def main(config_file, output_file):
with Open(config_file, 'r') as f:
config = json.load(f)
graph = dict()
for name, item in config.iteritems():
graph[name] = [] if "depends" not in item else item['depends']
with Open(output_file, 'w') as f:
f.write('#!/bin/bash\n\n')
for job in toposort(graph):
item = config[job]
param = ['-terse', '-cwd']
if "depends" in item:
param.append('-hold_jid')
param.append(','.join(['$' + x for x in item['depends']]))
if "array" in item:
param.append('-t')
assert(len(item['array']) > 0 and len(item['array']) < 4)
param.append(
''.join([
''.join(x)
for x in zip(['', '-', ':'], map(str, item['array']))
])
)
if 'stdout' in item:
param.append('-o')
param.append("'{}'".format(item['stdout']))
if 'stderr' in item:
param.append('-e')
param.append("'{}'".format(item['stderr']))
if "resources" in item:
assert(len(item['resources']) > 0)
param.append('-l')
param.append(','.join([
'='.join(x) for x in item['resources'].iteritems()
]))
if "params" in item:
assert(len(item['params']) > 0)
param.append(' '.join(item['params']))
query = ("{jobname}=`qsub -N '{name}' {parameters} {command} " + \
"| sed -e 's/[.].*$//'`").format(
name=job,
jobname=job,
parameters=' '.join(param),
command=cmd_to_string(item['cmd'])
)
f.write(query + '\n')
def test_toposort(self):
X = toposort(self.G)
Y = [3, 0, 2, 13, 8, 14, 6, 10, 9, 5, 1, 4, 7, 11, 12]
self.assertEqual(X, Y, "Topological sort is not working: " + \
str(X) + " != " + str(Y))
