Task #1415
Get rid of legacyheaders/
Description
The legacyheaders/ directory was meant as a temporary workaround to be able to move files to the new directory layout gradually, while keeping the build and the installed headers working all the time. The original idea (when the discussion started back in 2010 or so) was that this would be more or less gone by 5.0, but it has been quite persistently alive. So the goal would be to have all the headers from src/gromacs/legacyheaders/ moved into subdirectories like src/gromacs/domdec/ or src/gromacs/nbnxn/ or something, together with the source files that implement those functions and anything that belongs naturally together with them. Large parts of this should not be rocket science, and if people would contribute on the areas that they know, we could then see what are the problematic areas. The initial division can also be adjusted later as we grow wiser.
There are currently about 150 headers remaining, plus 38 from thread_mpi (the latter should be easy to move, once there is some clarify for #1411). Large parts of this will be easy, but the types/ subdirectory can be challenging.
This would allow us to clearly see the dependencies between the modules and draw reasonable division lines for the different libraries required for, e.g., #1165. Visualizing the dependencies between the parts with something like https://gerrit.gromacs.org/#/c/2908/ would provide a much clearer picture of where we are and what could be done to clarify the structure of the code.
Associated revisions
Move essential dynamics / flooding code to separate directory
Part of #1415 Get rid of legacyheaders.
Additional changes:
- provided doxygen-style documentation for functions in edsam.h
(partly copied over from edsam.c and removed there to avoid
duplication)
- uncrustified edsam.c and edsam.h
Change-Id: If4af498470c5200d50ac1d1b5537917c873380b5
Move pull code to separate subdirectory
Another part of #1415 Get rid of legacy headers.
Other changes:
- updated pulling-related include guards to new format
- updated documentation for doxygen
- updated .h includes
- uncrustified pull.h and pull_rotation.h
- updated copyright year for all files touched by this commit
Change-Id: Ief1ed3543b84f651d1bff01f1952b342850f5c22
Move more preprocessing files into the module
This removes the need for the gmx_objlib CMake object library, because
there is no longer random functionality orphaned in src/programs/gmx
(which is there because it was orphaned in src/kernel in release-4-6).
Moved legacyheaders/grompp.h to gmxpreprocess/grompp-impl.h since it
only declared structures that are (now) only used in that module (and
it no longer #includes stdio.h). gmxpreprocess/grompp.h now only
declares gmx_grompp().
Likewise, pdb2gmx, protonate and x2top now have their own
single-function headers.
Removed useless declaration of ncontrol from h_db.h
Removed grompp.h-related useless dependencies, declarations and
definitions from Generalized Born files.
Updated include and added C++ guards for files already within the
module (and new ones). Uncrustified, bumped copyrights
Refs #1415
Change-Id: Ie7967d7d7f61df684d530e3c2d982486a3cd128f
Move smalloc.h to utility/
One common header away from legacyheaders/.
Mostly mechanical replacement for the include paths, but removed a few
instances where the header was included more than once. Also, reordered
the headers a bit, mainly in C++ files.
Part of #1415.
Change-Id: Ic438d501ebf5eccc285655a9e8f2f625eb12f1d1
Move string2.* to utility/cstringutil.*
Another common header away from legacyheaders/.
Some associated #include cleanup.
This reintroduces some unwanted dependencies (like utility -> fileio),
but those need to be fixed separately.
Part of #1415.
Change-Id: Iffb2820019e2b41ef74bcabcd202364917e43d58
Move gmx_fatal.* to utility/fatalerror.*
One more included-by-all header to utility/.
Mainly mechanical replacement of include paths, some reordering in C++
files. Minor clean-up in the moved files.
gmx_fatal_collective.h not moved at this point, as it is unclear whether
it should go here, or somewhere else (utility/ should not depend on
t_commrec...).
Now, it's mainly types/simple.h that prevents removing some module-level
dependencies to legacyheaders/. Finding a good location for that (or
its contents, if it needs to be split), and reorganizing the code a bit
more should now allow really putting utility/ at the bottom of the
dependency stack where it belongs.
Part of #1415.
Change-Id: I6e487566d5bd7c9ec7a1455a2d31bd6d645bada3
Remove sysstuff.h
Replace this with those standard headers that are actually necessary for
the source files. There are likely several transitively covered header
dependencies now, but those can be resolved when they give problems.
One more header off from legacyheaders/.
Part of #1415.
Change-Id: I4cc3f0eec0f546dad929512e532d8efb11da3694
Move vec.h to math/
Most of the changes are scripted replacement of include paths.
Exceptions:
- #includes in the moved file were cleaned up slightly, and include
guards adjusted.
- Places where it was included as "gromacs/legacyheaders/vec.h" were
handled manually and the include order adjusted.
- Removal of unnecessary #include "vec.h" from update.h revealed some
transitive dependencies that were fixed. Some associated include
order cleanup in these files.
- Removed some duplicate includes.
- Remove dependency from linearalgebra/matrix.c to vec.h (only needed
for a single sqr()) to avoid a cyclic math <-> linearalgebra
dependency.
Part of #1415.
Change-Id: I7ece6eafa22139215510148807c5979f8950a885
Move part of macros.h to grompp-impl.h
Part of #1415.
Change-Id: I360ae1f220b6c51e90edbbe136053fd2e1c0ad5b
Move 'real' definition to utility/real.h
- types/simple.h still includes the new header to avoid touching all
code depending on this.
- Go through most files outside gmxlib and mdlib that included
types/simple.h, and checked whether headers from utility/ could
fulfill the needs. Replaced at least in places where this helped
fully remove legacyheaders/ dependencies.
- Some minor changes elsewhere to remove legacyheaders/ dependencies
from modules. Now linearalgebra/ and statistics/ don't depend on
legacyheaders, improving the layout of the dependency graph
significantly.
In the long run, this may be better outside utility/ to better
distinguish code that depends on 'real' from parts that do not.
Currently, it would create a lot of cyclic dependencies everywhere else.
Part of #1415.
Change-Id: I2aa1890357377d0d14c05b3968e1b36e1023458f
Move rvec and friends to math/vectypes.h
Adjust a few more types/simple.h includes to use only its component
parts. Now, math/ has only very few legacyheaders/ dependencies left.
Part of #1415
Change-Id: Iffeafa4fac5c5e0c744cf6deecac4eedaee2caf5
Reduced usage of typdefs.h
Preliminary step to move types out of legacyheader.
Renamed parameter called "matrix" because cppcheck gets
confused if a parameter is called the same as a type.
Part of #1415
Change-Id: I9207a7b8de7f092bab890da128abbb48a8d97b79
Move physics.* to math/units.*
- Remove some unnecessary #includes.
- Remove the dummy tests; easy to rewrite as usable tests using GTest if
someone needs those. They were anyways testing code that no one is
still calling, even though it was introduced several years ago.
Now gmxlib is free of *_test.c files.
Now, only one file using atom_id is keeping math/ dependent on
legacyheaders/.
Part of #1415.
Change-Id: I31312b92cf9f5d5129fbd90f31fcf27be2f7afaf
Removed legacyheaders/types/commrec_fwd.h from typedef.h
Related to #1415
Change-Id: I9a9dd7f1e62cfd040d183370d187f6a23ede78fa
Moved df_history utility routines from typedefs to new file.
Part of #1415.
Change-Id: Ia2b9e6e5342cb3bb5820894fb82ef2908d969bc6
Removed legacyheaders/typedefs.h
More cleaning up in legacyheaders. Mostly this patch involves
shuffling around include files, and adding a couple of forward
declarations. Renames gmxlib/typedefs.* to mdtypes/state.* and
introduces new utility/int64_to_int.cpp with header.
Introduced new directory mdtypes to resolve circular dependencies.
Right now state.* and history files
are the only files living there.
Part of #1415
Change-Id: I5dc59a2ca3bd1f9c5391f4b9deb9f116b30106fc
Moved inputrec.* from gmxlib and legacyheaders to mdtypes.
Part of #1415
Change-Id: Idb00712d1b6ea9648a36d349f670790aaaf2c6d4
Moved copyrite.* to fileio from gmxlib and legacyheaders.
Part of #1415
Change-Id: Id6cfb84cc683f88731fac7d80053aadc9b828806
Moved txtdump.* to fileio.
Some cleanups in edsam.cpp too.
Part of #1415
Change-Id: I6cd58951eff1bac0dad75dbd448a958e57c767e7
Merged legacyheaders/types/inputrec.h into mdtypes/inputrec.h
Part of #1415.
Change-Id: I39885a01474173170bc6a7a7c2e54e7f21d64370
Moved legacyheaders/types/energy.h to mdtypes.
Part of #1415
Change-Id: I65a00cc49110a09edfafc7520a7a480f73b5165c
Moved mdatom.h from legacyheader/types to mdtypes.
Add doxygen comments to the elements of the structure.
Part of #1415.
Change-Id: I811ad4782dd482ac7fe198c85c85b91af6e20b67
Merged legacyheaders/nrnb.h and types/nrnb.h to gmxlib.
Part of #1415
Change-Id: I33922419a6a5a7976bda12fd81e2d752eb0c5c6d
Combine enums.h and names*.
Combined enums.h and names* to mdtypes/md_enums.cpp/h.
Added doxygen comments to md_enums.h
Removed macros in inputrec.h to reduce cyclic dependencies.
Clean up of legacyheaders. By removing some unnecessary includes
from the files names.h and enums.h (now md_enums.h)
a lot of 'freeriders' showed up, therefore had to include
topology.h in many files.
Part of #1415
Change-Id: I12b8ef4f82b7aec806aea2eee7d77604e86dc576
Merged legacyheaders/types/ns.h and nblist.h to mdtypes/nblist.h
Also parts moved out of forcerec.h.
In order to make this work some parts of the forcerec structure
had to be made pointers, and the same for nblist structures.
Part of #1415.
Change-Id: Iaaadd76ccca001a11371b9a0ad1b75a727732f00
Moved legacyheaders/types/group.h to mdtypes.
Part of #1415.
Change-Id: I959941cf586b90e97359e8ec026dc923ff7f8aa5
Merged genborn.h from legacyheaders/types into mdlib/genborn.h
Part of #1415.
Change-Id: I2c9dcb827219649791183d016bf07d056a9ca049
Cleanups in legacyheader/types/commrec.h
Removed superfluous typedefs from above file.
Part of #1415.
Change-Id: If3d99dc24864d21dbbfa2eaf57fd5264f7d3d9ec
Moved domdec structures out of commrec.h.
In order to clean up the legacyheaders directory here the
structures relating to domain decomposition are taken out of
commrec.h and moved to a new file domdec/domdec_struct.h
To not introduce new cyclic dependencies modified the
interface of write_checkpoint and gmx_fatal_collective.
Part of #1415
Change-Id: I485a03eddbb87dcc236b7e2e7d85d03383d86f61
Merge remaining legacyheaders/types/ to mdtypes/
One cyclic dependency suppressed for now.
legacyheaders/ is no more.
Closes #1415 (but this just moves us to the next phase of the clean-up)
Change-Id: Ie80d24d347acb61216002a309cb4118f8dc99b6b
Broke up copyright.*
Split unrelated content into binaryinformation.* and pleasecite.*, and
move them to utility/. This removes functionality from fileio that does
not really belong there, and helps in removing cyclic dependencies.
One new cyclic dependency suppressed for now; it will disappear with
simplification of gmx_invsqrt().
Part of #1415.
Change-Id: I65f07768d46852783d30cf1a28dd22d614dde125
History
#1 Updated by Gerrit Code Review Bot over 3 years ago
Gerrit received a related patchset '1' for Issue #1415.
Uploader: Carsten Kutzner (ckutzne@gwdg.de)
Change-Id: If4af498470c5200d50ac1d1b5537917c873380b5
Gerrit URL: https://gerrit.gromacs.org/2961
#2 Updated by Gerrit Code Review Bot over 3 years ago
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Change-Id: Ief1ed3543b84f651d1bff01f1952b342850f5c22
Gerrit URL: https://gerrit.gromacs.org/2979
#3 Updated by Gerrit Code Review Bot over 3 years ago
Gerrit received a related patchset '1' for Issue #1415.
Uploader: Mark Abraham (mark.j.abraham@gmail.com)
Change-Id: Ie7967d7d7f61df684d530e3c2d982486a3cd128f
Gerrit URL: https://gerrit.gromacs.org/2993
#4 Updated by Gerrit Code Review Bot about 3 years ago
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Change-Id: Ic438d501ebf5eccc285655a9e8f2f625eb12f1d1
Gerrit URL: https://gerrit.gromacs.org/3311
#5 Updated by Gerrit Code Review Bot about 3 years ago
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#6 Updated by Gerrit Code Review Bot about 3 years ago
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#7 Updated by Gerrit Code Review Bot about 3 years ago
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#8 Updated by Gerrit Code Review Bot about 3 years ago
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#9 Updated by Gerrit Code Review Bot about 3 years ago
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#10 Updated by Roland Schulz about 3 years ago
I think we shouldn't have a new top level folder for each simulation method. This is getting quickly out of hand. We already have: imd, pulling, swap, essentialdynamics. Not as problematic (because the list probably wont grow quickly) but also quite long of a list is math related top-level folders (math, fft, linearalgebra, statistics). Would it make sense to make the last 3 subfolders?
I'm still a bit confused about the dependency checking scripts. What is the easiest approach to use them to know whether moving files into different (sub)folders will create cyclic dependencies?
#11 Updated by Teemu Murtola about 3 years ago
In general, I agree that the current subdirectories are possibly too fine-grained. But it is easier to first create smaller units and then combine them, than to try to figure out in advance what kind of bigger units make most sense. So I think that the current approach is reasonable, but we should aim for a smaller amount of top-level folders once it is clear what can be combined and makes sense to combine. Folders with just one or a few files don't really make much sense.
Roland Schulz wrote:
I think we shouldn't have a new top level folder for each simulation method. This is getting quickly out of hand. We already have: imd, pulling, swap, essentialdynamics.
I agree. My initial thought was to put all these special methods under a specialmd/ folder or similar.
Not as problematic (because the list probably wont grow quickly) but also quite long of a list is math related top-level folders (math, fft, linearalgebra, statistics). Would it make sense to make the last 3 subfolders?
Possibly. fft/ and linearalgebra/ have a special purpose of wrapping external libraries, and as such, have some relatively complex internal logic. But it would be simpler if there could be dependencies in both directions. This would, e.g., allow putting the definition of real and rvec into math/.
I'm still a bit confused about the dependency checking scripts. What is the easiest approach to use them to know whether moving files into different (sub)folders will create cyclic dependencies?
Currently, you need to run make dep-graphs and view doxygen/depgrahs/module-deps.dot.png. It currently only shows folders one level below src/gromacs/, but that is possible to change (but requires some thinking to keep things clear, both in the graph and elsewhere). I've been thinking of adding a proper cycle detection into the script, but that is complicated by the currently existing cycles. I'll see whether that would still be possible.
#12 Updated by Gerrit Code Review Bot about 3 years ago
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#13 Updated by Gerrit Code Review Bot about 3 years ago
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#14 Updated by Gerrit Code Review Bot about 3 years ago
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#15 Updated by Gerrit Code Review Bot about 3 years ago
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#16 Updated by Gerrit Code Review Bot about 3 years ago
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#17 Updated by Teemu Murtola about 3 years ago
Roland Schulz wrote:
I'm still a bit confused about the dependency checking scripts. What is the easiest approach to use them to know whether moving files into different (sub)folders will create cyclic dependencies?
As a reference, https://gerrit.gromacs.org/#/c/3380/ now allows you to run make doc-check, and it will report any new cyclic dependencies that the changes create. Hopefully, existing cycles will not lead to too many confusing results with the algorithm that is currently used. Until it gets merged, you can just cherry-pick it on top of any change (it shouldn't conflict with much of anything). Just try not to push the cherry-picked version. ;)
#18 Updated by Gerrit Code Review Bot over 1 year ago
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#19 Updated by Gerrit Code Review Bot over 1 year ago
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#20 Updated by Gerrit Code Review Bot over 1 year ago
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#21 Updated by Gerrit Code Review Bot over 1 year ago
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#22 Updated by Gerrit Code Review Bot over 1 year ago
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#23 Updated by Gerrit Code Review Bot over 1 year ago
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#24 Updated by Gerrit Code Review Bot over 1 year ago
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#25 Updated by Gerrit Code Review Bot over 1 year ago
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#26 Updated by Gerrit Code Review Bot over 1 year ago
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#27 Updated by Gerrit Code Review Bot over 1 year ago
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#29 Updated by Gerrit Code Review Bot over 1 year ago
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#31 Updated by Gerrit Code Review Bot over 1 year ago
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#33 Updated by Gerrit Code Review Bot over 1 year ago
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#34 Updated by Gerrit Code Review Bot over 1 year ago
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#35 Updated by Gerrit Code Review Bot over 1 year ago
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#36 Updated by Gerrit Code Review Bot over 1 year ago
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#37 Updated by Gerrit Code Review Bot over 1 year ago
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#38 Updated by Teemu Murtola over 1 year ago
- Status changed from New to Fix uploaded
- Target version changed from 5.x to 2016
#39 Updated by Teemu Murtola over 1 year ago
- Status changed from Fix uploaded to Resolved
Applied in changeset ca26ed983d1d628b0b7ccf603d9c7a68a4e8c91a.
#40 Updated by Teemu Murtola over 1 year ago
- Status changed from Resolved to Closed