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2019-08-07Removed temporary files to check Fortarn compilerMohammad Akhlaghi-2/+3
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.
2019-08-05Configuration: Checking that C and Fortran compilers workMohammad Akhlaghi-116/+199
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 ---------- conftest.c:9:19: fatal error: stdio.h: No such file or directory ^ compilation terminated. ---------- Fortran compiler ---------------- 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 ----------------
2019-07-29Checking software tarball checksums before building softwareMohammad Akhlaghi-3/+16
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.
2019-07-29Tip added at initial configuration notice on how to see progressMohammad Akhlaghi-0/+10
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.
2019-07-28Single wrapper instead of old ./configure, Makefile and ./for-groupMohammad Akhlaghi-0/+1224
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.