Reference system

The example Windows installation described below was done on the following system:
Machine: x64-based PC laptop
Operating system: Windows 10 Education
Processor: Intel Core i9, 2500 MHz, 14 cores
RAM: 32 GB

STEP 1: Download L-Galaxies 2020

OPTION 1: Download as zip file:

  1. Go to https://github.com/LGalaxiesPublicRelease/LGalaxies2020_PublicRepository
  2. From the drop-down list on the left, select the branch you wish to download:
    • "master" for the Yates+21a version of L-Galaxies 2020
    • "Yates2023" for the Yates+23 version of L-Galaxies 2020
  3. Click the green "Code" drop-down menu, and select "Download ZIP" [~5-20 MB]
  4. Move the downloaded file ([BRANCH_NAME].zip) to a suitable base directory.
  5. Using any un-zipping software (e.g. 7-Zip, or other), extract the model into a folder called /LGalaxies2020_PublicRepository-[BRANCH_NAME], hereafter, the "project root directory"
  6. Manually add an empty /output folder in the project root directory


OPTION 2: Download as a local Git repository:
This option requires having a GitHub account as well as Git and Git Bash on your Windows system. To download and install Git and Git Bash, follow the instructions at: https://github.com/git-guides/install-git Once you have Git and a GitHub account, proceed as follows:

  1. Open Git Bash
  2. Navigate to a directory where you'd like L-Galaxies kept:
    • cd [PATH TO CHOSEN FOLDER]
  3. Decide which branch you wish to download:
    • "master" for the Yates+21a version of L-Galaxies 2020
    • "Yates2023" for the Yates+23 version of L-Galaxies 2020
  4. Clone the repository:
    • git clone --branch [BRANCH_NAME] --single-branch https://github.com/[GITHUB_USERNAME]/ https://github.com/LGalaxiesPublicRelease/LGalaxies2020_PublicRepository


OPTION 3: Download as a local Git repository via the Eclipse IDE:
The L-Galaxies 2020 code can also be obtained from GitHub via the Eclipse IDE, which offers a more intuitive way of editing and debugging code using a Graphical User Interface (GUI). To install L-Galaxies 2020 this way, skip straight to STEP 8 below, where information on how to install Eclipse and synchronise it with L-Galaxies 2020 is provided.

STEP 2: Download spectrophotometric tables and treefiles

  1. Download the standard SpecPhotTables [~1.6 GB] [direct download]
  2. Move the downloaded .tar file (SpecPhotTables.tar) into the project root directory.
  3. Navigate to the project root directory.
  4. Unzip the file (using e.g. 7-Zip, or other)
    5. This will create a folder called /SpecPhotTables containing the downloaded spectrophotometic tables
  5. Download the treefiles (choose one of the following options):
    6. Millennium-I: Millennium-II:
    • Treefiles 40-79 [~6.0 GB compressed, ~13 GB uncompressed] 40 treefiles (standard test set)
    • Treefiles 0-511 [~92 GB compressed, ~185 GB uncompressed] All treefiles (full volume)
  6. Move the downloaded .tar file into the /MergerTrees directory, which is in the project root directory.
  7. Navigate to the /MergerTrees.
  8. >Unzip the treefiles
    9. This will create a folder called either /MR/treedata, /MRII/treedata, or /MRII containing the downloaded treefiles.

STEP 3: Install a Linux emulator, compiler, and C libraries

L-Galaxies requires a C compiler (e.g. gcc), the make command, and the GNU Scientific Libraries (GSL) to run. Most Windows distributions do not come these by default. If yours doesn't, the simplest solution is to download them via a Linux emulator. Here, we provide instructions for installing the popular gcc compiler via Cygwin. Other compilers (e.g. icc) and Linux emulators (e.g. MinGW) are also available.

  1. Go to: https://cygwin.com/install.html
  2. Click "setup-x86_64.exe" [~1.4 MB]
  3. Once downloaded, execute setup-x86_64.exe and begin following the instructions to install to the default location: C:\tools\cygwin
  4. In "Select packages", choose the "Full" view
  5. Select the following additional packages:
    • gcc-core 11.3.0-1 [~30.7 MB]
    • gcc-debuginfo 11.3.0-1 [~32.4 MB]
    • gsl 2.3-2 [~58 KB]
    • gsl-debuginfo 2.3-2 [~2.2 MB]
    • make 4.3-1 [~503 KB]
    • make-debuginfo 3.3-1 [~441 KB]
  6. Click "next"
  7. Click "next" again to complete the installation

N.B. We recommend you keep the setup-x86_64.exe installer on your system, as it can be run at any time to add/remove/update Cygwin tools.

STEP 4: Check compiler configuration

The L-Galaxies 2020 makefile needs to be told which C compiler to use and where the GSL libraries are stored. This information is provided by the user as a SYSTYPE configuration in the My_Makefile_compilers file, located in the project root directory.

SYSTYPE = "Linux" at the top of the file and un-commenting SYSTYPE = "cygwin". This set-up should be suitable for most Windows installations. It assumes the gcc compiler is to be used and that the GSL header files and libraries are stored in their default locations: /usr/local/include and /usr/local/lib (which is where cygwin should have put them). If your GSL files are not stored in these locations, you will need to change the GSL_INCL and GSL_LIBS paths accordingly. By default, no compiler optimisation flags are added to this configuration. Feel free to add ones of your own, if you wish.

You can check that gcc and gsl is installed on your system by executing the following commands in a cygwin64 terminal:



Common compiler issues

  1. Running with an old C standard: If your distribution is quite old, it may not be running with the latest C standard. If so, you may need to inform the compiler of this in My_Makefile_compilers by adding the -std flag to the CC call. (e.g. CC = gcc -std=C99 for systems running with C99).

  2. Running with old C libraries: Likewise, an old distribution may not have a version of the GNU C libraries (glibc). If so, you may need to install and build new C libraries following the instructions provided here (which is compilcated!). Alternatively, a quick hack (if you do have a recent version of the GSL libraries, see above), is to replace the #include <math.h> statements at the top of each L-Galaxies code .c file with #include <gsl/gsl_math.h>

  3. Multiple tentative definitions: If a compilation crashes with an error stating that "multiple tenative definitions of a global variable in different compilation units" are not allowed, you may need to add the -fcommon flag to the CC call in My_Makefile_compilers. Note that this flag is set by default when running with SYSTYPE = "cygwin".

  4. Shared libraries: If your system has shared GSL libraries (i.e. .so files), rather than local archived ones (i.e. .a files), you may need to replace the default -static flag for GSL_LIBS in My_Makefile_compilers with a -shared flag. You may also find that the GSL libraries are stored in /usr/include and /usr/lib (rather than /usr/local/include and /usr/local/lib), so should update the paths in My_Makefile_compilers accordingly.

  5. Shared object errors: Similarly, if you are getting errors like: "Relocation R_X86_64_32 against undefined symbol '[LGALAXIES_PARAMETER]' can not be used when making a shared object", then you may need to add the -fPIC flag to the CC call in My_Makefile_compilers

STEP 5: Compile and run the code

Compiling and running L-Galaxies 2020 is done as follows:

  1. In a cygwin64 terminal, navigate to the project root directory
  2. Compile the code:
    • make
  3. Run the code:
    • ./L-Galaxies ./input/[INPUT FILE]


There are four standard input files to choose from (for info on which to use, see STEP 7):


Once L-Galaxies 2020 has finished running, the output file(s) generated will be stored in the /outputs folder. These can be read in to python for analysis as described in STEP 6.

Straight out of the box, L-Galaxies 2020 will run on treefile 5 of Millennium-I with only redshift 0 data outputted. However, various other standard set-ups are also possible (see STEP 7).

STEP 6: Reading-in L-Galaxies 2020 outputs in python

L-Galaxies 2020 comes with a set of simple python scripts to read L-Galaxies output files (which, by default, are in binary format). This is done using the "output structure" provided (see "Changing which properties are outputted" in STEP 7). These python scripts also convert properties from code units to physical units, generate galaxy samples, and plot a few key relations. The scripts and output structures are in /AuxCode/Python.


To run these python scripts on your L-Galaxies output, simply execute the main_lgals.py file. This will generate a galaxy sample (using the selection criteria discussed below) which is saved to an .npy file in the /output/samples folder. It will also produce some plots in the /figures folder. To modify how main_lgals.py works, see below.


Switches
The main_lgals.py file contains a number of switches under "USER DEFINED INPUTS" which can be used to modify how/what data is read-in and made into samples. For example:


Sample Info
The type of L-Galaxies output to be read, and type of sample you want to generate, can also be set in main_lgals.py via the following variables:


Sample Types
There are four default sample types you can select when generating a sample from the L-Galaxies output file using main_lgals.py:

For more info on the exact selection criteria for these different sample types, see the make_lgals_sample.py file.


Note that the plots generated by these python scripts require latex syntax for some of the axis labels. If your Linux installation does not have (la)tex capabilities, you may need to install (some) of the following packages:


For more information on how to use/modify these python scripts, feel free to drop me an email (r.yates3 -at- herts.ac.uk).

(For those who prefer to handle data in IDL, there are some old IDL scripts available for reading-in/plotting L-Galaxies outputs. If you are interested in these, just drop me an email.)

STEP 7: Changing the model [OPTIONAL]

Default vs. Modified model
Input files (i.e. the .par files) are provided for the Default Model (DM) and Modified Model (MM) versions of L-Galaxies 2020 (see Yates+21a for details). In brief, the Default Model allows the majority of material released by supernovae and stellar winds to mix with the ambient ColdGas before some is blown out as galactic winds. The Modified Model allows the majority of this newly-released material to be directly ejected into the surrounding HotGas, without first mixing with the ColdGas. Depending on which model you want to use, the corresponding input file is one of the following:

Note that these input files are for runs on the Millenium-I merger trees. If you want to run on Millennium-II instead, see below.



Millennium-I vs. Millennium-II
By default, L-Galaxies 2020 will try to run on Millennium-I merger trees. To switch to Millennium-II, make sure you've downloaded some Millennium-II treefiles (see STEP 2), and then do the following:

  1. Open the My_Makefile_options file in the project root directory
  2. Uncomment the MRII switch
  3. Save and close My_Makefile_options
  4. Use the default model (DM) or modified model (MM) Millennium-II input files as the argument when running the code (see STEP 5 above):
    • input_MRII_W1_PLANCK_LGals2020_DM.par
    • input_MRII_W1_PLANCK_LGals2020_MM.par



Snapshot vs. Galaxytree mode
Snapshot mode (the default for L-Galaxies 2020) will only output data for a user-defined set of redshifts (i.e. snapshots). Galaxytree mode will instead output data from all snapshots, along with the IDs needed to link a given galaxy to its progenitors and descendents (note that this generates much larger output files).

To use/modify snapshot mode:

  1. Open desired_output_redshifts.txt in the /inputs folder
  2. Add the redshifts you wish to be outputted to the top of this file, one on each line, with an empty line at the end of your list (L-Galaxies will match these to their nearest snapshots automatically)
  3. Open the My_Makefile_options file in the project root directory
  4. Set the NOUT parameter to equal the number of redshifts you set to be outputted in desired_output_redshifts.txt
  5. Make sure that the GALAXYTREE switch is commented-out
  6. Save and close My_Makefile_options
  7. Compile and run L-Galaxies 2020 as described in STEP 5

To use galaxytree mode:
  1. Open the My_Makefile_options file in the project root directory
  2. Uncomment the GALAXYTREE switch
  3. Save and close My_Makefile_options
  4. Compile and run L-Galaxies 2020 as described in STEP 5



MCMC mode
For detailed instructions on how to run L-Galaxies in MCMC mode, in order to retune model parameters, see the MCMC instructions kindly provided by Marcel van Daalen.



Changing the output file name

  1. Open the input file you wish to use (see above) in the /inputs folder
  2. Change FileNameGalaxies to an appropriate name. This will be the prefix in the name of the output file(s) that L-Galaxies generates.
  3. Save and close the input file
  4. Compile and run L-Galaxies 2020 as described in STEP 5



Changing the treefiles used

  1. Open the input file you wish to use (see above) in the /inputs folder
  2. Set FirstFile to the first treefile you wish to use
  3. Set LastFile to the last treefile you wish to use
  4. Save and close the input file
  5. Compile and run L-Galaxies 2020 as described in STEP 5

To run L-Galaxies 2020 on the full set of Millennium-I or II trees, set FirstFile to 0 and LastFile to 511. For testing purposes on Millennium-I, treefile 5 alone is normally sufficient. For quick but statistically-significant runs on Millennium-I, treefiles 0-9 are normally sufficient. For quick but statistically-significant runs on Millennium-II, treefiles 40-79 are normally sufficient.



Model switches
L-Galaxies 2020 comes with a series of pre-defined model options (or "switches") that change e.g. the physics models used, the treefiles used, which properties are tracked/outputted, etc. These switches are defined in the My_Makefile_options file in the project root directory. There meanings should be quite self explanatory, but if you are unsure, feel free to ask! You are also able to add your own switches to your version of the code. These should be defined in My_Makefile_options and then utilised in the necessary code files via "ifdef statements" (or equivalent). For example, to create a switch which prevents the property BulgeMassRings from being outputted:

  1. Open My_Makefile_options in the project root directory
  2. Add the following line:
    • OPT += -DNO_BULGEMASSRINGS_OUTPUT
  3. Save and close My_Makefile_options
  4. Put the following ifdef statement around the instances of BulgeMassRings in h_galaxy_output.h and save.c (see below for more details):
    • #ifndef NO_BULGEMASSRINGS_OUTPUT
    • ...
    • #endif //NO_BULGEMASSRINGS_OUTPUT
  5. Save and close the code files
  6. Open the output structure .py file you are using
  7. Remove BulgeMassRings by either setting it to "False" in the properties_used dictionary (at the bottom of the .py file), or directly commenting it out:
    • # ('BulgeMassRings',numpy.float32,12),



Changing which properties are outputted
The L-Galaxies output structures define which properties are contained in the binary output files. The standard output structures (compatible with python) provided in each of the L-Galaxies 2020 branches are described below.

"master" branch:


"Yates2023" branch:
  • LGalaxy_snapshots_liteOutput.py: This is the standard output structure for outputs generated out-of-the-box by the "Yates2023" branch of L-Galaxies 2020. It assumes that snapshot mode has been selected and the standard set of model switches are turned on (see above), including the LITE_OUTPUT switch, which reduces the number of properties outputted.
  • LGalaxy_snapshots_normal.py: This output structure is for outputs generated in snapshot mode with the LITE_OUTPUT switched turned off.
  • LGalaxy_ringSFHs.py: This is the output structure to use (in snapshot mode) if chemical enrichment histories for individual elements in galaxy rings are required (i.e. if the OUTPUT_RINGS_EXTRA switch is turned on). Similar to the LGalaxy_snapshots_extraSFHs.py structure in the "master" branch.

You are also free to customise which properties are actually outputted by L-Galaxies 2020. This is done as follows:

  1. Open h_galaxy_output.h in the /code folder
  2. In the GALAXY_OUTPUT structure, add/comment-out the property you wish to be outputted/not outputted
    3. For example, to remove BulgeMassRings, either put it in a newly-defined #ifndef (see above) or directly comment it out:
    • // float BulgeMassRings[RNUM];
  3. Save and close h_galaxy_output.h
  4. Open save.c in the /code folder
  5. In the prepare_galaxy_for_output() function, add/comment-out the property you wish to be outputted/not outputted
    6. For example, to remove BulgeMassRings, either put it in a newly-defined #ifndef (see above) or directly comment it out:
    • // o->BulgeMassRings[ll] = g->BulgeMassRings[ll];
  6. Save and close save.c
  7. Open the output structure .py file you are using
  8. In the structure, add/comment-out the property you wish to be outputted/not outputted
    9. For example, to remove BulgeMassRings, set it to "False" in the properties_used dictionary (at the bottom of the .py file), or directly comment it out:
    • # ('BulgeMassRings',numpy.float32,12),
    The property in question will now be included/removed from the output file generated by L-Galaxies 2020.
Note: The majority of errors occurring when trying to read-in L-Galaxies output binaries into a python script come from a mis-match between the actual output and the output structure. Therefore, make sure you keep your output structure up-to-date with your code!



Processing binary_c data [Yates2023 branch only]
The Yates+23 version of L-Galaxies allows the inclusion of chemical yields and supernova rates from stellar populations containing binary stars, by utilising the binary stellar evolution (BSE) calculations made by the binary_c code. To do this, "ensemble" outputs from binary_c are loaded and converted into yield tables that can be read by L-Galaxies.

Standard versions of these tables are already generated and stored in the /YieldTables/binary_c_yields/default folder. However, if a different set of chemical elements is required (N.B. only 'H','He','C','N','O','Ne','Mg','Si','S','Ca', and 'Fe' are loaded by default), or if you want to use a new set of binary_c ensembles, then new yield tables can be easily generated by executing the process_binaryc_outputs.py script found in the /AuxCode/Python folder.

To change the chemical elements/isotoptes considered, simply modify the elements list under "INPUT VARIABLES" in process_binaryc_outputs.py. A new h_metals.h header file will automatically be written in the /code folder, which allows the new list of elements/isotopes chosen to be tracked in L-Galaxies.

To generate yield tables for a new set of binary_c ensembles, simply place the new ensemble .json files into the /YieldTables/binary_c_yields/new/ensembles folder and turn on the USE_NEW_ENSEMBLES switch in process_binaryc_outputs.py.

For more information on how to handle binary_c data with L-Galaxies, feel free to drop me an email (r.yates3 -at- herts.ac.uk).

STEP 7: L-Galaxies with the Eclipse IDE [OPTIONAL]

Although L-Galaxies 2020 can be used with any basic word processor and the command line, using an Interactive Development Environment (IDE) can make modifying, compiling, running, and debugging code significantly easier and more efficient. This can save a lot of time and energy in the long run. Therefore, we recommend an IDE (that is compatible with C makefile projects) is used when working with L-Galaxies. Below, we outline how to download, install, and synchronise the Java-based Eclipse IDE for L-Galaxies, which has already been extensively tried and tested with the code.


Install Cygwin:

  1. If you haven't already, complete STEP 3 above to install GSL and the gcc compiler via Cygwin.


Install jdk:
Eclipse is a java-based IDE, so it needs the Java Development Kit (JDK) to run. You can check if JDK is already installed on your system by opening a cygwin terminal and running java -version. If this command returns information on a Java "Runtime Environment", you probably have a working version of JDK installed. If you don't have JDK, you can install the latest version as a private user as follows:

  1. Go to: https://www.oracle.com/java/technologies/downloads/#jdk19-windows
  2. Click the download link for the Java SE Development Kit 19.0.1 x64 Installer
  3. Install to: C:\Program Files\Java\jdk-19\


Install Eclipse IDE:

  1. Go to: https://www.eclipse.org/downloads/packages/installer
  2. Click the download link for the Eclipse 2022-09 R x86_64 Installer for Windows
  3. Once downloaded, execute the installer on your system
  4. Select: Eclipse IDE for C/C++ Developers
  5. Confirm: Java 17+ VM: C:\Program Files\Java\jdk-19 and Installation Folder: C:\Users\[username]\eclipse\cpp-2022-09
  6. Accept the user agreement and click "launch"
  7. Confirm the defauly workspace path and click "launch" again.


Clone L-Galaxies 2020 repository:

  1. In the Eclipse IDE, click the "Open Perspective" button in the top right corner (symbol of a GUI interface with a plus sign)
  2. Select "Git"
  3. Click "Clone a Git Repository" (left)
  4. Enter the L-Galaxies 2020 repository URI: https://github.com/LGalaxiesPublicRelease/LGalaxies2020_PublicRepository
  5. Click "Next"
  6. Select which branch(es) you wish to clone and click "Next"
  7. Confirm the destination directory (this will become your git-synchronised project root directory).
  8. Click "Finish"
  9. Eclipse will now clone a local version of the L-Galaxies 2020 repository (progress bar in the bottom right corner)
  10. Once cloned, right click the name of the project in the left-hand panel (LGalaxies2020_PublicRepository)
  11. Click "Import projects..."
  12. In the new window, click "Finish"
    13. The L-Galaxies 2020 code is now ready to be used in the standard "C/C++ Perspective" in Eclipse


Define as a makefile project:

  1. Click the "C/C++ Perspective" button in the top right corner (symbol of a GUI interface with a letter "C")
  2. Click on the project name in the left-hand panel (LGalaxies2020_PublicRepository), so that it's highlighted
  3. Press Ctrl+n on the keyboard
  4. Select: "Convert to C/C++ project (Adds C/C++ Nature)" and click "Next"
  5. Select: "C project" (below the heading called "Convert to C or C++")
  6. Select: "Makefile project", and the "Cygwin GCC" toolchain
  7. Click "Finish"


Set-up a run configuration:

  1. In the "C/C++ perspective", click the project name in the left-hand panel (LGalaxies2020_PublicRepository), so that it's highlighted
  2. From the top menu bar, select "Run" > "Run configurations..."
  3. In the new window, click the "New Launch configuration" button (symbol of a blank page with a plus sign)
  4. Set "Name" in the right hand panel to: "LGalaxies2020_PublicRepository" (i.e. delete " Default")
  5. Set "C/C++ Application" to: "L-Galaxies.exe"
  6. Click the "(x) = Arguments" tab
  7. Under "Program arguments", add the local path to your preferred input file (e.g. ./input/input_MR_W1_PLANCK_LGals2020_DM.par)
  8. Click "Apply", then click "Close"


Add an output folder:

  1. In the "C/C++ perspective", right-click the project name in the left-hand panel (LGalaxies2020_PublicRepository)
  2. Select "New" > "Folder"
  3. In the new window, set Folder name as "output"
  4. Click "Finish"


Download treefiles and specphot tables:

  1. If you haven't already, complete STEP 2 above for this cloned L-Galaxies 2020 repository


Check compiler configuration:

  1. Complete STEP 4 above to check the gcc compiler is configured correctly for L-Galaxies 2020 on your system. For example, you may need to set the SYSTYPE to "cygwin" in My_Makefile_compilers.


Compile and run in Eclipse:

  1. In the "C/C++ perspective", click the project name in the left-hand panel (LGalaxies2020_PublicRepository), so that it's highlighted
  2. To compile: Click the "Build" button in the top left corner (symbol of a hammer)
  3. To run: Click the "Run" button in the top left corner (symbol of a green "play" sign)