ' + self.run_opts['output_dir'])
if check != 0:
self._stop(
'Error : the tmpdir for this run does not exist on the scrath')
check = os_utils.execute('test -d ' + self.myworkdir)
if check != 0:
self._stop('Error : the workdir does not exist or path is wrong')
check = os_utils.execute('test -d ' + self.storagedir)
if check != 0:
os_utils.execute('mkdir ' + self.storagedir)
check = os_utils.execute('test -d ' + self.storagedir + 'outputs')
if check != 0:
os_utils.execute('mkdir ' + self.storagedir + 'outputs')
check = os_utils.execute('test -d ' + self.storagedir + 'restarts')
if check != 0:
os_utils.execute('mkdir ' + self.storagedir + 'restarts')
return None
def check_existence_file(self, myfile):
exist = True
check = os_utils.execute('test -f ' + myfile)
if check != 0:
exist = False
return exist
def check_existence_dir(self, mydir):
exist = True
check = os_utils.execute('test -d ' + mydir)
if check != 0:
exist = False
return exist
def make_dir(self, dir):
os_utils.execute('mkdir ' + dir)
return None