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Until now, the hashbang of these two shell scripts was set to `/bin/bash',
hence assuming that GNU Bash exists on the host system! But this is an
extra requirement on the host operating system and these two scripts should
be written such that they operate on a POSIX shell (the generic `/bin/sh'
which can point to any shell program).
With this commit this has been implemented! We may confront some errors as
the system is run on other systems, but we should fix such errors and work
hard to make these two scripts as POSIX-compatible as possible (runnable on
any shell, so as not to force users to install Bash before running the
project).
This completes Task #15525.
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Until now, the main commands to run the project were these: `./project
configure' (to build the software), `./project prepare' (to possibly
arrange input datasets and build special configuration Makefiles) and
finally `./project make' to run the project.
The main logic behind the "prepare" phase `top-prepare.mk' is to build
configuration files that can be fed into the "make" step and optimize its
operation. For example when the total number of necessary inputs for the
majority of the analysis is not as large as the total number of
inputs. With "prepare" (when necessary), you go through the raw inputs,
select the ones that are necessary for the rest of the project. The output
of `top-prepare.mk' is a configuration file (a Make variable) that keeps
the IDs (numbers, names, etc). That configuration file would then be used
in the `top-make.mk' to identify the lower level targets and allow optimal
project organization and management.
But the last two are both part of the analysis, and while they indeed need
different calls to Make to be executed, many projects don't actually need a
preparation phase: ultimately, its an implementation choice by the project
developers and doesn't concern the project users (or the developers when
they are running it).
To avoid confusing the users, or simply annoying them when a projet doesn't
need it, with this commit, the top-level `top-prepare.mk' and `top-make.mk'
Makefiles are called with the single `./project make' command and
`./project prepare' has been dropped. I noticed this while writing the
paper on this system.
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Until now, the explanation for a missing static C library didn't actually
guide the users to look above and see the error message! So with this
commit, I edited it a little to be more clear (and mention to look
above). Also, I noticed that on Amazon AWS systems, the static C library is
installed as a separate package, so to help the users, I added the
necessary command and some better explanation.
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Until now Perl was built after Coreutils, but I recently noticed that
Coreutils actually uses Perl while creating its manpages. So it is now
built before Coreutils.
Also, while testing on an Amazon AWS EC2 server, we noticed that Coreutils
can't build its man page for `md5sum'. The problem was found to be due to
the fact that until now, we weren't actually setting LD_LIBRARY_PATH to our
installed library path in `basic.mk'. Therefore, it would crash because the
server had an older version of OpenSSL than the one that the template's
Coreutils was built with.
In the meantime (while addressing the issues above, because we only had one
thread on the AWS server) I also noticed a few programs that were using a
summarize compilation command (that just prints `CC xxx.c' instead of the
whole command) so I fixed them by adding `V=1'.
This bug was found by Idafen Santana Pérez.
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Until now, the configuration Makefiles (in
`reproduce/software/config/installation' and `reproduce/analysis/config')
had a `.mk' suffix, similar to the workhorse Makefiles. Although they are
indeed Makefiles, but given their nature (to only keep configuration
parameters), it is confusing (especially to early users) for them to also
have a `.mk' (similar to the analysis or software building Makefiles).
To address this issue, with this commit, all the configuration Makefiles
(in those directories) are now given a `.conf' suffix. This is also assumed
for all the files that are loaded.
The configuration (software building) and running of the template have been
checked with this change from scratch, but please report any error that may
not have been noticed.
THIS IS AN IMPORTANT CHANGE AND WILL CAUSE CRASHES OR UNEXPECTED BEHAVIORS
FOR PROJECTS THAT HAVE BRANCHED FROM THIS TEMPLATE. PLEASE CORRECT THE
SUFFIX OF ALL YOUR PROJECT'S CONFIGURATION MAKEFILES (IN THE DIRECTORIES
ABOVE), OTHERWISE THEY AREN'T AUTOMATICALLY LOADED ANYMORE.
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GNU Make 4.3 was just announced, so I have updated it here is well. This
was important because until now the installable version was in alpha-mode
(4.2.90), now its a stable version.
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In the previous commmit, I had forgot to add a `\' after the newly added
`sys_library_path' variable to the `high-level.mk' call.
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Until now, GCC wouldn't build properly on Debian-based operating systems
because `ld' needed to link with several necessary C library features like
`crti.o' and `crtn.o' (this is an `ld' issue, not GCC). The solution is to
add the directory containing them to `LIBRARY_PATH'. In the previous
commit, I actually searched for these files, but while testing on another
system, I noticed that it can be problematic (other architectures may
exist).
With this commit, we are actually finding the build architecture of the
running GCC (which is the same as the `ld') and using that to fix a fixed
directory to `LIBRARY_PATH'.
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Until now, to see if a working static C library and `sys/cdefs.h' exist, we
were checking absolute locations like `/usr/include/sys/cdefs.h' or
`/usr/lib/libc.a' and `/usr/lib64/libc.a'. But this is not robust because
on different systems, they can be in different locations.
With this commit, we actually use `find' to find the location of `libc.a'
and use that to add elements to CPPFLAGS and LDFLAGS. This should fix the
problem on systems that have them on non-standard locations.
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Until now, when find the versions of the TeXLive packages, we would assume
that `cat-date' is always present (because some packages don't have a
version!). However, apparently an update has been made in the TeXLive
Manager (`tlmgr') and `cat-date' is no longer present! As a result, none of
the TeXLive packages were being printed.
With this commit, it now assumes that `revision' is always present for
every package, but it also attempts to read `cat-date' (for backwards
compatability). When `cat-version' isn't present, it will try printing
`revision' and if that is also not present, it will print the date.
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After a new rebuild of the project, I noticed that we now need to also
build the `mweights' package.
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Until this commit, the checking of X11 installation done to ensure that
it is already available in the host system was crashing in macOS
systems. The reason is that the place of the X11 libraries use to be
`/opt/X11/lib' in macOS systems. With this commit, this issue has been
fixed by adding this directory to the LDFLAGS.
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Newer versions of Astropy package has been released. With this commit,
it has been updated. It has been increased from v3.2.1 to v4.0
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In markdown, to specify that part of the text should be shown as code we
need to put it between two `. But in `reproduce/software/make/README.md',
the code parts started with ` and finished in ' (like the file name above).
With this commit, this has been corrected and it will display properly on
web browsers.
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Now that its 2020, its necessary to include this year in the copyright
statements.
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Until this commit, the number `2' was missing in the checksum variable
name of that library. It was `libxml-checksum' but it should be
`libxml2-checksum'. With this commit, this issue has been fixed.
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An extra backslash in the prerequisites of Jeepney Python package was
causing a crash in the installation of that software. With this commit,
this problem has been fixed by removing the backslash.
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OpenMP takes a LONG TIME to build, so to keep things reproducible we are
explicitly disabling OpenMP, if a user needs OpenMP, its trivial to just
add it as a prerequisite of R. The problem is that in some scenarios (based
on other dependencies and when they were built in the build directory),
OpenMP may be present when R is being installed and in other it may not. We
don't want the result to be different between the two builds.
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With this commit, we now have the core R interpretter within the
template. We should later include instructions to install R packages
(possibly in a separate top-level Makefile like Python).
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Recent builds of the template need these three packages to build the PDF.
This was reported by Hamed Altafi.
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Until now we weren't including this package, but Alberto Madrigal recently
reported that his build of the template failed because it needed it.
With this commit, it is now being installed with the template.
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Until now, while building Perl, the `-Dlddlflags="-shared $$LDFLAGS"'
option was being used for all systems. However, this caused `symbol(s) not
found for architecture x86_64' problems on macOS systems.
With this commit, this configure option is only passed for GNU/Linux
systems. With it, Perl can be built nicely on both GNU/Linux and macOS.
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Newer versions of these packages have recently come out with major
improvements, so they have been updated in the template.
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Until now, Ghostscript was using some host system's X11 libraries during
its build (and later at run-time). We should ideally install all these
necessary libraries within the template (Task #15481). But right now we are
too busy.
As a temporary work-around we try building a small dummy program that links
with some of those libraries before attempting to built Ghostscript. If it
fails, then a notice is printed with the cause and explaining a temporary
solution is suggested: how to install those libraries on the system when
you have root access.
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Until now when building Matplotlib on macOS systems, we were using the
default C compiler. However, while Yahya Sefidbakht (previously) and
Mahdieh Nabavi (now) were trying to build the template, on their macOS
using the GNU Compiler Collection (GCC), we found that Matplotlib needs
special macOS headers that GCC doesn't recognize.
With this commit, when Matplotlib is being built on macOS systems, it uses
`clang' and this fixed the problem (so far checked on Mahdieh's machine).
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While working on a different branch to build the GNU C Library, I noticed a
few places in the template that need corrections which are now applied:
1. A new-line character after the "C compiler works" notice at the start
of the configure script.
2. Removing possible `::' in the `LD_LIBRARY_PATH' definition of
`basic.mk'. Note that its not necessary in the other steps because we
don't use any outside-defined `LD_LIBRARY_PATH'.
3. Building GMP for C++ and also with `--enable-fat'.
4. Removing the unpacked Perl tarball directory after its installation.
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These two packages are necessary to build the GNU C Library.
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Perl is necessary to build Texinfo and later to build LaTeX. Until now we
were just using the host operating system's installation of Perl, but in
some instances that Perl can be too old and not suppor the features
necessary. With this commit, Perl is now built from source during the basic
installation step of the template.
This was reported by Idafen Santana Pérez, after trying the pipeline on an
Amazon AWS EC2 system (a Linux distro by Amazon for its cloud services).
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When building the log4cxx tarball from its Git history, I noticed that
files with very long names are not packaged by tar (because by default
Automake uses the ancient v7 tar format that only supports file names less
than 99 characters).
So I build the tarball with the `tar-ustar' option to Automake (by
modifying the log4cxx source) and the resulting tarball was able to compile
and run successfully. This has been described above the rule to build
log4cxx and I also sent an email to their developing mailing list to inform
them of this problem. If they address it, I will remove the note on the
necessary corrections.
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Some minor corrections were made in the template:
- When making the distribution, `.swp' files (created by Vim) are also
removed.
- Autoconf is set as a prerequisite of Automake
I was also trying to add the Apache log4cxx, but its default 0.10.0 tarball
needs some patches, so I have just left it half done until someone actually
needs it and we apply the patch.
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Until now, the tarballs were the first normal prerequisite of the
software. As a result if their date changed, the whole software would be
re-built. However, for tarballs specifically, we actually check their
contents with a checksum, so their date is irrelevant (if its newer than
the built program, but has the same checksum, there is no need to re-build
the software).
Also, calling the tarball name as an argument to the building process (for
example `gbuild') was redundant. It is now automatically found from the
list of order-only prerequisites within `gbuild' and `cbuild' (similar to
how it was previously found in the `pybuild' for Python building).
A `README.md' file has also been placed in `reproduce/software/make' to
help describe the shared properties of the software building
Makefiles. This will hopefully grow much larger in the future.
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Python's `lmfit' module and all its major dependencies (`asteval',
`corner', `emcee' and `uncertainties') have been included in the template.
While doing this I noticed that if the tarballs are the last prerequisite
of each software building rule, then when building in parallel, the
template will immediately start building packages as soon as the first one
is downloaded. Not like the current way that it will attempt to download
several, then start building. For now, this has been implemented in the
Python build rules for all the modules and we'll later do the same for the
other programs and libraries. This also motivated a simplification of the
`pybuild' function: it now internally looks into the prerequisites and
selects the tarball from the prerequisite that is in the tarballs
directory.
This isn't a problem for the build, but I just don't understand why Python
can't recognize the version of `emcee', Python reads the version of `emcee'
as `0.0.0'! But it doesn't cause any crash in the build, so for now its
fine.
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The tarball of HEALPix includes multiple languages and doesn't include the
ready-to-run GNU Build System by default, we actually have to build the
`./configure' script for the C/C++ libraries. So it was necessary to also
include GNU Autoconf and GNU Automake as prerequisites of HEALPix.
However, the official GNU Autoconf tarball (dating from 2012) doesn't build
on modern systems, so I just cloned it from its source and bootstrapped it
and built its modern tarball which we are using here.
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The following software are added with this commit: eigency, esutil, flake8,
future, galsim, lsstdesccoord, pybind11 and pyflakes.
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As part of an effort to bring in all the dependencies of the LSST Science
pipeline (which includes the last commit), these software are now available
in the template.
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With this commit these three software packages are now installable with
this template.
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Carlos Morales Socorro reported that his LaTeX build was missing the
`trimspaces' package, so it is now included in the pipeline.
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Until now, some software were using the depreciated ADS URL
(`http://adsabs.harvard.edu....') and some were using the modern one
(`http://ui.adsabs.harvard.edu').
With this commit, to be consistent they all link to the modern URL.
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Since ImageMagick can take long to build, we are now building it in
parallel. Also, the part where we replace an `_' with `\_' in the software
version at the end of the configure script was removed. It is more
clear/readable that the actual rule that includes such a name deals with
the underline (as is the case for `sip_tpv' which already dealt with it).
Finally, I noticed that the checks at the start of `top-prepare' were
missing new-lines. I had forgot that the Make single-shell variable isn't
activated in this stage yet.
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In many real-world scenarios, `./project make' can really benefit from
having some basic information about the data before being run. For example
when quering a server. If we know how many datasets were downloaded and
their general properties, it can greatly optmize the process when we are
designing the solution to be run in `./project make'.
Therefore with this commit, a new phase has been added to the template's
design: `./project prepare'. In the raw template this is empty, because the
simple analysis done in the template doesn't warrant it. But everything is
ready for projects using the template to add preparation phases prior to
the analysis.
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It was some time since these three software were not updated! With this
commit the template now uses the most recent stable release of these
packages.
Also, the hosting server for ImageMagick was moved to my own webpage
because unfortunately ImageMagick removes its tarballs from its own
version.
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Until now we were calling it `Sextractor', but the official way of writing
it is `SExtractor'. With this commit, this has been corrected.
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Until now, we were assuming that the users would just clone the project in
Git. But after submitting arXiv:1909.11230, and trying to build directly
from the arXiv source, I noticed several problems that wouldn't allow users
to build it automatically. So I tried the build step by step and was able
to find a fix for the several issues that came up.
The scripting parts of the fix were primarily related to the fact that the
unpacked arXiv tarball isn't under version control, so some checks had to
be put there. Also, we wanted to make it easy to remove the extra files, so
an extra `--clean-texdit' option was added to `./project'.
Finally, some manual corrections were necessary (prior to running
`./project', which are now described in `README.md'. Most of the later
steps can be automated and we should do it later, I just don't have enough
time now.
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Users that are not familiar with the file structure of the project may
specify the current directory (to-level source directory) as their
build-directory. This will cause a crash right after answering the
questions, where `rm' will complain about `tex/build' not being deleted
because it exists as a directory.
To avoid such confusing situtations, the configure script now checks if the
build directory is actually a sub-directory of the source. If it is, it
will complain with a short message and abort. Also, a `CAUTION' statment
has been put in the initial description, right ontop of the question.
This bug was reported Carlos Allende Prieto and David Valls-Gabaud.
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Until now the SExtractor BibTeX entry has the first-name and family name in
the same field, while the family-name should be in curly braces. Also, it
was missing an ADS URL. So the default ADS generated BibTeX entry for
SExtractor is now used instead of the old one.
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New versions of astropy, bash, cmake, curl, findutils, gawk, gcc,
ghostscript, git, make, gsl had recently come so they are updated with this
commit.
About GNU Findutils and GNU Make: I was bootstrapping (building the tarball
of) these two separately separately because their standard tarball release
had problems on some systems. Both have been updated now so I am no longer
using my own webpage as their main URL.
A special note about GNU Make. I just noticed that during bootstrapping,
GNU Make would use the fixed version string of `4.2.90' for any commit!!!
But fortunately they have officially released their 4.2.90 version, so we
are safely using their own webpage. The only difference is the compression
format. My old bootstrapped build was `tar.lz', but the standard release is
`tar.gz'.
Also, all the basic programs (installed in `.local/bin') in `basic.mk' are
now existance-only dependencies (after a `|'). Because later programs just
use them at a very basic level, so there is no need to rebuild everything
when Bash gets updated for example.
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Until now, OpenMPI would complain about not having `ssh' or `rsh' as a
remote shell feature. However, such features should not be necessary in a
reproducible scenario and they also have major security issues.
With this commit, we are now using OpenMPI's `OMPI_MCA_plm_rsh_agent'
environment variable to disable any remote shell dependency for it (as
suggested by Boud). Therefore, any dependency for OpenSSH has been
removed. But I thought to keep the build instructions incase it may be
useful under some un-foreseen scenario. However, to discourage people from
building it, a notice was added ontop of the build instructions.
This bug was found, tested and solved thanks to Roberto Baena Gallé and
Boud Roukema.
This fixes bug #56724.
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Until now we have followed the convention of using space characters before
comment lines in recepies, not tabs. This has been corrected in one case.
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Until this commit, `fpack' and `funpack' were not installed by default
with the installation of CFITSIO. It is necessary to explicity do a
`make fpack' and `make funpack' to have them installed. With this
commit, these two programs have been added.
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Until this commit, the name of the variable for `beautifulsoup4'
checksum was wrong, and because of that, it was not able to install it.
With this commit, `beautifulsoup-checksum' has been replaced for
`beautifulsoup4-checksum' in the `reproduce/software/make/python.mk'
Makefile, and the problem has been fixed. This was not noticed
previously because this Python package is only installed when some high
level programs are requested to be installed.
With this commit the version of `imagemagick' program has been also
updated because the previous version is not available in the official
website anymore.
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