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

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

This guide is modified from section (d) of the worksheet inside Module 10 of Phys 6810 Computational Physics (Spring 2023).

NOTE: gprof does not work on macOS. Please use a linux machine (such as OSC)

To use gprof, compile and link the relevant codes with the -pg option:
Take a look at the Makefile make_hello_world and modify both the CFLAGS and LDFLAGS lines to include -pg

Compile and link the script by typing
    make -f make_hello_world

Execute the program
    ./hello_world.x

With the -pg flags, the execution will generate a file called gmon.out that is used by gprof.
The program has to exit normally (e.g. we can't stop with a ctrl-C).
Warning: Any existing gmon.out file will be overwritten.

Run gprof and save the output to a file (e.g., gprof.out) by
    gprof hello_world.x > gprof.out

We should at this point see a text file called gprof.out which contains the profile of hello_world.cpp
    vim gprof.out

# 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!

First try reading and following the instructions here

https://u.osu.edu/icemc/new-members-readme/

Then e-mail me at oindreeb@gmail.com with your problems 

Disclaimer: I wrote this for Owens, which I think will also work on Pitzer. I recommend following Steven's instructions, and use mine if it fails to build. J

1. Submit a batch job so the processing resources are not limited (change the project ID if needed.):

qsub -A PAS0654 -I -l nodes=1:ppn=4,walltime=2:00:00

2. Reset and load the following modules (copy and paste as it is):

module reset
module load cmake/3.7.2
module load python/2.7.latest
module load fftw3/3.3.5

3. Do echo $FFTW3_HOME and make sure it spits out "/usr/local/fftw3/intel/16.0/mvapich2/2.2/3.3.5". If it doesn't, do 

export FFTW3_HOME=/usr/local/fftw3/intel/16.0/mvapich2/2.2/3.3.5

Otherwise, just do

export FFTW_DIR=$FFTW3_HOME

4.  Do (Change DCMAKE_INSTALL_PREFIX and point it to the root source directory)

cmake -DCMAKE_C_COMPILER=`which gcc` \
-DCMAKE_CXX_COMPILER=`which g++` \
-DCMAKE_INSTALL_PREFIX=${HOME}/local/oakley/ROOT-6.12.06 \
-DBLAS_mkl_intel_LIBRARY=${MKLROOT}/lib/intel64 \
../root-6.12.06 2>&1 | tee cmake.log

It will configure root so it can be installed in the machine (takes about 5 minutes).

5. Once it is configured, do the following to build root (takes about 45 min)

make -j4 2>&1 | tee make.log

6. Once it's done, do 

make install

In order to run it, now go into the directory, then cd bin. Once you're in there you should see a .sh called 'thisroot.sh'. Type 'source thisroot.sh'. You should now be able to type 'root' and it will run. Note that you must source this EVERY time you log into OSC. The smart thing to do would be to put this into your bash script. 

(Second procedure from S. Prohira)

1. download ROOT: https://root.cern.ch/downloading-root (whatever the latest pro release is)

2. put the source tarball somewhere in your directory on ruby and expand it into the "source" folder

3. on ruby, open your ~/.bashrc file and add the following lines:

export CC="/usr/local/gnu/7.3.0/bin/gcc"
export CXX="/usr/local/gnu/7.3.0/bin/g++"
module load cmake
module load python
module load gnu/7.3.0

4. then run: source ~/.bashrc

5. make a "build" directory somewhere else on ruby called 'root' or 'root_build' and cd into that directory.

6. do: cmake /path/to/source/folder (e.g. the folder you expanded from the .tar file above. should finish with no errors.) here you can also include the -D flags that you want (such as minuit2 for the anita tools)
   -for example, the ANITA tools need you to do: cmake -Dminuit2:bool=true /path/to/source/folder.

7. do: make -j4 (or the way that Jorge did it above, if you want to submit it as a batch job (and not be a jerk running a job on the login nodes like i did))

8. add the following line to your .bashrc file (or .profile, whatever startup file you prefer):

source /path/to/root/build/directory/bin/thisroot.sh

9. enjoy root!

Source the attached env.sh file. Good to go!

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

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.

Attached is a set of slides on Getting Started with QC, a simulation monitoring project.  It has instructions on getting started in using a terminal window, and downloading, compiling and running AraSim, the simulation program for the ARA project.  AraSim has moved from the SVN repository to github, and so now you should be able to retrieve it, compile it using:

git clone https://github.com/ara-software/AraSim.git
cd AraSim
make
./AraSim

It will run without arguments, but the output might be silly. You can follow the instructions for running AraSim that are in the qc_Intro instructions, which will give them not silly results.  Those parts are still correct.

You might get some const expr errors if you are using ROOT 6, such as the ones in the first screen grab below.  As mentioned in the error messages, you need to change from const expr to not.  A few examples are shown in the next screen grab.

If you are here, you likely would also want to know how to install the prerequisites themselves. You might find this entry helpful then: http://radiorm.physics.ohio-state.edu/elog/How-To/4. It is only technically applicable to an older version that is designed for compatibility with ROOT5, but it will give you the idea.

These instructions are also superceded by an updated presentation at http://radiorm.physics.ohio-state.edu/elog/How-To/38

So, icemc has some needs (like Mathmore) and preferably root 6 that aren't installed on kingbeen and unity.

Here's what I did to get icecmc running on kingbee.

Throughout, $HOME=/home/clark.2668

• Try to install new version fo ROOT (6.08.06, which is the version Jacob uses on OSC) with CMAKE. Failed because Kingbee version of cmake is too old.
• Downloaded new version of CMAKE (3.11.0), failed because kingbee doesn't have C++11 support.
• Downloaded new version of gcc (7.33) and installed that in $HOME/QCtools/source/gcc-7.3. So I installed it "in place".
• Then, compiled the new version of CMAKE, also in place, so it's in $HOME/QCtools/source/cmake-3.11.0.
• Then, tried to compile ROOT, but it got upset because it couldn't find CXX11; so I added "export CC=$HOME/QCtools/source/gcc-7.3/bin/gcc" and then it could find it.
• Then, tried to compile ROOT, but couldn't because ROOT needs >python 2.7, and kingbee has python 2.6.
• So, downloaded latest bleeding edge version of python 3 (pyton 3.6.5), and installed that with optimiation flags. It's installed in $HOME/QCtools/tools/python-3.6.5-build.
• Tried to compile ROOT, and realized that I need to also compile the shared library files for python. So went back and compiled with --enable-shared as an argument to ./configure.
• Had to set the python binary, include, and library files custom in the CMakeCache.txt file.

Follow the instructions in the attached "getting_started_with_anita.pdf" file to download icemc, compile it, generate results, and plot those results.

Follow the instructions in the attached "getting_started_with_ara.pdf" file to download AraSim, compile it, generate results, and plot those results.

These are instructions I wrote for Rishabh Khandelwal to facilitate a "fast" start on Oakley at OSC. It was to help him run AraSim in batch jobs on Oakley.

It basically has you use software dependencies that I pre-installed on my OSC account at /users/PAS0654/osu0673/PhasedArraySimulation.

It also gives a "batch_processing" folder with examples for how to successfully run AraSim batch jobs (with correct output file management) on Oakley.

Sourcing these exact dependencies will not work on Owens or Ruby, sorry.

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/

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.

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)

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.

These documents contain information on how to run IceCube/ARA coincidence simulations and analysis. All technical information of where codes are stored and how to use them is detailed in the technical note. Other supportive information for physics understanding is in the powerpoint slides. The technical note will direct you to other documents in this elog in the places where you may need supplemental information.