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Until now, OpenMPI was being installed without any dependency. This was
fine because it would indeed build. But the moment you tried loading
something that depends on it (for example `mpi4py' through `astropy'), you
would get an error complaining that SSH isn't present.
With this commit, the pipeline now also installs OpenSSH to solve this
problem.
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Until now, we were relying on WCSLIB's internal checking and linking with
CFITSIO. But on one macOS system (not others that had no problem!), we
noticed that it complains with undefined symbol linking errors to CFITSIO
libraries.
With this commit, as a fast/ugly solution, we are explicity adding
`-lcfitsio' to WCSLIB's `LIBS' variable so all binaries are linked with it
automatically. We'll be in touch with the WCSLIB author to see if a better
solution can be found.
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Until now, we weren't explicitly disabling Java in the build of libffi
because there was no Java platform on the systems we tested. But recently
Yahya Sefidbakht report a crash in libffi (reported in bug #56716) because
of Java not being compiled properly.
Unfortunately libffi doesn't have a configure option to disable Java, but
it does have an internal macro (`NO_JAVA_RAW_API'). With this commit, we
we defined this macro in the `make' step, and it solved the problem.
This fixes bug #56716.
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Some of the software tarballs are directly available on their webpage (for
example due to build problems on systems, where we had to clone the
software and build its tarball ourselves until the next release). Until
now, only for these software, these tarballs were hosted on
`http://akhlaghi.org/src'. But now, I have moved a clone of the software
backup repository (including all its software) to
`http://akhlaghi.org/reproduce-software'.
To be more clear and have a single place for the backup software, the URL
of those software has also been updated in the project source.
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A new version of Gnuastro was recently released with many improvments and
bug fixes, so it is updated here too.
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Until now, we were just checking for the existance of a C and Fortran
compiler. But it can happen that even if they exist, they don't operate
properly, for example see some errors that have been reported until now in
P.S. (both on different macOS systems). But finding this source after the
programs have started is frustrating for the user.
With this commit, before we start building anything, we'll check these two
compilers with a simple program and see if they can indeed compile, and if
their compiled program can run. If it doesn't work an elaborate error
message is printed to help the users navigate to a solution.
Also, the building of `flock' within `configure.sh' has been moved just
before calling `basic.mk'. This was done so any warning/error message
is printed before actually building anything.
This fixes bug #56715.
P.S. The error messages:
C compiler
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conftest.c:9:19: fatal error: stdio.h: No such file or directory
^
compilation terminated.
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Fortran compiler
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dyld: Library not loaded: @rpath/libisl.10.dylib
Referenced from:
/path/to/anaconda2/gcc/libexec/gcc/x86_64-apple-darwin15.5.0/4.9.3/f951
Reason: image not found
gfortran: internal compiler error: Abort trap: 6
----------------
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Until now, in version 3.0.1, mpi4py couldn't be built with the most recent
version of OpenMPI. However, after trying the next version (3.0.2), I
noticed that it builds successfully without a problem.
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Until now, when you needed to completely clean a project (with `./project
make distclean') the Git hooks that are installed during configure time
would cause problems when committing (the `pre-commit' hook in particular
won't allow you to commit anything!).
With this commit, before deleting the software, the template first removes
these Git hooks.
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After making the previous commit, I noticed an extra line (redundantly
defining a wrong `BASH_ENV') that should have been deleted. It has been
corrected.
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Until now the only way to define the environment of the Make recipes was
through the exported Make variables (mostly in `initialize.mk' for the
analysis steps for example). However, there is only so much you can do with
environment variables! In some situations you want slightly more
complicated environment control, like setting an alias or running of
scripts (things that are commonly done in the `~/.bashrc' file of users to
configure their interactive, non-login shells).
With this commit, a `reproduce/software/bash/bashrc.sh' has been defined
for this job (which is currently empty!). Every major Make step of the
project adds this file as the `BASH_ENV' environment variable, so the shell
that is created to execute a recipe first executes this file, then the
recipe. Each top-level Makefile also defines a `PROJECT_STATUS' environment
variable that enables users to limit their envirnoment setup based on the
condition it is being setup (in particular in the early phase of
`basic.mk', where the user can't make any assumption about the programs and
has to write a portable shell script).
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After adding the libiconv library to the template, the C++ library uses
three of its functions (`libiconv', `libiconv_open' and
`libiconv_close'). However, it doesn't explicity link with it inside its
shared library!
I tried by exporting `LIBS=-liconv' before the GCC configure script but it
crashed as soon as it went on to the second GCC building stage (because
this environment variable was no longer present there). I also tried adding
the C++ configure option of `--enable-cstdio' to the GCC configure options
(so it doesn't use iconv according to the manual), but it made no change.
With this commit, as a brute-force solution, `patchelf --add-needed' is run
on the installed `libstdc++.so', so `libiconv.so' is explicitly included
inside the `libstdc++' shared library.
This bug was found by Roberto Baena Galle while trying to load Matplotlib
(which needed the C++ library).
This fixes bug #56702.
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Until now, there was no check on the integrity of the contents of the
downloaded/copied software tarballs, we only relied on the tarball
name. This could be bad for reproducibility and security, for example on
one server the name of a tarball may be the same but with different
content.
With this commit, the SHA512 checksums of all the software are stored in
the newly created `checksums.mk' (similar to how the versions are stored in
the `versions.mk'). The resulting variable is then defined for each
software and after downloading/copying the file we check to see if the new
tarball has the same checksum as the stored value. If it doesn't the script
will crash with an error, informing the user of the problem.
The only limitation now is a bootstrapping problem: if the host system
doesn't already an `sha512sum' executable, we will not do any checksum
verification until we install our `sha512sum' (as part of GNU
Coreutils). All the tarballs downloaded after GNU Coreutils are built will
have their checksums validated. By default almost all GNU/Linux systems
will have a usable `sha512sum' (its part of GNU Coreutils after all for a
long time: from the Coreutils Changelog file atleast since 2013).
This completes task #15347.
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The configuration step (building all the ncessary software) can take some
time. It is natual for the user to want to see how the build is going
(which software is being built at every moment). So far, we have only put a
"Inspecting status" section in `README-hacking.md' that describes a
solution, but some early users may not have read it yet.
With this commit a short tip was added in the initial installation notice
to inform the user of this very useful command.
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We recently moved the system's `rm' program absolute address to a shell
variable that is found during the `./project' script. But I had forgot to
account for the difference between the Make and Bash variable naming
differences. I had also forgot to add a value to the HOME variable.
With this commit both are corrected: the system's `rm' path is now called
`sys_rm' and the HOME variable is set.
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Until now, to work on a project, it was necessary to `./configure' it and
build the software. Then we had to run `.local/bin/make' to run the project
and do the analysis every time. If the project was a shared project between
many users on a large server, it was necessary to call the `./for-group'
script.
This way of managing the project had a major problem: since the user
directly called the lower-level `./configure' or `.local/bin/make' it was
not possible to provide high-level control (for example limiting the
environment variables). This was especially noticed recently with a bug
that was related to environment variables (bug #56682).
With this commit, this problem is solved using a single script called
`project' in the top directory. To configure and build the project, users
can now run these commands:
$ ./project configure
$ ./project make
To work on the project with other users in a group these commands can be
used:
$ ./project configure --group=GROUPNAME
$ ./project make --group=GROUPNAME
The old options to both configure and make the project are still valid. Run
`./project --help' to see a list. For example:
$ ./project configure -e --host-cc
$ ./project make -j8
The old `configure' script has been moved to
`reproduce/software/bash/configure.sh' and is called by the new `./project'
script. The `./project' script now just manages the options, then passes
control to the `configure.sh' script. For the "make" step, it also reads
the options, then calls Make. So in the lower-level nothing has
changed. Only the `./project' script is now the single/direct user
interface of the project.
On a parallel note: as part of bug #56682, we also found out that on some
macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set
to blank. This is no problem because RPATH is automatically set in macOS
and the executables and libraries contain the absolute address of the
libraries they should link with. But having `DYLD_LIBRARY_PATH' can
conflict with some low-level system libraries and cause very hard to debug
linking errors (like that reported in the bug report).
This fixes bug #56682.
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Until now we were only setting the `LD_LIBRARY_PATH' environment variable
for GNU/Linux systems. But macOS systems use the `DYLD_LIBRARY_PATH'.
With this commit, for better control over the environment, we are also
fixing `DYLD_LIBRARY_PATH' in all the places that we are setting the
general environment variables.
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Until now, like all other software, PatchELF would install with dynamic
linking. However, PatchELF links with `libstdc++' so on one system, I
noticed that PatchELF gives a segmentation fault and corrupts `libstdc++'
while correcting its RPATH (after installing GCC). The solution is to build
PatchELF statically.
With this commit, we force PatchELF to be built statically (it only
installs on GNU/Linux systems anyway, so there is no problem with static
linking on macOS). This solved the problem on that system.
While looking at its documentation, I also noticed that a new version of
PatchELF has been released after almost three years, so it has been updated
in the template also.
This fixes bug #56673.
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Some bugs have been fixed in the new version of WCSLIB, so it has been
updated in the template.
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More than two releases and bug fixes have been made to libgit2. So we are
now using a more recent version in the template.
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Configure script: when `texlive-ready-tlmgr' is not created, it is similar
to not having installed TeXLive. A check was added so in this scenario the
`./configure' script doesn't crash.
high-level.mk: `cairo' and `pixman' are now installed in parallel and with
`V=1' (so the full compilation and linking command is printed).
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In one of the last few commits, the commands in the recipe of libgit2 was
merged with `&&' so it stops if anything fails. But I had forgot to add a
`;' at the end of the `install_name_tool' command. This is corrected with
this commit.
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Until this commit, the addion of `-liconv' to `CXXFLAGS' in `high-level.mk'
dependend on `host_cc', but I had forgot that `host_cc' isn't defined for
`high-level.mk'. It is now defined for this Makefile also in the configure
script.
Also, the Standard C++ library depends on `libgcc_s.so.1', so after
building GCC, it was necessary to add Rpath to it.
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While doing a clean build, several issues were found in the pipeline and
corrected. The main issue was that with the recent installation of
`libiconv', the GCC standard C++ library depends on `libiconv', so we need
to explicity add an `-liconv' to any C++ compilation.
The other corrected points are:
- The C++ compiler is now explicitly defined in `CXX'.
- libgit2 and WCSLIB's recipes weren't using `&&' between statements, so
if there was an error, it would still build the target!
- The CMake bootstrapping script now builds much faster in parallel.
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While testing on a system with no Texinfo, we noticed that M4 depends on
Texinfo. To fix this problem, with this commit, it is now included in the
pipeline.
While doing a clean build, a few minor issues were also found and corrected
in the other rules.
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Until now, we were using the `--enable-single' configure-time option of
FFTW to build its single-precision library. The reason was that according
to the output of `./configure --help', this was equivalent to
`--enable-float'. However, the single precision library wasn't being built.
As a result, on systems that already had it, SExtractor would use the
system's library and on other systems, it would simply not pass the
configure step.
With this commit, we are now using `--enable-float' which fixes this
problem and installs the `libfftw3f*' libraries (showing that it is not
equal to `--enable-single'!). Also, some optimization flags were added to
hopefully make it faster.
This issue was found thanks to Zahra Sharbaf and Hamed Altafi.
This fixes bug #56588.
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Until now, we were letting the TeXLive installer use the default
CTAN-chosen mirror based on the host. But in many cases, this is not
efficient and sometimes those servers don't work.
With this commit, we manually set the server to use (`rit.edu'), which is
relatively fast and up to date. In this way, until we build TeXLive from
source, every user will be using the same CTAN mirror.
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On some Fedora systems, Wget's build conflicts with libiconv.
With this commit, we use Wget's `--without-libiconv-prefix' configure
option so it will be built without an outside libiconv.
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On some Fedora systems, libffi installs under `lib64', not `lib'. As a
result, Python's Setuptools can't find it and will not built (complaining
about not finding the `_ctypes' module).
With this commit, we fix this problem by explicitly putting a copy of
libffi's installed libraries within the `lib' directory.
This issue was found while testing the pipeline with Elham Saremi and Hamed
Altafi.
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Until now, we weren't explicitly setting the C and Fortran compiler
environment variables (`CC' and `F77'). As a result, if the user's system
had already set them, there would be a problem (and the system's compilers
would be used).
With this commit, we are explicitly setting these two environment variables
at the start of `high-level.mk'.
This bug was found after a discussion with Elham Saremi.
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An existing `libiconv' can cause a conflict with `pkg-config', this is why
`libiconv' depends on `pkg-config'. On a clean build, `pkg-config' is built
first. But when we don't have a clean build (and `libiconv' exists) there
will be a problem.
With this commit, before re-building `pkg-config', we'll remove any
possibly existing installation of `libiconv'.
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There was only a conflict with `.file-metadata'.
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While reviewing Prasenjit's commits, I noticed that we had forgot to add
the citation for TIDES, also to make things clear, the program/library
build rules are now sorted alphabetically.
Finally, I noticed that after building the TiKZ PDF figures, it is crashing
(like on Prasenjit's computer). After looking around, I noticed its because
we were setting the of the `TEXINPUTS' environment variable to be the
installed TeX Live directory (which was ultimately redundant because by
default TeX will look into where it was installed). The important thing is
just that we remove any possible value the host system has, not to set new
directories.
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Libiconv has to be installed before pkg-config otherwise there
would be a compilation error:
gconvert.c:61:2: error: #error GNU libiconv not in use but included
iconv.h is from libiconv
61 | #error GNU libiconv not in use but included iconv.h is from
libiconv
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TIDES is an ODE integrator with multiple-precision arithmetic.
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Several corrections were necessary in the basic build: 1) the
version of GCC on some systems includes an `_' which would cause
a crash when building the PDF. 2) libcharset had to be manually
added to the Git build.
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Prasenjit Saha reported that while building on a macOS, Git complained
about not finding `libiconv' functions. Therefore with this commit,
`libiconv' is also built as a dependency of Git.
Also, since the build of Binutils (and the subsequent GCC) doesn't depend
on the exact versions of the other basic software, they are set as
existance-only prerequsites (ignoring their timestamps). This is done to
avoid re-building when it is not needed.
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The comment above Gnuastro's build rule is not longer relevant, so it has
been removed.
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Until now, on GNU/Linux systems, GNU Binutils was built in parallel with
other programs. As a result, the moment that the Binutils executables (most
importantly `ld') are being installed, if another program is using them, we
can have a crash.
For some reason, this crash doesn't happen on Fedora or Arch Linux, but on
some Debian-based distors, it causes the following crash when we are
building Git (which happened to be built while Binuntils is being
installed):
credential-cache--daemon.o: file not recognized: File format not recognized
In a following run of `./configure' (when Binutils has been installed), Git
will build and install successfully.
To fix this problem, with this commit, all basic programs are now a
prerequisite of Binutils and Binutils is the sole prerequisite of GCC
(which is the final target of `basic.mk').
Also, the GCC configure options were re-ordered to be easier to read (the
`--with-*' options under each other, the `--enable-*' options under each
other and so on).
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Until now we hadn't noticed that Metastore's build doesn't include an
`rpath'. As a result I got a crash during a Git commit.
With this commit, on GNU/Linux systems, we now add rpath to the installed
Metastore executable. During the build, I also cleaned up the Metastore
build recipe to be more clear and readable (in particular we only check the
user name and group name when metastore is actually built).
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Until now, for some reason, the permission flags of `top.mk' were 755 (good
for an executable), not 644 (which is what they should be for a plain text
file that is run by another program).
This is corrected with this commit.
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The recent work by Raul to import Imfit is now merged into the master
branch. Only a few minor conflicts came up due to the update with CFITSIO
(that Raul also done in parallel on this branch).
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While trying to debug the installation of Imfit, we found out
that libcurl doesn't have rpath and is thus linking with the
host system's libraries. So rpath is now manually added to the
build of libcurl. We also found out that Imfit executables
don't have rpath, so it was added to them too.
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Until now, TeXlive would only attempt to download/update LaTeX packages,
but after some time, it will be necessary for it to update itself. When
this happens, it complains about running it with `update --self'.
To fix this problem, before installing/updating the LaTeX packages, we will
first update tlmgr in any case.
Also, we weren't removing the TeXlive package version file before appending
the values to it. So it was just repeating the packages every time it was
updated. With this commit, it is being removed on every new build.
Finally, the version of Git was updated to its most recent version.
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Until this commit, 'imfit' was installed using proper flags in order to
use our own libraries. However, it looks first of all to the default
system. As a consecuence, `imfit' program was linked to the host system
libraries, even when we told to use our own libraries!!
With this commit, the installation of `imfit' has been modified in order
to remove the default paths already set in the `SConstruct' script. By
doing this, only our paths are take into account for compiling the
program. It has been tested on Mac OS laptop and it works fine. Test on
GNU/Linux systems remain before merge into the main project branch.
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Until this commit, `fftw' was building single precission float library
because `scamp' had problem on using the default double precission
library. However,`imfit' and maybe other programs will use double
precission float libraries.
With this commit, `fftw' installation is done twice in order to build
single and double precission float libraries. It does not complain and
goes up to the end without crashing. However, more tests are needed in
order to ensure that there is not problem on having both libraries
because in principle, they share the same header file and that could
cause problems.
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`cfitsio' was recently updated and it cames up with a problem when
trying to build shared libraries (on Mac OS system laptop). This is
because the `configure' script for building `cfitsio' include by default
`rpath'.
With this commit, this issue is fixed by modifying the installation of
`cfitsio'. Using `sed', each ocurrence of `@rpath' in `configure' is
replaced by `$(ildir)'. Once it has been done, the installation of
`cfitsio' goes as normal.
In this commit, the version of the `cfitsio' has been also updated to
the most recent one.
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With this commit, I have corrected a typo in the installation of
`imfit'. In principle it is working on Mac OS system but when I tried to
install it in GNU/Linux system it crashed. It complains about a problem
with the `cfitsio' library:
/pathto/libcfitsio.a: error adding symbols: File format not recognized
As in the last commits done by Mohammad in the project, `cfitsio'
installation has been upgraded and also the installation has been
modified, I am going to try this new version. I will also check if it is
a problem about dynamic/static library.
It also seems that the installation is taking libraries and variables
from the host system, so I will check that everything used is from our
own programs/libraries.
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Until now, CFITSIO had several peculiar features which needed special
attention: 1) Its tarball didn't have a `.' in the version name and would
sometimes have extra `0's. 2) When unpacked it was just `cfitsio'. 3) It
hard coded the directory to search for cURL library. All of these forced us
to do a lot of extra steps for CFITSIO.
So I got in touch with them and fortunately they were very open to
correcting these issues and with version 3.47 all such issues have been
addressed in the tarball. Thanks to these changes, with this commit,
CFITSIO's build rule is now very similar to many other programs.
I also noticed that it has an optional `--with-bz2' feature to enable
unpacking `.fits.bz2' files. So this feature is also added.
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Until this commit, `imfit' paper was not included into the
acknowledgements.
With this commit, a bib tex file for `imfit' has been added. So, now it
is properly cited into the final paper.
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With this commit, `imfit' has been included into the project. As described
in the official webpage (http://www.mpe.mpg.de/~erwin/code/imfit/):
Imfit is a program for fitting astronomical images -- especially images
of galaxies, though it can in principle be used for fitting other
sources.
This program uses the `scons' program to build itself (not the traditional
GNU `configure' and `make' system). I have tested it by using an example
that can be found in the `examples' directory of the decompressed
tarball. It works fine without any error on my Mac OS system.
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