def Download(self, dirname, filelist): # {{{
if m.ispc():
#do nothing
return
#copy files from cluster to current directory
directory = '%s/%s/' % (self.executionpath, dirname)
issmscpin(self.hostname, self.login, self.port, directory, filelist)
def BuildKrigingQueueScript(self, modelname, solution, io_gather,
isvalgrind, isgprof): # {{{
#write queuing script
if not m.ispc():
fid = open(modelname + '.queue', 'w')
fid.write('#!/bin/sh\n')
if not isvalgrind:
if self.interactive:
fid.write('srun -np %i %s/kriging.exe %s/%s %s ' %
(self.np, self.codepath, self.executionpath,
modelname, modelname))
else:
fid.write(
'srun -np %i %s/kriging.exe %s/%s %s 2> %s.errlog >%s.outlog '
% (self.np, self.codepath, self.executionpath,
modelname, modelname, modelname, modelname))
elif isgprof:
fid.write('\n gprof %s/kriging.exe gmon.out > %s.performance'
& (self.codepath, modelname))
else:
#Add --gen-suppressions=all to get suppression lines
fid.write('LD_PRELOAD=%s \\\n' % self.valgrindlib)
fid.write('mpiexec -np %i %s --leak-check=full --suppressions=%s %s/kriging.exe %s/%s %s 2> %s.errlog >%s.outlog ' % \
(self.np,self.valgrind,self.valgrindsup,self.codepath,self.executionpath,modelname,modelname,modelname,modelname))
if not io_gather: #concatenate the output files:
fid.write('\ncat %s.outbin.* > %s.outbin' %
(modelname, modelname))
fid.close()
else: # Windows
fid = open(modelname + '.bat', 'w')
fid.write('@echo off\n')
if self.interactive:
fid.write('"%s/issm.exe" %s "%s/%s" %s ' %
(self.codepath, solution, self.executionpath,
modelname, modelname))
else:
fid.write('"%s/issm.exe" %s "%s/%s" %s 2> %s.errlog >%s.outlog' % \
(self.codepath,solution,self.executionpath,modelname,modelname,modelname,modelname))
fid.close()
#in interactive mode, create a run file, and errlog and outlog file
if self.interactive:
fid = open(modelname + '.errlog', 'w')
fid.close()
fid = open(modelname + '.outlog', 'w')
fid.close()
def BuildQueueScript(self, dirname, modelname, solution, io_gather,
isvalgrind, isgprof, isdakota,
isoceancoupling): # {{{
executable = 'issm.exe'
if isdakota:
version = IssmConfig('_DAKOTA_VERSION_')[0:2]
version = float(version)
if version >= 6:
executable = 'issm_dakota.exe'
if isoceancoupling:
executable = 'issm_ocean.exe'
#write queuing script
if not m.ispc():
fid = open(modelname + '.queue', 'w')
#fid.write('#!/bin/bash -l\n\n')
#fid.write('#SBATCH -N 1\n')
#fid.write('#SBATCH -J my_job\n')
#fid.write('#SBATCH --export=ALL\n\n')
fid.write('#!/bin/bash\n')
fid.write('#SBATCH --nodes=%i\n' % 1) #self.np)
fid.write('#SBATCH --ntasks=%i\n' % 1)
fid.write('#SBATCH --ntasks-per-node=%i\n' % 1)
fid.write('#SBATCH --cpus-per-task=%i\n' % 1)
fid.write('#SBATCH --job-name=%s\n' % modelname)
#fid.write('#SBATCH -t %i\n',cluster.time*60);
fid.write('#SBATCH -p smp \n')
fid.write('#SBATCH -o %s.outlog \n' % modelname)
fid.write('#SBATCH -e %s.errlog \n' % modelname)
fid.write('#SBATCH --get-user-env \n')
#fid.write('## Enlarge the stacksize. OpenMP-codes usually need a large stack. \n')
#fid.write('ulimit -s unlimited\n')
#fid.write('## This binds each thread to one core \n')
#fid.write('export OMP_PROC_BIND=TRUE \n')
#fid.write('## Number of threads as given by -c / --cpus-per-task \n')
#fid.write('export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK \n')
#fid.write('## This code snippet checks the task and thread distribution on the cores. \n')
#fid.write('srun /global/AWIsoft/xthi/xthi.intel | sort -n -k4,4 -k6,6 > xthi.log \n')
pth = self.executionpath + '/' + dirname
fid.write('srun %s/issm.exe %s %s %s > %s.log\n' %
(self.codepath, solution, pth, modelname, modelname))
def BuildQueueScript(self, dirname, modelname, solution, io_gather,
isvalgrind, isgprof, isdakota,
isoceancoupling): # {{{
executable = 'issm.exe'
if isdakota:
version = IssmConfig('_DAKOTA_VERSION_')[0:2]
version = float(version)
if version >= 6:
executable = 'issm_dakota.exe'
if isoceancoupling:
executable = 'issm_ocean.exe'
#write queuing script
if not m.ispc():
fid = open(modelname + '.queue', 'w')
fid.write('#!/bin/sh\n')
if not isvalgrind:
if self.interactive:
if IssmConfig('_HAVE_MPI_')[0]:
fid.write(
'mpiexec -np %i %s/%s %s %s/%s %s ' %
(self.np, self.codepath, executable, solution,
self.executionpath, dirname, modelname))
else:
fid.write('%s/%s %s %s/%s %s ' %
(self.codepath, executable, solution,
self.executionpath, dirname, modelname))
else:
if IssmConfig('_HAVE_MPI_')[0]:
fid.write(
'mpiexec -np %i %s/%s %s %s/%s %s 2> %s.errlog >%s.outlog '
% (self.np, self.codepath, executable, solution,
self.executionpath, dirname, modelname,
modelname, modelname))
else:
fid.write(
'%s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' %
(self.codepath, executable, solution,
self.executionpath, dirname, modelname, modelname,
modelname))
elif isgprof:
fid.write('\n gprof %s/%s gmon.out > %s.performance' %
(self.codepath, executable, modelname))
else:
#Add --gen-suppressions=all to get suppression lines
fid.write('LD_PRELOAD=%s \\\n' % self.valgrindlib)
if IssmConfig('_HAVE_MPI_')[0]:
fid.write('mpiexec -np %i %s --leak-check=full --suppressions=%s %s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % \
(self.np,self.valgrind,self.valgrindsup,self.codepath,executable,solution,self.executionpath,dirname,modelname,modelname,modelname))
else:
fid.write('%s --leak-check=full --suppressions=%s %s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % \
(self.valgrind,self.valgrindsup,self.codepath,executable,solution,self.executionpath,dirname,modelname,modelname,modelname))
if not io_gather: #concatenate the output files:
fid.write('\ncat %s.outbin.* > %s.outbin' %
(modelname, modelname))
fid.close()
else: # Windows
fid = open(modelname + '.bat', 'w')
fid.write('@echo off\n')
if self.interactive:
fid.write('"%s/%s" %s "%s/%s" %s ' %
(self.codepath, executable, solution,
self.executionpath, dirname, modelname))
else:
fid.write('"%s/%s" %s "%s/%s" %s 2> %s.errlog >%s.outlog' % \
(self.codepath,executable,solution,self.executionpath,dirname,modelname,modelname,modelname))
fid.close()
#in interactive mode, create a run file, and errlog and outlog file
if self.interactive:
fid = open(modelname + '.errlog', 'w')
fid.close()
fid = open(modelname + '.outlog', 'w')
fid.close()