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Date |
Author |
Subject |
Project |
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Draft
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Mon Apr 20 15:59:16 2026 |
Brian Clark, Hannah Hasan, Jude Rajasekera, and Carl Pfendner | Installing Software Pre-Requisites for Simulation and Analysis | Software |
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Instructions on installing simulation software prerequisites (ROOT, Boost, etc) on Linux computers.
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Draft
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Wed Apr 1 02:14:30 2026 |
Brian Clark | Advice for Using the Ray Trace Correlator | Analysis | 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.
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Draft
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Thu Mar 19 15:36:48 2026 |
Brian Clark | Advice for Using the Ray Trace Correlator | Analysis | 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.
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50
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Wed Jun 12 12:10:05 2024 |
Jacob Weiler | How to install AraSim on OSC | Software | # 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! |
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49
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Thu Sep 14 22:30:06 2023 |
Jason Yao | How to profile a C++ program | Software | 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 |
| Attachment 1: hello_world.cpp
|
#include <iostream>
#include <thread>
#include <chrono>
#include <cmath>
using namespace std;
void nap(){
// usleep(3000);
// this_thread::sleep_for(30000ms);
for (int i=0;i<1000000000;i++){
double j = sqrt(i^2);
}
}
int main(){
cout << "taking a nap" << endl;
nap();
cout << "hello world" << endl;
}
|
| Attachment 2: make_hello_world
|
SHELL=/bin/sh
# Note: Comments start with #. $(FOOBAR) means: evaluate the variable
# defined by FOOBAR= (something).
# This file contains a set of rules used by the "make" command.
# This makefile $(MAKEFILE) tells "make" how the executable $(COMMAND)
# should be create from the source files $(SRCS) and the header files
# $(HDRS) via the object files $(OBJS); type the command:
# "make -f make_program"
# where make_program should be replaced by the name of the makefile.
#
# Programmer: Dick Furnstahl (furnstahl.1@osu.edu)
# Latest revision: 12-Jan-2016
#
# Notes:
# * If you are ok with the default options for compiling and linking, you
# only need to change the entries in section 1.
#
# * Defining BASE determines the name for the makefile (prepend "make_"),
# executable (append ".x"), zip archive (append ".zip") and gzipped
# tar file (append ".tar.gz").
#
# * To remove the executable and object files, type the command:
# "make -f $(MAKEFILE) clean"
#
# * To create a zip archive with name $(BASE).zip containing this
# makefile and the SRCS and HDRS files, type the command:
# "make -f $(MAKEFILE) zip"
#
# * To create a gzipped tar file with name $(BASE).tar.gz containing this
# makefile and the source and header files, type the command:
# "make -f $(MAKEFILE) tarz"
#
# * Continuation lines are indicated by \ with no space after it.
# If you get a "missing separator" error, it is probably because there
# is a space after a \ somewhere.
#
###########################################################################
# 1. Specify base name, source files, header files, input files
###########################################################################
# The base for the names of the makefile, executable command, etc.
BASE= hello_world
# Put all C++ (or other) source files here. NO SPACES after continuation \'s.
SRCS= \
hello_world.cpp
# Put all header files here. NO SPACES after continuation \'s.
HDRS= \
# Put any input files you want to be saved in tarballs (e.g., sample files).
INPFILE= \
###########################################################################
# 2. Generate names for object files, makefile, command to execute, tar file
###########################################################################
# *** YOU should not edit these lines unless to change naming conventions ***
OBJS= $(addsuffix .o, $(basename $(SRCS)))
MAKEFILE= make_$(BASE)
COMMAND= $(BASE).x
TARFILE= $(BASE).tar.gz
ZIPFILE= $(BASE).zip
###########################################################################
# 3. Commands and options for different compilers
###########################################################################
#
# Compiler parameters
#
# CXX Name of the C++ compiler to use
# CFLAGS Flags to the C++ compiler
# CWARNS Warning options for C++ compiler
# F90 Name of the fortran compiler to use (if relevant)
# FFLAGS Flags to the fortran compiler
# LDFLAGS Flags to the loader
# LIBS A list of libraries
#
CXX= g++
CFLAGS= -g
CWARNS= -Wall -W -Wshadow -fno-common
MOREFLAGS= -Wpedantic -Wpointer-arith -Wcast-qual -Wcast-align \
-Wwrite-strings -fshort-enums
# add relevant libraries and link options
LIBS=
# LDFLAGS= -lgsl -lgslcblas
LDFLAGS=
###########################################################################
# 4. Instructions to compile and link, with dependencies
###########################################################################
all: $(COMMAND)
.SUFFIXES:
.SUFFIXES: .o .mod .f90 .f .cpp
#%.o: %.mod
# This is the command to link all of the object files together.
# For fortran, replace CXX by F90.
$(COMMAND): $(OBJS) $(MAKEFILE)
$(CXX) -o $(COMMAND) $(OBJS) $(LDFLAGS) $(LIBS)
# Command to make object (.o) files from C++ source files (assumed to be .cpp).
# Add $(MOREFLAGS) if you want additional warning options.
%.o: %.cpp $(HDRS) $(MAKEFILE)
$(CXX) -c $(CFLAGS) $(CWARNS) -o $@ $<
# Commands to make object (.o) files from Fortran-90 (or beyond) and
# Fortran-77 source files (.f90 and .f, respectively).
.f90.mod:
$(F90) -c $(F90FLAGS) -o $@ $<
.f90.o:
$(F90) -c $(F90FLAGS) -o $@ $<
.f.o:
$(F90) -c $(FFLAGS) -o $@ $<
##########################################################################
# 5. Additional tasks
##########################################################################
# Delete the program and the object files (and any module files)
clean:
/bin/rm -f $(COMMAND) $(OBJS)
/bin/rm -f $(MODIR)/*.mod
# Pack up the code in a compressed gnu tar file
tarz:
tar cfvz $(TARFILE) $(MAKEFILE) $(SRCS) $(HDRS) $(MODIR) $(INPFILE)
# Pack up the code in a zip archive
zip:
zip -r $(ZIPFILE) $(MAKEFILE) $(SRCS) $(HDRS) $(MODIR) $(INPFILE)
##########################################################################
# That's all, folks!
##########################################################################
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