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Until now, the Fortran compiler check wouldn't delete the files it creates
in the temporary software building directory.
With this commit, the cleaning steps have been added.
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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, 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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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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