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Analysis How-To » History » Version 11

Richard Trotta, 04/30/2019 01:56 PM

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h1. Analysis How-To
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h2. How should I analyze data?
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* Doing things locally will always be your best option for actual analysis. 
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** Fork a repo of hallc_replay_kaonlt %{color:red}and% UTIL_KAONLT for your own custom version that you can play with
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!fork.png!
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* Once you have forked the repo, clone hallc_replay_kaonlt to a local directory
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<pre><code class="bash">
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$USER> git clone https://github.com/USER/hallc_replay_kaonlt.git
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</code></pre>
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* Now the tricky part, UTIL_KAONLT is a submodule of hallc_replay_kaonlt so some intermediate steps will need to be made
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<pre><code class="bash">
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$USER/hallc_replay> git submodule --init --recursive
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</code></pre>
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** Check .gitmodules to make sure submod is listed
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<pre><code class="bash">
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[submodule "UTIL_KAONLT"]
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     path = UTIL_KAONLT
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     url = https://github.com/USER/UTIL_KAONLT
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     branch = <branchname>
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</code></pre>
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<pre><code class="bash">
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$USER/hallc_replay> git submodule update --recursive --remote
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</code></pre>
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* If HEAD is detached (check with git branch -a)
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<pre><code class="bash">
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$USER/hallc_replay> cd UTIL_KAONLT
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$USER/hallc_replay/UTIL_KAONLT> git branch -a
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* (HEAD detached at ###)
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</code></pre>
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* Check if head is really detached
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<pre><code class="bash">
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$USER/hallc_replay/UTIL_KAONLT> git symbolic-ref HEAD
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fatal: ref HEAD is not a symbolic ref
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</code></pre>
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<pre><code class="bash">
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$USER/hallc_replay/UTIL_KAONLT> git remote update
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Fetching origin
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</code></pre>
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* Change to master branch
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<pre><code class="bash">
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$USER/hallc_replay/UTIL_KAONLT> git checkout master
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Switched to branch 'master'
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Your branch is up-to-date with 'origin/master'
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</code></pre>
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* Pull and check branch again, everything should be set!
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<pre><code class="bash">
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$USER/hallc_replay/UTIL_KAONLT> git pull
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Already up-to-date
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$USER/hallc_replay/UTIL_KAONLT> git branch -a
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* master
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</code></pre>
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* Now that we have our repo locally we should set it up to pull from the “main” JeffersonLab version
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* First check your remote “origin” repo (this is where you will push to)
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<pre><code class="bash">
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$USER/hallc_replay> git remote -v
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origin https://github.com/USER/hallc_replay_kaonlt.git (fetch)
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origin https://github.com/USER/hallc_replay_kaonlt.git (push)
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</code></pre>
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* Next lets set up the “upstream” which is the JeffersonLab repo (DO NOT push HERE)
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<pre><code class="bash">
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$USER/hallc_replay> git remote add upstream https://github.com/JeffersonLab/hallc_replay_kaonlt.git
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$USER/hallc_replay> git remote -v
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origin https://github.com/USER/hallc_replay_kaonlt.git (fetch)
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origin https://github.com/USER/hallc_replay_kaonlt.git (push)
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upstream https://github.com/JeffersonLab/hallc_replay_kaonlt.git (fetch)
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upstream https://github.com/JeffersonLab/hallc_replay_kaonlt.git (push)
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</code></pre>
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* You will not be able to push to upstream unless you’re Stephen or me so don’t worry too much. Just be cautious.
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* A similar procedure can be performed with UTIL_KAONLT
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* Finally, let's talk about branches. Let’s add the develop branch to our local system…
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** First create a branch locally called develop and change to it
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<pre><code class="bash">
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$USER/hallc_replay> git branch develop
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$USER/hallc_replay> git checkout develop
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M  UTIL_KAONLT
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M  UTIL_OL
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Switched to branch 'develop'
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</code></pre>
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* Now simply pull develop
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<pre><code class="bash">
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$USER/hallc_replay> git pull origin develop
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</code></pre>
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* To create a new branch you must first create it in github
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!newbranch.png!
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* Then simply repeat the steps for setting up a branch from the previous slide
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h2. Getting .dat files from tape
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h1. Getting data from the MSS
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* If *.dat for a particular run is not in /cache/hallc/spring17/raw follow the instructions below...
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** In /cache/hallc.spring17/raw type: 
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<pre>
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> jcache get /mss/hallc/spring17/raw/<YourRawFile>.dat
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</pre>
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** This will take a little while to process. You can check the status of your process by typing:
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<pre>
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> jcache pendingRequest <JlabUserName>
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</pre>
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*->More information on using jcache can be found at* https://scicomp.jlab.org/docs/%20
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h2. Replaying
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* 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.
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* Before a batch submission, I highly encourage two preliminary steps
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## Do all debugging of replays locally, once this works move to the farm
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## 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)
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* 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.
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* Your final batch job submissions can be saved directly to tape.
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h2. Group environment
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* You can do replays under your farm directory or you can use our group environment.
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* 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).
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** This group environment is under /u/group/c-kaonlt
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** 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.
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** 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.
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* You may have issues with hcana, make sure you are in the JLab software environment version 2.1
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** source /site/12gev_phys/softenv.csh 2.1 (or .sh if using bash)
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* The group environment has a 100 gb quota and is backed up. This means two important things…
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## DO NOT save root files here! Ever!
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## It’s backed up so its good for important calibration work (*wink *wink)
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* 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).
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h2. Writing to tape
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* Writing to tape info, read - https://scicomp.jlab.org/docs/write-through-cache.
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* In your batch script, specify OUTPUT_FILE:/cache/hallc/kaonlt/USER/ROOTfiles/FILE.
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** Material in /cache is automatically copied to tape after some time if it is static
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** Small files (~1 MB) will not be backed up on tape
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** Once copied to tape, you can view the tape stub (NOT the file itself) under /mss/hallc/kaonlt/…
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** The tape does not handle overwriting well so if submit a job you must create a new "pass" directory…
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*** -->jput ... file.root /mss/hallc/kaonlt/USER/ROOTfiles/pass1/
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** The tape has FAR more space than we could get through so do not worry about "filling" it
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** Write to tape once you're happy with your code... just do it correctly
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h2. Few more words of warning
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* Do not write analysis to tape unless you are 100% certain it works correctly (and you don't want to repeat it very soon).
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* For farm jobs some info is included below -
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** See https://scicomp.jlab.org/docs/text_command_file for info on commands	
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** 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)
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** Farm/Auger project: c-kaonlt
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** For TEMPORARY output, write to volatile - /volatile/hallc/c-kaonlt/USER, this space is NOT backed up!
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** Specify the FULL path to this in your symbolic link
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** Make sure relvant directories are created
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* 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.