Kaon_LT Experiment

h1. Analysis How-To

{{>toc}}

h2. How should I analyze data?

* Doing things locally will always be your best option for actual analysis. 

** Fork a repo of hallc_replay_kaonlt %{color:red}and% UTIL_KAONLT for your own custom version that you can play with

!fork.png!

* Once you have forked the repo, clone hallc_replay_kaonlt to a local directory

<pre><code class="bash">

$USER> git clone https://github.com/USER/hallc_replay_kaonlt.git

</code></pre>

* Now the tricky part, UTIL_KAONLT is a submodule of hallc_replay_kaonlt so some intermediate steps will need to be made

<pre><code class="bash">

$USER/hallc_replay> git submodule --init --recursive

</code></pre>

** Check .gitmodules to make sure submod is listed

<pre><code class="bash">

[submodule "UTIL_KAONLT"]

     path = UTIL_KAONLT

     url = https://github.com/USER/UTIL_KAONLT

     branch = <branchname>

</code></pre>

<pre><code class="bash">

$USER/hallc_replay> git submodule update --recursive --remote

</code></pre>

* If HEAD is detached (check with git branch -a)

<pre><code class="bash">

$USER/hallc_replay> cd UTIL_KAONLT

$USER/hallc_replay/UTIL_KAONLT> git branch -a

* (HEAD detached at ###)

</code></pre>

* Check if head is really detached

<pre><code class="bash">

$USER/hallc_replay/UTIL_KAONLT> git symbolic-ref HEAD

fatal: ref HEAD is not a symbolic ref

</code></pre>

<pre><code class="bash">

$USER/hallc_replay/UTIL_KAONLT> git remote update

Fetching origin

</code></pre>

* Change to master branch

<pre><code class="bash">

$USER/hallc_replay/UTIL_KAONLT> git checkout master

Switched to branch 'master'

Your branch is up-to-date with 'origin/master'

</code></pre>

* Pull and check branch again, everything should be set!

<pre><code class="bash">

$USER/hallc_replay/UTIL_KAONLT> git pull

Already up-to-date

$USER/hallc_replay/UTIL_KAONLT> git branch -a

* master

</code></pre>

* 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)

<pre><code class="bash">

$USER/hallc_replay> git remote -v

origin https://github.com/USER/hallc_replay_kaonlt.git (fetch)

origin https://github.com/USER/hallc_replay_kaonlt.git (push)

</code></pre>

* Next lets set up the “upstream” which is the JeffersonLab repo (DO NOT push HERE)

<pre><code class="bash">

$USER/hallc_replay> git remote add upstream https://github.com/JeffersonLab/hallc_replay_kaonlt.git

$USER/hallc_replay> 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)

</code></pre>

* 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

<pre><code class="bash">

$USER/hallc_replay> git branch develop

$USER/hallc_replay> git checkout develop

M  UTIL_KAONLT

M  UTIL_OL

Switched to branch 'develop'

</code></pre>

* Now simply pull develop

<pre><code class="bash">

$USER/hallc_replay> git pull origin develop

</code></pre>

* To create a new branch you must first create it in github

!newbranch.png!

* Then simply repeat the steps for setting up a branch from the previous slide

h2. Getting .dat files from tape

* If *.dat for a particular run is not in /cache/hallc/spring17/raw follow the instructions below...

** In /cache/hallc.spring17/raw type: 

<pre>

> jcache get /mss/hallc/spring17/raw/<YourRawFile>.dat

</pre>

** This will take a little while to process. You can check the status of your process by typing:

<pre>

> jcache pendingRequest <JlabUserName>

</pre>

*->More information on using jcache can be found at* https://scicomp.jlab.org/docs/%20

h2. Replaying

* 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.

h2. Group environment

* 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).

h2. 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

h2. 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.