def getEnviron():
""" Load the environment variables needed for Spider.
If SPIDER_DIR is defined, the bin, man and proc folders will be
defined from it. If not, each of them should be defined separately.
"""
global SPIDER
env = Environ(os.environ)
SPIDER_PATH = env.getFirst((SPIDER_HOME, SPIDER_DIR), mandatory=True) #
# Scipion
# definition
# env.setInstalled(os.path.exists(SPIDER_DIR))
if SPIDER_PATH is None:
errors = ''
for var in [SPBIN_DIR, SPMAN_DIR, SPPROC_DIR]:
if not var in env:
errors += "\n Missing SPIDER variable: '%s'" % var
if len(errors):
print "ERRORS: " + errors
else:
env.update({SPBIN_DIR: join(SPIDER_PATH, 'bin') + '/', # Spider needs this extra slash at the end
SPMAN_DIR: join(SPIDER_PATH, 'man') + '/',
SPPROC_DIR: join(SPIDER_PATH, 'proc') + '/'
})
# Get the executable or 'spider' by default
SPIDER = join(env[SPBIN_DIR], env.get('SPIDER', 'spider_linux_mp_intel64'))
# expand ~ and vars
SPIDER = abspath(os.path.expanduser(os.path.expandvars(SPIDER)))
env.set('PATH', env[SPBIN_DIR], env.END)
return env
def getEnviron(cls):
""" Load the environment variables needed for Imagic.
IMAGIC_ROOT is set to IMAGIC_HOME MPI-related vars
are set if IMAGIC_HOME/openmpi path exists
IMAGIC_BATCH is needed for batch files to work.
"""
env = Environ(os.environ)
env.update({
'IMAGIC_ROOT': cls.getHome(),
'IMAGIC_BATCH': "1",
})
env.set('LD_LIBRARY_PATH', cls.getHome('lib'), env.BEGIN)
mpidir = cls.getHome('openmpi')
if os.path.exists(mpidir):
env.update({
'MPIHOME': mpidir,
'MPIBIN': mpidir + '/bin',
'OPAL_PREFIX': mpidir
})
env.set('PATH', mpidir + '/bin', env.BEGIN)
else:
print("Warning: IMAGIC_ROOT directory (", cls.getHome(),
") does not contain openmpi folder.\n",
"No MPI support will be enabled.")
return env
def getVmdEnviron():
""" Return the proper environ to launch VMD.
VMD_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = Environ(os.environ)
environ.set("PATH", os.path.join(os.environ["VMD_HOME"], "bin"), position=Environ.BEGIN)
return environ
def test_Environ(self):
""" Test the Environ class with its utilities. """
from pyworkflow.utils import Environ
env = Environ({
'PATH': '/usr/bin:/usr/local/bin',
'LD_LIBRARY_PATH': '/usr/lib:/usr/lib64'
})
env1 = Environ(env)
env1.set('PATH', '/usr/local/xmipp')
self.assertEqual(env1['PATH'], '/usr/local/xmipp')
self.assertEqual(env1['LD_LIBRARY_PATH'], env['LD_LIBRARY_PATH'])
env2 = Environ(env)
env2.set('PATH', '/usr/local/xmipp', position=Environ.BEGIN)
self.assertEqual(env2['PATH'],
'/usr/local/xmipp' + os.pathsep + env['PATH'])
self.assertEqual(env2['LD_LIBRARY_PATH'], env['LD_LIBRARY_PATH'])
env3 = Environ(env)
env3.update(
{
'PATH': '/usr/local/xmipp',
'LD_LIBRARY_PATH': '/usr/local/xmipp/lib'
},
position=Environ.END)
self.assertEqual(env3['PATH'],
env['PATH'] + os.pathsep + '/usr/local/xmipp')
self.assertEqual(
env3['LD_LIBRARY_PATH'],
env['LD_LIBRARY_PATH'] + os.pathsep + '/usr/local/xmipp/lib')
def getEnviron():
""" Load the environment variables needed for Spider.
If SPIDER_DIR is defined, the bin, man and proc folders will be
defined from it. If not, each of them should be defined separately.
"""
global SPIDER
env = Environ(os.environ)
SPIDER_DIR = env.getFirst(('SPIDER_HOME', 'SPIDER_DIR'), mandatory=True) #
# Scipion
# definition
if SPIDER_DIR is None:
errors = ''
for var in ['SPBIN_DIR', 'SPMAN_DIR', 'SPPROC_DIR']:
if not var in env:
errors += "\n Missing SPIDER variable: '%s'" % var
if len(errors):
print "ERRORS: " + errors
else:
env.update({
'SPBIN_DIR': join(SPIDER_DIR, 'bin') +
'/', # Spider needs this extra slash at the end
'SPMAN_DIR': join(SPIDER_DIR, 'man') + '/',
'SPPROC_DIR': join(SPIDER_DIR, 'proc') + '/'
})
# Get the executable or 'spider' by default
SPIDER = join(env['SPBIN_DIR'], env.get('SPIDER',
'spider_linux_mp_intel64'))
# expand ~ and vars
SPIDER = abspath(os.path.expanduser(os.path.expandvars(SPIDER)))
env.set('PATH', env['SPBIN_DIR'], env.END)
return env
def getChimeraEnviron():
""" Return the proper environ to launch chimera.
CHIMERA_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = Environ(os.environ)
environ.set('PATH', os.path.join(os.environ['CHIMERA_HOME'], 'bin'),
position=Environ.BEGIN)
return environ
def getVmdEnviron():
""" Return the proper environ to launch VMD.
VMD_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = Environ(os.environ)
environ.set('PATH', os.path.join(os.environ['VMD_HOME'], 'bin'),
position=Environ.BEGIN)
return environ
def getChimeraEnviron():
""" Return the proper environ to launch chimera.
CHIMERA_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = Environ(os.environ)
environ.set('PATH', os.path.join(os.environ['CHIMERA_HOME'], 'bin'),
position=Environ.BEGIN)
if "REMOTE_MESA_LIB" in os.environ:
environ.set('LD_LIBRARY_PATH', os.environ['REMOTE_MESA_LIB'],
position=Environ.BEGIN)
return environ
def getEnviron(cls):
""" Load the environment variables needed for Spider.
If SPIDER_HOME is defined, the bin, man and proc folders will be
defined from it. If not, each of them should be defined separately.
"""
env = Environ(os.environ)
if cls.getHome():
env.update( # Spider needs this extra slash at the end
{SPBIN_DIR: cls.getHome('spider/bin') + '/',
SPMAN_DIR: cls.getHome('spider/man') + '/',
SPPROC_DIR: cls.getHome('spider/proc') + '/'})
else:
errors = ''
for var in [SPBIN_DIR, SPMAN_DIR, SPPROC_DIR]:
if var not in env:
errors += "\n Missing SPIDER variable: '%s'" % var
if len(errors):
print("ERRORS: " + errors)
env.set('PATH', env[SPBIN_DIR], env.END)
return env
def getEnviron(cls):
""" Setup the environment variables needed to launch Relion. """
environ = Environ(os.environ)
binPath = os.pathsep.join([cls.getHome('bin'), Config.MPI_BINDIR])
libPath = os.pathsep.join([cls.getHome('lib'), cls.getHome('lib64'), pwem.Config.MPI_LIBDIR])
if binPath not in environ['PATH']:
environ.update({'PATH': binPath,
'LD_LIBRARY_PATH': libPath
}, position=Environ.BEGIN)
# Get Relion CUDA library path if defined
cudaLib = cls.getVar(RELIONTOMO_CUDA_LIB, pwem.Config.CUDA_LIB)
environ.addLibrary(cudaLib)
if 'RELION_MPI_LIB' in os.environ:
environ.addLibrary(os.environ['RELION_MPI_LIB'])
if 'RELION_MPI_BIN' in os.environ:
environ.set('PATH', os.environ['RELION_MPI_BIN'],
position=Environ.BEGIN)
return environ
def test_Environ(self):
""" Test the Environ class with its utilities. """
from pyworkflow.utils import Environ
env = Environ({'PATH': '/usr/bin:/usr/local/bin',
'LD_LIBRARY_PATH': '/usr/lib:/usr/lib64'
})
env1 = Environ(env)
env1.set('PATH', '/usr/local/xmipp')
self.assertEqual(env1['PATH'],'/usr/local/xmipp')
self.assertEqual(env1['LD_LIBRARY_PATH'], env['LD_LIBRARY_PATH'])
env2 = Environ(env)
env2.set('PATH', '/usr/local/xmipp', position=Environ.BEGIN)
self.assertEqual(env2['PATH'],'/usr/local/xmipp' + os.pathsep + env['PATH'])
self.assertEqual(env2['LD_LIBRARY_PATH'], env['LD_LIBRARY_PATH'])
env3 = Environ(env)
env3.update({'PATH': '/usr/local/xmipp',
'LD_LIBRARY_PATH': '/usr/local/xmipp/lib'},
position=Environ.END)
self.assertEqual(env3['PATH'],env['PATH'] + os.pathsep + '/usr/local/xmipp')
self.assertEqual(env3['LD_LIBRARY_PATH'],env['LD_LIBRARY_PATH'] + os.pathsep + '/usr/local/xmipp/lib')
