Reproducible source for XXXXXXXXXXXXXXXXX

Copyright (C) 2018-2025 Mohammad Akhlaghi mohammad@akhlaghi.org
See the end of the file for license conditions.

This is the reproducible project source for the paper titled "XXX XXXXX XXXXXX", by XXXXX XXXXXX, YYYYYY YYYYY and ZZZZZZ ZZZZZ that is published in XXXXX XXXXX.

To reproduce the results and final paper, the only dependency is a minimal Unix-based building environment including a C and C++ compiler (already available on your system if you have ever built and installed a software from source) and a downloader (Wget or cURL). Note that Git is not mandatory: if you don't have Git to run the first command below, go to the URL given in the command on your browser, and download the project's source (there is a button to download a compressed tarball of the project). If you have received this source from arXiv or Zenodo (without any .git directory inside), please see the "Building project tarball" section below.

$ git clone XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
$ cd XXXXXXXXXXXXXXXXXX
$ ./project configure
$ ./project make

This paper is made reproducible using Maneage (MANaging data linEAGE). To learn more about its purpose, principles and technicalities, please see README-hacking.md, or the Maneage webpage at https://maneage.org.

Building the project

This project was designed to have as few dependencies as possible without requiring root/administrator permissions.

1. Necessary dependencies:

   1.1: Minimal software building tools like C compiler, Make, and other tools found on any Unix-like operating system (GNU/Linux, BSD, Mac OS, and others). All necessary dependencies will be built from source (for use only within this project) by the ./project configure script (next step).

   1.2: (OPTIONAL) Tarball of dependencies. If they are already present (in a directory given at configuration time), they will be used. Otherwise, a downloader (wget or curl) will be necessary to download any necessary tarball. The necessary tarballs are also collected in the archived project on https://doi.org/10.5281/zenodo.XXXXXXX. Just unpack that tarball and you should see all the tarballs of this project's software. When ./project configure asks for the "software tarball directory", give the address of the unpacked directory that has all the tarballs. [[TO AUTHORS: UPLOAD THE SOFTWARE TARBALLS WITH YOUR DATA AND PROJECT SOURCE TO ZENODO OR OTHER SIMILAR SERVICES. THEN ADD THE DOI/LINK HERE. DON'T FORGET THAT THE SOFTWARE ARE A CRITICAL PART OF YOUR WORK'S REPRODUCIBILITY.]]

2. Configure the environment (top-level directories in particular) and build all the necessary software for use in the next step. It is recommended to set directories outside the current directory. Please read the description of each necessary input clearly and set the best value. Note that the configure script also downloads, builds and locally installs (only for this project, no root privileges necessary) many programs (project dependencies). So it may take a while to complete.

   $ ./project configure
   

3. Run the following command to reproduce all the analysis and build the final paper.pdf on 8 threads. If your CPU has a different number of threads, change the number (you can see the number of threads available to your operating system by running ./.local/bin/nproc)

   $ ./project make -j8
   

Building project tarball (possibly from arXiv)

If the paper is also published on arXiv, it is highly likely that the authors also uploaded/published the full project there along with the LaTeX sources. If you have downloaded (or plan to download) this source from arXiv, some minor extra steps are necessary as listed below. This is because this tarball is mainly tailored to automatic creation of the final PDF without using Maneage (only calling LaTeX, not using the './project' command)!

You can directly run 'latex' on this directory and the paper will be built with no analysis (all necessary built products are already included in the tarball). One important feature of the tarball is that it has an extra Makefile to allow easy building of the PDF paper without worring about the exact LaTeX and bibliography software commands.

Only building PDF using tarball (no analysis)

1. If you got the tarball from arXiv and the arXiv code for the paper is 1234.56789, then the downloaded source will be called 1234.56789 (no suffix). However, it is actually a .tar.gz file. So take these steps to unpack it to see its contents.

   $ arxiv=1234.56789
   $ mv $arxiv $arxiv.tar.gz
   $ mkdir $arxiv
   $ cd $arxiv
   $ tar xf ../$arxiv.tar.gz
   

2. No matter how you got the tarball, if you just want to build the PDF paper, simply run the command below. Note that this won't actually install any software or do any analysis, it will just use your host operating system (assuming you already have a LaTeX installation and all the necessary LaTeX packages) to build the PDF using the already-present plots data.

   $ make # Build PDF in tarball without doing analysis
   

3. If you want to re-build the figures from scratch, you need to make the following corrections to the paper's main LaTeX source (paper.tex): uncomment (remove the starting %) the line containing \newcommand{\makepdf}{}, see the comments above it for more.

Building full project from tarball (custom software and analysis)

As described above, the tarball is mainly geared to only building the final PDF. A few small tweaks are necessary to build the full project from scratch (download necessary software and data, build them and run the analysis and finally create the final paper).

1. If you got the tarball from arXiv, before following the standard procedure of projects described at the top of the file above (using the ./project script), its necessary to set its executable flag because arXiv removes the executable flag from the files (for its own security).

   $ chmod +x project
   

2. Make the following changes in two of the LaTeX files so LaTeX attempts to build the figures from scratch (to make the tarball; it was configured to avoid building the figures, just using the ones that came with the tarball).

   • paper.tex: uncomment (remove the starting %) of the line containing \newcommand{\makepdf}{}, see the comments above it for more.

   • tex/src/preamble-pgfplots.tex: set the tikzsetexternalprefix variable value to tikz/, so it looks like this: \tikzsetexternalprefix{tikz/}.

3. Remove extra files. In order to make sure arXiv can build the paper (resolve conflicts due to different versions of LaTeX packages), it is sometimes necessary to copy raw LaTeX package files in the tarball uploaded to arXiv. Later, we will implement a feature to automatically delete these extra files, but for now, the project's top directory should only have the following contents (where reproduce and tex are directories). You can safely remove any other file/directory.

   $ ls
   COPYING paper.tex project README-hacking.md README.md reproduce/ tex/
   

Building on older systems (+10 year old compilers)

Maneage builds almost all its software itself. But to do that, it needs a C and C++ compiler on the host. The C++ standard in particular is updated regularly. Therefore, gradually the basic software packages (that are used to build the internal Maneage C compiler and other necessary tools) will start using the newer language features in their newer versions. As a result, if a host doesn't update its compiler for more than a decade, some of the basic software may not get built.

Note that this is only a problem for the "basic" software of Maneage (that are used to build Maneage's own C compiler), not the high-level (or science) software. On GNU/Linux systems, the high-level software get built with Maneage's own C compiler. Therefore once Maneage's C compiler is built, you don't need to worry about the versions of the high-level software.

One solution to such cases is to downgrade the versions of the basic software that can't be built. For example, when building Maneage in August 2022 on a old Debian GNU/Linux system from 2010 (with GCC 4.4.5 and GNU C Library 2.11.3 and Linux kernel 2.6.32-5 on an amd64 architecture), the following low-level packages needed to be downgraded to slightly earlier versions.

As you can see above, fortunately most basic software in Maneage respect +10 year old compilers and are build-able there. So your higher-level science software should be buildable with out changing their versions. It is highly improbable that these downgrades will affect your final science result.

Building on ARM

As of 2021年10月13日, very little testing of Maneage has been done on arm64 (tested in aarch64). However, some testing has been done on the PinePhone, running Debian/Mobian. In principle default Maneage branch (not all high-level software have been tested) should run fully (configure + make) from the raw source to the final verified pdf. Some issues that you might need to be aware of are listed below.

Older packages

In old packages that may be still needed and that have an old config.guess file (e.g. from 2002, such as fftw2-2.1.5-4.2, that are not in the base Maneage branch) may crash during the build. A workaround is to provide an updated (e.g. 2018) 'config.guess' file (automake --add-missing --force-missing --copy) in 'reproduce/software/patches/' and copy it over the old file during the build of the package.

An un-killable running job

Vampires may be a problem on the pinephone/aarch64. A "vampire" is defined here as a job that is in the "R" (running) state, using nearly 95-100% of a cpu, for an extremely long time (hours), without producing any output to its log file, and is immune to being killed by the user or root with 'kill -9'. A reboot and relaunch of the './project configure --existing-conf' command is the only solution currently known (as of 2021年10月13日) for vampires. These are known to have occurred with linux-image-5.13-sunxi64.

RAM/swap space

Adding atleast 3 Gb of swap space (man swapon, man mkswap, man dd) on the eMMC may help to reduce the chance of having errors due to the lack of RAM.

Time scale

On the PinePhone v1.2b, apart from the time wasted by vampires, expect roughly 24 hours' wall time in total for the full 'configure' phase. The default 'maneage' example calculations, diagrams and pdf production are light and should be very fast.

Building in containers

Containers are a common way to build projects in an independent filesystem and an almost independent operating system without the overhead (in size and speed) of a virtual machine. As a result, containers allow easy movement of built projects from one system to another without rebuilding. However, they are still large binary files (+1 Gigabytes) and may not be usable in the future (for example with new software versions not reading old images or old/new kernel issues). Containers are thus good for execution/testing phases of a project, but shouldn't be what you archive for the long term!

It is therefore very important that if you want to save and move your maneaged project within containers, be sure to commit all your project's source files and push them to your external Git repository (you can do these within the container as explained below). This way, you can always recreate the container with future technologies too. Generally, if you are developing within a container, its good practice to recreate it from scratch every once in a while, to make sure you haven't forgot to include parts of your work in your project's version-controlled source. In the sections below we also describe how you can use the container only for the software environment and keep your data and project source on your host.

If you have the necessary software tarballs and input data (optional features described below) you can disable internet. In this situation, the configuration and analysis will be exactly reproduced, the final LaTeX macros will be created, and all results will be verified successfully. However, no final paper.pdf will be created to visualize/combine everything in one easy-to-read file. Until task 15267 is complete, Maneage only needs internet to install TeXLive packages (using TeXLive's own package manager tlmgr) in the ./project configure phase. This won't stop the configuration (since all the analysis can still be reproduced). We are working on completing this task as soon as possible, but until then, if you want to disable internet and you want to build the final PDF, please disable internet after the configuration phase. Note that only the necessary TeXLive packages are installed (~350 MB), not the full TeXLive collection!

The container technologies that Maneage has a high-level interface for (with the reproduce/software/shell directory) are listed below. Each has a dedicated shell script in that directory with an (almost) identical interface. See the respective *-README.md file in that directory for more details, as well as running your desired script with --help or reading its comments at the top of the file.

• Apptainer: useful in high performance computing (HPC) facilities (where you do not have root permissions). Apptainer is fully free and open source software. Apptainer containers can only be created and used on GNU/Linux operating systems, but are stored as a single file (very easy to manage).

• Docker: requires root access, but useful on virtual private servers (VPSs). Docker images are stored and managed by a root-level daemon, so you can only manage them through its own interface (making containers by all users visible and accessible to all other users of a system by default). A docker container build on a GNU/Linux host can also be executed on Windows or macOS. However, while the Docker engine and its command-line interface on GNU/Linux are free and open source software, its desktop application (with a GUI and components necessary for Windows or macOS) is not (requires payment for large companies).

Copyright information

This file is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This file is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this file. If not, see https://www.gnu.org/licenses/.