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This is an archived project. Repository and other project resources are read-only.
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Jeremy Auguste
oar
Commits
61528e9e
Commit
61528e9e
authored
7 years ago
by
Jeremy Auguste
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Added batchoar script (WIP)
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61528e9e
#!/usr/bin/env python
# coding: utf-8
import
argparse
import
yaml
import
itertools
import
subprocess
import
logging
from
collections
import
deque
from
.
import
oargen
def
argparser
():
parser
=
argparse
.
ArgumentParser
()
parser
.
add_argument
(
'
job_file
'
,
help
=
"
YAML file which contains all the jobs to launch
"
)
parser
.
add_argument
(
'
destination
'
,
help
=
"
New directory to create used to store outputs
"
)
parser
.
add_argument
(
'
-b
'
,
'
--besteffort
'
,
action
=
"
store_true
"
,
help
=
"
Launch job in besteffort mode
"
)
parser
.
add_argument
(
'
-t
'
,
'
--time
'
,
default
=
"
10
"
,
help
=
"
Default maximum duration of the jobs (format: h[:m[:s]])
"
)
parser
.
add_argument
(
'
-g
'
,
'
--gpu
'
,
action
=
"
store_true
"
,
help
=
"
If True, reserves only cores with GPUs
"
)
parser
.
add_argument
(
'
-c
'
,
'
--core
'
,
default
=
1
,
type
=
int
,
help
=
"
Number of cores to reserve
"
)
parser
.
add_argument
(
'
-H
'
,
'
--host
'
,
help
=
"
Name of the host (SQL LIKE syntax accepted)
"
)
parser
.
add_argument
(
'
-i
'
,
'
--interactive
'
,
action
=
"
store_true
"
,
help
=
"
Launch job in interactive mode
"
)
parser
.
add_argument
(
'
-C
'
,
'
--checkpoint
'
,
type
=
int
,
metavar
=
"
SECONDS
"
,
help
=
"
Enable checkpoint signals with the given delay (in seconds)
"
)
parser
.
add_argument
(
'
-j
'
,
'
--max-jobs
'
,
type
=
int
,
default
=-
1
)
parser
.
add_argument
(
'
--print-commands
'
,
action
=
"
store_true
"
,
help
=
"
Print each individual command
"
)
parser
.
add_argument
(
'
-r
'
,
'
--run
'
,
action
=
"
store_true
"
,
help
=
"
Run the command
"
)
parser
.
add_argument
(
'
-l
'
,
'
--logger
'
,
default
=
'
INFO
'
,
choices
=
[
'
DEBUG
'
,
'
INFO
'
,
'
WARNING
'
,
'
ERROR
'
,
'
CRITICAL
'
],
help
=
"
Logging level: DEBUG, INFO (default), WARNING, ERROR
"
)
args
=
parser
.
parse_args
()
numeric_level
=
getattr
(
logging
,
args
.
logger
.
upper
(),
None
)
if
not
isinstance
(
numeric_level
,
int
):
raise
ValueError
(
"
Invalid log level: {}
"
.
format
(
args
.
logger
))
logging
.
basicConfig
(
level
=
numeric_level
)
return
args
def
load_variables
(
yaml_variables
):
variable_names
=
[]
variables
=
[]
for
name
,
values
in
yaml_variables
.
items
():
variable_names
.
append
(
name
)
variables
.
append
(
values
)
return
variable_names
,
itertools
.
product
(
*
variables
)
def
load_flags
(
yaml_flags
,
args
):
flags
=
{}
for
command_flag
,
oar_flag
in
yaml_flags
.
items
():
if
getattr
(
args
,
oar_flag
):
flags
[
command_flag
]
=
command_flag
else
:
flags
[
command_flag
]
=
""
return
flags
def
load_job
(
job_name
,
job
,
var_names
,
var_tuples
,
constants
,
flags
,
precommand
):
for
name
,
value
in
constants
.
items
():
job
=
job
.
replace
(
f
"
$
{
name
}
$
"
,
str
(
value
))
job_name
=
job_name
.
replace
(
f
"
$
{
name
}
$
"
,
str
(
value
))
for
flag
,
str_flag
in
flags
.
items
():
job
=
job
.
replace
(
f
"
@
{
flag
}
@
"
,
str_flag
)
job_name
=
job_name
.
replace
(
f
"
@
{
flag
}
@
"
,
str_flag
)
if
precommand
:
job
=
f
"
{
precommand
}
{
job
}
"
jobs
=
[]
for
var_tuple
in
var_tuples
:
new_job
=
job
new_job_name
=
job_name
for
var_name
,
var
in
zip
(
var_names
,
var_tuple
):
new_job
=
new_job
.
replace
(
f
"
%
{
var_name
}
%
"
,
str
(
var
))
new_job_name
=
new_job_name
.
replace
(
f
"
%
{
var_name
}
%
"
,
str
(
var
))
jobs
.
append
((
new_job_name
,
new_job
))
return
jobs
def
load_jobs
(
yaml_in
,
args
):
yaml_jobs
=
yaml
.
load
(
yaml_in
)
var_names
,
var_tuples
=
load_variables
(
yaml_jobs
[
"
variables
"
])
constants
=
yaml_jobs
[
"
constants
"
]
flags
=
load_flags
(
yaml_jobs
[
"
flags
"
],
args
)
try
:
precommand
=
yaml_jobs
[
"
environment
"
][
"
precommand
"
]
except
KeyError
:
precommand
=
""
jobs
=
[]
for
job_name
,
job
in
yaml_jobs
[
"
jobs
"
].
items
():
jobs
.
extend
(
load_job
(
job_name
,
job
,
var_names
,
var_tuples
,
constants
,
flags
,
precommand
))
return
jobs
def
extract_job_id
(
cmd_output
):
for
line
in
cmd_output
.
splitlines
():
if
line
.
startswith
(
"
OAR_JOB_ID=
"
):
return
line
.
split
(
'
=
'
)[
1
]
return
None
def
main
():
args
=
argparser
()
with
open
(
args
.
job_file
)
as
fin
:
jobs
=
load_jobs
(
fin
,
args
)
anteriors
=
deque
()
for
job_name
,
job
in
jobs
:
if
len
(
anteriors
)
<
args
.
max_jobs
:
anterior
=
None
else
:
anterior
=
anteriors
.
pop
()
oar_command
=
oargen
.
prepare_oarsub
(
args
.
gpu
,
args
.
host
,
args
.
core
,
args
.
time
,
command
=
job
,
command_is_string
=
True
,
name
=
job_name
,
besteffort
=
args
.
besteffort
,
checkpoint
=
args
.
checkpoint
,
anterior
=
anterior
)
cmd_output
=
oargen
.
run_oarsub
(
oar_command
,
print_cmd
=
args
.
print_commands
,
fake_run
=
not
args
.
run
,
return_output
=
True
)
if
cmd_output
is
not
None
:
job_id
=
extract_job_id
(
cmd_output
)
if
job_id
is
None
:
logging
.
warning
(
"
Job
'
{}
'
seems to have failed to launch...
"
.
format
(
job_name
))
else
:
anteriors
.
appendleft
(
job_id
)
if
__name__
==
'
__main__
'
:
main
()
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