General Processes
for doing research
This page is for my own reference to recall oft-repeated tasks...
Logging onto Networks
Because I used to always forget the command!
To log in to OU: ssh -XY $user@ouhep02.nhn.ou.edu (or other OU HEP machines like 06)
I usually work in my user name's folder on /raid02 where there's lots of space.
To log in to LXPLUS (faster at CERN): ssh -XY $user@lxplus5.cern.ch
(be careful of the version that you log in to - ask someone since LXPLUS gets updated but not all associated packages might work with new versions)
A Great Statistics Course
These lectures by Roger Barlow given at SLAC are a pretty great overview of useful statistical methods. They follow well from his book, "Statistics: A Guide to the Use of Statistical Methods in the Physical Sciences".
How to Find and Check Out / Check In Athena Code
Basically: Use this great Twiki page!
To work with CERN code, first you might have to find it in the directory of version-controlled (SVN) Athena code.
1. Go to: https://svnweb.cern.ch/trac/atlasoff/browser
2. Click "log in" on the upper right, open a new tab and navigate to this link again. This extra step is due to a glitch in how SVN handles the browser.
3. Now you've reached the repository of code and can browse through it to find the code you want to check out.
To check out the code, use Bash to navigate to the location you want to place the code (such as testarea/17.3.4.8). If you haven't done so, first set up your directory:
asetup 17.3.4.8,here --dbrelease=current
Now use the cmt command to check out the code:
cmt co -r $branchname location/of/code
Here, $branchname represents the full name shown when you expand "branches", and location/of/code is the directory of code you want to check out, starting from ATLAS's root directory (shown as root/ at the top of the page - don't include the root/).
Can also check out code with the svn co command. In the location you want the code:
svn co svn+ssh://svn.cern.ch/reps/atlasoff/location/of/code/as/shown/in/trac/browser
At CERN, instead use this command:
svn co svn+ssh://svn.cern.ch/reps/atlasusr/location/of/code...
4. To check the code back in, use the commands on the twiki page...if working on branch (as I usually am), from the package directory (the folder that has the cmt, src, etc folders in it):
svn switch $SVNROOT/<path-to-package>/<package>/branches/<package>-ii-jj-kk-branch
where you can find the ii-jj-kk numbers to use in the online directory of Athena code.
Switching to the branch only has to be done once per login and automatically updates the branch as well.
Then commit the code as usual:
svn ci -m "commit message here"
If SVN says it found a conflict in the code, you can choose p to postpone the commit. Then navigate to the file with the conflict and edit it. The lines with >>>>> will show you the conflict. Edit the file to what you want it to be, save and close, re-compile the package to check for errors, then do:
svn resolved filelocation/filename.extension
To check the status of any other conflicting files, do: svn status
Then do the commit again.
Preparing to Run Athena Code
After setting up your environment as described in the ATLAS Software Training, do the following to prepare an lxplus session:
ssh -Yl $user@lxplus.cern.ch [note which lxplus node it logs into]
Whether you're working on LXPLUS or OUHEP, every time you log in you must run an asetup command (unless you've included it in a setup file) in order to run ATLAS code commands. To do this, navigate to your test area directory (such as .../$user/testarea), create a directory for the release you wish to run (such as 17.2.7.4.1) and type:
asetup 17.2.7.4.1
To run code:
- To run a make or a gmake, navigate to your cmt directory and type 'gmake clean' and then 'gmake'
(cmt config
required one time per checkout if you didn't use cmt co to check out)
- To run a python script or job options file directly, type
athena file.extension
(in the run directory)