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pbsCoat.py
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Created
Tue, Aug 20, 15:11
Size
3 KB
Mime Type
text/x-python
Expires
Thu, Aug 22, 15:11 (2 d)
Engine
blob
Format
Raw Data
Handle
20038269
Attached To
R3127 blackdynamite
pbsCoat.py
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#!/usr/bin/env python
from
BlackDynamite
import
*
import
os
,
stat
import
subprocess
import
re
import
socket
admissible_params
=
{
"walltime"
:
str
,
"email"
:
str
,
"nproc"
:
int
,
"pbs_option"
:
[
str
],
"module"
:
[
str
],
"mpiprocs"
:
int
,
"ncpus"
:
int
,
"cwd"
:
bool
}
default_params
=
{
"walltime"
:
"48:00:00"
,
"cwd"
:
True
}
help
=
{
"walltime"
:
"Specify the wall time for the runs"
,
"email"
:
"Specify the email to notify"
,
"nproc"
:
"Force the number of processors and update the run"
,
"pbs_option"
:
"Allow to provide additional PBS options"
,
"module"
:
"List of module to load"
,
"ncpus"
:
"Number of cpus per nodes"
,
"mpiprocs"
:
"Number of mpi processus per nodes"
,
"cwd"
:
"Run by default in the run folder"
}
def
launch
(
run
,
params
):
_exec
=
run
.
getExecFile
()
head
=
\
"""#!/bin/bash
#PBS -l walltime={0}
"""
.
format
(
params
[
"walltime"
])
if
(
"email"
in
params
):
head
+=
"#PBS -m abe
\n
"
head
+=
"#PBS -M {0}
\n
"
.
format
(
params
[
"email"
])
pbs_head_name
=
"#PBS -N {0}_{1}
\n
"
.
format
(
run
[
"run_name"
],
run
.
id
)
head
+=
pbs_head_name
run
[
"state"
]
=
"PBS submit"
if
(
"nproc"
in
params
):
run
[
"nproc"
]
=
params
[
"nproc"
]
nproc
=
run
[
"nproc"
]
if
(
"mpiprocs"
in
params
or
"npcus"
in
params
):
args
=
[]
if
"ncpus"
in
params
:
npernode
=
params
[
"ncpus"
]
args
.
append
(
"ncpus={0}"
.
format
(
npernode
))
if
"mpiprocs"
in
params
:
npernode
=
min
(
params
[
"mpiprocs"
],
nproc
)
args
.
append
(
"mpiprocs={0}"
.
format
(
npernode
))
select
=
max
(
1
,
nproc
/
npernode
)
args
.
insert
(
0
,
"#PBS -l select={0}"
.
format
(
select
))
select_str
=
":"
.
join
(
args
)
print
select_str
head
+=
select_str
+
"
\n
"
else
:
head
+=
"#PBS -l nodes="
+
str
(
nproc
)
+
"
\n
"
if
(
"pbs_option"
in
params
):
for
i
in
params
[
"pbs_option"
]:
head
+=
"#PBS {0}
\n
"
.
format
(
i
)
if
(
"module"
in
params
):
for
i
in
params
[
"module"
]:
head
+=
"module load {0}
\n
"
.
format
(
i
)
run
.
update
()
head
+=
"""
export BLACKDYNAMITE_HOST=__BLACKDYNAMITE__dbhost__
export BLACKDYNAMITE_SCHEMA=__BLACKDYNAMITE__study__
export BLACKDYNAMITE_STUDY=__BLACKDYNAMITE__study__
export BLACKDYNAMITE_RUN_ID=__BLACKDYNAMITE__run_id__
export BLACKDYNAMITE_USER="""
+
params
[
"user"
]
+
"""
on_kill()
{
updateRuns.py --updates \"state = PBS killed\" --truerun
exit 0
}
on_stop()
{
updateRuns.py --updates \"state = PBS stopped\" --truerun
exit 0
}
# Execute function on_die() receiving TERM signal
#
trap on_stop SIGUSR1
trap on_stop SIGTERM
trap on_kill SIGUSR2
trap on_kill SIGKILL
"""
if
(
params
[
"cwd"
]):
head
+=
"""
cd __BLACKDYNAMITE__run_path__
"""
_exec
[
"file"
]
=
run
.
replaceBlackDynamiteVariables
(
head
)
+
_exec
[
"file"
]
f
=
open
(
_exec
[
"filename"
],
'w'
)
f
.
write
(
_exec
[
"file"
])
f
.
close
()
# os.chmod(_exec["filename"], stat.S_IRWXU)
print
(
"execute qsub ./"
+
_exec
[
"filename"
])
print
(
"in dir "
)
subprocess
.
call
(
"pwd"
)
if
(
params
[
"truerun"
]
==
True
):
ret
=
subprocess
.
call
(
"qsub "
+
_exec
[
"filename"
],
shell
=
True
)
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