...
Set
...
up
...
a
...
working
...
area
...
on
...
linux
...
- I
...
- set
...
- up
...
- an
...
- area
...
- in
...
- my
...
- Glast
...
- Users
...
- area
...
- . For example
No Format $USHERNFS/RealData
...
...
where
...
- USHERNFS
...
- is
...
- /nfs/slac/g/glast/users/glground/usher
...
- Use
...
- this
...
- space
...
- to
...
- store
...
- the
...
- top
...
- level
...
- job
...
- options
...
- file
...
- for
...
- controlling
...
- the
...
- job
...
- (I
...
- still
...
- rely
...
- on
...
- the
...
- basicOptions
...
- file
...
- as
...
- much
...
- as
...
- possible)
...
Setting
...
up
...
the
...
environment
...
- Set
...
- CMTPATH.
...
- Here
...
- it
...
- is
...
- convenient
...
- to
...
- point
...
- to
...
- one
...
- of
...
- the
...
- builds
...
- already
...
- done
...
- for
...
- us
...
- by
...
- the
...
- Release
...
- Manager.
...
- You
...
- can
...
- find
...
- the
...
- specific
...
- paths
...
- on
...
- the
...
...
...
...
- .
...
- Pick
...
- one
...
- of
...
- the
...
- builds
...
- and
...
- you
...
- will
...
- see
...
- the
...
- path
...
- to
...
- it
...
- on
...
- the
...
- resulting
...
- page.
...
- Set
...
- the
...
- CMTPATH:
...
in
...
- csh:
No Format setenv CMTPATH
...
/nfs/farm/g/glast/u09/builds/rh9_gcc32/GlastRelease/GlastRelease-
...
in bash:v6r0No Format CMTPATH=/nfs/farm/g/glast/u09/builds/rh9_gcc32/GlastRelease/GlastRelease-
...
v6r0; export CMTPATH
...
- Setup
...
- the
...
- Gleam
...
- environment.
...
- Batch
...
- jobs
...
- inherit
...
- the
...
- environment
...
- of
...
- the
...
- submitting
...
- process.
...
- So,
...
- "source"
...
- the
...
- setup
...
- file
...
- (note
...
- that
...
- you
...
- will
...
- need
...
- to
...
- check
...
- the
...
- Gleam
...
- version
...
- number
...
- to
...
- do
...
- this):
...
in
...
- csh:
...
No Format source $CMTPATH/Gleam/(gleam version)/cmt/setup.csh
...
in
...
- bash:
...
No Format source $\{CMTPATH}/Gleam/(gleam version)/cmt/setup.sh
...
- Setup
...
- the
...
- top
...
- level
...
- job
...
- options
...
- environment
...
- variable
...
- to
...
- point
...
- to
...
- your
...
- top
...
- level
...
- job
...
- options
...
- file.
...
- For
...
- example:
...
in
...
- csh:
...
No Format setenv JOBOPTIONS $USHERNFS/RealData/readdigi_runrecon.txt
...
in
...
- bash:
...
No Format JOBOPTIONS=$\{USHERNFS}/RealData/readdigi_runrecon.txt; export JOBOPTIONS;
- Before you can run a job you need to reset the permissions (why?)
No Format chmod u+=rwx *
...
does the trick for me.chmod g+=rw *
Submit the batch job
- Use "bsub" to submit to the batch system (see the Glast batch farm page for more information):
No Format bsub -q long -o $USHERNFS/RealData/recon.out -R rhel4 $CMTPATH/Gleam/
...
v5r8p1/rh9_gcc32/Gleam.exe
...
- use "bjobs" to check on the status of the job
In theory this can be done from a shell script...
- But I could not get the following to work. Basically, when I source readdigi_runrecon.csh it tells me that it can't find Gleam, essentially because the CMTPATH is undefined.
What can I say other than it is for these types of reasons that I don't like linux...
| No Format |
|---|
#!/bin/csh
#
#echo 'Default read digi - run recon starting at:' ; date
#
unsetenv LD_LIBRARY_PATH
setenv CMTPATH /nfs/farm/g/glast/u09/builds/rh9_gcc32/GlastRelease/GlastRelease-HEAD1.420
pushd $CMTPATH/Gleam/v5r8p1/cmt
source setup.csh
#
popd
setenv JOBOPTIONS $USHERNFS/RealData/readdigi_runrecon.txt
bsub -q xlong -G glastgrp -o $USHERNFS/RealData/recon.out $CMTPATH/Gleam/v5r8p1/rh9_gcc32/Gleam.exe
#
#echo 'Default read digi - run recon ending at:' ; date
|