Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
P
param_runner
Manage
Activity
Members
Plan
Wiki
Code
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Locked files
Deploy
Releases
Container Registry
Analyze
Contributor analytics
Repository analytics
Insights
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
BioHPC
param_runner
Commits
0b0901c7
There was an error fetching the commit references. Please try again later.
Commit
0b0901c7
authored
8 years ago
by
David Trudgian
Browse files
Options
Downloads
Patches
Plain Diff
Bump version, fix bin for modules
parent
5dd9d13e
No related merge requests found
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
bin/param_runner
+10
-4
10 additions, 4 deletions
bin/param_runner
setup.py
+1
-1
1 addition, 1 deletion
setup.py
with
11 additions
and
5 deletions
bin/param_runner
+
10
−
4
View file @
0b0901c7
...
@@ -88,11 +88,16 @@ def main():
...
@@ -88,11 +88,16 @@ def main():
if
'
gres
'
in
p
.
vals
:
if
'
gres
'
in
p
.
vals
:
gres
=
str
(
p
.
vals
[
'
gres
'
])
gres
=
str
(
p
.
vals
[
'
gres
'
])
sbatch_cmd
=
[
'
sbatch
'
,
'
-N
'
,
nodes
,
'
-p
'
,
partition
,
'
-t
'
,
time_limit
,
'
--gres
'
,
gres
,
'
-oparam_runner_%j.out
'
]
sbatch_cmd
=
'
sbatch
'
+
'
-N
'
+
nodes
+
'
-p
'
+
partition
+
'
-t
'
+
time_limit
+
'
--gres
'
+
gres
+
'
-oparam_runner_%j.out
'
else
:
else
:
sbatch_cmd
=
[
'
sbatch
'
,
'
-N
'
,
nodes
,
'
-p
'
,
partition
,
'
-t
'
,
time_limit
,
'
-oparam_runner_%j.out
'
]
sbatch_cmd
=
'
sbatch
'
+
'
-N
'
+
nodes
+
'
-p
'
+
partition
+
'
-t
'
+
time_limit
+
'
-oparam_runner_%j.out
'
batch_script
=
"
#!/bin/bash
\n
"
batch_script
=
"
#!/bin/bash
\n
"
if
'
modules
'
in
p
.
vals
.
keys
():
for
mod_name
in
p
.
vals
[
'
modules
'
]:
batch_script
+=
"
module add %s
\n
"
%
mod_name
batch_script
+=
python_exe
batch_script
+=
python_exe
batch_script
+=
'
-u
'
batch_script
+=
'
-u
'
batch_script
+=
this_script
batch_script
+=
this_script
...
@@ -101,9 +106,10 @@ def main():
...
@@ -101,9 +106,10 @@ def main():
batch_script
+=
'
2>&1
\n
'
batch_script
+=
'
2>&1
\n
'
logger
.
debug
(
sbatch_cmd
)
logger
.
debug
(
sbatch_cmd
)
logger
.
debug
(
batch_script
)
sbatch_proc
=
subprocess
.
Popen
(
sbatch_cmd
,
stdin
=
subprocess
.
PIPE
,
stdout
=
subprocess
.
PIPE
,
sbatch_proc
=
subprocess
.
Popen
(
sbatch_cmd
,
shell
=
True
,
stdin
=
subprocess
.
PIPE
,
stdout
=
subprocess
.
PIPE
,
stderr
=
subprocess
.
PIPE
)
stderr
=
subprocess
.
PIPE
,
env
=
os
.
environ
.
copy
()
)
stdout
,
stderr
=
sbatch_proc
.
communicate
(
batch_script
)
stdout
,
stderr
=
sbatch_proc
.
communicate
(
batch_script
)
...
...
This diff is collapsed.
Click to expand it.
setup.py
+
1
−
1
View file @
0b0901c7
...
@@ -10,7 +10,7 @@ def read(fname):
...
@@ -10,7 +10,7 @@ def read(fname):
setup
(
setup
(
name
=
"
param_runner
"
,
name
=
"
param_runner
"
,
version
=
"
1.0.0a
2
"
,
version
=
"
1.0.0a
4
"
,
author
=
"
David Trudgian
"
,
author
=
"
David Trudgian
"
,
author_email
=
"
david.trudgian@utsouthwestern.edu
"
,
author_email
=
"
david.trudgian@utsouthwestern.edu
"
,
description
=
(
"
Parameter exploration on SLURM clusters.
"
),
description
=
(
"
Parameter exploration on SLURM clusters.
"
),
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment