ELOG How-To

Jacob Weiler, How to install AraSim on OSC, Software

Wed, 12 Jun 2024 12:10:05 -0400

# 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 .b

Jason Yao, How to profile a C++ program, Software

Thu, 14 Sep 2023 22:30:06 -0400

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

Alan Salcedo , Doing IceCube/ARA coincidence analysis,

Thu, 08 Jun 2023 16:29:45 -0400

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.

William Luszczak, PUEO simulation stack installation instructions, Software

Mon, 24 Apr 2023 11:51:42 -0400

These are instructions I put together as I was first figuring out how to compile PueoSim/NiceMC. This was originally done on machines running CentOS 7, however has since been replicated on the OSC machines (running RedHat 7.9 I think?). I generally try to avoid any `module load` type prerequisites, instead opting to compile any dependencies from source. You _might_ be able to get this to work by `module load`ing e.g. fftw, but try this at your own peril.

#pueoBuilder Installation Tutorial

This tutorial will guide you through the process of building the tools included in pueoBuilder from scratch, including the prerequisites and any environment variables that you will need to set. This sort of thing is always a bit of a nightmare process for me, so hopefully this guide can help you skip some of the frustration that I ran into. I did not have root acces on the system I was building on, so the instructions below are what I had to do to get things working with local installations. If you have root access, then things might be a bit easier. For reference I'm working on CentOS 7, other operating systems might have different problems that arise.

##Prerequisites
As far as I can tell, the prerequisites that need to be built first are:

-Python 3.9.18 (Apr. 6 2024 edit by Jason Yao, needed for ROOT 6.26-14)
-cmake 3.21.2 (I had problems with 3.11.4)
-gcc 11.1.0 (9.X will not work) (update 4/23/24: If you are trying to compile ROOT 6.30, you might need to downgrade to gcc 10.X, see note about TBB in "Issues I ran into" at the end)
-fftw 3.3.9
-gsl 2.7.1 (for ROOT)
-ROOT 6.24.00
-OneTBB 2021.12.0 (if trying to compile ROOT 6.30)

###CMake
You can download the source files for CMake here: https://cmake.org/download/. Untar the source files with:

tar -xzvf cmake-3.22.1.tar.gz

Compiling CMake is as easy as following the directions on the website: https://cmake.org/instal

Alex M, OSC License Request,

Tue, 02 Aug 2022 14:34:15 -0400

Some programs on OSC require authorized access to use in the form of a license. The license will be automatically read if it is available whenever you open a program on OSC, provided you have access to the license. In order to have access to a license, you need to fill out the attached form and send it to Amy to forward to OSC. Available programs (at least some of) which require a license can be found here: https://www.osc.edu/resources/available_software/software_list . Replace the name of the program at the top of the form with the desired software.

William Luszczak, "Help! AnitaBuildTools/PueoBuilder can't seem to find FFTW!", Software

Fri, 04 Feb 2022 13:06:25 -0500

Disclaimer: This might not be the best solution to this problem. I arrived here after a lot of googling and stumbling across this thread with a similar problem for an unrelated project: https://github.com/xtensor-stack/xtensor-fftw/issues/52. If you're someone who actually knows cmake, maybe you have a better solution.

When compiling both pueoBuilder and anitaBuildTools, I have run into a cmake error that looks like:

CMake Error at /apps/cmake/3.17.2/share/cmake-3.17/Modules/FindPackageHandleStandardArgs.cmake:164 (message):
  Could NOT find FFTW (missing: FFTW_LIBRARIES)

(potentially also missing FFTW_INCLUDES). Directing CMake to the pre-existing FFTW installations on OSC does not seem to do anything to resolve this error. From what I can tell, this might be related to how FFTW is built, so to get around this we need to build our own installation of FFTW using cmake instead of the recommended build process. To do this, grab the whatever version of FFTW you need from here: http://www.fftw.org/download.html (for example, I needed 3.3.9). Untar the source file into whatever directory you're working in:

tar -xzvf fftw-3.3.9.tar.gz

Then make a build directory and cd into it:

mkdir install cd install

Now build using cmake, using the flags shown below.

cmake -DCMAKE_INSTALL_PREFIX=$(path_to_install_loc) -DBUILD_SHARED_LIBS=ON -DENABLE_OPENMP=ON -DENABLE_THREADS=ON ../fftw-3.3.9

For example, I downloaded and untarred the source file in `/scratch/wluszczak/fftw/`, and my install prefix was `/scratch/wluszczak/fftw/install/`. In principle this installation prefix can be anywhere you have write access, but for the sake of organization I usually try to keep everything in one place.

Once you have configured cmake, go ahead and install:

&nbs



Keith McBride, NASA Proposal fellowships, Other
Tue, 05 Nov 2019 16:22:16 -0500
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.


Amy , How to start a new undergrad hire, Other
Fri, 11 Oct 2019 13:43:35 -0400
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.


Dustin Nguyen, Advice (not mine) on writing HEP stuff , Other
Thu, 25 Jul 2019 16:50:43 -0400
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. 


Justin Flaherty, Installing PyROOT for Python 3 on Owens, Software
Thu, 11 Jul 2019 10:05:37 -0400
In order to get PyROOT working for Python 3, you must build ROOT with a flag that specifies Python 3 in the installation.  This method will create a folder titled root-6.16.00 in your current directory, so organize things how you see fit. Then the steps are relatively simple:

wget https://root.cern/download/root_v6.16.00.source.tar.gz

tar -zxf root_v6.16.00.source.tar.gz

cd root-6.16.00

mkdir obj

cd obj

cmake .. -Dminuit2=On -Dpython3=On

make -j8

If you wish to do a different version of ROOT, the steps should be the same:

wget https://root.cern/download/root_v<version>.source.tar.gz

tar -zxf root_v<version>.source.tar.gz

cd root-<version>

mkdir obj

cd obj

cmake .. -Dminuit2=On -Dpython3=On

make -j8