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bob
gridtk
Commits
931decce
Commit
931decce
authored
Mar 28, 2014
by
Manuel Günther
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Improved behavior when multiple jobs are re-submitted at the same time.
parent
4a1fbb81
Changes
4
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Showing
4 changed files
with
15 additions
and
6 deletions
+15
-6
gridtk/models.py
gridtk/models.py
+2
-2
gridtk/script/jman.py
gridtk/script/jman.py
+10
-2
gridtk/sge.py
gridtk/sge.py
+2
-1
setup.py
setup.py
+1
-1
No files found.
gridtk/models.py
View file @
931decce
...
...
@@ -292,9 +292,9 @@ class Job(Base):
deps
=
str
(
sorted
(
list
(
set
([
dep
.
unique
for
dep
in
self
.
get_jobs_we_wait_for
()]))))
if
dependencies
<
len
(
deps
):
deps
=
deps
[:
dependencies
-
3
]
+
'...'
return
format
.
format
(
self
.
unique
,
job_id
,
queue
,
status
,
self
.
name
,
deps
,
command_line
)
return
format
.
format
(
self
.
unique
,
job_id
,
queue
[:
12
]
,
status
,
self
.
name
,
deps
,
command_line
)
else
:
return
format
.
format
(
self
.
unique
,
job_id
,
queue
,
status
,
self
.
name
,
command_line
)
return
format
.
format
(
self
.
unique
,
job_id
,
queue
[:
12
]
,
status
,
self
.
name
,
command_line
)
...
...
gridtk/script/jman.py
View file @
931decce
...
...
@@ -90,6 +90,14 @@ def get_ids(jobs):
return
indexes
def
get_memfree
(
memory
,
parallel
):
"""Computes the memory required for the memfree field."""
number
=
int
(
memory
.
rstrip
(
string
.
ascii_letters
))
memtype
=
memory
.
lstrip
(
string
.
digits
)
if
not
memtype
:
memtype
=
"G"
return
"%d%s"
%
(
number
*
parallel
,
memtype
)
def
submit
(
args
):
"""Submission command"""
...
...
@@ -115,7 +123,7 @@ def submit(args):
if
args
.
qname
!=
'all.q'
:
kwargs
[
'hvmem'
]
=
args
.
memory
if
args
.
parallel
is
not
None
:
kwargs
[
'pe_opt'
]
=
"pe_mth %d"
%
args
.
parallel
kwargs
[
'memfree'
]
=
"%d%s"
%
(
int
(
args
.
memory
.
rstrip
(
string
.
ascii_letters
))
*
args
.
parallel
,
args
.
memory
.
lstrip
(
string
.
digits
)
)
kwargs
[
'memfree'
]
=
get_memfree
(
args
.
memory
,
args
.
parallel
)
kwargs
[
'dry_run'
]
=
args
.
dry_run
kwargs
[
'stop_on_failure'
]
=
args
.
stop_on_failure
...
...
@@ -140,7 +148,7 @@ def resubmit(args):
kwargs
[
'hvmem'
]
=
args
.
memory
if
args
.
parallel
is
not
None
:
kwargs
[
'pe_opt'
]
=
"pe_mth %d"
%
args
.
parallel
kwargs
[
'memfree'
]
=
"%d%s"
%
(
int
(
args
.
memory
.
rstrip
(
string
.
ascii_letters
))
*
args
.
parallel
,
args
.
memory
.
lstrip
(
string
.
digits
)
)
kwargs
[
'memfree'
]
=
get_memfree
(
args
.
memory
,
args
.
parallel
)
if
args
.
io_big
:
kwargs
[
'io_big'
]
=
True
if
args
.
no_io_big
:
...
...
gridtk/sge.py
View file @
931decce
...
...
@@ -154,7 +154,8 @@ class JobManagerSGE(JobManager):
logger
.
debug
(
"Re-submitting job '%s' with dependencies '%s' to the grid."
%
(
job
,
deps
))
self
.
_submit_to_grid
(
job
,
job
.
name
,
job
.
get_array
(),
deps
,
job
.
log_dir
,
**
arguments
)
self
.
session
.
commit
()
# commit after each job to avoid failures of not finding the job during execution in the grid
self
.
session
.
commit
()
self
.
unlock
()
...
...
setup.py
View file @
931decce
...
...
@@ -9,7 +9,7 @@ if sys.version_info[:2] < (2, 7) or ((3,0) <= sys.version_info[:2] < (3,2)):
setup
(
name
=
'gridtk'
,
version
=
'1.1.
3
a0'
,
version
=
'1.1.
4
a0'
,
description
=
'SGE Grid and Local Submission and Monitoring Tools for Idiap'
,
url
=
'http://github.com/idiap/gridtk'
,
...
...
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