-
Notifications
You must be signed in to change notification settings - Fork 2
/
submit_job.py
311 lines (248 loc) · 9.99 KB
/
submit_job.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
"""
A script for submitting nengo_mpi jobs to the scheduling queue
on either scinet bgq or scinet gpc.
"""
import os
import os.path as path
import string
import subprocess
import argparse
import datetime
import math
import re
def write_gpc_jobfile(
filename, n_procs, network_file, network_name,
working_dir, wall_time, exe_loc, t, log, merged, timing,
envs, ranks_per_node=8):
network_file = path.split(network_file)[-1]
with open(filename, 'w') as outf:
outf.write("#!/bin/bash\n")
outf.write("# MOAB/Torque submission script for SciNet GPC\n")
outf.write("#\n")
n_nodes = int(math.ceil(float(n_procs) / ranks_per_node))
line = (
"#PBS -l nodes=%d:ppn=%d,walltime=%s"
"\n" % (n_nodes, ranks_per_node, wall_time))
outf.write(line)
outf.write("#PBS -N %s\n" % network_name)
outf.write("#PBS -m abe\n")
outf.write("#PBS -e %s.err\n" % network_name)
outf.write("#PBS -o %s.out\n\n" % network_name)
outf.write(
"# load modules (must match modules used for compilation)\n")
outf.write("module load intel/14.0.1\n")
outf.write("module load python/2.7.5\n")
outf.write("module load openmpi/intel/1.6.4\n")
outf.write("module load cxxlibraries/boost/1.55.0-intel\n")
outf.write("module load gcc/4.8.1\n")
outf.write("module load hdf5/1813-v18-openmpi-intel\n")
outf.write("module load use.own\n")
outf.write("module load nengo\n\n")
for e in envs:
outf.write("export %s\n" % e)
if envs:
outf.write("\n")
outf.write("cd %s\n" % working_dir)
outf.write("cp ${PBS_NODEFILE} .\n\n")
outf.write("# EXECUTION COMMAND;\n")
outf.write(
"mpirun -np {p} --mca pml ob1 {exe_loc} --noprog {log} {merged} "
"{timing} {network_file} {t}\n".format(
p=n_procs, ranks_per_node=ranks_per_node, exe_loc=exe_loc,
log=log, merged=merged, timing=timing,
network_file=network_file, t=t))
def write_bgq_jobfile(
filename, n_procs, network_file, network_name,
working_dir, wall_time, exe_loc, t, log, merged, timing,
envs, ranks_per_node=16):
n_nodes = math.ceil(float(n_procs) / ranks_per_node)
n_nodes = int(max(64, n_nodes))
network_file = path.split(network_file)[-1]
with open(filename, 'w') as outf:
outf.write('#!/bin/sh\n')
outf.write('# @ job_name = %s\n' % network_name)
outf.write('# @ job_type = bluegene\n')
outf.write('# @ comment = "nengo_mpi BGQ Job"\n')
outf.write('# @ error = %s.err\n' % network_name)
outf.write('# @ output = %s.out\n' % network_name)
outf.write('# @ bg_size = %s\n' % n_nodes)
outf.write('# @ wall_clock_limit = %s\n' % wall_time)
outf.write('# @ bg_connectivity = Torus\n')
outf.write('# @ queue \n')
outf.write(
'runjob --np {p} --ranks-per-node={ranks_per_node} '
'--envs OMP_NUM_THREADS=1 HOME=$HOME {envs} --cwd={wd} : '
'{exe_loc} --noprog {log} {merged} {timing} '
'{network_file} {t}'.format(
p=n_procs, ranks_per_node=ranks_per_node, exe_loc=exe_loc,
log=log, merged=merged, timing=timing,
network_file=network_file,
t=t, wd=working_dir, envs=' '.join(envs)))
def handle_non_cluster(
n_procs, network_file, network_name,
working_dir, exe_loc, t, log, merged, timing, ranks_per_node):
old_dir = os.getcwd()
os.chdir(working_dir)
command = (
"mpirun -np {p} --mca pml ob1 {exe_loc} --noprog {log} {merged} "
"{timing} {network_file} {t}\n".format(
p=n_procs, ranks_per_node=ranks_per_node, exe_loc=exe_loc,
log=log, merged=merged, timing=timing,
network_file=network_file, t=t))
try:
output = subprocess.check_output(
command.split(), stderr=subprocess.STDOUT)
except subprocess.CalledProcessError as e:
print e.output
raise
with open(network_name+'.out', 'w') as f:
f.write(output)
os.chdir(old_dir)
return output
def make_directory_name(experiments_dir, network_name, add_date=True):
if add_date:
working_dir = path.join(experiments_dir, network_name + "_")
date_time_string = str(datetime.datetime.now()).split('.')[0]
date_time_string = reduce(
lambda y, z: string.replace(y, z, "_"),
[date_time_string, ":", " ", "-"])
working_dir += date_time_string
else:
working_dir = path.join(experiments_dir, network_name)
return working_dir
def make_sym_link(target, name):
try:
os.remove(name)
except OSError:
pass
os.symlink(target, name)
def submit_job(
network_file, n_procs, log, merged=False, timing=False, t=1.0,
wall_time=None, rpn=0, envs=None, dir=None, add_date=True):
platform = ''
host_name = os.getenv("HOSTNAME")
if host_name:
if 'gpc' in host_name:
platform = 'gpc'
elif 'bgq' in host_name:
platform = 'bgq'
if not platform:
print("Not on known cluster. Attempting to run the network, "
"rather than submitting as a job.")
if rpn == 0:
ranks_per_node = {'gpc': 8, 'bgq': 16, '': 8}[platform]
else:
ranks_per_node = rpn
if log:
log = " --log " + log
merged = "--merged" if merged else ""
timing = "--timing" if timing else ""
if wall_time is None:
wall_time = {
'gpc': '0:15:00', 'bgq': '0:30:00', '': '0:15:00'}[platform]
else:
wall_time = wall_time
# Checks envs - \S matches any non-whitespace character
envs = [] if envs is None else envs
pattern = '\S+=\S+'
for e in envs:
assert re.match(pattern, e), "``envs`` supplied in incorrect format."
# Define constants
exe_loc = path.join(os.getenv('HOME'), 'nengo_mpi/bin/nengo_mpi')
experiments_dir = (
path.join(os.getenv('SCRATCH'), "experiments")
if dir is None else dir)
network_name = path.basename(network_file)
network_name = path.splitext(network_name)[0]
print "Network name: ", network_name
# Create directory to run the job from
working_dir = make_directory_name(
experiments_dir, network_name, add_date=add_date)
if not path.isdir(working_dir):
os.makedirs(working_dir)
# Create convenience `latest` symlink
make_sym_link(working_dir, path.join(experiments_dir, 'latest'))
# Make a symlink in the working dir to the
# file containing the network that we want to load and simulate
make_sym_link(
path.join(os.getcwd(), network_file),
path.join(working_dir, path.basename(network_file)))
if platform not in ['gpc', 'bgq']:
if envs:
raise Exception(
"Cannot supply environment variables on non-cluster. Instead, "
"set environment variables in calling shell.")
handle_non_cluster(
n_procs, path.basename(network_file), network_name,
working_dir, exe_loc, t, log, merged, timing, ranks_per_node)
return
submit_script = "submit_script.sh"
submit_script_path = path.join(working_dir, submit_script)
# Create the job file in the working dir
if platform == 'gpc':
write_gpc_jobfile(
submit_script_path, n_procs, network_file, network_name,
working_dir, wall_time, exe_loc, t, log, merged, timing,
envs, ranks_per_node)
elif platform == 'bgq':
write_bgq_jobfile(
submit_script_path, n_procs, network_file, network_name,
working_dir, wall_time, exe_loc, t, log, merged, timing,
envs, ranks_per_node)
else:
raise NotImplementedError()
os.chdir(working_dir)
# Submit to queue
if platform == 'gpc':
job_id = subprocess.check_output(['qsub', submit_script])
job_id = job_id.split('.')[0]
elif platform == 'bgq':
job_id = subprocess.check_output(['llsubmit', submit_script])
job_id = job_id.split('"')[1]
else:
raise NotImplementedError()
# Create a file in the directory with the job_id as its name
open(job_id, 'w').close()
print "Job ID: ", job_id
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description="Submit a nengo_mpi simulation using either "
"BGQ llsubmit or GPC qsub.")
parser.add_argument(
'network', default="", type=str,
help="The network file to run.")
parser.add_argument(
'-p', type=int, default=1024,
help="Number of processors.")
parser.add_argument(
'--log', default="", type=str,
help="Location to save results to.")
parser.add_argument(
'--merged', action="store_true",
help="Supply to run using merged mpi communication.")
parser.add_argument(
'--timing', action="store_true",
help="Supply to collect timing information.")
parser.add_argument(
'-t', default=1.0, type=float,
help="The simulation time.")
parser.add_argument(
'-w', default=None,
help="Upper bound on required wall time.")
parser.add_argument(
'--rpn', default=0, type=int, help="MPI Ranks per node.")
parser.add_argument(
'--envs', default=None, nargs='*',
help="Environment variables to run the job with.")
parser.add_argument(
'--dir', default=None,
help="Path to store the experiment directories.")
parser.add_argument(
'--add-date', action='store_true',
help="Whether to add date to experiment directory names.")
# Parse args
args = parser.parse_args()
print args
submit_job(
args.network, args.p, args.log, args.merged, args.timing, args.t,
args.w, args.rpn, args.envs, args.dir, args.add_date)