def _setup_munge(self):
"""
Setup Munge (used by Slurm as a user auth mechanism)
"""
log.debug("Setting up Munge (for Slurm)...")
if not os.path.exists('/etc/munge'):
# Munge not installed so grab it
misc.run("apt-get update; apt-get install munge libmunge-dev -y")
misc.run("/usr/sbin/create-munge-key")
misc.append_to_file('/etc/default/munge', 'OPTIONS="--force"')
misc.run("service munge start")
log.debug("Done setting up Munge")
# Copy the munge key to cluster NFS
if not os.path.exists(self.app.path_resolver.slurm_root_nfs):
misc.make_dir(self.app.path_resolver.slurm_root_nfs)
nfs_munge_key = os.path.join(self.app.path_resolver.slurm_root_nfs, 'munge.key')
shutil.copyfile('/etc/munge/munge.key', nfs_munge_key)
os.chmod(nfs_munge_key, 0400)
log.debug("Copied /etc/munge/munge.key to {0}".format(nfs_munge_key))
def _configure_sge(self):
log.info("Setting up SGE...")
SGE_config_file = '%s/galaxyEC2.conf' % self.app.path_resolver.sge_root
with open(SGE_config_file, 'w') as f:
print >> f, _get_sge_install_conf(
self.app, self.app.cloud_interface.get_private_ip())
os.chown(SGE_config_file,
pwd.getpwnam("sgeadmin")[2],
grp.getgrnam("sgeadmin")[2])
log.debug("Created SGE install template as file '%s'" %
SGE_config_file)
fix_libc()
log.debug("Setting up SGE.")
self._fix_util_arch()
if misc.run(
'cd %s; ./inst_sge -m -x -auto %s' %
(self.app.path_resolver.sge_root, SGE_config_file),
"Setting up SGE did not go smoothly",
"Successfully set up SGE"):
log.debug("Successfully setup SGE; configuring SGE")
log.debug("Adding parallel environments")
pes = ['SGE_SMP_PE', 'SGE_MPI_PE']
for pe in pes:
pe_file_path = os.path.join('/tmp', pe)
with open(pe_file_path, 'w') as f:
print >> f, conf_manager.load_conf_template(
getattr(conf_manager, pe)).safe_substitute()
misc.run('cd %s; ./bin/lx24-amd64/qconf -Ap %s' %
(self.app.path_resolver.sge_root, pe_file_path))
log.debug("Creating queue 'all.q'")
SGE_allq_file = '%s/all.q.conf' % self.app.path_resolver.sge_root
all_q_template = conf_manager.load_conf_template(
conf_manager.SGE_ALL_Q_TEMPLATE)
if self.app.config.hadoop_enabled:
all_q_params = {
"slots":
int(commands.getoutput("nproc")),
"prolog_path":
os.path.join(
paths.P_HADOOP_HOME,
paths.P_HADOOP_INTEGRATION_FOLDER + "/hdfsstart.sh"),
"epilog_path":
os.path.join(
paths.P_HADOOP_HOME,
paths.P_HADOOP_INTEGRATION_FOLDER + "/hdfsstop.sh")
}
else:
all_q_params = {
"slots": int(commands.getoutput("nproc")),
"prolog_path": 'NONE',
"epilog_path": 'NONE'
}
with open(SGE_allq_file, 'w') as f:
print >> f, all_q_template.substitute(all_q_params)
os.chown(SGE_allq_file,
pwd.getpwnam("sgeadmin")[2],
grp.getgrnam("sgeadmin")[2])
log.debug("Created SGE all.q template as file '%s'" %
SGE_allq_file)
misc.run(
'cd %s; ./bin/lx24-amd64/qconf -Mq %s' %
(self.app.path_resolver.sge_root, SGE_allq_file),
"Error modifying all.q", "Successfully modified all.q")
log.debug("Configuring users' SGE profiles")
misc.append_to_file(
paths.LOGIN_SHELL_SCRIPT,
"\nexport SGE_ROOT=%s" % self.app.path_resolver.sge_root)
misc.append_to_file(paths.LOGIN_SHELL_SCRIPT,
"\n. $SGE_ROOT/default/common/settings.sh\n")
# Write out the .sge_request file for individual users
sge_request_template = conf_manager.load_conf_template(
conf_manager.SGE_REQUEST_TEMPLATE)
sge_request_params = {
'psql_home': self.app.path_resolver.pg_home,
'galaxy_tools_dir': self.app.path_resolver.galaxy_tools,
}
users = ['galaxy', 'ubuntu']
for user in users:
sge_request_file = os.path.join('/home', user, '.sge_request')
with open(sge_request_file, 'w') as f:
print >> f, sge_request_template.substitute(
sge_request_params)
os.chown(sge_request_file,
pwd.getpwnam(user)[2],
grp.getgrnam(user)[2])
return True
return False
