def test_make_new_header_pmem_limits(self, mock_cluster_overhead, mock_clusterdata):
sf = SubmitFilter(
[],
[x + "\n" for x in SCRIPTS[6].split("\n")]
)
mock_clusterdata.return_value = {
'TOTMEM': 4096 << 20,
'PHYSMEM': 3072 << 20,
'NP': 8,
'NP_LCD': 2,
}
mock_cluster_overhead.return_value = 0
sf.parse_header()
header = submitfilter.make_new_header(sf)
self.assertEqual(header, [
'#!/bin/bash',
'#PBS -l nodes=1:ppn=4',
'#PBS -l pmem=1g',
'#PBS -m n'
'',
'',
], msg='header with existing mem set')
self.assertEqual(get_warnings(), [
"Unable to determine clustername, using default delcatty (no PBS_DEFAULT)",
"Warning, requested %sb pmem per node, this is more than the available pmem (%sb), this job will never start." % (1 << 30, (3072 << 20) / 8 )
])
def test_make_new_header_add_missing(self):
"""
Test make_new_header
add missing mail / unless present
add pvmem unless defined
VSC_NODE_PARTITION
"""
partname = "mypartition"
os.environ["VSC_NODE_PARTITION"] = partname
sf = SubmitFilter([], [x + "\n" for x in SCRIPTS[1].split("\n")])
sf.parse_header()
self.assertEqual(sf.header, ["#!/bin/bash"], msg="minimal header from minimal script")
header = submitfilter.make_new_header(sf)
self.assertEqual(
header,
[
"#!/bin/bash",
"# No mail specified - added by submitfilter",
"#PBS -m n",
"# No pmem or vmem limit specified - added by submitfilter (server found: delcatty)",
"#PBS -l vmem=4720302336",
"# Adding PARTITION as specified in VSC_NODE_PARTITION",
"#PBS -W x=PARTITION:%s" % partname,
],
msg="added missing defaults and pratiton information to header",
)
del os.environ["VSC_NODE_PARTITION"]
def main(arguments=None):
"""Main function"""
if arguments is None:
arguments = sys.argv
sf = SubmitFilter(arguments, sys.stdin.readline)
sf.parse_header()
header = make_new_header(sf)
# flush it so it doesn't get mixed with stderr
sys.stdout.flush()
sys.stderr.flush()
# prebody is not stripped of the newline
sys.stdout.write("\n".join(header+[sf.prebody]))
for line in sf.stdin:
sys.stdout.write(line)
# print all generated warnings
# flush it so it doesn't get mixed with stderr
sys.stdout.flush()
for warn in ["%s\n" % w for w in get_warnings()]:
sys.stderr.write(warn)
sys.stderr.flush()
sys.exit(0)
def test_make_new_header_add_missing(self):
"""
Test make_new_header
add missing mail / unless present
add pvmem unless defined
VSC_NODE_PARTITION
"""
partname = 'mypartition'
os.environ['VSC_NODE_PARTITION'] = partname
sf = SubmitFilter(
[],
[x + "\n" for x in SCRIPTS[1].split("\n")]
)
sf.parse_header()
self.assertEqual(sf.header, ['#!/bin/bash'], msg='minimal header from minimal script')
header = submitfilter.make_new_header(sf)
self.assertEqual(header, [
'#!/bin/bash',
'# No mail specified - added by submitfilter',
'#PBS -m n',
'# No pmem or vmem limit specified - added by submitfilter (server found: delcatty)',
'#PBS -l vmem=4720302336',
'# Adding PARTITION as specified in VSC_NODE_PARTITION',
'#PBS -W x=PARTITION:%s' % partname,
], msg='added missing defaults and pratiton information to header')
del os.environ['VSC_NODE_PARTITION']
def test_make_new_header_ignore_indentation(self):
sf = SubmitFilter([], [x + "\n" for x in SCRIPTS[5].split("\n")])
sf.parse_header()
header = submitfilter.make_new_header(sf)
self.assertEqual(
header,
["#!/bin/bash", "#PBS -l nodes=1:ppn=4", "#PBS -l vmem=1g", "#PBS -m n", ""],
msg="header with an indented line",
)
def test_make_new_header_with_existing_mem(self):
sf = SubmitFilter([], [x + "\n" for x in SCRIPTS[4].split("\n")])
sf.parse_header()
header = submitfilter.make_new_header(sf)
self.assertEqual(
header,
["#!/bin/bash", "#PBS -l nodes=1:ppn=4", "#PBS -l mem=10g", "#PBS -m n" "", ""],
msg="header with existing mem set",
)
def test_gather_state(self):
"""Test gather_state"""
h = SubmitFilter(["-q", "verylong"], [x + "\n" for x in SCRIPTS[0].split("\n")])
h.parse_header()
os.environ["PBS_DEFAULT"] = "master15.delcatty.gent.vsc"
allpmem = 67630407680
state, newopts = h.gather_state(MASTER_REGEXP)
self.assertTrue("l" in state, msg='state retruned by gather_state always contains key "l"')
self.assertEqual(
state,
{
"e": "error_testrun.txt",
"m": "bea",
"l": {
"_nrcores": 80,
"_ppn": 16,
"vmem": "500mb",
"_vmem": 500 * 2 ** 20,
"_nrnodes": 5,
"nodes": "5:ppn=16",
"walltime": "11:25:00",
"pmem": "%s" % (allpmem / 2),
"_pmem": allpmem / 2,
},
"o": "output_testrun.txt",
"N": "testrun",
"q": "verylong",
"_cluster": "delcatty",
},
msg="expected state %s" % state,
)
self.assertEqual(
newopts,
[
"testrun",
"output_testrun.txt",
"nodes=5:ppn=16,pmem=%s" % (allpmem / 2),
"error_testrun.txt",
"walltime=11:25:00",
"vmem=500mb",
"bea",
"short",
"verylong",
],
msg="expected newopts %s" % newopts,
)
del os.environ["PBS_DEFAULT"]
def test_parse(self):
h = SubmitFilter(["-q", "verylong"], [x + "\n" for x in SCRIPTS[0].split("\n")])
# stdin is an iterator
self.assertTrue(hasattr(h.stdin, "next"), "stdin is an iterator")
h.parse_header()
self.assertEqual(
h.header,
[
"#!/bin/sh",
"#",
"#",
"#PBS -N testrun",
"#PBS -o output_testrun.txt -l nodes=5:ppn=all,pmem=half",
"#PBS -e error_testrun.txt",
"#PBS -l walltime=11:25:00",
"#PBS -l vmem=500mb",
"#PBS -m bea",
"#PBS -q short",
"#",
],
msg="Found header %s" % h.header,
)
self.assertEqual(h.prebody, "cd $VSC_HOME\n", msg="found prebody '%s'" % h.prebody)
self.assertEqual(h.dprefix, "#PBS", msg="found expected headers dprefix %s" % h.dprefix)
self.assertEqual(
h.stdin.next(), "##logs to stderr by default, redirect this to stdout\n", msg="stdin at expected position"
)
self.assertEqual(
h.allopts,
[
("N", "testrun"),
("o", "output_testrun.txt"),
("l", "nodes=5:ppn=all,pmem=half"),
("e", "error_testrun.txt"),
("l", "walltime=11:25:00"),
("l", "vmem=500mb"),
("m", "bea"),
("q", "short"),
("q", "verylong"),
],
msg="found alloptions in order %s" % h.allopts,
)
self.assertEqual(
h.occur, [3, 4, 4, 5, 6, 7, 8, 9, None], msg="expected ordered occurence of options %s" % h.occur
)
def test_gather_state(self):
"""Test gather_state"""
h = SubmitFilter(['-q', 'verylong'],
[x + "\n" for x in SCRIPTS[0].split("\n")])
h.parse_header()
os.environ['PBS_DEFAULT'] = "master15.delcatty.gent.vsc"
overhead = 2842984448
allpmem = 67630407680 - overhead
state, newopts = h.gather_state(MASTER_REGEXP)
self.assertTrue(
'l' in state,
msg='state retruned by gather_state always contains key "l"')
self.assertEqual(state, {
'e': 'error_testrun.txt',
'm': 'bea',
'l': {
'_nrcores': 80,
'_ppn': 16,
'vmem': '500mb',
'_vmem': 500 * 2**20,
'_nrnodes': 5,
'nodes': '5:ppn=16',
'walltime': '11:25:00',
'pmem': '%s' % (allpmem / 2),
'_pmem': allpmem / 2,
},
'o': 'output_testrun.txt',
'N': 'testrun',
'q': 'verylong',
'_cluster': 'delcatty'
},
msg="expected state %s" % state)
self.assertEqual(newopts, [
'testrun',
'output_testrun.txt',
'nodes=5:ppn=16,pmem=%s' % (allpmem / 2),
'error_testrun.txt',
'walltime=11:25:00',
'vmem=500mb',
'bea',
'short',
'verylong',
],
msg="expected newopts %s" % newopts)
del os.environ['PBS_DEFAULT']
def test_parse(self):
h = SubmitFilter(['-q', 'verylong'],
[x + "\n" for x in SCRIPTS[0].split("\n")])
# stdin is an iterator
self.assertTrue(hasattr(h.stdin, 'next'), "stdin is an iterator")
h.parse_header()
self.assertEqual(h.header, [
'#!/bin/sh',
'#',
'#',
'#PBS -N testrun',
'#PBS -o output_testrun.txt -l nodes=5:ppn=all,pmem=half',
'#PBS -e error_testrun.txt',
'#PBS -l walltime=11:25:00',
'#PBS -l vmem=500mb',
'#PBS -m bea',
'#PBS -q short',
'#',
],
msg="Found header %s" % h.header)
self.assertEqual(h.prebody,
"cd $VSC_HOME\n",
msg="found prebody '%s'" % h.prebody)
self.assertEqual(h.dprefix,
'#PBS',
msg="found expected headers dprefix %s" % h.dprefix)
self.assertEqual(
h.stdin.next(),
"##logs to stderr by default, redirect this to stdout\n",
msg="stdin at expected position")
self.assertEqual(h.allopts, [
('N', 'testrun'),
('o', 'output_testrun.txt'),
('l', 'nodes=5:ppn=all,pmem=half'),
('e', 'error_testrun.txt'),
('l', 'walltime=11:25:00'),
('l', 'vmem=500mb'),
('m', 'bea'),
('q', 'short'),
('q', 'verylong'),
],
msg="found alloptions in order %s" % h.allopts)
self.assertEqual(h.occur, [3, 4, 4, 5, 6, 7, 8, 9, None],
msg="expected ordered occurence of options %s" %
h.occur)
def test_gather_state(self):
"""Test gather_state"""
h = SubmitFilter(
['-q', 'verylong'],
[ x + "\n" for x in SCRIPTS[0].split("\n")]
)
h.parse_header()
os.environ['PBS_DEFAULT'] = "master15.delcatty.gent.vsc"
overhead = 2842984448
allpmem = 67630407680 - overhead
state, newopts = h.gather_state(MASTER_REGEXP)
self.assertTrue('l' in state, msg='state retruned by gather_state always contains key "l"')
self.assertEqual(state, {
'e': 'error_testrun.txt',
'm': 'bea',
'l': {
'_nrcores': 80,
'_ppn': 16,
'vmem': '500mb',
'_vmem': 500*2**20,
'_nrnodes': 5,
'nodes': '5:ppn=16',
'walltime': '11:25:00',
'pmem': '%s' % (allpmem/2),
'_pmem': allpmem/2,
},
'o': 'output_testrun.txt',
'N': 'testrun',
'q': 'verylong',
'_cluster': 'delcatty'
}, msg="expected state %s" % state)
self.assertEqual(newopts, [
'testrun',
'output_testrun.txt',
'nodes=5:ppn=16,pmem=%s' % (allpmem/2),
'error_testrun.txt',
'walltime=11:25:00',
'vmem=500mb',
'bea',
'short',
'verylong',
], msg="expected newopts %s" % newopts)
del os.environ['PBS_DEFAULT']
def test_make_new_header_ignore_indentation(self):
sf = SubmitFilter(
[],
[x + "\n" for x in SCRIPTS[5].split("\n")]
)
sf.parse_header()
header = submitfilter.make_new_header(sf)
self.assertEqual(header, [
'#!/bin/bash',
'#PBS -l nodes=1:ppn=4',
'#PBS -l vmem=1g',
'#PBS -m n',
'',
], msg='header with an indented line')
def test_make_new_header_with_existing_mem(self):
sf = SubmitFilter(
[],
[x + "\n" for x in SCRIPTS[4].split("\n")]
)
sf.parse_header()
header = submitfilter.make_new_header(sf)
self.assertEqual(header, [
'#!/bin/bash',
'#PBS -l nodes=1:ppn=4',
'#PBS -l mem=4g',
'#PBS -m n'
'',
'',
], msg='header with existing mem set')
def test_make_new_header_with_existing_mem(self):
sf = SubmitFilter(
[],
[x + "\n" for x in SCRIPTS[4].split("\n")]
)
sf.parse_header()
header = submitfilter.make_new_header(sf)
self.assertEqual(header, [
'#!/bin/bash',
'#PBS -l nodes=1:ppn=4',
'#PBS -l mem=10g',
'#PBS -m n'
'',
'',
], msg='header with existing mem set')
def test_make_new_header(self):
"""Test make_new_header resource replacement"""
sf = SubmitFilter(
[],
[x + "\n" for x in SCRIPTS[2].split("\n")]
)
sf.parse_header()
header = submitfilter.make_new_header(sf)
self.assertEqual(header, [
'#!/bin/bash',
'#PBS -l nodes=3:ppn=8',
'#PBS -l vmem=75524837376',
'#PBS -l pmem=32393711616',
'#PBS -m n',
], msg='modified header with resources replaced')
def test_make_new_header(self):
"""Test make_new_header resource replacement"""
sf = SubmitFilter(
[],
[x + "\n" for x in SCRIPTS[2].split("\n")]
)
sf.parse_header()
header = submitfilter.make_new_header(sf)
self.assertEqual(header, [
'#!/bin/bash',
'#PBS -l nodes=3:ppn=8',
'#PBS -l vmem=75524837376',
'#PBS -l pmem=32393711616',
'#PBS -m n',
], msg='modified header with resources replaced')
def test_parse(self):
h = SubmitFilter(
['-q', 'verylong'],
[x + "\n" for x in SCRIPTS[0].split("\n")]
)
# stdin is an iterator
self.assertTrue(hasattr(h.stdin, 'next'), "stdin is an iterator")
h.parse_header()
self.assertEqual(h.header,
['#!/bin/sh', '#', '#',
'#PBS -N testrun',
'#PBS -o output_testrun.txt -l nodes=5:ppn=all,pmem=half',
'#PBS -e error_testrun.txt',
'#PBS -l walltime=11:25:00',
'#PBS -l vmem=500mb',
'#PBS -m bea',
'#PBS -q short',
'#',
], msg="Found header %s" % h.header)
self.assertEqual(h.prebody, "cd $VSC_HOME\n", msg="found prebody '%s'" % h.prebody)
self.assertEqual(h.dprefix, '#PBS', msg="found expected headers dprefix %s" % h.dprefix)
self.assertEqual(h.stdin.next(),
"##logs to stderr by default, redirect this to stdout\n",
msg="stdin at expected position")
self.assertEqual(h.allopts,
[('N', 'testrun'),
('o', 'output_testrun.txt'),
('l', 'nodes=5:ppn=all,pmem=half'),
('e', 'error_testrun.txt'),
('l', 'walltime=11:25:00'),
('l', 'vmem=500mb'),
('m', 'bea'),
('q', 'short'),
('q', 'verylong'),
], msg="found alloptions in order %s" % h.allopts)
self.assertEqual(h.occur,
[3, 4, 4, 5, 6, 7, 8, 9, None],
msg="expected ordered occurence of options %s" % h.occur)
def test_make_new_header_basic(self):
"""Basic test for make_new_header"""
sf = SubmitFilter(["-q", "verylong"], [x + "\n" for x in SCRIPTS[0].split("\n")])
sf.parse_header()
old_header = sf.header[:]
header = submitfilter.make_new_header(sf)
self.assertEqual(old_header, sf.header, msg="make_new_header leaves original unmodified")
modresourcesidx = 4
self.assertEqual(
header.pop(modresourcesidx),
"#PBS -o output_testrun.txt -l nodes=5:ppn=16,pmem=32393711616",
msg="replace the resource header as expected",
)
sf.header.pop(modresourcesidx)
self.assertEqual(header, sf.header, msg="all other header lines unmodified")
def test_make_new_header_warn(self):
"""
Test make_new_header warnings
ideal ppn
vmem too high
"""
reset_warnings()
sf = SubmitFilter(
[],
[x + "\n" for x in SCRIPTS[3].split("\n")]
)
sf.parse_header()
header = submitfilter.make_new_header(sf)
self.assertEqual(header, sf.header, msg='unmodified header')
self.assertEqual(get_warnings(), [
'The chosen ppn 4 is not considered ideal: should use either lower than or multiple of 3',
'Warning, requested 1099511627776b vmem per node, this is more than the available vmem (86142287872b), this job will never start.',
], msg='warnings for ideal ppn and vmem too high')
def test_make_new_header_basic(self):
"""Basic test for make_new_header"""
sf = SubmitFilter(
['-q', 'verylong'],
[x + "\n" for x in SCRIPTS[0].split("\n")]
)
sf.parse_header()
old_header = sf.header[:]
header = submitfilter.make_new_header(sf)
self.assertEqual(old_header, sf.header, msg='make_new_header leaves original unmodified')
modresourcesidx = 4
self.assertEqual(header.pop(modresourcesidx),
'#PBS -o output_testrun.txt -l nodes=5:ppn=16,pmem=32393711616',
msg='replace the resource header as expected')
sf.header.pop(modresourcesidx)
self.assertEqual(header, sf.header, msg='all other header lines unmodified')
def test_make_new_header_warn(self):
"""
Test make_new_header warnings
ideal ppn
vmem too high
"""
reset_warnings()
sf = SubmitFilter(
[],
[x + "\n" for x in SCRIPTS[3].split("\n")]
)
sf.parse_header()
header = submitfilter.make_new_header(sf)
self.assertEqual(header, sf.header, msg='unmodified header')
self.assertEqual(get_warnings(), [
'The chosen ppn 4 is not considered ideal: should use either lower than or multiple of 3',
'Warning, requested 1099511627776b vmem per node, this is more than the available vmem (86142287872b), this job will never start.',
], msg='warnings for ideal ppn and vmem too high')
def test_make_new_header_add_missing(self):
"""
Test make_new_header
add missing mail / unless present
add pvmem unless defined
VSC_NODE_PARTITION
"""
partname = 'mypartition'
os.environ[submitfilter.ENV_NODE_PARTITION] = partname
reserv = 'magicreserv'
os.environ[submitfilter.ENV_RESERVATION] = reserv
sf = SubmitFilter(
[],
[x + "\n" for x in SCRIPTS[1].split("\n")]
)
sf.parse_header()
self.assertEqual(sf.header, ['#!/bin/bash'], msg='minimal header from minimal script')
header = submitfilter.make_new_header(sf)
self.assertEqual(header, [
'#!/bin/bash',
'# No mail specified - added by submitfilter',
'#PBS -m n',
'# No pmem or vmem limit specified - added by submitfilter (server found: delcatty)',
'#PBS -l vmem=4720302336',
'# Adding PARTITION as specified in VSC_NODE_PARTITION',
'#PBS -W x=PARTITION:%s' % partname,
'# Adding reservation as specified in VSC_RESERVATION',
'#PBS -W x=FLAGS:ADVRES:%s' % reserv,
], msg='added missing defaults and pratiton information to header')
del os.environ[submitfilter.ENV_NODE_PARTITION]
del os.environ[submitfilter.ENV_RESERVATION]
def main(arguments=None):
"""Main function"""
if arguments is None:
arguments = sys.argv
# This error could otherwise result in empty PBS_O_WORKDIR
try:
os.getcwd()
except OSError as e:
sys.stderr.write("ERROR: Unable to determine current workdir: %s (PWD deleted?)." % e)
sys.stderr.flush()
sys.exit(1)
sf = SubmitFilter(arguments, sys.stdin.readline)
sf.parse_header()
header = make_new_header(sf)
# flush it so it doesn't get mixed with stderr
sys.stdout.flush()
sys.stderr.flush()
# prebody is not stripped of the newline
sys.stdout.write("\n".join(header+[sf.prebody]))
for line in sf.stdin:
sys.stdout.write(line)
# print all generated warnings
# flush it so it doesn't get mixed with stderr
sys.stdout.flush()
for warning in ["%s\n" % w for w in get_warnings()]:
sys.stderr.write(warning)
sys.stderr.flush()
sys.exit(0)
def main(arguments=None):
"""Main function"""
if arguments is None:
arguments = sys.argv
# This error could otherwise result in empty PBS_O_WORKDIR
try:
os.getcwd()
except OSError as e:
sys.stderr.write("ERROR: Unable to determine current workdir: %s (PWD deleted?)." % e)
sys.stderr.flush()
sys.exit(1)
sf = SubmitFilter(arguments, sys.stdin.readline)
sf.parse_header()
header = make_new_header(sf)
# flush it so it doesn't get mixed with stderr
sys.stdout.flush()
sys.stderr.flush()
# prebody is not stripped of the newline
sys.stdout.write("\n".join(header+[sf.prebody]))
for line in sf.stdin:
sys.stdout.write(line)
# print all generated warnings
# flush it so it doesn't get mixed with stderr
sys.stdout.flush()
for warning in ["%s\n" % w for w in get_warnings()]:
sys.stderr.write(warning)
sys.stderr.flush()
sys.exit(0)
