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()
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.name,self.login,self.port,directory,filelist)
def issmdir():
"""
ISSMDIR - Get ISSM_DIR environment variable
Usage:
ISSM_DIR=issmdir()
"""
if not m.ispc():
ISSM_DIR = os.environ['ISSM_DIR']
else:
ISSM_DIR = os.environ['ISSM_DIR_WIN']
if m.strcmpi(ISSM_DIR[-1], '/') or m.strcmpi(ISSM_DIR[-1], '\\'):
ISSM_DIR = ISSM_DIR[:-1] #shave off the last '/'
if not ISSM_DIR:
raise RuntimeError(
"issmdir error message: 'ISSM_DIR' environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!"
)
return ISSM_DIR
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('mpiexec -np %i %s/kriging.exe %s/%s %s ' % (self.np,self.codepath,self.executionpath,modelname,modelname))
else:
fid.write('mpiexec -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 issmscpout(host, path, login, port, packages):
"""
ISSMSCPOUT send packages to a host, using scp on unix, and pscp on windows
usage: issmscpout(host,path,packages)
"""
#get hostname
hostname = gethostname()
#if hostname and host are the same, do a simple copy
if m.strcmpi(host, hostname):
for package in packages:
here = os.getcwd()
os.chdir(path)
try:
os.remove(package)
except OSError as e:
pass
subprocess.call('ln -s %s %s' %
(os.path.join(here, package), path),
shell=True)
os.chdir(here)
else:
if m.ispc():
#use the putty project pscp.exe: it should be in the path.
#get ISSM_DIR variable
if 'ISSM_DIR_WIN' in os.environ:
ISSM_DIR = os.environ['ISSM_DIR_WIN'][1:-2]
else:
raise OSError(
"issmscpout error message: could not find ISSM_DIR_WIN environment variable."
)
username = input('Username: (quoted string) ')
key = input('Key: (quoted string) ')
for package in packages:
try:
subprocess.check_call(
'%s/externalpackages/ssh/pscp.exe -l "%s" -pw "%s" %s %s:%s'
% (ISSM_DIR, username, key, package, host, path),
shell=True)
except CalledProcessError as e:
raise CalledProcessError(
"issmscpout error message: could not call putty pscp.")
else:
#just use standard unix scp
#create string of packages being sent
string = ''
for package in packages:
string += ' ' + package
string += ' '
if port:
subprocess.call('scp -P %d %s %s@localhost:%s' %
(port, string, login, path),
shell=True)
else:
subprocess.call('scp %s %s@%s:%s' %
(string, login, host, path),
shell=True)
def issmssh(host, login, port, command):
"""
ISSMSSH - wrapper for OS independent ssh command.
usage:
issmssh(host,command)
"""
#first get hostname
hostname = gethostname()
#if same as host, just run the command.
if m.strcmpi(host, hostname):
subprocess.call(command, shell=True)
else:
if m.ispc():
#use the putty project plink.exe: it should be in the path.
#get ISSM_DIR variable
if 'ISSM_DIR_WIN' in os.environ:
ISSM_DIR = os.environ['ISSM_DIR_WIN'][1:-2]
else:
raise OSError(
"issmssh error message: could not find ISSM_DIR_WIN environment variable."
)
username = input('Username: (quoted string) ')
key = input('Key: (quoted string) ')
subprocess.call(
'%s/externalpackages/ssh/plink.exe -ssh -l "%s" -pw "%s" %s "%s"'
% (ISSM_DIR, username, key, host, command),
shell=True)
else:
#just use standard unix ssh
if port:
subprocess.call('ssh -l %s -p %d localhost "%s"' %
(login, port, command),
shell=True)
else:
subprocess.call('ssh -l %s %s "%s"' % (login, host, command),
shell=True)
# The following code was added to fix:
# "IOError: [Errno 35] Resource temporarily unavailable"
# on the Mac when trying to display md after the solution.
# (from http://code.google.com/p/robotframework/issues/detail?id=995)
# Make FreeBSD use blocking I/O like other platforms
import sys
import fcntl
from os import O_NONBLOCK
fd = sys.stdin.fileno()
flags = fcntl.fcntl(fd, fcntl.F_GETFL)
fcntl.fcntl(fd, fcntl.F_SETFL, flags & ~O_NONBLOCK)
fd = sys.stdout.fileno()
flags = fcntl.fcntl(fd, fcntl.F_GETFL)
fcntl.fcntl(fd, fcntl.F_SETFL, flags & ~O_NONBLOCK)
def issmscpin(host, login, port, path, packages):
"""
ISSMSCPIN get packages from host, using scp on unix, and pscp on windows
usage: issmscpin(host,packages,path)
"""
#first get hostname
hostname = gethostname()
#first be sure packages are not in the current directory, this could conflict with pscp on windows.
#remove warnings in case the files do not exist
for package in packages:
try:
os.remove(package)
except OSError as e:
pass
#if hostname and host are the same, do a simple copy
if m.strcmpi(hostname, host):
for package in packages:
try:
shutil.copy(os.path.join(path, package),
os.getcwd()) #keep going, even if success=0
except OSError as e:
pass
else:
if m.ispc():
#use the putty project pscp.exe: it should be in the path.
#get ISSM_DIR variable
if 'ISSM_DIR_WIN' in os.environ:
ISSM_DIR = os.environ['ISSM_DIR_WIN'][1:-2]
else:
raise OSError(
"issmscpin error message: could not find ISSM_DIR_WIN environment variable."
)
username = raw_input('Username: (quoted string) ')
key = raw_input('Key: (quoted string) ')
for package in packages:
try:
subprocess.check_call(
'%s/externalpackages/ssh/pscp.exe -l "%s" -pw "%s" %s:%s %s'
% (ISSM_DIR, username, key, host,
os.path.join(path, package), os.getcwd()),
shell=True)
except CalledProcessError as e:
raise CalledProcessError(
"issmscpin error message: could not call putty pscp.")
else:
#just use standard unix scp
#string to copy multiple files using scp:
string = '\{' + ','.join([str(x) for x in packages]) + '\}'
if port:
subprocess.call(
'scp -P %d %s@localhost:%s %s/. ' %
(port, login, os.path.join(path, string), os.getcwd()),
shell=True)
else:
subprocess.call(
'scp %s@%s:%s %s/.' %
(login, host, os.path.join(path, string), os.getcwd()),
shell=True)
#check scp worked
for package in packages:
if not os.path.exists(os.path.join('.', package)):
raise OSError(
"issmscpin error message: could not call scp on *nix system."
)