Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
pegasus-isi
ACME-Workflow
Commits
84106ab3
Commit
84106ab3
authored
Mar 15, 2015
by
Juve, Gideon
Browse files
Update scripts for new directory structure
parent
85be8191
Changes
3
Hide whitespace changes
Inline
Side-by-side
bin/acme-amwg.sh
View file @
84106ab3
...
...
@@ -2,8 +2,42 @@
set
-e
if
[
$#
-ne
1
]
;
then
echo
"Usage:
$0
diag140804.csh"
function
usage
()
{
echo
"Usage:
$0
-case CASENAME -script diag140804.csh"
}
if
[
$#
-eq
0
]
;
then
usage
exit
1
fi
while
[
"$#"
-ne
0
]
;
do
case
"
$1
"
in
-case
)
shift
CASENAME
=
$1
;;
-script
)
shift
SCRIPT
=
$1
;;
*
)
usage
exit
1
;;
esac
shift
done
if
[
-z
"
$CASENAME
"
]
;
then
usage
echo
"ERROR: Specify CASENAME"
exit
1
fi
if
[
-z
"
$SCRIPT
"
]
;
then
usage
echo
"ERROR: Specify SCRIPT"
exit
1
fi
...
...
@@ -20,9 +54,7 @@ fi
module load ncl
module load nco
# Chmod the templated script for this stage
chmod
755
$1
/bin/csh
$PWD
/
$SCRIPT
||
true
# Run the script on the service node
./
$1
||
true
exit
0
bin/acme-output.sh
View file @
84106ab3
...
...
@@ -3,7 +3,7 @@
set
-e
function
usage
()
{
echo
"Usage:
$0
-stage N"
echo
"Usage:
$0
-case CASENAME
-stage N"
}
if
[
$#
-eq
0
]
;
then
...
...
@@ -13,6 +13,10 @@ fi
while
[
$#
-ne
0
]
;
do
case
"
$1
"
in
-case
)
shift
CASENAME
=
$1
;;
-stage
)
shift
STAGE
=
$1
...
...
@@ -25,36 +29,41 @@ while [ $# -ne 0 ]; do
shift
done
if
[
-z
"
$CASENAME
"
]
;
then
echo
"ERROR: Specify -casename"
usage
exit
1
fi
if
[
-z
"
$STAGE
"
]
;
then
echo
"ERROR: Specify -stage"
usage
exit
1
fi
# Get the case name
CASE
=
$(
./xmlquery CASE
-valonly
-silent
)
# Get the full path to the run directory
RUNDIR
=
$(
./xmlquery RUNDIR
-valonly
-silent
)
RUNDIR
=
$(
cd
$RUNDIR
&&
pwd
)
CASEROOT
=
$PWD
/
$CASENAME
# Get the workflow scratch directory
DIR
=
$(
pwd
)
# Make the stage output dir
STAGEDIR
=
$DIR
/
${
CASE
}
-stage
${
STAGE
}
STAGEDIR
=
$DIR
/
${
CASE
NAME
}
-stage
${
STAGE
}
mkdir
$STAGEDIR
# Get the full path to the run directory
RUNDIR
=
$(
cd
$CASEROOT
&&
./xmlquery RUNDIR
-valonly
-silent
)
RUNDIR
=
$(
cd
$RUNDIR
&&
pwd
)
# Touch this file here so that it will always exist, even if it is empty
# for the first stage
touch
outputs_to_ignore
# For each of the new files
for
f
in
$(
ls
${
RUNDIR
}
/
${
CASE
}
.
*
${
RUNDIR
}
/
*
.log.
*
.gz
${
RUNDIR
}
/rpointer.
*
|
grep
-v
-f
outputs_to_ignore
)
;
do
for
f
in
$(
ls
${
RUNDIR
}
/
${
CASE
NAME
}
.
*
${
RUNDIR
}
/
*
.log.
*
.gz
${
RUNDIR
}
/rpointer.
*
|
grep
-v
-f
outputs_to_ignore
)
;
do
# Symlink it to the output dir
ln
-s
$f
${
STAGEDIR
}
/
$(
basename
$f
)
done
# Update the ignore file to ignore outputs from the current stage
ls
${
RUNDIR
}
/
${
CASE
}
.
*
${
RUNDIR
}
/
*
.log.
*
>
outputs_to_ignore
ls
${
RUNDIR
}
/
${
CASE
NAME
}
.
*
${
RUNDIR
}
/
*
.log.
*
>
outputs_to_ignore
bin/acme-run.sh
View file @
84106ab3
#!/bin/bash
#!/bin/bash
-l
set
-e
function
usage
()
{
echo
"Usage:
$0
[-continue] -stage N -stop STOP_OPTION -n STOP_N"
echo
"Usage:
$0
[-continue]
-case CASENAME
-stage N -stop STOP_OPTION -n STOP_N"
}
if
[
$#
-eq
0
]
;
then
...
...
@@ -14,6 +14,10 @@ fi
CONTINUE_RUN
=
FALSE
while
[
"$#"
-ne
0
]
;
do
case
"
$1
"
in
-case
)
shift
CASENAME
=
$1
;;
-continue
)
CONTINUE_RUN
=
TRUE
;;
...
...
@@ -37,11 +41,18 @@ while [ "$#" -ne 0 ]; do
shift
done
echo
CASENAME
$CASENAME
echo
STOP_N
$STOP_N
echo
STOP_OPTION
$STOP_OPTION
echo
CONTINUE_RUN
$CONTINUE_RUN
echo
STAGE
$STAGE
if
[
-z
"
$CASENAME
"
]
;
then
echo
"ERROR: Specify -case"
usage
exit
1
fi
if
[
-z
"
$STAGE
"
]
;
then
echo
"ERROR: Specify -stage"
usage
...
...
@@ -60,6 +71,14 @@ if [ -z "$STOP_OPTION" ]; then
exit
1
fi
export
CASENAME
export
CASEROOT
=
$PWD
/
$CASENAME
cd
$CASENAME
# Make sure that the run directory is correct
./xmlchange
-file
env_run.xml
-id
RUNDIR
-val
$CASEROOT
/run
# We never want to resubmit the jobs in the Pegasus workflow
./xmlchange
-file
env_run.xml
-id
RESUBMIT
-val
0
...
...
@@ -78,12 +97,9 @@ fi
./xmlchange
-file
env_run.xml
-id
CHECK_TIMING
-val
FALSE
./xmlchange
-file
env_run.xml
-id
SAVE_TIMING
-val
FALSE
# Get the case name
CASE
=
$(
./xmlquery CASE
-valonly
-silent
)
# This script often returns non-zero, so we need to mask the failure
# We use exitcode.successmessage to detect failures
./
$CASE
.run
||
true
/bin/csh
./
$CASE
NAME
.run
||
true
exit
0
Write
Preview
Supports
Markdown
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!
Cancel
Please
register
or
sign in
to comment