Age | Commit message (Collapse) | Author | Lines |
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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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Now that its 2020, its necessary to include this year in the copyright
statements.
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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, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.
Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.
Also, some of the software versions were also updated after some checks
with their webpages.
This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).
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