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2020-01-20IMPORTANT!!! Configuration Makefiles now have a .conf suffixMohammad Akhlaghi-2/+2
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.
2020-01-01Copyright statements updated to include 2020Mohammad Akhlaghi-1/+1
Now that its 2020, its necessary to include this year in the copyright statements.
2019-10-31Minor corrections in distribution and autoconf prerequisite of automakeMohammad Akhlaghi-2/+2
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.
2019-10-30Tarballs set as order-only prerequisites, not needed for build callsMohammad Akhlaghi-28/+32
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.
2019-05-01Problem in generic CMake rule correctedMohammad Akhlaghi-2/+5
In the recent correction of backslashes, I had missed adding an `&&' before the `rm' command of the generic CMake building rule (`cbuild' of `build-rules.mk'). With this commit, this has been corrected. A multi-threaded Make was also added to build OpenMPI (which takes long and is often built alone because it takes so long and other things depend on it) and the HDF5 library.
2019-04-30End-of-line Backslashs no longer right under each otherMohammad Akhlaghi-52/+53
When we need to quote the new-line character we end the line with a backslash (`\'). Until now, our convention has been to put all such backslashes under each other to help in visual inspection. But this causes a lot of confusion in version control: if only one line's length is larger, the whole block will be marked as changed and thus makes it hard to visually see the actual change. It also makes debuging the code (adding some temporary lines) hard. With this commit, I went through all the files and tried to fix all such cases so only a single white space character is between the last command character and the backslash. Where there was an empty line (ending with a backslash, to help in visually separating the code into blocks), I put the backslash right under the previous line's. This completes task #15259.
2019-04-30Running PatchELF on all programs after CoreutilsMohammad Akhlaghi-5/+6
Even though the Coreutils configure script says that it adds `rpath' to its executables, its executables don't have it. As a result, it goes to use the host operating system libraries, causing failures when they don't match with the template. Unfortunately after some tests with the configure script, I couldn't find any way to include `rpath'! Even though `-rpath-link' is present in all linking commands during Coreutils' build, the installed files still don't have it! So I was forced to use PatchELF. However, one problem is that Coreutils installs many programs, not just one like Bash or AWK. As a brute-force solution, with this commit, we are running PatchELF on all the installed programs. It won't hurt those that already have it, but it will fix all those that don't. With this commit, I am also making the following non-related small changes: - In `build-rules.mk', the `&&' characters were placed at the start of the line for better readability. - Bash, Readline and NCURSES are now built in parallel on systems that support it (during `basic.mk').
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-0/+120
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).