# Installing AraSim on OSC

Readding this because I realized it was deleted when I went looking for it

Quick Links:
- https://github.com/ara-software/AraSim # AraSim github repo (bottom has installation instructions that are sort of right)
- Once AraSim is downloaded: AraSim/UserGuideTex/AraSimGuide.pdf (manual for AraSim) might have to be downloaded if you can't view pdf's where you write code

Step 1: 
We need to add in the dependancies. AraSim needs multiple different packages to be able to run correctly. The easiest way on OSC to get these without a headache is to add the following to you .bashrc for your user.

cvmfs () {
    module load gnu/4.8.5
    export CC=`which gcc`
    export CXX=`which g++`
    if [ $# -eq 0 ]; then
        local version="trunk"
    elif [ $# -eq 1 ]; then
        local version=$1
    else
        echo "cvmfs: takes up to 1 argument, the version to use"
        return 1
    fi
    echo "Loading cvmfs for AraSim"
    echo "Using /cvmfs/ara.opensciencegrid.org/${version}/centos7/setup.sh"
    source "/cvmfs/ara.opensciencegrid.org/${version}/centos7/setup.sh"
    #export JUPYTER_CONFIG_DIR=$HOME/.jupyter
    #export JUPYTER_PATH=$HOME/.local/share/jupyter
    #export PYTHONPATH=/users/PAS0654/alansalgo1/.local/bin:/users/PAS0654/alansalgo1/.local/bin/pyrex:$PYTHONPATH
}

If you want to view my bashrc
- /users/PAS1977/jacobweiler/.bashrc

Reload .bashrc
- source ~/.bashrc

Step 2:
Go to directory that you want to put AraSim and type: 
- git clone https://github.com/ara-software/AraSim.git
This will download the github repo

Step 3:
We need to use make and load sourcing
- cd AraSim
- cvmfs
- make
wait and it should compile the code 

Step 4:
We want to do a test run with 100 neutrinos to make sure that it does *actually* run
Try: - ./AraSim SETUP/setup.txt
This errored for me (probably you as well) 
Switch from frequency domain to time domain in the setup.txt
- cd SETUP
- open setup.txt 
- scroll to bottom
- Change SIMULATION_MODE = 1
- save
- cd .. 
- ./AraSim SETUP/setup.txt 
This should run quickly and now you have AraSim setup!

Log into kingbee.mps.ohio-state.edu first, then log into radiorm.physics.ohio-state.edu.

From Keith Stewart 03/16/17:  It appears that radiorm SSH from offsite is closed. So you will need to be on an OSU network physically or via VPN. fox is also blocked from offsite as well. Kingbee should still be available for now. If you want to use it as a jump host to get to radiorm without VPN. However, you will want to get comfortable with the VPN before it is a requirement.

Carl 03/16/17:  I could log in even while using a hard line and plugged in directly to the network.

From Bryan Dunlap 12/16/17:  I have set up the group permissions on the elog directory so you and your other designated people can edit files.  I have configured sudo to allow you all to restart the elogd service.  Once you have edited the file [/home/elog/elog.cfg I think], you can then type

sudo /sbin/service elogd restart

to restart the daemon so it re-reads the config. Sudo will prompt you for your password before it executes the command.

One really useful thing in here is how to describe "Value Added" to visitors.

Okay, so our group has two "project" spaces on OSC (the Ohio Supercomputer). The first is for Amy's group, and is a project workspace called "PAS0654". The second is the CCAPP Condo (literally, CCAPP has some pre-specified rental time, and hence "condo") on OSC, and this is project PCON0003.

When you are signed up for the supercomputer, one of two things happen:

1. You will be given a username under the PAS0654 group, and in which case, your username will be something like osu****. Connolly home drive is /users/PAS0654/osu****. Beatty home drive is /users/PAS0174/osu****. CCAPP home drive is /users/PCON0003/pcon****.
2. You will be given a username under the PCON0003 group, and in which case, your username will be something like cond****.

If you are given a osu**** username, you must make sure to be added to the CCAPP Condo so that you can use Ruby compute resources. It will not be automatic.

Some current group members, and their OSC usernames. In parenthesis is the project space they are found in.

Current Users

osu0673: Brian Clark (PAS0654)

cond0068: Jorge Torres-Espinosa (PCON0003)

osu8619: Keith McBride (PAS0174)

osu9348: Julie Rolla (PAS0654)

osu9979: Lauren Ennesser (PAS0654)

osu6665: Amy Connolly (PAS0654)

Past Users

osu0426: Oindree Banerjee (PAS0654)

osu0668: Brian Dailey (PAS0654)

osu8620: Jacob Gordon (PAS0174)

osu8386: Sam Stafford (ANITA analysis in /fs/scratch/osu8386) (PAS0174)

cond0091: Judge Rajasekera (PCON0003)

So, ARA has five stations down in the ice that are taking data. Weekly, a member of the collaboration checks on the detectors to make sure that they are healthy.

This means things like making sure they are triggering at approximately the right rates, are taking cal pulsers, that the box isn't too hot, etc.

Here are some resources to get you started. Usual ara username and password apply in all cases.

• On this page, you can scroll down to "Monitoring Shifts": http://ara.icecube.wisc.edu/wiki/index.php/ARA_Operations
• This is a link to an example report with very nice commentary about what to expect as normal, etc: http://ara.physics.wisc.edu/docs/0016/001610/002/edited_notes_for_monitoring_report.pdf
• This is a link to another example report that is considered typical: http://ara.physics.wisc.edu/docs/0013/001317/001/Monitor-May-11_May-18.pdf
• And another: http://ara.physics.wisc.edu/cgi-bin/DocDB/ShowDocument?docid=1616

Also, the page where all of the plots live is here: http://aware.wipac.wisc.edu/

Thanks, and good luck monitoring! Ask someone whose done it before when in doubt.

Brian

PDF of advice by Andy Buckley (U Glasgow) on writing a HEP thesis (and presumably HEP papers too) that was forwarded by John Beacom to the CCAPP mailing list a few months back. 

If an undergrad has been working with the group on a volunteer basis, they will need that clarified, so that they have not up to then we working for pay without training.  There is a form that they sign saying they have been working as a volunteer.

Below is an email that Pam sent in July 2019 outlining what they need.  Other things to remember:

Undergrads receive emails from the department to remind them about orientation and scheduling prior to first day of hire, and other emails from ASC. They receive more information at orientation.

They will need to show ID.  

If an undergrad (or any hire) does not waive retirement/OPERs within 30 days, they will have to have this deducted from their paycheck. This is another reason that orientation is important.
 
For the person hiring them:
 
1.      Tell your admin (Lisa) asap who, when, etc you want to hire. ASAP is important because (Pam) will process over 75 undergraduates hires in the Fall and over 100 in the summer. Each takes 20 days on average (see below)
2.      On the first day of employment – ask your new hire if they have completed their orientation with the ASC.
 

From: Hood, Pam 
Sent: Tuesday, July 23, 2019 4:49 PM
To: 'physics-all@lists.osu.edu' <physics-all@lists.osu.edu>
Subject: Undergraduate Fall Hires
 
Hello all,
 
Fall is almost upon us and I am working on having positions ready to fill as well as posting on the OSU student job site and Federal Work study job boards. In order to plan my workflow, if you would let me know:
 
1.      Approximately how many undergraduate student assistants you plan to hire and at what rate of pay. Our department’s current average rate of pay is $10.00 - $10.50/hour, however it does depend on the position. Range is $8.55 - $14.00/hour.
 
2.      A brief summary of job duties and responsibilities (i.e. assisting in research for ______)
 
3.      Request for posting OR
 
4.      If you have specific student that has been a non-paid volunteer that you would like to hire, they need to sign a waiver prior to orientation.  Please see attached for volunteer waiver.
 
5.      Please indicate if your start date varies from August 20. And it may vary based on multiply factors i.e. signatures, workflow, etc.
 
6.      All terminations for summer ungraduated student workers OR
 
7.      If you are intending to continue employment but require a reduction in hours worked in order to comply with policy Please see attached policy for min/max hours.
 
 
I have attempted to answer all the FAQs that I noted in the “summer undergraduate hiring wave” in italics, however please let me know if you have questions. As always, it is ASC policy to not start any employee prior to orientation and it will take a minimum of 10 days from the time the contract is signed by both the student and the supervisor– please encourage your students to sign asap or it lengthens the process significantly.
 
I will do my best to facilitate this process for you. Students Buck ID# and email is extremely helpful. If you need the hire to start August 20, please send me the information via email by July 31, 2019. If you respond later or request a hire after July 31, I will estimate the hire date at the time of submittal.
 
Thanks,
 
Pam

Here is a useful link for astroparticle grad students related proposals from NASA:

https://nspires.nasaprs.com/external/solicitations/summary.do?solId=%7BE16CD59F-29DD-06C0-8971-CE1A9C252FD4%7D&path=&method=init

Full email I received regarding this information was:

_______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________

ROSES-19 Amendment adds a new program element to ROSES-2019: Future Investigators in NASA Earth and Space Science and Technology (FINESST), the ROSES Graduate Student Research Program Element, E.6.

Through FINESST, the Science Mission Directorate (SMD) solicits proposals from accredited U.S. universities and other eligible organizations for graduate student-designed and performed research projects that contribute to SMD's science, technology and exploration goals.

A Notice of Intent is not requested for E.6 FINESST. Proposals to FINESST are due by February 4, 2020.

Potential proposers who wish to participate in the optional pre-proposal teleconference December 2, 2019 from 1:00-2:30 p.m. Eastern Time may (no earlier than 30 minutes prior to the start time) call 1-888-324-3185 (U.S.-only Toll Free) or 1-630-395-0272 (U.S. Toll) and use Participant Passcode: 8018549. Restrictions may prevent the use of a toll-free number from a mobile or free-phone or from telephones outside the U.S. For U.S. TTY-equipped callers or other types of relay service no earlier than 30 minutes before the start of the teleconference, call 711 and provide the same conference call number/passcode. Email HQ-FINESST@mail.nasa.gov any teleconference agenda suggestions and questions by November 25, 2019. Afterwards, questions and responses, with identifying information removed, will be posted on the NSPIRES page for FINESST under "other documents".

FINESST awards research grants with a research mentor as the principal investigator and the listed graduate student listed as the "student participant". Unlike the extinct NASA Earth and Space Science Fellowships (NESSF), the Future Investigators (FIs) are not trainees or fellows. Students with existing NESSF awards seeking a third year of funding, may not submit proposals to FINESST. Instead, they may propose to NESSF20R. Subject to a period of performance restriction, some former NESSFs may be eligible to submit proposals to FINESST.

On or about November 1, 2019, this Amendment to the NASA Research Announcement "Research Opportunities in Space and Earth Sciences (ROSES) 2019" (NNH19ZDA001N) will be posted on the NASA research opportunity homepage at http://solicitation.nasaprs.com/ROSES2019 and will appear on the RSS feed at: https://science.nasa.gov/researchers/sara/grant-solicitations/roses-2019/

Questions concerning this program element may be directed to HQ-FINESST@mail.nasa.gov.

Here is an old email thread about how to ship a station to Pole.

Bought 951 Non-Resin Soldering Flux. This is the preferred variety. This could be found on this website https://www.kester.com/products/product/951-soldering-flux. 

The amount of Flux that was bought was 1 Gallon (Lasts quite some time). The price was $83.86 with approximate shipping of $43. This was done with a Pcard and a tax exempt form. 

The website used to purchase this was https://www.alliedelec.com/kester-solder-63-0000-0951/70177935/

If you are trying to use the Ray Trace Correlator with AraRoot, you will probably encounter some issues as you go. Here is some advice that Carl Pfendner found, and Brian Clark compiled.

Please note that it is extremely important that your AntennaInfo.sqlite table in araROOT contain the ICRR versions of both Testbed and Station1. Testbed seems to have fallen out of practice of being included in the SQL table. Also, Station1 is the ICRR (earliest) version of A1, unlike the ATRI version which is logged as ARA01. This will cause seg faults in the intial setup of the timing and geometry arrays that seem unrelated to pure geometry files. If you get a seg-fault in the "setupSizes" function or the Detector call of the "setupPairs" function, checking your SQL file is a good idea. araROOT branch 3.13 has such a source table with Testbed and Station1 included.

Which combination of Makefile/Makefile.arch/StandardDefinitions.mk works can be machine specific (frustratingly). Sometimes the best StandardDefinitions.mk is found int he make_timing_arrays example.

Common Things to Check

1: Did you "make install" the Ray Trace Correlator after you made it?

2: Do you have the setup.txt file?

3: Do you have the "data" directory?

Common Errors

1: If the Ray Trace Correlator compiles, and you execute a binary, and get the following:

     ******** Begin Correlator ********, this one!
     Pre-icemodel test
     terminate called after throwing an instance of 'std::out_of_range'
     what():  basic_string::substr
     Aborted

Check to make sure have the "data" directory.
 

Sometimes you need to fit a function to a histogram in ROOT. Attached is code for how to do that in the simple case of a power law fit.

To run the example, you should type "root fitSnr.C" in the command line. The code will access the source histogram (hstrip1nsr.root, which is actually ANITA-2 satellite data). The result is stripe1snrfit.png.

On Nov 28 2017, Brian Connolly came and visited and taught us how to do basic data analysis in R.

He in particular showed us how to do a Linear Discriminant Analysis (LDA) and Principal Component Analysis (PCA).

Attached are three of the data files Carl Pfendner prepared for us to analyze (ARA data, including simulation, force triggers, and RF triggers).

Also attached is some R code that shows how to set up the LDA and the PCA and how to plot their result. You are meant to run each line of the code in r by hand (this is not a functioning R script I don't think).

Go here (https://www.r-project.org/) to learn how to download R. You will also probably have to download GGFortify. To do that, open an r session, and type "install.packages('ggfortify')".

Quick C++ program for pulling waveforms out of deep ARA station data. If you are using AraRoot, you would put this inside your "analysis" directory and add it to your CMakeLists.txt.

Here is some C++ code and an associated makefile to find effective volumes from AraSim output files.

It computes error bars on the effective volumes using the relevant AraSim function.

Compile like "make -f veff.mk"

Run like "./veff thrown_radius thrown_depth AraOut.1.root AraOut.2.root...."

Attaching some scripts that help processing the effective volumes. This is an extension of what Brian Clark did in a previous post (http://radiorm.physics.ohio-state.edu/elog/How-To/27)

There are 4 files attached:

- veff_aeff2.C and veff_aeff2.mk. veff_aeff2.C produces Veff_des$1.txt ($1 can be A or B or C). This file contains the following columns: energy, veff, veff_error, veff1 (PA), veff2 (LPDA), veff3 (bicone), respectively. However, the energies are not sorted.

-veff.sh: this bash executable runs veff_aeff2.C for all (that's what the "*" in the executable is for) the root output files, for a given design (A, B, C). You need to modify the location of your output files, though. Run like "./veff.sh A", which will execute veff_aeff2.C and produce the veff text files. Do the same for B or C.

-make_plot.py: takes Veff_des$1.txt, sorts energies out, plots the effective volumes vs. energies, and produces a csv file containing the veffs (just for the sake of copying and pastting on the spreadsheets). Run like "pyhton make_plot.py".

Say you want to plot two TH2Ds with on the same pad but different color paletettes?

This is possible, but requires a touch of fancy ROOT-ing. Actually, it's not that much, it just takes a lot of time to figure it out. So here it is.

Fair warning, the order of all the gPad->Modified's etc seems very important to no seg fault.

In include the main (demo.cc) and the Makefile.

PBS has the option of having arrays of jobs in case you want to easily submit multiple similar jobs. The only difference in them is the array index, which you can use in your PBS script to run each task with a different set of input arguments, or any other operation that requires a unique index.

You need to add the following lines to your submitter file:

#PBS -t array_min-array_max%increment

#PBS -t 1-100%5

For Mac and Windows:

https://osuasc.teamdynamix.com/TDClient/KB/ArticleDet?ID=14542
For Linux, in case some of your students need it:

https://osuasc.teamdynamix.com/TDClient/KB/ArticleDet?ID=17908

From Sam 01/25/17:  It doesn't work from my Ubuntu 14 machine.  My VPN setup in 14 does not have the "Software Token Authentication" option on the screen as shown in the instructions.  It fails on connection attempt.  
The instructions specify Ubuntu 16; perhaps there is a way to make it work on 14, but I don't know what it is.