diff options
30 files changed, 937 insertions, 783 deletions
diff --git a/.dir-locals.el b/.dir-locals.el index 8c3e759..dae2993 100644 --- a/.dir-locals.el +++ b/.dir-locals.el @@ -9,8 +9,8 @@ ;; ;; For more information see (info "(emacs) Directory Variables") ;; -;; Copyright (C) 2017 Mosè Giordano <mose@gnu.org> -;; Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org> +;; Copyright (C) 2017-2020 Mosè Giordano <mose@gnu.org> +;; Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> ;; ;; Copying and distribution of this file, with or without modification, ;; are permitted in any medium without royalty provided the copyright diff --git a/.file-metadata b/.file-metadata Binary files differindex ca6abc5..0daa3df 100644 --- a/.file-metadata +++ b/.file-metadata @@ -9,7 +9,7 @@ # To help readability, please add new files based on the length of the # line you wish to add. # -# Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, # are permitted in any medium without royalty provided the copyright @@ -33,16 +33,14 @@ mmap_* build .local .build -LOCAL.mk Makefile tex/tikz .gnuastro .DS_Store .texlive* +LOCAL.conf tex/pipeline LOCAL_tmp.mk LOCAL_old.mk gnuastro-local.conf - -reproduce/BDIR/ -reproduce/SURVEY/ +.compiler_test_dir_please_delete
\ No newline at end of file diff --git a/README-hacking.md b/README-hacking.md index 5e202b3..82b40e3 100644 --- a/README-hacking.md +++ b/README-hacking.md @@ -1,7 +1,8 @@ Reproducible paper template =========================== -Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> +Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2020 Raul Infante-Sainz <infantesainz@gmail.com>\ See the end of the file for license conditions. This project contains a **fully working template** for doing reproducible @@ -176,7 +177,7 @@ evolving, so some details may be different in them. The more recent ones can be used as a good working example besides the default template. - Infante-Sainz et - al. ([2019](https://ui.adsabs.harvard.edu/abs/2019MNRAS.tmp.2729I), + al. ([2020](https://ui.adsabs.harvard.edu/abs/2020MNRAS.491.5317I), MNRAS, 491, 5317): The version controlled project source is available [on GitLab](https://gitlab.com/infantesainz/sdss-extended-psfs-paper) and is also archived on Zenodo with all the necessary software tarballs: @@ -279,28 +280,20 @@ example if you run `.local/bin/ls` you will be using the `ls` of the template, which is problably different from your system's `ls` (run them both with `--version` to check). -Once the project is configured for your system, `./project prepare` and -`./project make` will do the basic preparations and run the project's -analysis with the custom version of software. The `project` script is just -a wrapper, and with the commands above, it will call `top-prepare.mk` and -`top-make.mk` (both are in the `reproduce/analysis/make` directory). - -In the template, no particular preparation is necessary, so it will -immediately finish and instruct you to run `./project make`. But in some -projects, it can be very useful to do some very basic preparatory steps on -the input data that can greatly optimize running of `./project make`. For -example, you may need to query a server, to find how many input files there -are. Once that number is known in the preparation phase, `./project make` -can parallelize the analysis much more effectively. +Once the project is configured for your system, `./project make` will do +the basic preparations and run the project's analysis with the custom +version of software. The `project` script is just a wrapper, and with the +`make` argument, it will first call `top-prepare.mk` and `top-make.mk` +(both are in the `reproduce/analysis/make` directory). In terms of organization, `top-prepare.mk` and `top-make.mk` have an -identical design, only a minor difference. So, let's continue the -template's architecture with `top-make.mk`. Once you understand that, -you'll clearly understand `top-prepare.mk` also. These very high-level -files are relatively short and heavily commented so hopefully the -descriptions in each comment will be enough to understand the general -details. As you read this section, please also look at the contents of the -mentioned files and directories to fully understand what is going on. +identical design, only minor differences. So, let's continue the template's +architecture with `top-make.mk`. Once you understand that, you'll clearly +understand `top-prepare.mk` also. These very high-level files are +relatively short and heavily commented so hopefully the descriptions in +each comment will be enough to understand the general details. As you read +this section, please also look at the contents of the mentioned files and +directories to fully understand what is going on. Before starting to look into the top `top-make.mk`, it is important to recall that Make defines dependencies by files. Therefore, the @@ -328,17 +321,17 @@ variables/configurations) and _workhorse-Makefiles_ (Makefiles that actually contain analysis/processing rules). The configuration-Makefiles are those that satisfy these two wildcards: -`reproduce/software/config/installation/*.mk` (for building the necessary +`reproduce/software/config/installation/*.conf` (for building the necessary software when you run `./project configure`) and -`reproduce/analysis/config/*.mk` (for the high-level analysis, when you run -`./project make`). These Makefiles don't actually have any rules, they just -have values for various free parameters throughout the configuration or -analysis. Open a few of them to see for yourself. These Makefiles must only -contain raw Make variables (project configurations). By "raw" we mean that -the Make variables in these files must not depend on variables in any other -configuration-Makefile. This is because we don't want to assume any order -in reading them. It is also very important to *not* define any rule, or -other Make construct, in these configuration-Makefiles. +`reproduce/analysis/config/*.conf` (for the high-level analysis, when you +run `./project make`). These Makefiles don't actually have any rules, they +just have values for various free parameters throughout the configuration +or analysis. Open a few of them to see for yourself. These Makefiles must +only contain raw Make variables (project configurations). By "raw" we mean +that the Make variables in these files must not depend on variables in any +other configuration-Makefile. This is because we don't want to assume any +order in reading them. It is also very important to *not* define any rule, +or other Make construct, in these configuration-Makefiles. Following this rule-of-thumb enables you to set these configure-Makefiles as a prerequisite to any target that depends on their variable @@ -379,8 +372,8 @@ Let's see how this design is implemented. Please open and inspect `top-make.mk` it as we go along here. The first step (un-commented line) is to import the local configuration (your answers to the questions of `./project configure`). They are defined in the configuration-Makefile -`reproduce/software/config/installation/LOCAL.mk` which was also built by -`./project configure` (based on the `LOCAL.mk.in` template of the same +`reproduce/software/config/installation/LOCAL.conf` which was also built by +`./project configure` (based on the `LOCAL.conf.in` template of the same directory). The next non-commented set of the top `Makefile` defines the ultimate @@ -444,7 +437,7 @@ project is designed to grow in this framework. File modification dates (meta data) ----------------------------------- -While git does an excellent job at keeping a history of the contents of +While Git does an excellent job at keeping a history of the contents of files, it makes no effort in keeping the file meta data, and in particular the dates of files. Therefore when you checkout to a different branch, files that are re-written by Git will have a newer date than the other @@ -492,7 +485,7 @@ mind are listed below. - Do not use any constant numbers (or important names like filter names) in the workhorse-Makefiles or paper's LaTeX source. Define such constants as logically-grouped, separate configuration-Makefiles in - `reproduce/analysis/config/XXXXX.mk`. Then set this + `reproduce/analysis/config/XXXXX.conf`. Then set this configuration-Makefiles file as a pre-requisite to any rule that uses the variable defined in it. @@ -551,6 +544,27 @@ First custom commit $ git remote rename origin template-origin # Rename current/only remote to "template-origin". $ git branch -m template # Rename current/only branch to "template". $ git checkout -b master # Create and enter new "master" branch. + $ pwd # Just to confirm where you are. + ``` + + - **Prepare to build project**: The `./project configure` command of the + next step will build the different software packages within the + "build" directory (that you will specify). Nothing else on your system + will be touched. However, since it takes long, it is useful to see + what it is being built at every instant (its almost impossible to tell + from the torrent of commands that are produced!). So open another + terminal on your desktop and navigate to the same project directory + that you cloned (output of last command above). Then run the following + command. Once every second, this command will just print the date + (possibly followed by a non-existant directory notice). But as soon as + the next step starts building software, you'll see the names of + software get printed as they are being built. Once any software is + installed in the project build directory it will be removed. Again, + don't worry, nothing will be installed outside the build directory. + + ```shell + # On another terminal (go to top project directory) + $ ./project --check-config ``` - **Test the template**: Before making any changes, it is important to @@ -566,22 +580,11 @@ First custom commit ```shell $ ./project configure # Build the project's software environment (can take an hour or so). - $ ./project prepare # Pre-processing preparations (doing nothing in the raw template). $ ./project make # Do the processing and build paper (just a simple demo in the template). # Open 'paper.pdf' and see if everything is ok. ``` - - **Software building status**: While the `./project configure` command of - the step above is busy building all the different software, you can - check the status by running the following command in another terminal - (but same project source directory). See the "Inspecting status" - section below for more. - - ```shell - $ while true; do echo; date; ls .build/software/build-tmp; sleep 1; done - ``` - - **Setup the remote**: You can use any [hosting facility](https://en.wikipedia.org/wiki/Comparison_of_source_code_hosting_facilities) that supports Git to keep an online copy of your project's version @@ -637,7 +640,8 @@ First custom commit - `reproduce/analysis/make/top-make.mk`: Delete the `delete-me` line in the `makesrc` definition. Just make sure there is no empty line - between the `download \` and `verify \` lines. + between the `download \` and `verify \` lines (they should be + directly under eachother). - `reproduce/analysis/make/verify.mk`: In the final recipe, under the commented line `Verify TeX macros`, remove the full line that @@ -654,7 +658,7 @@ First custom commit ``` - Disable verification of outputs by removing the `yes` from - `reproduce/analysis/config/verify-outputs.mk`. Later, when you are + `reproduce/analysis/config/verify-outputs.conf`. Later, when you are ready to submit your paper, or publish the dataset, activate verification and make the proper corrections in this file (described under the "Other basic customizations" section below). This is a @@ -685,7 +689,7 @@ First custom commit $ echo "tex/src/delete-me.mk merge=ours" >> .gitattributes $ echo "tex/src/delete-me-demo.mk merge=ours" >> .gitattributes $ echo "reproduce/analysis/make/delete-me.mk merge=ours" >> .gitattributes - $ echo "reproduce/analysis/config/delete-me-num.mk merge=ours" >> .gitattributes + $ echo "reproduce/analysis/config/delete-me-num.conf merge=ours" >> .gitattributes $ git add .gitattributes ``` @@ -710,6 +714,19 @@ First custom commit Copyright (C) 2020 YOUR NAME <YOUR@EMAIL.ADDRESS> ``` + - **Configure Git for fist time**: If you have never used Git, then you + have to configure it with some basic information in order to have + essential information in the commit messages (ignore this step if you + have already done it). Git will include your name and e-mail address + information in each commit. You can also specify your favorite text + editor for making the commit (`emacs`, `vim`, etc.). + + ```shell + $ git config --global user.name "YourName YourSurname" + $ git config --global user.email your-email@example.com + $ git config --global core.editor vim + ``` + - **Your first commit**: You have already made some small and basic changes in the steps above and you are in the `master` branch. So, you can officially make your first commit in your project's history. But @@ -750,29 +767,29 @@ Other basic customizations - **High-level software**: The template installs all the software that your project needs. You can specify which software your project needs - in `reproduce/software/config/installation/TARGETS.mk`. The necessary - software are classified into two classes: 1) programs or libraries - (usually written in C/C++) which are run directly by the operating - system. 2) Python modules/libraries that are run within Python. By - default `TARGETS.mk` only has GNU Astronomy Utilities (Gnuastro) as - one scientific program and Astropy as one scientific Python - module. Both have many dependencies which will be installed into your - project during the configuration step. To see a list of software that - are currently ready to be built in the template, see - `reproduce/software/config/installation/versions.mk` (which has their - versions also), the comments in `TARGETS.mk` describe how to use the - software name from `versions.mk`. Currently the raw pipeline just uses - Gnuastro to make the demonstration plots. Therefore if you don't need - Gnuastro, go through the analysis steps in `reproduce/analysis` and - remove all its use cases (clearly marked). + in `reproduce/software/config/installation/TARGETS.conf`. The + necessary software are classified into two classes: 1) programs or + libraries (usually written in C/C++) which are run directly by the + operating system. 2) Python modules/libraries that are run within + Python. By default `TARGETS.conf` only has GNU Astronomy Utilities + (Gnuastro) as one scientific program and Astropy as one scientific + Python module. Both have many dependencies which will be installed + into your project during the configuration step. To see a list of + software that are currently ready to be built in the template, see + `reproduce/software/config/installation/versions.conf` (which has + their versions also), the comments in `TARGETS.conf` describe how to use + the software name from `versions.conf`. Currently the raw pipeline just + uses Gnuastro to make the demonstration plots. Therefore if you don't + need Gnuastro, go through the analysis steps in `reproduce/analysis` + and remove all its use cases (clearly marked). - **Input dataset**: The input datasets are managed through the - `reproduce/analysis/config/INPUTS.mk` file. It is best to gather all + `reproduce/analysis/config/INPUTS.conf` file. It is best to gather all the information regarding all the input datasets into this one central file. To ensure that the proper dataset is being downloaded and used by the project, it is also recommended get an [MD5 checksum](https://en.wikipedia.org/wiki/MD5) of the file and include - that in `INPUTS.mk` so the project can check it automatically. The + that in `INPUTS.conf` so the project can check it automatically. The preparation/downloading of the input datasets is done in `reproduce/analysis/make/download.mk`. Have a look there to see how these values are to be used. This information about the input datasets @@ -806,7 +823,7 @@ Other basic customizations in the project, it will stop and print the problematic file and its expected and calculated checksums. First set the value of `verify-outputs` valiable in - `reproduce/analysis/config/verify-outputs.mk` to `yes`. Then go to + `reproduce/analysis/config/verify-outputs.conf` to `yes`. Then go to `reproduce/analysis/make/verify.mk`. The verification of all the files is only done in one recipe. First the files that go into the plots/figures are checked, then the LaTeX macros. Validation of the @@ -956,8 +973,8 @@ for the benefit of others. - *Environment of each recipe*: If you need to define a special environment (or alises, or scripts to run) for all the recipes in - your Makefiles, you can use the Bash startup file - `reproduce/software/bash/bashrc.sh`. This file is loaded before every + your Makefiles, you can use a Bash startup file + `reproduce/software/shell/bashrc.sh`. This file is loaded before every Make recipe is run, just like the `.bashrc` in your home directory is loaded everytime you start a new interactive, non-login terminal. See the comments in that file for more. @@ -1226,25 +1243,6 @@ for the benefit of others. $ git clone my-project-git.bundle ``` - - **Inspecting software building status**: When you run `./project - configure`, several programs and libraries start to get configured and - build (in many cases, simultaneously). To understand the building - process, or for debugging a strange situation, it is sometimes useful - to know which programs are being built at every moment. To do this, - you can look into the `.build/software/build-tmp` directory (from the - top project directory). This temporary directory is only present while - building the software. At every moment, it contains the unpacked - source tarball directories of the all the packages that are being - built. After a software is successfully installed in your project, it - is removed from this directory. To automatically get a listing of this - directory every second, you can run the command below (on another - terminal while the software are being built). Press `CTRL-C` to stop - it and return back to the command-line). - - ```shell - $ while true; do echo; date; ls .build/software/build-tmp; sleep 1; done - ``` - @@ -21,7 +21,6 @@ received this source from arXiv, please see the respective section below. $ git clone XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX $ cd XXXXXXXXXXXXXXXXXX $ ./project configure -$ ./project prepare $ ./project make ``` @@ -77,20 +76,7 @@ requiring root/administrator permissions. $ ./project configure ``` -3. In some cases, the project's analysis may need some preparations to - optimize its processing. This is usually mainly related to input data, - and some very basic calculations that can help the management of the - overall lproject in the main/next step. To do the basic preparations, - please run this command to do the preparation 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`) - - ```shell - $ ./project prepare -j8 - ``` - -4. Run the following command to reproduce all the analysis and build the +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`) @@ -1,4 +1,4 @@ -#!/bin/bash +#!/bin/sh # # High-level script to manage the project. # Run `./project --help' for a description of how to use it. @@ -33,9 +33,11 @@ host_cc=0 operation= build_dir= input_dir= +check_config= make_targets= software_dir= clean_texdir=0 +prepare_redo=0 existing_conf=0 scriptname="./project" minmapsize=10000000000 @@ -65,14 +67,12 @@ print_help() { # Print the output. cat <<EOF Usage: $scriptname configure [OPTIONS] - $scriptname prepare [OPTIONS] $scriptname make [OPTIONS] Top-level script to manage the reproducible project. The high-level operation is defined by the (mandatory) second argument: configure - Configure project for this machine (e.g., build software). - prepare - Low-level preparations to optimize building with 'make'. make - Run the project (do analysis and build outputs). RECOMMENDATION: If this is the first time you are configuring this @@ -97,6 +97,7 @@ Configure options: -i, --input-dir=STR Directory containing input datasets (optional). -m, --minmapsize=INT [Gnuastro] Minimum number of bytes to use RAM. -s, --software-dir=STR Directory containing necessary software tarballs. + --check-config During configuration, show what is being built. --clean-texdir Remove possibly existing build-time subdirectories under the project's 'tex/' directory (can happen when source is from arXiv for example). @@ -108,6 +109,7 @@ Configure and Make options: Make options: -d, --debug=FLAGS Print various types of debugging information. + -p, --prepare-redo Re-do preparation (only done automatically once). Mandatory or optional arguments to long options are also mandatory or optional for any corresponding short options. @@ -144,12 +146,11 @@ func_operation_set() { fi } -while [[ $# -gt 0 ]] +while [ $# -gt 0 ] do case $1 in # Main operation. configure) func_operation_set $1; shift;; - prepare) func_operation_set $1; shift;; make) func_operation_set $1; shift;; @@ -161,8 +162,8 @@ do -e*|--existing-conf=*) on_off_option_error --existing-conf -e;; --host-cc) host_cc=1; shift;; --host-cc=*) on_off_option_error --host-cc;; - -i|--inputdir) input_dir="$2"; check_v "$1" "$input_dir"; shift;shift;; - -i=*|--inputdir=*) input_dir="${1#*=}"; check_v "$1" "$input_dir"; shift;; + -i|--input-dir) input_dir="$2"; check_v "$1" "$input_dir"; shift;shift;; + -i=*|--input-dir=*) input_dir="${1#*=}"; check_v "$1" "$input_dir"; shift;; -i*) input_dir=$(echo "$1" | sed -e's/-i//'); check_v "$1" "$input_dir"; shift;; -m|--minmapsize) minmapsize="$2"; check_v "$1" "$minmapsize"; shift;shift;; -m=*|--minmapsize=*) minmapsize="${1#*=}"; check_v "$1" "$minmapsize"; shift;; @@ -170,6 +171,8 @@ do -s|--software-dir) software_dir="$2"; check_v "$1" "$software_dir"; shift;shift;; -s=*|--software-dir=*) software_dir="${1#*=}"; check_v "$1" "$software_dir"; shift;; -s*) software_dir=$(echo "$1" | sed -e's/-s//'); check_v "$1" "$software_dir"; shift;; + --check-config) check_config=1; shift;; + --check-config=*) on_off_option_error --check-config;; --clean-texdir) clean_texdir=1; shift;; --clean-texdir=*) on_off_option_error --clean-texdir;; @@ -183,12 +186,17 @@ do -'?'|--help) print_help; exit 0;; -'?'*|--help=*) on_off_option_error --help -?;; - # Make options (note that Make's `debug' can take values, but when called - # without any value, it is like giving it a value of `a'): + # Make options + # ------------ + # + # Note that Make's `debug' can take values, but when called without any + # value, it is like giving it a value of `a'): -d|--debug) if [ x"$2" = x ]; then debug=a; shift; else debug="$2"; check_v debug "$debug"; shift;shift; fi;; -d=*|--debug=*) debug="${1#*=}"; check_v debug "$debug"; shift;; -d*) debug=$(echo "$1" | sed -e's/-d//'); check_v debug "$debug"; shift;; + -p|--prepare-redo) prepare_redo=1; shift;; + -p=*|--prepare-redo=*) on_off_option_error --prepare-redo; shift;; # Unrecognized option: -*) echo "$scriptname: unknown option '$1'"; exit 1;; @@ -202,6 +210,44 @@ done +# Check configuration status +# -------------------------- +if ! [ x$check_config = x ]; then + # Find the color option to pass to `ls'. Note that `--color' (for GNU + # Coreutils `ls') should be checked first because it also has `-G', but + # for something else. + if ls --color 2> /dev/null > /dev/null; then coloropt="--color=auto" + elif ls -G 2> /dev/null > /dev/null; then coloropt="-G" + else coloropt="" + fi + + # Print a notice to let the user know what is happening. + cat <<EOF + +This is an infinite loop that will print what software are being built at +every moment. It is actually a listing ('ls' command) of the temporary +directory where software source code are unpacked while they are being +built. If the project isn't being configured, the output (every second) +will either be empty (only a date) or a with an error about a non-existant +directory. This feature is thus only useful when the project's software are +being built. + +EOF + + # Run the infinite loop. + while true; do + echo; + echo "$(date) [[press CTRL-C to stop]]"; + ls $coloropt .build/software/build-tmp || junk=1; + sleep 1; + done + exit 0 +fi + + + + + # Basic group settings # -------------------- if ! [ x$group = x ]; then @@ -252,48 +298,10 @@ controlled_env() { -# Error messages -# -------------- -# -# Having the error messages here helps the over-all process be more -# readable. -print_error_abort() { - case $1 in - prepare) - cat <<EOF - -The project isn't configured for this system, or the configuration wasn't -successful. To configure the project, please use this command: - - $ ./project configure - -(TIP: if you have already ran this command once, run it with '-e' to use -the previous configuration, run with '--help' for more info) - -EOF - exit 1; - ;; - make) - cat <<EOF - -The project preparation hasn't been completed, or it wasn't successful. To -prepare the project prior to building it, please use this command: - - $ ./project prepare - -EOF - exit 1; - ;; - esac -} - - - - # Do requested operation # ---------------------- perms="u+r,u+w,g+r,g+w,o-r,o-w,o-x" -configscript=./reproduce/software/bash/configure.sh +configscript=./reproduce/software/shell/configure.sh case $operation in # Build the project's software. @@ -313,7 +321,7 @@ case $operation in # `reproduce/*/bash' should need executable flags, so we are giving # them executable flags by default. If any other file in your project # needs such flags, add them here. - chmod +x reproduce/software/bash/* reproduce/analysis/bash/* + chmod +x reproduce/software/shell/* reproduce/analysis/bash/* # If the user requested, clean the TeX directory from the extra # (to-be-built) directories that may already be there (and will not @@ -356,30 +364,44 @@ case $operation in - # Run the input management. - prepare) + # Run the project. + make) # Make sure the configure script has been completed properly # (`configuration-done.txt' exists). if ! [ -f .build/software/configuration-done.txt ]; then - print_error_abort $operation - fi + cat <<EOF - # Run input-preparations in control environment - controlled_env reproduce/analysis/make/top-prepare.mk - ;; +The project is either (1) not configured on this system, or (2) the +configuration wasn't successful. +(1) If it hasn't been configured at all, use the command below to configure +it (set a build directory and let it build its necessary software in it). + $ ./project configure +(2) If it has been configured, but the configuration failed in a step, you +can re-configure it using your previous settings with the command +below. All successful steps will be skipped, allowing a fast completion. + $ ./project configure -e - # Run the project - make) +If there was a problem, please let us know by filling this online form: + http://savannah.nongnu.org/support/?func=additem&group=reproduce - # Make sure the configure script has been completed properly - # (`configuration-done.txt' exists). - if ! [ -f .build/software/preparation-done.mk ]; then - print_error_abort $operation +EOF + exit 1 + fi + + # Run data preparation phase (optionally build Makefiles with + # special values for optimizing the main `top-make.mk'). But note + # that data preparation is only done automatically the first time + # the project is built (when `.build/software/preparation-done.mk' + # doesn't yet exist). After that, if the user wants to re-do the + # preparation they have to use the `--prepare-redo' option. + if ! [ -f .build/software/preparation-done.mk ] \ + || [ x"$prepare_redo" = x1 ]; then + controlled_env reproduce/analysis/make/top-prepare.mk fi # Run the actual project. @@ -392,9 +414,14 @@ case $operation in # Operation not specified. *) - echo "No operation defined." - echo "Please run with '--help' for more information." - echo "Available operations are: 'configure', 'prepare', or 'make')." + cat <<EOF + +No operation defined! + +Please run with '--help' for more information. +(TIP: available operations are: 'configure' or 'make'). + +EOF exit 1 ;; esac diff --git a/reproduce/analysis/bash/download-multi-try b/reproduce/analysis/bash/download-multi-try index dec2539..7a5f8f2 100755 --- a/reproduce/analysis/bash/download-multi-try +++ b/reproduce/analysis/bash/download-multi-try @@ -51,11 +51,13 @@ set -e -# Input arguments and necessary sanity checks. +# Input arguments and necessary sanity checks. Note that the 5th argument +# (backup servers) isn't mandatory. inurl="$3" outname="$4" lockfile="$2" downloader="$1" +backupservers="$5" if [ "x$downloader" = x ]; then echo "$0: downloader (first argument) not given."; exit 1; fi @@ -73,6 +75,13 @@ fi +# Separate the actual filename, to possibly use backup server. +urlfile=$(echo "$inurl" | awk -F "/" '{print $NF}') + + + + + # Try downloading multiple times before crashing. counter=0 maxcounter=10 @@ -107,8 +116,19 @@ while [ ! -f "$outname" ]; do if [ x"$lockfile" = xnolock ]; then if ! $downloader $outname $inurl; then rm -f $outname; fi else + # Try downloading from the requested URL. flock "$lockfile" bash -c \ "if ! $downloader $outname $inurl; then rm -f $outname; fi" + + # If it failed, try the backup server(s). + if [ ! -f "$outname" ]; then + if [ x"$backupservers" != x ]; then + for bs in "$backupservers"; do + flock "$lockfile" bash -c \ + "if ! $downloader $outname $bs/$urlfile; then rm -f $outname; fi" + done + fi + fi fi done diff --git a/reproduce/analysis/config/verify-outputs.conf b/reproduce/analysis/config/verify-outputs.conf index e580e04..0542c53 100644 --- a/reproduce/analysis/config/verify-outputs.conf +++ b/reproduce/analysis/config/verify-outputs.conf @@ -1,3 +1,2 @@ # To disable verification of output datasets set this variable to yes - verify-outputs = diff --git a/reproduce/analysis/make/download.mk b/reproduce/analysis/make/download.mk index e4f2ccd..cf5bfa4 100644 --- a/reproduce/analysis/make/download.mk +++ b/reproduce/analysis/make/download.mk @@ -24,9 +24,10 @@ # Download input data # -------------------- # -# The input dataset properties are defined in `$(pconfdir)/INPUTS.mk'. For -# this template we only have one dataset to enable easy processing, so all -# the extra checks in this rule may seem redundant. +# The input dataset properties are defined in +# `$(pconfdir)/INPUTS.conf'. For this template we only have one dataset to +# enable easy processing, so all the extra checks in this rule may seem +# redundant. # # In a real project, you will need more than one dataset. In that case, # just add them to the target list and add an `elif' statement to define it diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index a4acff7..ce4e488 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -141,6 +141,12 @@ export SHELL := $(installdir)/bin/bash export CPPFLAGS := -I$(installdir)/include export LD_LIBRARY_PATH := $(installdir)/lib +# Until we build our own C library, without this, the project's GCC won't +# be able to compile anything if the host C library isn't in a standard +# place: in particular Debian-based operatings sytems. On other systems, it +# will be empty. +export CPATH := $(SYS_CPATH) + # RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is # ultimately redundant. But on some systems, even having a single value # causes crashs (see bug #56682). So we'll just give it no value at all. @@ -151,9 +157,9 @@ export DYLD_LIBRARY_PATH := # remote-shell accesss through this environment variable. export OMPI_MCA_plm_rsh_agent=/bin/false -# Recipe startup script, see `reproduce/software/bash/bashrc.sh'. +# Recipe startup script. export PROJECT_STATUS := make -export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh +export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh @@ -242,7 +248,7 @@ distclean: clean # `rm', not our own. $$sys_rm -rf $(BDIR) $$sys_rm -f Makefile .gnuastro .local .build - $$sys_rm -f $(pconfdir)/LOCAL.mk $(gconfdir)/gnuastro-local.conf + $$sys_rm -f $(pconfdir)/LOCAL.conf $(gconfdir)/gnuastro-local.conf @@ -299,10 +305,11 @@ $(packagecontents): paper.pdf | $(texdir) # directories (when building in a group structure, there will be # `build-user1', `build-user2' and etc), are just temporary LaTeX # build files and don't have any relevant/hand-written files in - # them. 2) The `LOCAL.mk' and `gnuastro-local.conf' files just have - # this machine's local settings and are irrelevant for anyone else. + # them. 2) The `LOCAL.conf' and `gnuastro-local.conf' files just + # have this machine's local settings and are irrelevant for anyone + # else. rm -rf $$dir/tex/build/build* - rm $$dir/reproduce/software/config/installation/LOCAL.mk + rm $$dir/reproduce/software/config/installation/LOCAL.conf rm $$dir/reproduce/software/config/gnuastro/gnuastro-local.conf # When submitting to places like arXiv, they will just run LaTeX diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index af6bdc5..67db364 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -38,7 +38,7 @@ # # Note that if you don't want the final PDF and just want the processing # and file outputs, you can remove the value of `pdf-build-final' in -# `reproduce/analysis/config/pdf-build.mk'. +# `reproduce/analysis/config/pdf-build.conf'. $(mtexdir)/project.tex: $(mtexdir)/verify.tex # If no PDF is requested, or if LaTeX isn't available, don't @@ -62,7 +62,7 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex echo "can check by running './.local/bin/latex --version'), _AND_" echo "make sure that the 'pdf-build-final' variable has a value." echo "'pdf-build-final' is defined in: " - echo "'reproduce/analysis/config/pdf-build.mk'." + echo "'reproduce/analysis/config/pdf-build.conf'." echo echo "If you don't have LaTeX within the project, please re-run" echo "'./project configure -e' when you have internet access." diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk index 1f0613c..36f25e7 100644 --- a/reproduce/analysis/make/prepare.mk +++ b/reproduce/analysis/make/prepare.mk @@ -19,7 +19,9 @@ # Final-target # # Without this file, `./project make' won't work. -$(BDIR)/software/preparation-done.mk: +prepare-dep = $(subst prepare, ,$(makesrc)) +$(BDIR)/software/preparation-done.mk: \ + $(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex) # If you need to add preparations define targets above to do the # preparations, then set the value below to `yes'. Recall that just diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index 000c1fd..30d537a 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -21,7 +21,7 @@ # Load the local configuration (created after running # `./project configure'). -include reproduce/software/config/installation/LOCAL.mk +include reproduce/software/config/installation/LOCAL.conf @@ -50,7 +50,7 @@ include reproduce/software/config/installation/LOCAL.mk # # Controlling this requires two variables that are available at this stage: # -# - `GROUP-NAME': from `LOCAL.mk' (which was built by `./project configure'). +# - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure'). # - `reproducible_paper_group_name': value to the `--group' option. # # The analysis is only done when both have the same group name. Note that @@ -63,7 +63,7 @@ include reproduce/software/config/installation/LOCAL.mk # # If you are just interested in the processing and don't want to build the # PDF, you can skip the creatation of the final PDF by removing the value -# of `pdf-build-final' in `reproduce/analysis/config/pdf-build.mk'. +# of `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'. ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME)) all: paper.pdf else diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index 5ce120d..1778c6b 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -25,7 +25,7 @@ # Load the local configuration (created after running # `./project configure'). -include reproduce/software/config/installation/LOCAL.mk +include reproduce/software/config/installation/LOCAL.conf @@ -37,19 +37,7 @@ include reproduce/software/config/installation/LOCAL.mk # See `top-make.mk' for complete explanation. ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME)) all: $(BDIR)/software/preparation-done.mk - @echo ""; - echo "----------------" - echo "Project preparation has been completed without any errors." - echo "" - echo "Please run the following command to start building the project." - echo "(Replace '8' with the number of CPU threads on your system)" - echo "" - if [ "x$(GROUP-NAME)" = x ]; then \ - echo " $$ ./project make"; \ - else \ - echo " $$ ./project make --group=$(GROUP-NAME) -j8"; \ - fi - echo "" + @echo "Project preparation is complete."; else all: @if [ "x$(GROUP-NAME)" = x ]; then \ @@ -59,6 +47,7 @@ all: echo "Project is configured for groups, please run"; \ echo " $$ ./project prepare --group=$(GROUP-NAME) -j8"; \ fi + exit 1 endif @@ -87,5 +76,5 @@ makesrc = initialize \ # # See `top-make.mk' for complete explanation. project-phase = prepare -include reproduce/analysis/config/*.mk +include reproduce/analysis/config/*.conf include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk) diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk index a04bce4..f0bcf10 100644 --- a/reproduce/analysis/make/verify.mk +++ b/reproduce/analysis/make/verify.mk @@ -33,7 +33,7 @@ verify-print-tips = \ echo "If you are still developing your project, you can disable"; \ echo "verification by removing the value of the variable in the"; \ echo "following file (from the top project source directory):"; \ - echo " reproduce/analysis/config/verify-outputs.mk"; \ + echo " reproduce/analysis/config/verify-outputs.conf"; \ echo; \ echo "If this is the final version of the file, you can just copy"; \ echo "and paste the calculated checksum (above) for the file in"; \ diff --git a/reproduce/software/bibtex/missfits.tex b/reproduce/software/bibtex/missfits.tex new file mode 100644 index 0000000..85a1645 --- /dev/null +++ b/reproduce/software/bibtex/missfits.tex @@ -0,0 +1,18 @@ +%% Copyright (C) 2020 Surena Fatemi <surena.fatemi@ipm.ir> +%% +%% Copying and distribution of this file, with or without modification, +%% are permitted in any medium without royalty provided the copyright +%% notice and this notice are preserved. This file is offered as-is, +%% without any warranty. + +@ARTICLE{missfits, + author = {{Marmo}, C. and {Bertin}, E.}, + title = "{MissFITS and WeightWatcher: Two Optimised Tools for Managing FITS Data.}", + journal = {Astronomical Data Analysis Software and Systems XVII}, + year = 2008, + volume = {394}, + series = {Astronomical Society of the Pacific Conference Series}, + pages = {619}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2008ASPC..394..619M}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +}
\ No newline at end of file diff --git a/reproduce/software/config/installation/LOCAL.mk.in b/reproduce/software/config/installation/LOCAL.conf.in index 1045f72..0579218 100644 --- a/reproduce/software/config/installation/LOCAL.mk.in +++ b/reproduce/software/config/installation/LOCAL.conf.in @@ -12,5 +12,6 @@ BDIR = @bdir@ INDIR = @indir@ DEPENDENCIES-DIR = @ddir@ +SYS_CPATH = @sys_cpath@ DOWNLOADER = @downloader@ GROUP-NAME = @groupname@ diff --git a/reproduce/software/config/installation/TARGETS.mk b/reproduce/software/config/installation/TARGETS.conf index 0352d53..bb402be 100644 --- a/reproduce/software/config/installation/TARGETS.mk +++ b/reproduce/software/config/installation/TARGETS.conf @@ -18,17 +18,17 @@ # All software that are currently available for installation can be seen in # the following file. # -# reproduce/software/config/installation/versions.mk +# reproduce/software/config/installation/versions.conf # # Please add any software that you need for your project in the respective -# part below (using its name in `versions.mk', but without the `-version' +# part below (using its name in `versions.conf', but without the `-version' # part). Just note that if a program/library is a dependency of another, # you don't need to include it here (it will be installed before the # higher-level software anyway). # # Note that many low-level software will be installed before those that are # installed in this step. They are clearly distinguished from the -# higher-level (optional) software in `versions.mk'. These low-level +# higher-level (optional) software in `versions.conf'. These low-level # software MUST NOT be added here. diff --git a/reproduce/software/config/installation/checksums.mk b/reproduce/software/config/installation/checksums.conf index a1a3767..4a5d8aa 100644 --- a/reproduce/software/config/installation/checksums.mk +++ b/reproduce/software/config/installation/checksums.conf @@ -43,7 +43,7 @@ libiconv-checksum = 365dac0b34b4255a0066e8033a8b3db4bdb94b9b57a9dca17ebf2d779139 libtool-checksum = a6eef35f3cbccf2c9e2667f44a476ebc80ab888725eb768e91a3a6c33b8c931afc46eb23efaee76c8696d3e4eed74ab1c71157bcb924f38ee912c8a90a6521a4 lzip-checksum= 0349b4c6c0b41e601b7ee381c3254d741397beb3ef9354c08162f346f131f4f48f6613ee0a610cdc6d827530df634f884ecfeee35215b10045a40fee76f8e938 m4-checksum = a92cad4441b3fd7c033837389ca3499494523d364a5fda043d92c517051510f1758b3b837f0477f42d2258a179ab79a4993e5d1694ef2673db6d96d1faff84fe -make-checksum = 6ebf886a394c61eea53dc0fa277b00cda263861e8e647608e0fce549cd619946981224408ee519bbd71068e9424798d3c5791451f60ff06d766f563142703d32 +make-checksum = 9a1185cc468368f4ec06478b1cfa343bf90b5cd7c92c0536567db0315b0ee909af53ecce3d44cfd93dd137dbca1ed13af5713e8663590c4fdd21ea635d78496b metastore-checksum = b2a5fdde9de5ddc1e6c368d5da1b2e97e4fdbaa138a7be281ccb40a81dd4a9bb1849d36b2d5d3f01205079bace60441f82a7002097ff3a7037340a35b0f1574a mpc-checksum = 72d657958b07c7812dc9c7cbae093118ce0e454c68a585bfb0e2fa559f1bf7c5f49b93906f580ab3f1073e5b595d23c6494d4d76b765d16dde857a18dd239628 mpfr-checksum = d583555d08863bf36c89b289ae26bae353d9a31f08ee3894520992d2c26e5683c4c9c193d7ad139632f71c0a476d85ea76182702a98bf08dde7b6f65a54f8b88 @@ -71,9 +71,9 @@ zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff # ------------------------------------------ # # These are programs and libraries that are optional, The ones in -# `reproduce/software/config/installation/TARGETS.mk' will be built as part -# of a project. To specify a software there, just remove the `-checksum' -# suffix from the list below. +# `reproduce/software/config/installation/TARGETS.conf' will be built as +# part of a project. To specify a software there, just remove the +# `-checksum' suffix from the list below. apachelog4cxx-checksum = aa59ce549c2c5cbeec031361dfce09cdfc3e62ee3bc9ecbc809507b7ec878c14409b98536b7d13c27690809c8e9d5ebafc3589c9fb5e4aecd5cc064943ae7d6b apr-checksum = daa140c83c7e2c45c3980d9dc81d34fa662bebd050653562c39572d0ddf2eaedb71767c518a59d77f59db9b32e00221ef48b9f72ec3666c4521dd511969f3706 apr-util-checksum = 84da76e9b64da2de0996d4d6f3ab3f23db3724eb6352d218e0e8196bcc0b0a5d4fe791f41b4cc350ce3d04cce3bb3cf8bfb513d777d0cd030928368e6b55a536 @@ -111,6 +111,7 @@ libtiff-checksum = d213e5db09fd56b8977b187c5a756f60d6e3e998be172550c2892dbdb4b2a libtirpc-checksum = 392f391f9fc1bd68d81dc44e4058831a64b32790b5c8c37338b0ab416fad2ae4d16389e632596734dba09780347918cc65c6f134e0c1afd09e81ec250785ed23 libxml2-checksum = cb7784ba4e72e942614e12e4f83f4ceb275f3d738b30e3b5c1f25edf8e9fa6789e854685974eed95b362049dbf6c8e7357e0327d64c681ed390534ac154e6810 minizip-checksum = 56b5443f79d1a0a5f563a563f7b1c27b0b0fc5ba5b37248367b204a89a9373df7d12ea802c678f3f39c987d5f1766003eac3dd31b643773afa4463a3f6406628 +missfits-checksum = 32727f5eb30573a1cedacb8900e2536867e4815059eee32e64e3db65be9291b8a91b9f45b2c9f3cf6fc2a8cc448012ea3d502bdd9dee516008e17d5086aee795 netpbm-checksum = 064720f8a9d0a502488e1af4daecdbf3936910996507ca6f311073a0ad842346692a148eb1ddf7b717f7b108f60500246cb4b83f4d3665f5fc285a84ae1d63d6 openblas-checksum = 91b3074eb922453bf843158b4281cde65db9e8bbdd7590e75e9e6cdcb486157f7973f2936f327bb3eb4f1702ce0ba51ae6729d8d4baf2d986c50771e8f696df0 openmpi-checksum = 760716974cb6b25ad820184622e1ee7926bc6fda87db6b574f76792bc1ca99522e52195866c14b7cb2df5a4981efdaf9f71d2c5533cc0e8e45c2c4b3b74cbacc @@ -144,7 +145,7 @@ yaml-checksum = 13d2197135946204323dbfccafa0ac7b3d05437e920545a56f46811fd7319c01 asn1crypto-checksum = 44d442a6ddfa971e31e24712fe084368356deb5e1c4c3b3e813e0910931860215bc1c4f9eb2c4bd4fdef607c324086c096e9357068646efd28c97f2d4f85c62f asteval-checksum = 4d64900b2f7dfdd098d6c8c102f9d9fd46f9ec265a54330e7d94479ba41f0ee0698855658e18b8b32b9c255159eb9a085af5f0306eb6508663d3fea7d2e00b4a astropy-checksum = c32e874d208f312f894643ab5b3d71dc37630e544da0ceb5ee998d752f9a055d32f6e4319f2cb6928637aaf8573bac58d2882bd636b6a89f5501e3ac7e5ab681 -astroquery-checksum = 0da57f687ac0aa7611cd97085771d79c99e9ac8c11f0828fcbc7390faf24e1e87d86812020e0ae8be1749f5f2ae9cb3733e5922d38a897a9e212247175c28e52 +astroquery-checksum = 43846791d8469a26cf6bb8819db58b830cfe50a34bc0091c2e843dd7dc78b1317530855d432a3a567a9f6a6f4d2682382a32edc91ea01716246b99b3625ec521 beautifulsoup4-checksum = 7aa77bc6008bbcbbbe91b0a850007ab237d2832b63a787fbd94b7cbf47d4276b185e0c61c134df73221406458edff2b75b6b8c2b53b543aa3bb1b0e2202dac5a certifi-checksum = 6a6bf1ff98caefcdbf78a8c83e11e155368bacdd806f0ae0c6afa8f513667df6598e594b3584de61acdca3d6049f4a776937f2aa8672b602bd6db7b737f6074e cffi-checksum = af4fe47cf5d6f1126222898365cfa21e9f11d0e71b87d869014dbb37af30dca9ddf50c989030d0f610f50e8099e8dfd08a688d8c3629abbcc4f0294f5f91b817 diff --git a/reproduce/software/config/installation/texlive.mk b/reproduce/software/config/installation/texlive-packages.conf index 6760eba..6760eba 100644 --- a/reproduce/software/config/installation/texlive.mk +++ b/reproduce/software/config/installation/texlive-packages.conf diff --git a/reproduce/software/config/installation/versions.mk b/reproduce/software/config/installation/versions.conf index 988f668..1b678ad 100644 --- a/reproduce/software/config/installation/versions.mk +++ b/reproduce/software/config/installation/versions.conf @@ -41,7 +41,7 @@ libiconv-version = 1.16 libtool-version = 2.4.6 lzip-version= 1.20 m4-version = 1.4.18 -make-version = 4.2.90 +make-version = 4.3 metastore-version = 1.1.2-23-fa9170b mpc-version = 1.1.0 mpfr-version = 4.0.2 @@ -69,9 +69,9 @@ zlib-version = 1.2.11 # ------------------------------------------ # # These are programs and libraries that are optional, The ones in -# `reproduce/software/config/installation/TARGETS.mk' will be built as part -# of a project. To specify a software there, just remove the `-version' -# suffix from the list below. +# `reproduce/software/config/installation/TARGETS.conf' will be built as +# part of a project. To specify a software there, just remove the +# `-version' suffix from the list below. apachelog4cxx-version = 0.10.0-603-014954db apr-version = 1.7.0 apr-util-version = 1.6.1 @@ -108,6 +108,7 @@ libtiff-version = 4.0.10 libtirpc-version = 1.1.4 libxml2-version = 2.9.9 minizip-version = 2.9.2 +missfits-version = 2.8.0 openblas-version = 0.3.5 openmpi-version = 4.0.1 openssh-version = 8.0p1 @@ -139,7 +140,7 @@ yaml-version = 0.2.2 asn1crypto-version = 0.24.0 asteval-version = 0.9.16 astropy-version = 4.0 -astroquery-version = 0.3.9 +astroquery-version = 0.4 beautifulsoup4-version = 4.7.1 certifi-version = 2018.11.29 cffi-version = 1.12.2 diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md index fc04dfb..d71a3d5 100644 --- a/reproduce/software/make/README.md +++ b/reproduce/software/make/README.md @@ -2,7 +2,7 @@ Software building instructions ============================== This directory contains Makefiles that are called by the high-level -`reproduce/software/bash/configure.sh` script. The main target for the +`reproduce/software/shell/configure.sh` script. The main target for the installation of each software is a simple plain text file that contains the name of the software and its version (which is put in the paper in the end). Once built, these plain-text files are all put in the proper diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index e7d00df..212c738 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -34,9 +34,9 @@ # Top level environment include reproduce/software/make/build-rules.mk -include reproduce/software/config/installation/LOCAL.mk -include reproduce/software/config/installation/versions.mk -include reproduce/software/config/installation/checksums.mk +include reproduce/software/config/installation/LOCAL.conf +include reproduce/software/config/installation/versions.conf +include reproduce/software/config/installation/checksums.conf lockdir = $(BDIR)/locks tdir = $(BDIR)/software/tarballs @@ -48,7 +48,7 @@ ibidir = $(BDIR)/software/installed/version-info/proglib # We'll need the system's PATH for making links to low-level programs we # won't be building ourselves. -syspath := $(PATH) +syspath := $(PATH) # As we build more programs, we want to use this project's built programs # and libraries, not the host's. @@ -58,7 +58,15 @@ export PKG_CONFIG_PATH := $(ildir)/pkgconfig export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS) -export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH) \ + +# This is the "basic" tools where we are relying on the host operating +# system, but are slowly populating our basic software envirnoment. To run +# (system or template) programs, `LD_LIBRARY_PATH' is necessary, so here, +# we'll first tell the programs to look into any possible pre-defined +# `LD_LIBRARY_PATH', then we'll add our own newly installed libraries. We +# will also make sure that there is no "current directory" in it (by +# removing a starting or trailing `:' and any occurance of `::'. +export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH):$(ildir) \ | sed -e's/::/:/g' -e's/^://' -e's/:$$//') # RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is @@ -66,14 +74,18 @@ export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH) \ # causes crashs (see bug #56682). So we'll just give it no value at all. export DYLD_LIBRARY_PATH := -# Recipe startup script, see `reproduce/software/bash/bashrc.sh'. +# Recipe startup script. export PROJECT_STATUS := configure_basic -export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh +export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh # Define the top-level basic programs (that don't depend on any other). top-level-programs = low-level-links gcc all: $(foreach p, $(top-level-programs), $(ibidir)/$(p)) +# Servers to use as backup, later this should go in a file that is not +# under version control (the actual server that the tarbal comes from is +# irrelevant). +backupservers = http://akhlaghi.org/reproduce-software @@ -176,7 +188,7 @@ $(tarballs): $(tdir)/%: | $(lockdir) mergenames=0; \ c=$(m4-checksum); \ w=http://akhlaghi.org/reproduce-software/m4-1.4.18-patched.tar.gz; \ - elif [ $$n = make ]; then c=$(make-checksum); w=https://alpha.gnu.org/gnu/make; \ + elif [ $$n = make ]; then c=$(make-checksum); w=https://ftp.gnu.org/gnu/make; \ elif [ $$n = metastore ]; then c=$(metastore-checksum); w=http://akhlaghi.org/reproduce-software; \ elif [ $$n = mpc ]; then c=$(mpc-checksum); w=http://ftp.gnu.org/gnu/mpc; \ elif [ $$n = mpfr ]; then c=$(mpfr-checksum); w=http://www.mpfr.org/mpfr-current;\ @@ -228,15 +240,19 @@ $(tarballs): $(tdir)/%: | $(lockdir) \ touch $(lockdir)/download; \ $(downloadwrapper) "$$downloader" $(lockdir)/download \ - $$tarballurl "$@.unchecked"; \ + $$tarballurl "$@.unchecked" "$(backupservers)"; \ fi; \ \ \ if type sha512sum > /dev/null 2>/dev/null; then \ checksum=$$(sha512sum "$@.unchecked" | awk '{print $$1}'); \ - echo "$*: should be '$$c', is '$$checksum'"; \ - if [ x$$checksum = x$$c ]; then mv "$@.unchecked" "$@"; \ - else echo "ERROR: Non-matching checksum for '$*'."; exit 1; \ + if [ x"$$checksum" = x"$$c" ]; then \ + mv "$@.unchecked" "$@"; \ + else \ + echo "ERROR: Non-matching checksum for '$*'."; \ + echo "Checksum should be: $$c"; \ + echo "Checksum is: $$checksum"; \ + exit 1; \ fi; \ else mv "$@.unchecked" "$@"; \ fi; @@ -658,6 +674,66 @@ $(ibidir)/bash: $(ibidir)/readline \ +# The `-shared' flag will cause problems while building Perl on macOS, so +# we'll only use this configuration option when we are GNU/Linux +# systems. However, since the whole option must be used (which includes `=' +# and empty space), its easier to define the variable as a Make variable +# outside the recipe, not as a shell variable inside it. +ifeq ($(on_mac_os),yes) +perl-conflddlflags = +else +perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS" +endif +$(ibidir)/perl: | $(ibidir)/bash \ + $(tdir)/perl-$(perl-version).tar.gz + major_version=$$(echo $(perl-version) \ + | sed -e's/\./ /g' \ + | awk '{printf("%d", $$1)}'); \ + base_version=$$(echo $(perl-version) \ + | sed -e's/\./ /g' \ + | awk '{printf("%d.%d", $$1, $$2)}'); \ + cd $(ddir) \ + && rm -rf perl-$(perl-version) \ + && if ! tar xf $(word 1,$(filter $(tdir)/%,$|)); then \ + echo; echo "Tar error"; exit 1; \ + fi \ + && cd perl-$(perl-version) \ + && sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \ + -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \ + Configure > Configure-tmp \ + && mv -f Configure-tmp Configure \ + && chmod +x Configure \ + && ./Configure -des \ + -Dusethreads \ + -Duseshrplib \ + -Dprefix=$(idir) \ + -Dvendorprefix=$(idir) \ + -Dprivlib=$(idir)/share/perl$$major_version/core_perl \ + -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/core_perl \ + -Dsitelib=$(idir)/share/perl$$major_version/site_perl \ + -Dsitearch=$(idir)/lib/perl$$major_version/$$basever/site_perl \ + -Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \ + -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \ + -Dscriptdir=$(idir)/bin/core_perl \ + -Dsitescript=$(idir)/bin/site_perl \ + -Dvendorscript=$(idir)/bin/vendor_perl \ + -Dinc_version_list=none \ + -Dman1ext=1perl \ + -Dman3ext=3perl \ + -Dcccdlflags='-fPIC' \ + $(perl-conflddlflags) \ + -Dldflags="$$LDFLAGS" \ + && make SHELL=$(ibdir)/bash -j$(numthreads) \ + && make SHELL=$(ibdir)/bash install \ + && cd .. \ + && rm -rf perl-$(perl-version) \ + && cd $$topdir \ + && echo "Perl $(perl-version)" > $@ + + + + + # Coreutils # --------- # @@ -677,8 +753,10 @@ $(ibidir)/bash: $(ibidir)/readline \ # The echo after the PatchELF loop is to avoid a crash if the last # file that PatchELF encounters is not usable (and it returns with # an error). +# +# Coreutils uses Perl to create man pages! $(ibidir)/coreutils: $(ibidir)/openssl \ - | $(ibidir)/bash \ + | $(ibidir)/perl \ $(tdir)/coreutils-$(coreutils-version).tar.xz cd $(ddir) \ && rm -rf coreutils-$(coreutils-version) \ @@ -847,17 +925,17 @@ $(ibidir)/wget: $(ibidir)/libiconv \ # there is no access to the system's PATH. $(ibidir)/diffutils: | $(ibidir)/coreutils \ $(tdir)/diffutils-$(diffutils-version).tar.xz - $(call gbuild, diffutils-$(diffutils-version), static, , V=1) \ + $(call gbuild, diffutils-$(diffutils-version), static,,V=1) \ && echo "GNU Diffutils $(diffutils-version)" > $@ $(ibidir)/file: | $(ibidir)/coreutils \ $(tdir)/file-$(file-version).tar.gz - $(call gbuild, file-$(file-version), static) \ + $(call gbuild, file-$(file-version), static,,V=1) \ && echo "File $(file-version)" > $@ $(ibidir)/findutils: | $(ibidir)/coreutils \ $(tdir)/findutils-$(findutils-version).tar.xz - $(call gbuild, findutils-$(findutils-version), static, , V=1) \ + $(call gbuild, findutils-$(findutils-version), static,,V=1) \ && echo "GNU Findutils $(findutils-version)" > $@ $(ibidir)/gawk: $(ibidir)/gmp \ @@ -910,13 +988,13 @@ $(ibidir)/gmp: | $(ibidir)/m4 \ $(ibidir)/glibtool: | $(ibidir)/m4 \ $(tdir)/libtool-$(libtool-version).tar.xz $(call gbuild, libtool-$(libtool-version), static, \ - --program-prefix=g) \ + --program-prefix=g, V=1) \ && ln -s $(ibdir)/glibtoolize $(ibdir)/libtoolize \ && echo "GNU Libtool $(libtool-version)" > $@ $(ibidir)/grep: | $(ibidir)/coreutils \ $(tdir)/grep-$(grep-version).tar.xz - $(call gbuild, grep-$(grep-version), static) \ + $(call gbuild, grep-$(grep-version), static,,V=1) \ && echo "GNU Grep $(grep-version)" > $@ $(ibidir)/libbsd: | $(ibidir)/coreutils \ @@ -927,7 +1005,7 @@ $(ibidir)/libbsd: | $(ibidir)/coreutils \ $(ibidir)/m4: | $(ibidir)/coreutils \ $(ibidir)/texinfo \ $(tdir)/m4-$(m4-version).tar.gz - $(call gbuild, m4-$(m4-version), static) \ + $(call gbuild, m4-$(m4-version), static,,V=1) \ && echo "GNU M4 $(m4-version)" > $@ # Metastore is used (through a Git hook) to restore the source modification @@ -997,7 +1075,7 @@ $(ibidir)/metastore: $(needlibbsd) \ -e's|@GROUP[@]|'$$group'|g' \ -e's|@BINDIR[@]|$(ibdir)|g' \ -e's|@TOP_PROJECT_DIR[@]|'$$current_dir'|g' \ - reproduce/software/bash/git-$$f > .git/hooks/$$f \ + reproduce/software/shell/git-$$f > .git/hooks/$$f \ && chmod +x .git/hooks/$$f; \ done; \ fi \ @@ -1020,63 +1098,6 @@ $(ibidir)/mpfr: $(ibidir)/gmp \ $(call gbuild, mpfr-$(mpfr-version), static, , , make check) \ && echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@ -# The `-shared' flag will cause problems while building Perl on macOS, so -# we'll only use this configuration option when we are GNU/Linux -# systems. However, since the whole option must be used (which includes `=' -# and empty space), its easier to define the variable as a Make variable -# outside the recipe, not as a shell variable inside it. -ifeq ($(on_mac_os),yes) -perl-conflddlflags = -else -perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS" -endif -$(ibidir)/perl: | $(ibidir)/coreutils \ - $(tdir)/perl-$(perl-version).tar.gz - major_version=$$(echo $(perl-version) \ - | sed -e's/\./ /g' \ - | awk '{printf("%d", $$1)}'); \ - base_version=$$(echo $(perl-version) \ - | sed -e's/\./ /g' \ - | awk '{printf("%d.%d", $$1, $$2)}'); \ - cd $(ddir) \ - && rm -rf perl-$(perl-version) \ - && if ! tar xf $(word 1,$(filter $(tdir)/%,$|)); then \ - echo; echo "Tar error"; exit 1; \ - fi \ - && cd perl-$(perl-version) \ - && sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \ - -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \ - Configure > Configure-tmp \ - && mv -f Configure-tmp Configure \ - && chmod +x Configure \ - && ./Configure -des \ - -Dusethreads \ - -Duseshrplib \ - -Dprefix=$(idir) \ - -Dvendorprefix=$(idir) \ - -Dprivlib=$(idir)/share/perl$$major_version/core_perl \ - -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/core_perl \ - -Dsitelib=$(idir)/share/perl$$major_version/site_perl \ - -Dsitearch=$(idir)/lib/perl$$major_version/$$basever/site_perl \ - -Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \ - -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \ - -Dscriptdir=$(idir)/bin/core_perl \ - -Dsitescript=$(idir)/bin/site_perl \ - -Dvendorscript=$(idir)/bin/vendor_perl \ - -Dinc_version_list=none \ - -Dman1ext=1perl \ - -Dman3ext=3perl \ - -Dcccdlflags='-fPIC' \ - $(perl-conflddlflags) \ - -Dldflags="$$LDFLAGS" \ - && make SHELL=$(ibdir)/bash -j$(numthreads) \ - && make SHELL=$(ibdir)/bash install \ - && cd .. \ - && rm -rf perl-$(perl-version) \ - && cd $$topdir \ - && echo "Perl $(perl-version)" > $@ - - $(ibidir)/pkg-config: | $(ibidir)/coreutils \ $(tdir)/pkg-config-$(pkgconfig-version).tar.gz # An existing `libiconv' can cause a conflict with `pkg-config', @@ -1101,7 +1122,7 @@ $(ibidir)/pkg-config: | $(ibidir)/coreutils \ $(ibidir)/sed: | $(ibidir)/coreutils \ $(tdir)/sed-$(sed-version).tar.xz - $(call gbuild, sed-$(sed-version), static) \ + $(call gbuild, sed-$(sed-version), static,,V=1) \ && echo "GNU Sed $(sed-version)" > $@ $(ibidir)/texinfo: | $(ibidir)/perl \ @@ -1111,7 +1132,7 @@ $(ibidir)/texinfo: | $(ibidir)/perl \ $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/info; \ $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/install-info; \ fi \ - && echo "GNU Texinfo $(sed-version)" > $@ + && echo "GNU Texinfo $(texinfo-version)" > $@ $(ibidir)/which: | $(ibidir)/coreutils \ $(tdir)/which-$(which-version).tar.gz @@ -1161,6 +1182,15 @@ endif # programs (http://savannah.nongnu.org/bugs/?56294). Therefore, we'll set # all other basic programs as Binutils prerequisite and GCC (the final # basic target) ultimately just depends on Binutils. +# +# The `ld' linker of Binutils needs several `*crt*.o' file to run. On some +# systems these object files aren't installed in standard places. We +# defined `LIBRARY_PATH' and that fixed the problem for many +# systems. However, some software (for example ImageMagick) over-write +# `LIBRARY_PATH', therefore there is no other way than to put a link to +# these necessary files in our local build directory. IMPORTANT NOTE: +# later, when we build the GNU C Library in the project, we should remove +# this step. $(ibidir)/binutils: | $(ibidir)/sed \ $(ibidir)/wget \ $(ibidir)/grep \ @@ -1174,6 +1204,7 @@ $(ibidir)/binutils: | $(ibidir)/sed \ $(ibidir)/diffutils \ $(ibidir)/coreutils \ $(gcc-prerequisites) + if [ x$(on_mac_os) = xyes ]; then \ $(call makelink,as); \ $(call makelink,ar); \ @@ -1181,9 +1212,17 @@ $(ibidir)/binutils: | $(ibidir)/sed \ $(call makelink,nm); \ $(call makelink,ps); \ $(call makelink,ranlib); \ - echo "" > $@; \ + echo "" > $@; \ else \ - $(call gbuild, binutils-$(binutils-version), static) \ + $(call gbuild, binutils-$(binutils-version), static, \ + --with-lib-path=$(sys_library_path), \ + -j$(numthreads) ) \ + && if ! [ x"$(sys_library_path)" = x ]; then \ + for f in $(sys_library_path)/*crt*.o; do \ + b=$$($(ibdir)/basename $$f); \ + ln -s $$f $(ildir)/$$b; \ + done; \ + fi \ && echo "GNU Binutils $(binutils-version)" > $@; \ fi @@ -1222,15 +1261,27 @@ $(ibidir)/gcc: | $(ibidir)/binutils \ ccinfo=$$(gcc --version | awk 'NR==1'); \ echo "C compiler (""$$ccinfo"")" > $@; \ else \ + current_dir=$$(pwd); \ rm -f $(ibdir)/gcc* $(ibdir)/g++ $(ibdir)/gfortran $(ibdir)/gcov*;\ rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc*; \ rm -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64*;\ \ ln -fs $(ildir) $(idir)/lib64; \ - \ - cd $(ddir); \ + \ + in_ram=$$(df $(ddir) \ + | awk 'NR==2{print ($$4>10000000) ? "yes" : "no"}'); \ + if [ $$in_ram = "yes" ]; then odir=$(ddir); \ + else \ + odir=$(BDIR)/software/build-tmp-gcc; \ + if [ -d $$odir ]; then rm -rf $$odir; fi; \ + mkdir $$odir; \ + fi; \ + cd $$odir; \ rm -rf gcc-$(gcc-version); \ - tar xf $(word 1,$(filter $(tdir)/%,$|)) \ + tar xf $(word 1,$(filter $(tdir)/%,$|)); \ + if [ $$odir != $(ddir) ]; then \ + ln -s $$odir/gcc-$(gcc-version) $(ddir)/gcc-$(gcc-version); \ + fi \ && cd gcc-$(gcc-version) \ && mkdir build \ && cd build \ @@ -1257,15 +1308,24 @@ $(ibidir)/gcc: | $(ibidir)/binutils \ && make SHELL=$(ibdir)/bash -j$(numthreads) \ && make SHELL=$(ibdir)/bash install \ && cd ../.. \ - && rm -rf gcc-$(gcc-version) \ + && tempname=$$odir/gcc-$(gcc-version)/build/rpath-temp-copy \ && if [ "x$(on_mac_os)" != xyes ]; then \ patchelf --add-needed $(ildir)/libiconv.so $(ildir)/libstdc++.so; \ for f in $$(find $(idir)/libexec/gcc) $(ildir)/libstdc++*; do \ - if ldd $$f &> /dev/null; then \ - patchelf --set-rpath $(ildir) $$f; \ + isdynamic=$$(file $$f | grep "dynamically linked"); \ + if [ x"$$isdynamic" != x ]; then \ + cp $$f $$tempname; \ + patchelf --set-rpath $(ildir) $$tempname; \ + mv $$tempname $$f; echo "corrected"; \ fi; \ done; \ fi \ + && rm -rf gcc-$(gcc-version) \ + && cd $$current_dir \ + && if [ "$$odir" != "$(ddir)" ]; then \ + rm -rf $$odir; \ + rm $(ddir)/gcc-$(gcc-version); \ + fi \ && ln -sf $(ibdir)/gcc $(ibdir)/cc \ && echo "GNU Compiler Collection (GCC) $(gcc-version)" > $@; \ fi diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk index cbde70b..f3ca7d2 100644 --- a/reproduce/software/make/build-rules.mk +++ b/reproduce/software/make/build-rules.mk @@ -1,7 +1,7 @@ # Generic configurable recipes to build packages with GNU Build system or # CMake. This is Makefile is not intended to be run directly, it will be -# imported into `dependencies-basic.mk' and `dependencies.mk'. They should -# be activated with Make's `Call' function. +# imported into `basic.mk' and `high-level.mk'. They should be activated +# with Make's `Call' function. # # Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> # diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index ac46f3a..5f1d2b2 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -28,11 +28,11 @@ # Top level environment include reproduce/software/make/build-rules.mk -include reproduce/software/config/installation/LOCAL.mk -include reproduce/software/config/installation/TARGETS.mk -include reproduce/software/config/installation/texlive.mk -include reproduce/software/config/installation/versions.mk -include reproduce/software/config/installation/checksums.mk +include reproduce/software/config/installation/LOCAL.conf +include reproduce/software/config/installation/TARGETS.conf +include reproduce/software/config/installation/versions.conf +include reproduce/software/config/installation/checksums.conf +include reproduce/software/config/installation/texlive-packages.conf lockdir = $(BDIR)/locks tdir = $(BDIR)/software/tarballs @@ -70,8 +70,8 @@ all: $(foreach p, $(top-level-programs), $(ibidir)/$(p)) \ .SHELLFLAGS := --noprofile --norc -ec export CCACHE_DISABLE := 1 export PATH := $(ibdir) -export CXX := $(ibdir)/g++ export CC := $(ibdir)/gcc +export CXX := $(ibdir)/g++ export SHELL := $(ibdir)/bash export F77 := $(ibdir)/gfortran export LD_RUN_PATH := $(ildir):$(il64dir) @@ -79,14 +79,31 @@ export PKG_CONFIG_PATH := $(ildir)/pkgconfig export LD_LIBRARY_PATH := $(ildir):$(il64dir) export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig +# Until we build our own C library, without this, our GCC won't be able to +# compile anything! Note that on most systems (in particular +# non-Debian-based), `sys_cpath' will be empty. +export CPATH := $(sys_cpath) + # RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is # ultimately redundant. But on some systems, even having a single value # causes crashs (see bug #56682). So we'll just give it no value at all. export DYLD_LIBRARY_PATH := -# Recipe startup script, see `reproduce/software/bash/bashrc.sh'. +# On Debian-based OSs, the basic C libraries are in a target-specific +# location, not in standard places. Until we merge the building of the C +# library, it is thus necessary to include this location here. On systems +# that don't need it, `sys_library_path' is just empty. This is necessary +# for `ld'. +export LIBRARY_PATH := $(sys_library_path) + +# Recipe startup script, see `reproduce/software/shell/bashrc.sh'. export PROJECT_STATUS := configure_highlevel -export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh +export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh + +# Servers to use as backup, later this should go in a file that is not +# under version control (the actual server that the tarbal comes from is +# irrelevant). +backupservers = http://akhlaghi.org/reproduce-software # Building flags: # @@ -168,6 +185,7 @@ tarballs = $(foreach t, apachelog4cxx-$(apachelog4cxx-version).tar.lz \ libtirpc-$(libtirpc-version).tar.bz2 \ libxml2-$(libxml2-version).tar.gz \ minizip-$(minizip-version).tar.gz \ + missfits-$(missfits-version).tar.gz \ netpbm-$(netpbm-version).tar.gz \ openblas-$(openblas-version).tar.gz \ openmpi-$(openmpi-version).tar.gz \ @@ -268,6 +286,7 @@ $(tarballs): $(tdir)/%: | $(lockdir) mergenames=0 c=$(minizip-checksum); w=https://github.com/nmoinvaz/minizip/archive/$(minizip-version).tar.gz + elif [ $$n = missfits ]; then c=$(missfits-checksum); w=https://www.astromatic.net/download/missfits elif [ $$n = netpbm ]; then c=$(netpbm-checksum); w=http://akhlaghi.org/reproduce-software elif [ $$n = openblas ]; then mergenames=0 @@ -325,7 +344,7 @@ $(tarballs): $(tdir)/%: | $(lockdir) touch $(lockdir)/download downloader="wget --no-use-server-timestamps -O" $(downloadwrapper) "$$downloader" $(lockdir)/download \ - $$tarballurl "$@.unchecked" + $$tarballurl "$@.unchecked" "$(backupservers)" fi # Make sure this is the expected tarball. Note that we now have a @@ -601,7 +620,7 @@ $(ibidir)/hdf5: $(ibidir)/openmpi \ # HEALPix includes the source of its C, C++, Python (and several other # languages) libraries within one tarball. We will include the Python # installation only when any other Python module is requested (in -# `TARGETS.mk'). +# `TARGETS.conf'). # # Note that the default `./configure' script is an interactive script which # is hard to automate. So we need to go into the `autotools' directory of @@ -647,7 +666,7 @@ $(ibidir)/healpix: $(ibidir)/cfitsio \ && echo "HEALPix $(healpix-version) \citep{healpix}" > $@ $(ibidir)/libjpeg: | $(tdir)/jpegsrc.$(libjpeg-version).tar.gz - $(call gbuild, jpeg-9b, static) \ + $(call gbuild, jpeg-9b, static,,V=1) \ && echo "Libjpeg $(libjpeg-version)" > $@ $(ibidir)/libnsl: $(ibidir)/libtirpc \ @@ -1017,12 +1036,15 @@ $(ibidir)/imfit: $(ibidir)/gsl \ fi \ && echo "Imfit $(imfit-version) \citep{imfit2015}" > $@ - $(ibidir)/minizip: $(ibidir)/cmake \ | $(tdir)/minizip-$(minizip-version).tar.gz $(call cbuild, minizip-$(minizip-version), static) \ && echo "minizip $(minizip-version)" > $@ +$(ibidir)/missfits: | $(tdir)/missfits-$(missfits-version).tar.gz + $(call gbuild, missfits-$(missfits-version), static) \ + && cp $(dtexdir)/missfits.tex $(ictdir)/ \ + && echo "MissFITS $(missfits-version) \citep{missfits}" > $@ # Netpbm is a prerequisite of Astrometry-net, it contains a lot of programs. # This program has a crazy dialogue installation which is override using the @@ -1135,7 +1157,10 @@ $(ibidir)/xlsxio: $(ibidir)/expat \ | $(tdir)/xlsxio-$(xlsxio-version).tar.gz export LDFLAGS="-lbz2 -lbsd"; \ $(call cbuild, xlsxio-$(xlsxio-version), static) \ - && echo "XLSX I/O $(xlsxio-version)" > $@ + && echo "XLSX I/O $(xlsxio-version)" > $ + + + @@ -1216,7 +1241,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co #else #forbiber = $(ibidir)/libnsl #endif -$(itidir)/texlive: reproduce/software/config/installation/texlive.mk \ +$(itidir)/texlive: reproduce/software/config/installation/texlive-packages.conf \ $(itidir)/texlive-ready-tlmgr \ $(forbiber) diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index 8c7b6f0..fef1605 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -185,7 +185,7 @@ $(pytarballs): $(tdir)/%: h=$(pytopurl)/$$hash/SecretStorage-$(secretstorage-version).tar.gz elif [ $$n = asn ]; then h=fc/f1/8db7daa71f414ddabfa056c4ef792e1461ff655c2ae2928a2b675bfed6b4; c=$(asn1crypto-checksum) elif [ $$n = asteval ]; then h=50/3f/29b7935c6dc09ee96dc347edc66c57e8ef68d595dd35b763a36a117acc8c; c=$(asteval-checksum) - elif [ $$n = astroquery ]; then h=61/50/a7a08f9e54d7d9d97e69433cd88231e1ad2901811c9d1ae9ac7ccaef9396; c=$(astroquery-checksum) + elif [ $$n = astroquery ]; then h=e2/af/a3cd3b30745832a0e81f5f13327234099aaf5d03b7979ac947a888e68e91; c=$(astroquery-checksum) elif [ $$n = astropy ]; then h=de/96/7feaca4b9be134128838395a9d924ea0b389ed4381702dcd9d11ae31789f; c=$(astropy-checksum) elif [ $$n = beautifulsoup ]; then h=80/f2/f6aca7f1b209bb9a7ef069d68813b091c8c3620642b568dac4eb0e507748; c=$(beautifulsoup4-checksum) elif [ $$n = certifi ]; then h=55/54/3ce77783acba5979ce16674fc98b1920d00b01d337cfaaf5db22543505ed; c=$(certifi-checksum) @@ -259,7 +259,7 @@ $(pytarballs): $(tdir)/%: touch $(lockdir)/download downloader="wget --no-use-server-timestamps -O" $(downloadwrapper) "$$downloader" $(lockdir)/download \ - $$tarballurl "$@.unchecked" + $$tarballurl "$@.unchecked" "$(backupservers)" fi # Make sure this is the expected tarball. Note that we now have a @@ -373,12 +373,9 @@ $(ipydir)/asteval: $(ipydir)/numpy \ $(call pybuild, tar xf, asteval-$(asteval-version), , \ ASTEVAL $(asteval-version)) -$(ipydir)/astroquery: $(ipydir)/numpy \ - $(ipydir)/astropy \ +$(ipydir)/astroquery: $(ipydir)/astropy \ $(ipydir)/keyring \ - $(ipydir)/html5lib \ $(ipydir)/requests \ - $(ipydir)/beautifulsoup4 \ | $(tdir)/astroquery-$(astroquery-version).tar.gz $(call pybuild, tar xf, astroquery-$(astroquery-version), ,\ Astroquery $(astroquery-version)) @@ -386,6 +383,9 @@ $(ipydir)/astroquery: $(ipydir)/numpy \ $(ipydir)/astropy: $(ipydir)/h5py \ $(ipydir)/scipy \ $(ipydir)/numpy \ + $(ipydir)/pyyaml \ + $(ipydir)/html5lib \ + $(ipydir)/beautifulsoup4 \ | $(tdir)/astropy-$(astropy-version).tar.gz $(call pybuild, tar xf, astropy-$(astropy-version)) \ && cp $(dtexdir)/astropy.tex $(ictdir)/ \ diff --git a/reproduce/software/bash/bashrc.sh b/reproduce/software/shell/bashrc.sh index b2a151f..b2a151f 100755 --- a/reproduce/software/bash/bashrc.sh +++ b/reproduce/software/shell/bashrc.sh diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/shell/configure.sh index f7fa9c8..6e1b5fb 100755 --- a/reproduce/software/bash/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -1,4 +1,4 @@ -#! /bin/bash +#! /bin/sh # # Necessary preparations/configurations for the reproducible project. # @@ -38,11 +38,11 @@ cdir=reproduce/software/config sbdir=$cdir/installation -pconf=$sbdir/LOCAL.mk -ptconf=$sbdir/LOCAL_tmp.mk -poconf=$sbdir/LOCAL_old.mk -depverfile=$cdir/installation/versions.mk -depshafile=$cdir/installation/checksums.mk +pconf=$sbdir/LOCAL.conf +ptconf=$sbdir/LOCAL_tmp.conf +poconf=$sbdir/LOCAL_old.conf +depverfile=$cdir/installation/versions.conf +depshafile=$cdir/installation/checksums.conf # --------- Delete for no Gnuastro --------- glconf=$cdir/gnuastro/gnuastro-local.conf # ------------------------------------------ @@ -57,7 +57,8 @@ glconf=$cdir/gnuastro/gnuastro-local.conf # In case someone opens the files output from the configuration scripts in # a text editor and wants to edit them, it is important to let them know # that their changes are not going to be permenant. -function create_file_with_notice() { +create_file_with_notice () +{ if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1" then echo "#" >> "$1" @@ -81,7 +82,8 @@ function create_file_with_notice() { # # Since the build directory will go into a symbolic link, we want it to be # an absolute address. With this function we can make sure of that. -function absolute_dir() { +absolute_dir () +{ if stat "$1" 1> /dev/null; then echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")" else @@ -93,6 +95,415 @@ function absolute_dir() { +# Check for C/C++ compilers +# ------------------------- +# +# To build the software, we'll need some basic tools (the compilers in +# particular) to be present. +hascc=0; +if type cc > /dev/null 2>/dev/null; then + if type c++ > /dev/null 2>/dev/null; then export CC=cc; hascc=1; fi +else + if type gcc > /dev/null 2>/dev/null; then + if type g++ > /dev/null 2>/dev/null; then export CC=gcc; hascc=1; fi + else + if type clang > /dev/null 2>/dev/null; then + if type clang++ > /dev/null 2>/dev/null; then export CC=clang; hascc=1; fi + fi + fi +fi +if [ $hascc = 0 ]; then + cat <<EOF +______________________________________________________ +!!!!!!! C/C++ Compiler NOT FOUND !!!!!!! + +To build the project's software, the host system needs to have basic C and +C++ compilers. The executables that were checked are 'cc', 'gcc' and +'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++ +compiler. If you have a relevant compiler that is not checked, please get +in touch with us (with the form below) so we add it: + + https://savannah.nongnu.org/support/?func=additem&group=reproduce +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + exit 1 +fi + + + + + +# Special directory for compiler testing +# -------------------------------------- +# +# This directory will be deleted when the compiler testing is finished. +compilertestdir=.compiler_test_dir_please_delete +if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi + + + + + +# Check C compiler +# ---------------- +gcc_works=0 +testprog=$compilertestdir/test +testsource=$compilertestdir/test.c +echo; echo; echo "Checking host C compiler..."; +cat > $testsource <<EOF +#include <stdio.h> +#include <stdlib.h> +int main(void){printf("...C compiler works.\n"); + return EXIT_SUCCESS;} +EOF +if $CC $testsource -o$testprog && $testprog; then + rm $testsource $testprog +else + rm $testsource + cat <<EOF + +______________________________________________________ +!!!!!!! C compiler doesn't work !!!!!!! + +Host C compiler ('gcc') can't build a simple program. + +A working C compiler is necessary for building the project's software. +Please use the error message above to find a good solution and re-run the +project configuration. + +If you can't find a solution, please send the error message above to the +link below and we'll try to help + +https://savannah.nongnu.org/support/?func=additem&group=reproduce + +TIP: Once you find the solution, you can use the '-e' option to use +existing configuration: + + $ ./project configure -e + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + exit 1 +fi + + + + + +# See if the linker accepts -Wl,-rpath-link +# ----------------------------------------- +# +# `-rpath-link' is used to write the information of the linked shared +# library into the shared object (library or program). But some versions of +# LLVM's linker don't accept it an can cause problems. +cat > $testsource <<EOF +#include <stdio.h> +#include <stdlib.h> +int main(void) {return EXIT_SUCCESS;} +EOF +if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null > /dev/null; then + export rpath_command="-Wl,-rpath-link=$instdir/lib" +else + export rpath_command="" +fi +rm -f $testprog $testsource + + + + + +# See if we need the dynamic-linker (-ldl) +# ---------------------------------------- +# +# Some programs (like Wget) need dynamic loading (using `libdl'). On +# GNU/Linux systems, we'll need the `-ldl' flag to link such programs. But +# Mac OS doesn't need any explicit linking. So we'll check here to see if +# it is present (thus necessary) or not. +cat > $testsource <<EOF +#include <stdio.h> +#include <dlfcn.h> +int +main(void) { + void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY); + return 0; +} +EOF +if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then + needs_ldl=no; +else + needs_ldl=yes; +fi +rm -f $testprog $testsource + + + + + +# See if the C compiler can build static libraries +# ------------------------------------------------ + +# We are manually only working with shared libraries: because some +# high-level programs like Wget and cURL need dynamic linking and if we +# build the libraries statically, our own builds will be ignored and these +# programs will go and find their necessary libraries on the host system. +# +# Another good advantage of shared libraries is that we can actually use +# the shared library tool of the system (`ldd' with GNU C Library) and see +# exactly where each linked library comes from. But in static building, +# unless you follow the build closely, its not easy to see if the source of +# the library came from the system or our build. +static_build=no + + + + + +# If we are on a Mac OS system +# ---------------------------- +# +# For the time being, we'll use the existance of `otool' to see if we are +# on a Mac OS system or not. Some tools (for example OpenSSL) need to know +# this. +# +# On Mac OS, the building of GCC crashes sometimes while building libiberty +# with CLang's `g++'. Until we find a solution, we'll just use the host's C +# compiler. +if type otool > /dev/null 2>/dev/null; then + host_cc=1 + on_mac_os=yes + cat <<EOF + +______________________________________________________ +!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! + +The GNU Compiler Collection (GCC, including compilers for C, C++, Fortran +and etc) is currently not built on macOS systems for this project. To build +the project's necessary software on this system, we need to use your +system's C compiler. + +Project's configuration will continue in 5 seconds. +______________________________________________________ + +EOF + sleep 5 +else + host_cc=0 + on_mac_os=no +fi + + + + + +# Necessary C library element positions +# ------------------------------------- +# +# On some systems (in particular Debian-based OSs), the static C library +# and necessary headers in a non-standard place, and we can't build GCC. So +# we need to find them first. The `sys/cdefs.h' header is also in a +# similarly different location. +sys_cpath="" +sys_library_path="" +if [ x"$$on_mac_os" != xyes ]; then + + # Get the GCC target name of the compiler, when its given, special + # C libraries and headers are in a sub-directory of the host. + gcctarget=$(gcc -v 2>&1 \ + | tr ' ' '\n' \ + | awk '/\-\-target/' \ + | sed -e's/\-\-target=//') + if [ x"$gcctarget" != x ]; then + if [ -f /usr/lib/$gcctarget/libc.a ]; then + export sys_library_path=/usr/lib/$gcctarget + export sys_cpath=/usr/include/$gcctarget + fi + fi + + # For a check: + #echo "sys_library_path: $sys_library_path" + #echo "sys_cpath: $sys_cpath" +fi + + + + + +# See if a link-able static C library exists +# ------------------------------------------ +# +# After building GCC, we must use PatchELF to correct its RPATHs. However, +# PatchELF links internally with `libstdc++'. So a dynamicly linked +# PatchELF cannot be used to correct the links to `libstdc++' in general +# (on some systems this causes no problem, but on others it doesn't!). +# +# However, to build a Static PatchELF, we need to be able to link with the +# static C library, which is not always available on some GNU/Linux +# systems. Therefore we need to check this here. If we can't build a static +# PatchELF, we won't build any GCC either. +if [ x"$host_cc" = x0 ]; then + echo; echo; echo "Checking if static C library is available..."; + cat > $testsource <<EOF +#include <stdio.h> +#include <stdlib.h> +#include <sys/cdefs.h> +int main(void){printf("...yes\n"); + return EXIT_SUCCESS;} +EOF + cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc" + if $cc_call && $testprog; then + gccwarning=0 + good_static_libc=1 + rm $testsource $testprog + else + echo; echo "Compilation command:"; echo "$cc_call" + good_static_libc=0 + rm $testsource + gccwarning=1 + host_cc=1 + cat <<EOF + +_______________________________________________________ +!!!!!!!!!!!! Warning !!!!!!!!!!!! + +The 'sys/cdefs.h' header cannot be included, or a usable static C library +('libc.a', in any directory) cannot be used with the current settings of +this system. SEE THE ERROR MESSAGE ABOVE. + +Because of this, we can't build GCC. You either 1) don't have them, or 2) +the default system environment aren't enough to find them. + +1) If you don't have them, your operating system provides them as separate +packages that you must manually install. Please look into your operating +system documentation or contact someone familiar with it. For example on +some Redhat-based GNU/Linux distributions, the static C library package can +be installed with this command: + + $ sudo yum install glibc-static + +2) If you have 'libc.a' and 'sys/cdefs.h', but in a non-standard location (for +example in '/PATH/TO/STATIC/LIBC/libc.a' and +'/PATH/TO/SYS/CDEFS_H/sys/cdefs.h'), please run the commands below, then +re-configure the project to fix this problem. + + $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS" + $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS" + +_______________________________________________________ + +EOF + fi +fi + +# Print a warning if GCC is not meant to be built. +if [ x"$gccwarning" = x1 ]; then + cat <<EOF + +PLEASE SEE THE WARNINGS ABOVE. + +Since GCC is pretty low-level, this configuration script will continue in 5 +seconds and use your system's C compiler (it won't build a custom GCC). But +please consider installing the necessary package(s) to complete your C +compiler, then re-run './project configure'. + +Project's configuration will continue in 5 seconds. + +EOF + sleep 5 +fi + + + + + +# Fortran compiler +# ---------------- +# +# If GCC is ultimately build within the project, the user won't need to +# have a fortran compiler, we'll build it internally for high-level +# programs. However, when the host C compiler is to be used, the user needs +# to have a Fortran compiler available. +if [ $host_cc = 1 ]; then + + # See if a Fortran compiler exists. + hasfc=0; + if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi + if [ $hasfc = 0 ]; then + cat <<EOF +______________________________________________________ +!!!!!!! Fortran Compiler NOT FOUND !!!!!!! + +The project won't be building its own GCC (which includes a Fortran +compiler) on this system. If you need software that need a Fortran +compiler, it will crash with an error. Fortran is necessary for many +lower-level scientific programs, hence this warning. Currently we search +for 'gfortran'. If you have a Fortran compiler that is not checked, please +get in touch with us (with the form below) so we add it: + + https://savannah.nongnu.org/support/?func=additem&group=reproduce + +Project's configuration will continue in 5 seconds. +______________________________________________________ + +EOF + sleep 5 + else + + # See if the Fortran compiler works + testsource=$compilertestdir/test.f + echo; echo; echo "Checking host Fortran compiler..."; + echo " PRINT *, \"... Fortran Compiler works.\"" > $testsource + echo " END" >> $testsource + if gfortran $testsource -o$testprog && $testprog; then + rm $testsource $testprog + else + rm $testsource + cat <<EOF + +______________________________________________________ +!!!!!!! Fortran compiler doesn't work !!!!!!! + +Host Fortran compiler ('gfortran') can't build a simple program. + +A working Fortran compiler is necessary for building some of the project's +software. Please use the error message above to find a good solution and +re-run the project configuration. + +If you can't find a solution, please send the error message above to the +link below and we'll try to help + +https://savannah.nongnu.org/support/?func=additem&group=reproduce + +TIP: Once you find the solution, you can use the '-e' option to use +existing configuration: + + $ ./project configure -e + +Project's configuration will continue in 5 seconds. +______________________________________________________ + +EOF + sleep 5 + fi + fi +fi + + + + + +# Delete the compiler testing directory +# ------------------------------------- +# +# This directory was made above to make sure the necessary compilers can be +# run. +rm -rf $compilertestdir + + + + + # Inform the user # --------------- # @@ -117,7 +528,7 @@ EOF # What to do with possibly existing configuration file # ---------------------------------------------------- # -# `LOCAL.mk' is the top-most local configuration for the project. If it +# `LOCAL.conf' is the top-most local configuration for the project. If it # already exists when this script is run, we'll make a copy of it as backup # (for example the user might have ran `./project configure' by mistake). printnotice=yes @@ -239,7 +650,7 @@ EOF bdir= currentdir=$(pwd) junkname=pure-junk-974adfkj38 - while [ x$bdir == x ] + while [ x$bdir = x ] do # Ask the user (if not already set on the command-line). if [ x"$build_dir" = x ]; then @@ -264,10 +675,12 @@ EOF fi fi - # Make sure the given directory is not a subdirectory of the - # source directory. + # If its given, make sure it isn't a subdirectory of the source + # directory. if ! [ x"$bdir" = x ]; then - if [[ $bdir == $currentdir* ]]; then + echo "Given build directory: $bdir" + if echo "$bdir/" \ + | grep '^'$currentdir 2> /dev/null > /dev/null; then # If it was newly created, it will be empty, so delete it. if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi @@ -299,10 +712,10 @@ if [ x"$input_dir" = x ]; then else indir=$input_dir fi -mk20name=$(awk '!/^#/ && $1=="MK20DATA" {print $3}' $adir/INPUTS.mk) -mk20md5=$(awk '!/^#/ && $1=="MK20MD5" {print $3}' $adir/INPUTS.mk) -mk20size=$(awk '!/^#/ && $1=="MK20SIZE" {print $3}' $adir/INPUTS.mk) -mk20url=$(awk '!/^#/ && $1=="MK20URL" {print $3}' $adir/INPUTS.mk) +mk20name=$(awk '!/^#/ && $1=="MK20DATA" {print $3}' $adir/INPUTS.conf) +mk20md5=$(awk '!/^#/ && $1=="MK20MD5" {print $3}' $adir/INPUTS.conf) +mk20size=$(awk '!/^#/ && $1=="MK20SIZE" {print $3}' $adir/INPUTS.conf) +mk20url=$(awk '!/^#/ && $1=="MK20URL" {print $3}' $adir/INPUTS.conf) if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then cat <<EOF @@ -387,6 +800,7 @@ if [ $rewritepconfig = yes ]; then sed -e's|@bdir[@]|'"$bdir"'|' \ -e's|@indir[@]|'"$indir"'|' \ -e's|@ddir[@]|'"$ddir"'|' \ + -e's|@sys_cpath[@]|'"$sys_cpath"'|' \ -e's|@downloader[@]|'"$downloader"'|' \ -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \ $pconf.in >> $pconf @@ -630,195 +1044,7 @@ fi -# Check for C/C++ compilers -# ------------------------- -# -# To build the software, we'll need some basic tools (the compilers in -# particular) to be present. -hascc=0; -if type cc > /dev/null 2>/dev/null; then - if type c++ > /dev/null 2>/dev/null; then hascc=1; fi -else - if type gcc > /dev/null 2>/dev/null; then - if type g++ > /dev/null 2>/dev/null; then hascc=1; fi - else - if type clang > /dev/null 2>/dev/null; then - if type clang++ > /dev/null 2>/dev/null; then hascc=1; fi - fi - fi -fi -if [ $hascc = 0 ]; then - cat <<EOF -______________________________________________________ -!!!!!!! C/C++ Compiler NOT FOUND !!!!!!! - -To build the project's software, the host system needs to have basic C and -C++ compilers. The executables that were checked are 'cc', 'gcc' and -'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++ -compiler. If you have a relevant compiler that is not checked, please get -in touch with us (with the form below) so we add it: - - https://savannah.nongnu.org/support/?func=additem&group=reproduce -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -EOF - exit 1 -fi - - - - - -# Check C compiler -# ---------------- -gcc_works=0 -testprog=$tmpblddir/test-c -testsource=$tmpblddir/test.c -echo; echo; echo "Checking host C compiler..."; -echo "#include <stdio.h>" > $testsource -echo "#include <stdlib.h>" >> $testsource -echo "int main(void){printf(\"...C compiler works.\n\");" >> $testsource -echo " return EXIT_SUCCESS;}" >> $testsource -if gcc $testsource -o$testprog && $testprog; then - rm $testsource $testprog -else - rm $testsource - cat <<EOF - -______________________________________________________ -!!!!!!! C compiler doesn't work !!!!!!! - -Host C compiler ('gcc') can't build a simple program. - -A working C compiler is necessary for building the project's software. -Please use the error message above to find a good solution and re-run the -project configuration. - -If you can't find a solution, please send the error message above to the -link below and we'll try to help - -https://savannah.nongnu.org/support/?func=additem&group=reproduce - -TIP: Once you find the solution, you can use the '-e' option to use -existing configuration: - - $ ./project configure -e - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -EOF - exit 1 -fi - - - - - -# See if the linker accepts -Wl,-rpath-link -# ----------------------------------------- -# -# `-rpath-link' is used to write the information of the linked shared -# library into the shared object (library or program). But some versions of -# LLVM's linker don't accept it an can cause problems. -oprog=$sdir/rpath-test -cprog=$sdir/rpath-test.c -echo "#include <stdio.h>" > $cprog -echo "int main(void) {return 0;}" >> $cprog -if [ x$CC = x ]; then CC=gcc; fi; -if $CC $cprog -o$oprog -Wl,-rpath-link &> /dev/null; then - export rpath_command="-Wl,-rpath-link=$instdir/lib" -else - export rpath_command="" -fi -rm -f $oprog $cprog - - - - - -# See if we need the dynamic-linker (-ldl) -# ---------------------------------------- -# -# Some programs (like Wget) need dynamic loading (using `libdl'). On -# GNU/Linux systems, we'll need the `-ldl' flag to link such programs. But -# Mac OS doesn't need any explicit linking. So we'll check here to see if -# it is present (thus necessary) or not. -oprog=$sdir/ldl-test -cprog=$sdir/ldl-test.c -cat > $cprog <<EOF -#include <stdio.h> -#include <dlfcn.h> -int -main(void) { - void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY); - return 0; -} -EOF -if gcc $cprog -o$oprog &> /dev/null; then needs_ldl=no; else needs_ldl=yes; fi -rm -f $oprog $cprog - - - - - -# See if the C compiler can build static libraries -# ------------------------------------------------ - -# We are manually only working with shared libraries: because some -# high-level programs like Wget and cURL need dynamic linking and if we -# build the libraries statically, our own builds will be ignored and these -# programs will go and find their necessary libraries on the host system. -# -# Another good advantage of shared libraries is that we can actually use -# the shared library tool of the system (`ldd' with GNU C Library) and see -# exactly where each linked library comes from. But in static building, -# unless you follow the build closely, its not easy to see if the source of -# the library came from the system or our build. -static_build=no - -#oprog=$sdir/static-test -#cprog=$sdir/static-test.c -#echo "#include <stdio.h>" > $cprog -#echo "int main(void) {return 0;}" >> $cprog -#if [ x$CC = x ]; then CC=gcc; fi; -#if $CC $cprog -o$oprog -static &> /dev/null; then -# export static_build="yes" -#else -# export static_build="no" -#fi -#rm -f $oprog $cprog -#if [ $printnotice = yes ] && [ $static_build = "no" ]; then -# cat <<EOF -#_________________________________________________________________________ -#!!!!!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!! -# -#Your system's C compiler ('$CC') doesn't support building static -#libraries. Therefore the dependencies will be built dynamically. This means -#that they will depend more strongly on changes/updates in the host -#system. For high-level applications (like most research projects in natural -#sciences), this shouldn't be a significant problem. -# -#But generally, for reproducibility, its better to build static libraries -#and programs. For more on their difference (and generally an introduction -#on linking), please see the link below: -# -#https://www.gnu.org/software/gnuastro/manual/html_node/Linking.html -# -#If you have other compilers on your system, you can select a different -#compiler by setting the 'CC' environment variable before running -#'./project configure'. -# -#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -# -#EOF -# sleep 5 -#fi - - - - - -# inform the user that the build process is starting +# Inform the user that the build process is starting # ------------------------------------------------- if [ $printnotice = yes ]; then tsec=10 @@ -839,12 +1065,13 @@ will be installed in: **TIP**: you can see which software is being installed at every moment with the following command. See "Inspecting status" section of 'README-hacking.md' for more. In short, run it while the project is being -configured (in another terminal, but on this same directory: '`pwd`'): +configured (in another terminal, but on this same directory: 'pwd'): - $ while true; do echo; date; ls .build/software/build-tmp; sleep 1; done + $ ./project --check-config -------------------------- +Project's configuration will continue in $tsec seconds. +------------------------- EOF sleep $tsec @@ -854,241 +1081,6 @@ fi -# If we are on a Mac OS system -# ---------------------------- -# -# For the time being, we'll use the existance of `otool' to see if we are -# on a Mac OS system or not. Some tools (for example OpenSSL) need to know -# this. -# -# On Mac OS, the building of GCC crashes sometimes while building libiberty -# with CLang's `g++'. Until we find a solution, we'll just use the host's C -# compiler. -if type otool > /dev/null 2>/dev/null; then - host_cc=1 - on_mac_os=yes -else - on_mac_os=no -fi - - - - - -# See if GCC can be built -# ----------------------- -# -# On some GNU/Linux distros, the C compiler is broken into `multilib' (for -# 32-bit and 64-bit support, with their own headers). On these systems, -# `/usr/include/sys/cdefs.h' and `/usr/lib/libc.a' are not available by -# default. So GCC will crash with different ugly errors! The only solution -# is that user manually installs the `multilib' part as root, before -# running the configure script. -# -# Note that `sys/cdefs.h' may be available in other directories (for -# example `/usr/include/x86_64-linux-gnu/') that are automatically included -# in an installed GCC. HOWEVER during the build of GCC, all those other -# directories are ignored. So even if they exist, they are useless. -gccwarning=0 -if [ $host_cc = 0 ]; then - if ! [ -f /usr/include/sys/cdefs.h ]; then - host_cc=1 - gccwarning=1 - cat <<EOF - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -This system doesn't have '/usr/include/sys/cdefs.h'. Because of this, the -project can't build its custom GCC to ensure better reproducibility. We -strongly recommend installing the proper package (for your operating -system) that installs this necessary file. For example on some Debian-based -GNU/Linux distros, you need these two packages: 'gcc-multilib' and -'g++-multilib'. -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -EOF - fi - - if [ -f /usr/lib/libc.a ] || [ -f /usr/lib64/libc.a ]; then - # This is just a place holder - host_cc=$host_cc - else - host_cc=1 - gccwarning=1 - cat <<EOF - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -This system doesn't have '/usr/lib/libc.a' or '/usr/lib64/libc.a'. Because -of this, the project can't build its custom GCC to ensure better -reproducibility. We recommend installing the proper package (for your -operating system) that installs this necessary file. - -Some possible solutions: - 1. On some Debian-based GNU/Linux distros, these two packages may fix the - problem: 'gcc-multilib' and 'g++-multilib'. - 2. (BE CAREFUL!) If you have '/usr/lib/x86_64-linux-gnu' but don't have - '/usr/lib64', then running the following command might fix this - particular problem by making a symbolic link. - $ sudo ln -s /usr/lib/x86_64-linux-gnu /usr/lib64 - After the configure script is finished, delete the link with 'rm - /usr/lib64' (you won't need it any more as far as this project is - concerned). -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -EOF - fi -fi - -# See if a link-able static C library exists -# ------------------------------------------ -# -# After building GCC, we must use PatchELF to correct its RPATHs. However, -# PatchELF links internally with `libstdc++'. So a dynamicly linked -# PatchELF cannot be used to correct the links to `libstdc++' in general -# (on some systems this causes no problem, but on others it doesn't!). -# -# However, to build a Static PatchELF, we need to be able to link with the -# static C library, which is not always available on some GNU/Linux -# systems. Therefore we need to check this here. If we can't build a static -# PatchELF, we won't build any GCC either. -if [ $host_cc = 0 ]; then - testprog=$tmpblddir/test-c - testsource=$tmpblddir/test.c - echo; echo; echo "Checking if static C library is available..."; - echo "#include <stdio.h>" > $testsource - echo "#include <stdlib.h>" >> $testsource - echo "int main(void){printf(\"...yes\");" >> $testsource - echo " return EXIT_SUCCESS;}" >> $testsource - if gcc $testsource -o$testprog -static -lc && $testprog; then - good_static_libc=1 - rm $testsource $testprog - else - good_static_libc=0 - rm $testsource - gccwarning=1 - host_cc=1 - cat <<EOF - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -A usable static C library ('libc.a', in any directory) cannot be linked in -the current settings of this system. Because of this we can't build a -static PatchELF, hence we can't build GCC. - -If you have 'libc.a', but in a non-standard location (for example in -'/PATH/TO/STATIC/LIBC/libc.a'), please run this command, then re-configure -the project to fix this problem. - -export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS" - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -EOF - fi -fi - -# Print a warning if GCC is not meant to be built. -if [ $gccwarning = 1 ]; then - cat <<EOF - -PLEASE SEE THE WARNINGS ABOVE. - -Since GCC is pretty low-level, this configuration script will continue in 5 -seconds and use your system's C compiler (it won't build a custom GCC). But -please consider installing the necessary package(s) to complete your C -compiler, then re-run './project configure'. - -EOF - sleep 5 -fi - - - - - -# Fortran compiler -# ---------------- -# -# If GCC is ultimately build within the project, the user won't need to -# have a fortran compiler, we'll build it internally for high-level -# programs. However, when the host C compiler is to be used, the user needs -# to have a Fortran compiler available. -if [ $host_cc = 1 ]; then - - # See if a Fortran compiler exists. - hasfc=0; - if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi - if [ $hasfc = 0 ]; then - cat <<EOF -______________________________________________________ -!!!!!!! Fortran Compiler NOT FOUND !!!!!!! - -Because the project won't be building its own GCC (which includes a Fortran -compiler), you need to have a Fortran compiler available. Fortran is -commonly necessary for many lower-level scientific programs. Currently we -search for 'gfortran'. If you have a Fortran compiler that is not checked, -please get in touch with us (with the form below) so we add it: - - https://savannah.nongnu.org/support/?func=additem&group=reproduce - -Note: GCC will not be built because you are either using the '--host-cc' -option, or you are using an operating system that currently has bugs when -building GCC. -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -EOF - exit 1 - fi - - # See if the Fortran compiler works - testprog=$tmpblddir/test-f - testsource=$tmpblddir/test.f - echo; echo; echo "Checking host Fortran compiler..."; - echo " PRINT *, \"... Fortran Compiler works.\"" > $testsource - echo " END" >> $testsource - if gfortran $testsource -o$testprog && $testprog; then - rm $testsource $testprog - else - rm $testsource - cat <<EOF - -______________________________________________________ -!!!!!!! Fortran compiler doesn't work !!!!!!! - -Host Fortran compiler ('gfortran') can't build a simple program. - -A working Fortran compiler is necessary for building some of the project's -software. Please use the error message above to find a good solution and -re-run the project configuration. - -If you can't find a solution, please send the error message above to the -link below and we'll try to help - -https://savannah.nongnu.org/support/?func=additem&group=reproduce - -TIP: Once you find the solution, you can use the '-e' option to use -existing configuration: - - $ ./project configure -e - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -EOF - exit 1 - fi -fi - - - - - # Number of threads for basic builds # ---------------------------------- # @@ -1181,6 +1173,32 @@ fi +# Paths needed by the host compiler (only for `basic.mk') +# ------------------------------------------------------- +# +# At the end of the basic build, we need to build GCC. But GCC will build +# in multiple phases, making its own simple compiler in order to build +# itself completely. The intermediate/simple compiler doesn't recognize +# some system specific locations like `/usr/lib/ARCHITECTURE' that some +# operating systems use. We thus need to tell the intermediate compiler +# where its necessary libraries and headers are. +if [ x"$sys_library_path" != x ]; then + if [ x"$LIBRARY_PATH" = x ]; then + export LIBRARY_PATH="$sys_library_path" + else + export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path" + fi + if [ x"$CPATH" = x ]; then + export CPATH="$sys_cpath" + else + export CPATH="$CPATH:$sys_cpath" + fi +fi + + + + + # Build basic software # -------------------- # @@ -1188,13 +1206,14 @@ fi # Bash, Make, or AWK. In this step, we'll install such low-level basic # tools, but we have to be very portable (and use minimal features in all). echo; echo "Building necessary software (if necessary)..." -make -f reproduce/software/make/basic.mk \ +make -k -f reproduce/software/make/basic.mk \ + sys_library_path=$sys_library_path \ good_static_libc=$good_static_libc \ rpath_command=$rpath_command \ static_build=$static_build \ + numthreads=$numthreads \ needs_ldl=$needs_ldl \ on_mac_os=$on_mac_os \ - numthreads=$numthreads \ host_cc=$host_cc \ -j$numthreads @@ -1215,11 +1234,13 @@ else numthreads=$jobs fi .local/bin/env -i HOME=$bdir \ - .local/bin/make -f reproduce/software/make/high-level.mk \ + .local/bin/make -k -f reproduce/software/make/high-level.mk \ + sys_library_path=$sys_library_path \ rpath_command=$rpath_command \ static_build=$static_build \ numthreads=$numthreads \ on_mac_os=$on_mac_os \ + sys_cpath=$sys_cpath \ host_cc=$host_cc \ -j$numthreads @@ -1279,8 +1300,8 @@ fi # After everything is installed, we'll put all the names and versions in a # human-readable paragraph and also prepare the BibTeX citation for the # software. -function prepare_name_version() { - +prepare_name_version () +{ # First see if the (possible) `*' in the input arguments corresponds to # anything. Note that some of the given directories may be empty (no # software installed). @@ -1385,9 +1406,9 @@ echo `.local/bin/date` > $finaltarget # The configuration is now complete, we can inform the user on the next # step(s) to take. if [ x$reproducible_paper_group_name = x ]; then - buildcommand="./project prepare -j8" + buildcommand="./project make -j8" else - buildcommand="./project prepare --group=$reproducible_paper_group_name -j8" + buildcommand="./project make --group=$reproducible_paper_group_name -j8" fi cat <<EOF diff --git a/reproduce/software/bash/git-post-checkout b/reproduce/software/shell/git-post-checkout index f6366dc..f6366dc 100755 --- a/reproduce/software/bash/git-post-checkout +++ b/reproduce/software/shell/git-post-checkout diff --git a/reproduce/software/bash/git-pre-commit b/reproduce/software/shell/git-pre-commit index 9d550db..9d550db 100755 --- a/reproduce/software/bash/git-pre-commit +++ b/reproduce/software/shell/git-pre-commit |