Instructions on installing simulation software prerequisites (ROOT, Boost, etc) on Linux computers.

Doing large runs of ShelfMC can be time intensive. However, if you have access to a computing cluster like Ruby or KingBee, where you are given a node with multiple processors, ShelfMC runs can be optimized by utilizing all available processors on a node. The multithread_shelfmc.sh script automates these runs for you. The script and instructions are attached below.

These scripts allow you to do thousands of ShelfMC runs while varying certain parameters of your choice. As is, the attenuation length, reflection, ice thickness, firn depth, station depth is varied over certain rages; in total, the whole Parameter Space Scan does 5250 runs on a cluster like Ruby or KingBee. The scripts and instructions are attached below. 

Jacob Here, Just want to add how I got AnitaTools to see FFTW:

1) echo $FFTW3_HOME to find where the lib and include dir is.

2) Next add the following line to the start of cmake/modules/FindFFTW.cmake

'set ( FFTW_ROOT full/path/you/got/from/step/1)'

Brief, experience-based instructions on installing the AnitaTools package on the Oakley OSC cluster.

Batch jobs on OSC are initiated through the Portable Batch System (PBS).  This is the recommended way to run stuff on OSC clusters.
Attached is a sample PBS script that copies files to temporary storage on the OSC cluster (also recommended) and runs an analysis program.
Info on batch processing is at https://www.osc.edu/supercomputing/batch-processing-at-osc.
     This will tell you how to submit and manage batch jobs.
More resources are available at www.osc.edu.

PBS web site: /www.pbsworks.com

The PBS user manual is at www.pbsworks.com/documentation/support/PBSProUserGuide10.4.pdf.

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 

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.

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.

On ruby, users get charged for the full node, even if you aren't using all 20 cores, so it's a pain if you want to run a bunch of serial jobs. There is, however, a thing called the 'parallel command processor' (pcp) which is provided on ruby, (https://www.osc.edu/resources/available_software/software_list/parallel_command_processor) that makes it very simple.

essentially, you make a text file filled with commands, one command per line, and then you give it to the parallel command processor and it submits each line of your text file as an individual job. the nice thing about this is that you don't have to think about it. you just give it the file and go, and it will use all cores on the full node in the most efficient way possible.

below i provide 2 examples, a very simple one to show you how it works, and a more complicated one. in both files, i make the command file inside of a loop. you don't need to do this-you can make the file in some other way if you choose to. note that you can also do this from within an interactive job. more instructions at the above link.

test.pbs  is just a minimal thing, where you need to submit the same command but with some value that needs to be incremented 1000 times (e.g. 1000 different jobs).

effvol.pbs is more involved, and shows some important steps if your job produces a lot of output, where you use the $TMPDIR or the pbs workdir. (if you don't know what that is, you probably don't need to use it). each command in this file stores an output file to the $TMPDIR directory. this directory is accessed faster than the directories where you store your files, and so your jobs run faster. at the end of the script, all of the output files from all of the run jobs, are copied to my home directory, because $TMPDIR is deleted after each job. also this file shows the sourcing of a particular bash profile for submitted jobs (if you need this. some programs work differently when submitted than jobs run on the login nodes on ruby).

i recommend reading the above link for more information. the pcp is very useful on ruby!

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

ANITA Binned Analysis: https://github.com/osu-particle-astrophysics/BinnedAnalysis

GENETIS Bicone: https://github.com/mclowdus/BiconeEvolution

GENETIS Dipole: https://github.com/hchasan/XF-Scripts

ANITA Build tool: https://github.com/anitaNeutrino/anitaBuildTool

ANITA Hackathon: https://github.com/anitaNeutrino/hackathon2017

ICEMC: https://github.com/anitaNeutrino/icemc

Brian's Github: https://github.com/clark2668?tab=repositories

Note that you *may* need permissions for some of these. Please email Lauren (ennesser.1@buckeyemail.osu.edu ), Julie (JulieRolla@gmail.com), AND Brian (clark.2668@buckeyemail.osu.edu ) if you have any issues with permssions. Please state which GitHub links you are looking to view. 

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

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

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

OSC added ARA's CVMFS repository on Pitzer and Owens. This has been already done in UW's cluster thanks to Ben Hokanson-Fasig and Brian Clark. With CVMFS, all the dependencies are compiled and stored in a single folder (container), meaning that the user can just source the paths to the used environmental variables and not worry about installing them at all. This is very useful, since it usually takes a considerable amount of time to get those dependencies and properly install/debug the ARA software. To use the software, all you have to do is:

Libraries and executables are stored here, in case you want to reference those dependencies as your environmental variables: /cvmfs/ara.opensciencegrid.org/trunk/centos7/

Even if you're not in the ARA collaboration, you can benefit from this through the fact that ROOT6 is installed and compiled in the container. In order to use it you just need to run the same bash command, and ROOT 6 will be available for you to use.

Feel free to email any questions to Brian Clark or myself.

--------

Technical notes: 

The ARA software was compiled with gcc version 4.8.5. In OSC, that compiler can be loaded by doing module load gnu/4.8.5. If you're using any other compiler, you'll get a warning telling you that if you do any compilation against the ARA software, you may need to add the -D_GLIBCXX_USE_CXX11_ABI=0 flag to your Make file. 

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:

    make install -j $(nproc)

Where $(nproc) is the number of threads you want to use. On OSC I used $(nproc)=4 for compiling the ANITA tools and it finished in a reasonable amount of time.

Once this has finished, cd to your install directory and remove everything except the `include` and `lib64` folders:

    cd $(path_to_install_dir) #You might already be here if you never left
    rm *
    rm -r CMakeFiles

Now we need to rebuild with slightly different flags:

    cmake -DCMAKE_INSTALL_PREFIX=$(path_to_install_loc) -DBUILD_SHARED_LIBS=ON -DENABLE_OPENMP=ON -DENABLE_THREADS=ON -DENABLE_FLOAT=ON ../fftw-3.3.9
    make install -j $(nproc)

At the end of the day, your fftw install directory should have the following files:

    include/fftw3.f  
    include/fftw3.f03
    include/fftw3.h  
    include/fftw3l.f03  
    include/fftw3q.f03 
    lib64/libfftw3f.so          
    lib64/libfftw3f_threads.so.3      
    lib64/libfftw3_omp.so.3.6.9  
    lib64/libfftw3_threads.so
    lib64/libfftw3f_omp.so        
    lib64/libfftw3f.so.3        
    lib64/libfftw3f_threads.so.3.6.9  
    lib64/libfftw3.so            
    lib64/libfftw3_threads.so.3
    lib64/libfftw3f_omp.so.3      
    lib64/libfftw3f.so.3.6.9    
    lib64/libfftw3_omp.so             
    lib64/libfftw3.so.3          
    lib64/libfftw3_threads.so.3.6.9
    lib64/libfftw3f_omp.so.3.6.9  
    lib64/libfftw3f_threads.so  
    lib64/libfftw3_omp.so.3           
    lib64/libfftw3.so.3.6.9

Once fftw has been installed, export your install directory (the one with the include and lib64 folders) to the following environment variable:

    export FFTWDIR=$(path_to_install_loc)

Now you should be able to cd to your anitaBuildTools directory (or pueoBuilder directory) and run their associated build scripts:

    ./buildAnita.sh

or:

    ./pueoBuilder.sh

And hopefully your tools will magically compile (or at least, you'll get a new set of errors that are no longer related to this problem).

If you're running into an error that looks like:
        
    CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
    Please set them or make sure they are set and tested correctly in the CMake files:
    FFTWF_LIB (ADVANCED)

then pueoBuilder/anitaBuildTools can't seem to find your fftw installation (or files that are supposed to be included in that installation), try rebuilding FFTW with different flags according to which files it seems to think are missing.

If it seems like pueoBuilder can't seem to find your FFTW installation at all (i.e. you're getting some error that looks like missing: FFTW_LIBRARIES or missing: FFTW_INCLUDES, check the environment variables that are supposed to point to your local FFTW installation (`$FFTWDIR`) and make sure there are the correct files in the `lib` and `include` subdirectories. 

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/install/, but since we're doing a local build, we'll use the `configure` script instead of the listed `bootstrap` script. As an example, suppose that I downloaded the above tar file to `/scratch/wluszczak/cmake`: 

    mkdir install
    cd cmake-3.22.1
    ./configure --prefix=/scratch/wluszczak/cmake/install
    make
    make install

You should additionally add this directory to your `$PATH` variable:

    export PATH=/scratch/wluszczak/cmake/install/bin:$PATH
    

To check to make sure that you are using the correct version of CMake, run:

    cmake --version

and you should get:

    cmake version 3.22.1

    CMake suite maintained and supported by Kitware (kitware.com/cmake).

### gcc 11.1.0

Download the gcc source from github here: https://github.com/gcc-mirror/gcc/tags. I used the 11.1.0 release, though there is a more recent 11.2.0 release that I have not tried. Once you have downloaded the source files, untar the directory:

    tar -xzvf gcc-releases-gcc-11.1.0.tar.gz

Then install the prerequisites for gcc:
    
    cd gcc-releases-gcc-11.1.0
    contrib/download_prerequisites

One of the guides I looked at also recommended installing flex separately, but I didn't seem to need to do this, and I'm not sure how you would go about it without root priviledges, though I imagine it's similar to the process for all the other packages here (download the source and then build by providing an installation prefix somewhere)

After you have installed the prerequisites, create a build directory:

    cd ../
    mkdir build
    cd build

Then configure GCC for compilation like so:

    ../gcc-releases-gcc-11.1.0/configure -v --prefix=/home/wluszczak/gcc-11.1.0 --enable-checking=release --enable-languages=c,c++,fortran --disable-multilib --program-suffix=-11.1

I don't remember why I installed to my home directory instead of the /scratch/ directories used above. In principle the installation prefix can go wherever you have write access. Once things have configured, compile gcc with:

    make -j $(nproc)
    make install

Where `$(nproc)` is the number of processing threads you want to devote to compilation. More threads will run faster, but be more taxing on your computer. For reference, I used 8 threads and it took ~15 min to finish. 

Once gcc is built, we need to set a few environment variables:

    export PATH=/home/wluszczak/gcc-11.1.0/bin:$PATH
    export LD_LIBRARY_PATH=/home/wluszczak/gcc-11.1.0/lib64:$LD_LIBRARY_PATH

We also need to make sure cmake uses this compiler:

    export CC=/home/wluszczak/gcc-11.1.0/bin/gcc-11.1
    export CXX=/home/wluszczak/gcc-11.1.0/bin/g++-11.1
    export FC=/home/wluszczak/gcc-11.1.0/bin/gfortran-11.1

If your installation prefix in the configure command above was different, substitute that directory in place of `/home/wluszczak/gcc-11.1.0` for all the above export commands. To easily set these variables whenever you want to use gcc-11.1.0, you can stick these commands into a single shell script:

    #load_gcc11.1.sh
    export PATH=/home/wluszczak/gcc-11.1.0/bin:$PATH
    export LD_LIBRARY_PATH=/home/wluszczak/gcc-11.1.0/lib64:$LD_LIBRARY_PATH

    export CC=/home/wluszczak/gcc-11.1.0/bin/gcc-11.1
    export CXX=/home/wluszczak/gcc-11.1.0/bin/g++-11.1
    export FC=/home/wluszczak/gcc-11.1.0/gfortran-11.1

(again substituting your installation prefix in place of mine). You can then set all these environment variables by simply running:
    
    source load_gcc11.1.sh

Once this is done, you can check that gcc-11.1.0 is properly installed by running:

    gcc-11.1 --version

Note that plain old

    gcc --version

might still point to an older version of gcc. This is fine though. 

###FFTW 3.3.9
Grab the source code for the appropriate versino of FFTW from here: http://www.fftw.org/download.html

However, do NOT follow the installation instructions on the webpage. Those instructions might work if you have root privileges, but I personally couldn't seem to to get things to work that way. Instead, we're going to build fftw with cmake. Untar the fftw source files:

    tar -xzvf fftw-3.3.9.tar.gz

Make a build directory and cd into it:
    
    mkdir build
    cd build

Now build using cmake, using the flags shown below. For reference, I downloaded and untarred the source file in `/scratch/wluszczak/fftw/build`, so adjust your install prefix accordingly to point to your own build directory that you created in the previous step.

    cmake -DCMAKE_INSTALL_PREFIX=/scratch/wluszczak/fftw/build/ -DBUILD_SHARED_LIBS=ON -DENABLE_OPENMP=ON -DENABLE_THREADS=ON ../fftw-3.3.9
    make install -j $(nproc)

Now comes the weird part. Remove everything except the `include` and `lib64` directories in your build directory (if you installed to a different `CMAKE_INSTALL_PREFIX`, the include and lib64 directories might be located there instead. The important thing is that you want to remove everything, but leave the `include` and `lib64` directories untouched):

    rm *
    rm -r CMakeFiles

Now rebuild fftw, but with an additional flag:

    cmake -DCMAKE_INSTALL_PREFIX=/scratch/wluszczak/fftw/build/ -DBUILD_SHARED_LIBS=ON -DENABLE_OPENMP=ON -DENABLE_THREADS=ON -DENABLE_FLOAT=ON ../fftw-3.3.9
    make install -j $(nproc)

At the end of the day, your fftw install directory should have the following files:

    include/fftw3.f  
    include/fftw3.f03
    include/fftw3.h  
    include/fftw3l.f03  
    include/fftw3q.f03 
    lib64/libfftw3f.so          
    lib64/libfftw3f_threads.so.3      
    lib64/libfftw3_omp.so.3.6.9  
    lib64/libfftw3_threads.so
    lib64/libfftw3f_omp.so        
    lib64/libfftw3f.so.3        
    lib64/libfftw3f_threads.so.3.6.9  
    lib64/libfftw3.so            
    lib64/libfftw3_threads.so.3
    lib64/libfftw3f_omp.so.3      
    lib64/libfftw3f.so.3.6.9    
    lib64/libfftw3_omp.so             
    lib64/libfftw3.so.3          
    lib64/libfftw3_threads.so.3.6.9
    lib64/libfftw3f_omp.so.3.6.9  
    lib64/libfftw3f_threads.so  
    lib64/libfftw3_omp.so.3           
    lib64/libfftw3.so.3.6.9

Why do we have to do things this way? I don't know, I'm bad at computers. Maybe someone more knowledgeable knows. I found that when I didn't do this step, I'd run into errors that pueoBuilder could not find some subset of the required files (either the ones added by building with `-DENABLE_FLOAT`, or the ones added by building without `-DENABLE_FLOAT`). 

Once fftw has been installed, export your install directory (the one with the include and lib64 folders) to the following environment variable:

    export FFTWDIR=/scratch/wluszczak/fftw/build

Again, substituting your own fftw install prefix that you used above in place of `/scratch/wluszczak/fftw/build`

###gsl 2.7.1
gsl 2.7.1 is needed for the `mathmore` option in ROOT. If you have an outdated version of gsl, ROOT will still compile, but it will skip installing `mathmore` and `root-config --has-mathmore` will return `no`. To fix this, grab the latest source code for gsl from here: https://www.gnu.org/software/gsl/. Untar the files to a directory of your choosing:

    tar -xzvf gsl-latest.tar.gz

For some reason I also installed gsl to my home directory, but in principle you can put it wherever you want. 

    mkdir /home/wluszczak/gsl
    ./configure --prefix=/home/wluszczak/gsl
    make
    make check
    make install

To make sure ROOT can find this installation of gsl, you'll again need to set an environment variable prior to building ROOT:

    export GSL_ROOT_DIR=/home/wluszczak/gsl/
    
I also added this to my $PATH variable, though I don't remember if that was required to get things working or not:

    export PATH=/home/wluszczak/gsl/bin/:$PATH 
    export LD_LIBRARY_PATH=/home/wluszczak/gsl/lib:$LD_LIBRARY_PATH

###Python 3.9.18
Apr. 6, 2024 edit by Jason Yao:
I was able to follow this entire ELOG to install root 6.24.00, but I also was getting warnings/errors that seem to be related to Python,
so I went ahead and installed Python 3.9.18 (and then a newer version of ROOT just for fun).
Note that even though we can `module load python/3.9-2022.05` on OSC, I am 90% sure that this provided Python instance is no good as far as ROOT is concerned.

Head over to https://www.python.org/downloads/release/python-3918/ to check out the source code.
You can run
    wget https://www.python.org/ftp/python/3.9.18/Python-3.9.18.tgz
to download it on OSC; then, run
    tar -xzvf Python-3.9.18.tgz
    cd Python-3.9.18

Next we will compile Python from source. I used this website for this step.
I wanted to install to `${HOME}/usr/Python-3.9.18/install`, so
    ./configure --prefix=${HOME}/usr/Python-3.9.18/install --enable-shared
Note that we must have the flag `--enable-shared` "to ensure that shared libraries are built for Python. By not doing this you are preventing any application which wants to use Python as an embedded environment from working" according to this guy.
(The corresponding error when you try to compile ROOT later on would look like "...can not be used when making a shared object; recompile with -fPIC...")

After configuration,
    make -j8 && make install
(using 8 threads)

After installation, head over to the install directory, and then
    cd bin
You should see `pip3` and `python3.9`. If you run
    ./python3
you should see the Python interactive terminal
    Python 3.9.18 (main, Apr  5 2024, 22:49:51) 
    [GCC 11.1.0] on linux
    Type "help", "copyright", "credits" or "license" for more information.
    >>>
Add the python3 in this folder to your PATH variable. For example, 
    export PATH=${HOME}/usr/Python-3.9.18/install/bin:${PATH}
 

While we are in the python install directory, we might as well also use the `pip3` there to install numpy:
    ./pip3 install numpy
(I am not sure if this is absolutely needed by ROOT, but probably)

Next comes the important bit. You need to add the `lib/` directory inside you python installation to the environment variable $LD_LIBRARY_PATH
    export LD_LIBRARY_PATH=${HOME}/usr/Python-3.9.18/install/lib:$LD_LIBRARY_PATH
according to stackoverflow. Without this step I ran into errors when compiling ROOT.

###ROOT 6.24.00
Download the specific version of ROOT that you need from here: https://root.cern/install/all_releases/

You might need to additionally install some of the dependencies (https://root.cern/install/dependencies/), but it seems like everything I needed was already installed on my system. 

Untar the source you downloaded:
    
    tar -xzvf root_v6.24.00.source.tar.gz

Make some build and install directories:

    mkdir build install
    cd build

Run CMake, but be sure to enable the fortan, mathmore and minuit2 options. For reference, I had downloaded and untarred the source files to `/scratch/wluszczak/root`. Your installation and source paths will be different.

    cmake -DCMAKE_INSTALL_PREFIX=/scratch/wluszczak/root/install/ /scratch/wluszczak/root/root-6.24.00/ -Dfortran=ON -Dminuit2=ON -Dmathmore=ON

Note: if you end up with an error related to compiling XROOTD, then add -Dxrootd=OFF to the original cmake command above.

Then proceed to start the build:

    cmake --build . --target install -j $(nproc)
    

If everything has worked then after the above command finishes running, you should be able to run the following file to finish setting up ROOT:

    source ../install/bin/thisroot.sh

##pueoBuilder
By this point, you should have working installations of CMake 3.21.2, gcc-11.1.0, fftw 3.3.9, and ROOT 6.24.00. Additionally, the following environment variables should have been set:

    export PATH=/scratch/wluszczak/cmake/install/bin:$PATH

    export PATH=/home/wluszczak/gcc-11.1.0/bin:$PATH
    export LD_LIBRARY_PATH=/home/wluszczak/gcc-11.1.0/lib64:$LD_LIBRARY_PATH

    export CC=/home/wluszczak/gcc-11.1.0/bin/gcc-11.1
    export CXX=/home/wluszczak/gcc-11.1.0/bin/g++-11.1
    export FC=/home/wluszczak/gcc-11.1.0/gfortran-11.1

    export FFTWDIR=/scratch/wluszczak/fftw/build

At this point, the hard work is mostly done. Check out pueoBuilder with:

    git clone git@github.com:PUEOCollaboration/pueoBuilder 

set the following environment variables:

    export PUEO_BUILD_DIR=/scratch/wluszczak/PUEO/pueoBuilder
    export PUEO_UTIL_INSTALL_DIR=/scratch/wluszczak/PUEO/pueoBuilder
    export NICEMC_SRC=${PUEO_BUILD_DIR}/components/nicemc
    export NICEMC_BUILD=${PUEO_BUILD_DIR}/build/components/nicemc
    export PUEOSIM_SRC=${PUEO_BUILD_DIR}/components/pueoSim
    export LD_LIBRARY_PATH=${PUEO_UTIL_INSTALL_DIR}/lib:$LD_LIBRARY_PATH

Where $PUEO_BUILD_DIR and $PUEO_UTIL_INSTALL_DIR point to where you cloned pueoBuilder to (in my case, `/scratch/wluszczak/PUEO/pueoBuilder`. Now you should be able to just run:

    ./pueoBuilder.sh

Perform a prayer to the C++ gods while you're waiting for it to compile, and hopefully at the end of the day you'll have a working set of PUEO software. 

##Issues I Ran Into
If you already have an existing installation of ROOT, you may still need to recompile to make sure you're using the same c++ standard that the PUEO software is using. I believe the pre-compiled ROOT binaries available through their website are insufficient, though maybe someone else has been able to get those working. 

If you're running into errors about c++ standard or compiler version even after you have installed gcc-11.1.0, then for some reason your system isn't recognizing your local installation of gcc-11.1.0. Check the path variables ($PATH and $LD_LIBRARY_PATH) to make sure the gcc-11.1.0 `bin` directory is being searched.

If you're running into an error that looks like:
        
    CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
    Please set them or make sure they are set and tested correctly in the CMake files:
    FFTWF_LIB (ADVANCED)

then pueoBuilder can't seem to find your fftw installation (or files that are supposed to be included in that installation), try rebuilding with different flags according to which files it seems to think are missing.

If it seems like pueoBuilder can't seem to find your fftw installation at all (i.e. you're getting some error that looks like `missing: FFTW_LIBRARIES` or `missing: FFTW_INCLUDES`), check the environment variables that are supposed to point to your fftw installation (`$FFTWDIR`) and make sure there are the correct files in the `lib` and `include` subdirectories. 

Update: 6/23/24: The latest version of ROOT (6.30) will fail to compile on OSC unless you manually compile TBB as well. An easy workaround is to simply downgrade to ROOT 6.24, however if you really need ROOT 6.30 you can follow the instructions below to install TBB and compile ROOT:

You will first need to downgrade to GCC 10.X. TBB will not compile with GCC 11. This can be done by following the GCC installation isntructions above, except starting with GCC 10 source code instead of GCC 11.

To install TBB yourself, download the source code (preferably the .tar.gz file) from here: https://github.com/oneapi-src/oneTBB/releases/tag/v2021.12.0. Move the file to the directory where you want to install TBB and untar it with:

    tar -xzvf oneTBB-2021.12.0.tar.gz

Make some build and install directories:

    mkdir build install
    cd build

Then configure cmake:

    cmake -DCMAKE_INSTALL_PREFIX=/path/to/tbb/install

Then compile with:

    cmake --build .

Once this has finished running, you can add the installation to you $PATH and $LD_LIBRARY_PATH variables:

    export PATH=/path/to/tbb/install/bin:$PATH
    export LD_LIBRARY_PATH=/path/to/tbb/install/lib64:$LD_LIBRARY_PATH

You can then proceed as normal, except when compiling root you will need one additional cmake flag (Dbuiltin_tbb=ON):

  cmake -DCMAKE_INSTALL_PREFIX=/scratch/wluszczak/root/install/ /scratch/wluszczak/root/root-6.24.00/ -Dfortran=ON -Dminuit2=ON -Dmathmore=ON -Dbuiltin_tbb=ON

And hopefully this should work. This process is a little bit more involved than just downgrading ROOT, so try to avoid going down this route unless absolutely necessary.

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