Developing for ABINIT¶
Introducing ABINIT to new developers¶
WARNING : some parts are severely outdated …
This tutorial introduces ABINIT to new developers. We want here to give a first insight into the internals of ABINIT. In other words, you will look at what’s under the hood. Being an ABINIT user is not required, though it will help a lot, in particular when writing a test case for your contribution. Some experience in programming is necessary if you want to take maximum benefit from this tutorial. In particular, some ease with Fortran 90, 95 or 2003 will be truly welcome. Familiarity with the unix command line will be important as well.
The ABINIT package is aimed at being used by different groups of people, without mandatory control by the main contributors of the ABINIT group. In the same way, the ABINIT development project is fundamentally open to the contributions of many people, including ones not located in Louvain-la-neuve or other major development sites of ABINIT. These external contributors are de facto members of the ABINIT group.
People using the code might consider adding their personal subroutines in their local branch, without trying to make them part of the official ABINIT package. However, this has two drawbacks for them: in subsequent versions, their modifications will not be incorporated, so that they might have to check and modify the interface for each new version; moreover, their addition is not tested by other users of the code, and some nasty bugs might remain unnoticed. Our opinion is that it would also be nicer from them to share the fruits of their coding efforts with other users of the code, in the spirit of GPL open source and linux development.
Of course, these collaborative efforts entail complications as well. In particular, the collaboration between distant developers should be carefully planned, since orthogonal modifications of the same piece of code by two different people at the same time is very likely to happen, generating conflicts in the code and a large waste of time when it has to be synchronized. It is also mandatory, in order to have a contribution merged into ABINIT, to use a well-defined coding style, to provide test case files, and to comment the modifications and additions as much as possible, in order to facilitate maintenance and the future modifications. This is verified by a number of scripts, known as abirules, checking for the presence of documentation, absence of unused variables, etc…
A lot of information for the ABINIT developers can be found in the developer’s corner of the ABINIT wiki, especially, an overview of ABINIT development, git(lab) specificities, buildbot and the test farm, as well as in the ABINIT doc.
The main goals of this tutorial are to provide you with a useful understanding of the source tree structure and the build process, as well as to sensibilize you to the rules and procedures followed for the development of ABINIT. In the example we have chosen, we will suppose that you want to add an input variable to the code and create a corresponding subroutine. For simplicity, we will now imagine that you have designed a new exchange-correlation functional and that you want to test it with ABINIT. In reality, xc functionals are treated almost exclusively through the libxc library. Here are the steps we will take:
- Get the source and compile the code.
- Identify the subroutines to modify.
- Add the new input variable and its associated routine.
- Add a test to the test suite.
- Create a patch for the project leader.
For this tutorial, your input variable will be a real number called ” tutorial “. The task devoted to your routine is just to print this variable.
Get the source and compile the code¶
There are two ways of getting the source code of ABINIT:
- directly from the ABINIT web site (abinit.org/) by downloading the latest production tarball;
- from the ABINIT gitlab git repository. This is favored, as it allows easier integration and merging, testing, etc…
While the first method is commonplace, the second one requires you to know how to use git(lab). Please see the ABINIT gitlab Wiki section.
Once you have got the tarball, uncompress it by typing:
tar xvzf abinit-<version> .tar.gz
Q1. If you need off-line documentation, in which directories will you look?
Q2. Where can you find the tests?
Q3. What do the numbers in the names of the ” src ” subdirectories stand for?
Q4. In the source subdirectories, what do the abinit.src files contain? In your opinion, what is their purpose?
Q5. What kind of tests are available? How important do you think they are?
Now you can try to build ABINIT. Information on how to do it is stored inside the INSTALL file. Please read it now.
Before actually starting the compilation, type:
and read carefully the output. You might then find useful to have a look at the template for config files stored in ~abinit/doc/build/config-template.ac9 which will provide you with more details on the configuration. Other example config files in that subdirectory can be used to set up your build more quickly. If you have a configuration file called ~/.abinit/build/hostname.ac (with hostname equal to the $HOSTNAME shell variable for your machine) ABINIT’s configure will load it at runtime.
The compilation will likely take more than 10 minutes. In the meantime, you can proceed to the next task.
Identify the subroutines to modify¶
At this point, you have to discover which parts of the code will have to be modified in order to have your contribution correctly integrated. First choose randomly a few subroutines in one of the ” src/* ” subdirectories and have a look at them, in particular their headers. Then try to answer the following questions:
Q6. How would you identify the subroutines involved in the treatment of input variables?
Q7. Where are the routines handling exchange-correlation? Which input variables are they strongly related to?
Q8. Which subroutine would you choose as a parent for yours?
Q9. Where is the wrtout subroutine? What is its purpose? How does it work?
Add the new input variable and its associated routine¶
Please examine the file ~abinit/doc/developers/programmer_guide.txt and ~abinit/doc/developers/rules_coding.txt. This might help writing your own subroutine. To actually start, go to the subdirectory you’ve identified before and type:
sh ../../developers/various/mkroutine.sh handle_tutorial
This will create a file named m_handle_tutorial.F90 , handle_tutorial being the name of your subroutine. Note that since 2018 all routines in abinit must be contained in modules, to ensure interfaces will be generated and tested by the compiler.
Add treatment code for your input variable to the files you have identified
previously. Then write your subroutine, and add a call to it at a suitable
place. When you’re done, issue
./config/scripts/makemake from the top source
directory, to have the build system aware of the presence of your new routine.
Last but not least, rebuild abinit.
Add a test to the test suite¶
Since your contribution is to be integrated into the version 7 (8, 9 …) of ABINIT, all associated tests should go to the ~abinit/tests/v7/ directory (or v8/ or v9/ ....) Wander a little bit around the subdirectories of tests/ , and have a look at their content. Examine one of the input files, contained in the v7 (8, 9 …) subdirectory. Note in particular the content at the bottom of the file. Each test is identified by an index, attributed after consulting the ABINIT coordinator. Say it was decided that your contribution will be checked by test 99. Read the Web documentation that describes how to add a new test
Q10. What do you need to do in order to have a new test added?
Implement your test and issue
./runtests.py v7 in the tests/
subdirectory, to check that it works fine.
Create a patch for the project leader¶
There are two ways of creating a patch, depending on whether you are using git or not. If yes, you just have to add your new files, commit your changes with a comment, then push to gitlab and issue a “pull request”. This procedure is highly recommended, as it is very fast and as the project leader will be provided with a lot of flexibility and information to handle your contribution. If not, you have to create a patch with a full description of your changes and send it by email.
To merge your contribution correctly, the project leader needs patches both in universal format and where new files are considered empty in the old version.
Q11. Which options will you give to the diff command to produce the patch ?
Q12. How will you proceed exactly to create it ?
4 Solutions to questions¶
Even if we provide you here with the answers to some of the questions, we highly recommend you to try by yourself before looking at them. Please read this section only as a last resort.
R1. In ~abinit/doc/ , of course.
R2. In ~abinit/tests/ , of course.
R3. They correspond to a hierarchical structuring of the dependencies within ABINIT. The higher the level, the more the dependencies on lower levels.
R4. They contain the list of source files to be compiled, and are processed to create the makefiles for each directory. Thanks to their presence, developers do not need to know all the internals of the build system (autoconf, m4, etc…).
R5. The available documentation describes all tests in detail and stresses their importance quite enough. Just read the suggested files.
R6. I would issue a grep command for a random input variable in order to trace the handling of input variables throughout the code.
R7. These routines can be found in ~abinit/src/56_xc , and are driven by the ixc input variable.
R8. The ~abinit/src/56_xc/drivexc.F90 routine, for instance.
R9. Look in ~abinit/src/14_hidewrite/wrtout.F90 , the header contains detailed explanations.
R10. You can follow the wiki documentation that describes how to add a new test
R11. “-u -r -N”.
R12. Supposing that you have downloaded ABINIT 8.8.3, the following set of commands will do:
mv abinit-8.8.3 abinit-8.8.3-tutorial
tar xvzf /path/to/abinit/tarball/abinit-8.8.3.tar.gz
mv abinit-8.8.3 abinit-8.8.3-orig
diff -urN abinit-8.8.3-orig abinit-8.8.3-tutorial > abinit-8.8.3-tutorial.patch
gzip --best abinit-8.8.3-tutorial.patch