Analysis How-To » History » Revision 6
- Table of contents
- Analysis How-To
How should I analyze data?¶
- Doing things locally will always be your best option for actual analysis.
- Fork a repo of hallc_replay_kaonlt and UTIL_KAONLT for your own custom version that you can play with
- Once you have forked the repo, clone hallc_replay_kaonlt to a local directory
$USER> git clone https://github.com/USER/hallc_replay_kaonlt.git
- Now the tricky part, UTIL_KAONLT is a submodule of hallc_replay_kaonlt so some intermediate steps will need to be made
$USER> git submodule --init --recursive
- Check .gitmodules to make sure submod is listed
[submodule "UTIL_KAONLT"] path = UTIL_KAONLT url = https://github.com/USER/UTIL_KAONLT branch = <branchname>
$USER> git submodule update --recursive --remote
- Check .gitmodules to make sure submod is listed
- If HEAD is detached (check with git branch -a)
$USER> git branch -a * (HEAD detached at ###)
- Check if head is really detached
$USER> git symbolic-ref HEAD fatal: ref HEAD is not a symbolic ref
$USER> git remote update Fetching origin
- Change to master branch
$USER> git checkout master Switched to branch 'master' Your branch is up-to-date with 'origin/master'
- Pull and check branch again, everything should be set!
$USER> git pull Already up-to-date $USER> git branch -a * master
- Now that we have our repo locally we should set it up to pull from the “main” JeffersonLab version
- First check your remote “origin” repo (this is where you will push to)
$USER> git remote -v origin https://github.com/USER/hallc_replay_kaonlt.git (fetch) origin https://github.com/USER/hallc_replay_kaonlt.git (push)
- Next lets set up the “upstream” which is the JeffersonLab repo (DO NOT push HERE)
$USER> git remote add upstream https://github.com/JeffersonLab/hallc_replay_kaonlt.git $USER> git remote -v origin https://github.com/USER/hallc_replay_kaonlt.git (fetch) origin https://github.com/USER/hallc_replay_kaonlt.git (push) upstream https://github.com/JeffersonLab/hallc_replay_kaonlt.git (fetch) upstream https://github.com/JeffersonLab/hallc_replay_kaonlt.git (push)
- You will not be able to push to upstream unless you’re Stephen or me so don’t worry too much. Just be cautious.
- A similar procedure can be performed with UTIL_KAONLT
- Finally, let's talk about branches. Let’s add the develop branch to our local system…
- First create a branch locally called develop and change to it
- Now simply pull develop
- To create a new branch you must first create it in github
- Then simply repeat the steps for setting up a branch from the previous slide
- Before we can analyze we must replay. This should be done in the farm to save yourself time and local cpu effort. The easiest way is to do a batch job submission, but this comes with some prep work.
- Before a batch submission, I highly encourage two preliminary steps
- Do all debugging of replays locally, once this works move to the farm
- Once on the farm you have two options; your ifarm version or our group (discussed soon). This is for final debugging purposes to assure everything works in the farm, then you can submit a batch job. Save the root files in /volatile/hallc/c-kaonlt/<USER> (note: volatile is NOT backed up)
- There is a batch script I have created and Stephen as changed with the help of Brad to assure it will not mess things up. Again, I highly recommend the two above steps before moving onto this script or you will be wasting time and resources.
- Your final batch job submissions can be saved directly to tape.
- You can do replays under your farm directory or you can use our group environment.
- We have set up a group environment with a version of our repo that currently mimics the cdaq as close as possible (although an updated hcana is used).
- This group environment is under /u/group/c-kaonlt
- I have made a directory USERS which you can use for person replay scripts and environments. DO NOT change any replays that are not under USERS without contacting Stephen or me first.
- There is an hcana already set up here, use this for any group replays. If you would like to use a different version of hcana please use your farm directory. If I find a hcana in USERS I will destroy it.
- You may have issues with hcana, make sure you are in the JLab software environment version 2.1
- source /site/12gev_phys/softenv.csh 2.1 (or .sh if using bash)
- The group environment has a 100 gb quota and is backed up. This means two important things…
- DO NOT save root files here! Ever!
- It’s backed up so its good for important calibration work (*wink *wink)
- Upon the request of Stephen, any improper use of this environment will incur a penalty of one beer/bottle of single malt or an owl shift (depending upon severity).
Writing to tape¶
- Writing to tape info, read - https://scicomp.jlab.org/docs/write-through-cache.
- In your batch script, specify OUTPUT_FILE:/cache/hallc/kaonlt/USER/ROOTfiles/FILE.
- Material in /cache is automatically copied to tape after some time if it is static
- Small files (~1 MB) will not be backed up on tape
- Once copied to tape, you can view the tape stub (NOT the file itself) under /mss/hallc/kaonlt/…
- The tape does not handle overwriting well so if submit a job you must create a new "pass" directory…
- -->jput ... file.root /mss/hallc/kaonlt/USER/ROOTfiles/pass1/
- The tape has FAR more space than we could get through so do not worry about "filling" it
- Write to tape once you're happy with your code... just do it correctly
Few more words of warning¶
- Do not write analysis to tape unless you are 100% certain it works correctly (and you don't want to repeat it very soon).
- For farm jobs some info is included below -
- See https://scicomp.jlab.org/docs/text_command_file for info on commands
- Do not set CPU above 1 (it will slow your job down in the queue and hcana is single threaded anyway so you gain nothing)
- Farm/Auger project: c-kaonlt
- For TEMPORARY output, write to volatile - /volatile/hallc/c-kaonlt/USER, this space is NOT backed up!
- Specify the FULL path to this in your symbolic link
- Make sure relvant directories are created
- You can use our work environment (/work/hallc/kaon), but this is not backed up and I will no be setting up an environment similar to group there. It’s a good place to put personal scripts if you don’t want to take up space in your farm directory.