Analysis How-To » History » Revision 14
Revision 13 (Richard Trotta, 04/30/2019 03:52 PM) → Revision 14/18 (Richard Trotta, 04/30/2019 03:53 PM)
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/
** 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.