[gmx-developers] slightly odd-looking code

jan rtm443x at googlemail.com
Tue Mar 24 23:24:24 CET 2020


Hi all,
I got the git repo from <https://github.com/gromacs/gromacs>, used
HEAD and started compiling.

I guess I should use the right tag, bit I could not see a tag that
looked like the release the tarball says it is, which is 2020.1 so I
just compiled it (with cygwin) even though it's had commits more
recently.

Anyway I hit this:

/cygdrive/c/Users/jan/Desktop/gromacs_git/gromacs/src/external/thread_mpi/src/tmpi_init.cpp:476:42:
error: ‘strdup’ was not declared in this scope; did you mean ‘strcmp’?
  476 |                     threads[i].argv[j] = strdup( (*argv)[j] );

which comes from

#if !(defined( _WIN32 ) || defined( _WIN64 ) )
    threads[i].argv[j] = strdup( (*argv)[j] );   //  <--- this line
#else
    threads[i].argv[j] = _strdup( (*argv)[j] );
#endif

so it looks like it didn't pick up I'm running in windows.
I'm not so familiar with make (or these build tools generally), but I
poked around in the makefile (generated by cmake I assume) but could
not see where to add the symbol for _WIN64

Since I understand it has been compiled and tested under MSVC2017
I'll try that tomorrow.

cheers

jan



On 24/03/2020, Paul Bauer <paul.bauer.q at gmail.com> wrote:
> Hello,
>
> I agree with Mark that the webinars should be a good start to have an idea
> a out the code.
>
> Concerning the error you are getting, this shouldn't happen if you work and
> build from a git repository. But it is still something I think should be
> fixed (especially because I have been the one pushing for it against Mark's
> objections)
>
> Cheers
>
> Paul
>
> On Tue, 24 Mar 2020, 19:50 Mark Abraham, <mark.j.abraham at gmail.com> wrote:
>
>> Hi gmx developers!
>>
>>
>> On Tue, 24 Mar 2020 at 15:29, jan <rtm443x at googlemail.com> wrote:
>>
>>> Hi all,
>>> given what's said below I need to be clear about where I am.
>>> I'm a back-end dev specialising somewhat in SQL/RDBMSs + data
>>> management (but not data analysis of any note), with plenty of
>>> experience of other languages etc. however I have never done any
>>> x86/x64 as such, I normally use high-level languages, I have no
>>> experience at all with GPUs and (as already mentioned) my C/C++ is
>>> neolithic, and I've no experience with the modern c/c++ build tools.
>>> My linux is not great.  And the nearest I can get to your kind of
>>> mathematics is a background in classical logic ie. not very close at
>>> all.
>>>
>>> None of these bother me; all are fixable, but it will take time. I'll
>>> need a minimal amount of guidance to get gowing - "read this" is fine
>>> but I'll need no handholding, and you don't have time for that anyway.
>>>
>>
>> Great - you're coming at the questions from a totally different
>> perspective, which is healthy for everyone, but that's going to give you
>> a
>> steep learning curve. There's some useful recorded webinars from BioExcel
>> given by particularly Paul, Szilard, Carsten, and I over recent years
>> that
>> are a good starting point for understanding how the code operates at run
>> time, but you should look for something else for "intro to molecular
>> dynamics for non-scientists." There's a bunch of material online - has
>> anybody got suggestions?
>>
>> First things first, I need to compile this stuff up.
>>> I'm using windows + cygwin - is this the best environment or do you
>>> recommend working entirely in Linux?
>>>
>>
>> We test in CI on Windows + MSVC, so that works fine, but there has been
>> no
>> love on cygwin for about a decade. It's almost certainly fixable, but
>> never
>> been a priority. So go native one way or the other :-)
>>
>> I've followed the instructions to get it working on cygwin and got
>>> stuck. Compilation fails with
>>>
>>> C:\Program Files\Python38\python.exe: can't open file
>>>
>>> '/cygdrive/c/Users/jan/Desktop/gromacs/gromacs-2020.1/admin/createFileHash.py':
>>> [Errno 2] No such file or directory
>>> CMake Error at cmake/gmxGenerateVersionInfoRelease.cmake:115 (file):
>>>   file failed to open for reading (No such file or directory):
>>>
>>> /cygdrive/c/Users/jan/Desktop/gromacs/gromacs-2020.1/computed_checksum
>>>
>>> computed_checksum indeed doesn't exist. What now?
>>>
>>
>> Sigh, that's broken implementation of a new feature that I never thought
>> was worth its cost. Don't know how to fix it.
>>
>> The above is going by
>>> <http://manual.gromacs.org/documentation/current/install-guide/index.html
>>> >
>>>
>>> Other problem is that untarring the tarball works, however on windows
>>> it's natural to use something like 7-zip. This doesn't work and I lost
>>> a couple of hours to that (certainly not the fault of the instructions
>>> but FYI anyway).
>>>
>>> Comments below too
>>>
>>>
>>> On 24/03/2020, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>> > Hi,
>>> >
>>> > Jan, the biggest bang-for-buck optimizations relevant to Folding at Home
>>> are
>>> > to
>>> >
>>> > a) offer to build them an OpenCL-enabled GROMACS "core" (ie the
>>> > version
>>> of
>>> > GROMACS that they run, when they run GROMACS). Currently they seem to
>>> run
>>> > all GPU jobs with OpenCL and OpenMM, which is nice but leaves a lot of
>>> > throughput on the table. The GROMACS OpenCL port is mature and stable,
>>> runs
>>> > on AMD/NVIDIA/Intel current GPUs, and should present no more
>>> > driver/user
>>> > problems than their OpenMM one. Their concept of a GPU slot is a
>>> > single
>>> GPU
>>> > accompanied by a single CPU thread/, whereas the GROMACS OpenCL port
>>> would
>>> > prefer multiple dedicated cores. That's still better than leaving GPUs
>>> > empty if there's not enough OpenMM jobs in the queue, though the
>>> > actual
>>> > performance will be woeful compared to GROMACS when you give it a
>>> healthy
>>> > chunk of CPU cores also. Could even be better than OpenMM's GPU core,
>>> > depending how modern that one is, too ;-) The GROMACS CUDA port is
>>> better
>>> > still (and in 2020 can do a decent job even with only a single CPU
>>> core),
>>> > but they have made a philosophical choice to use OpenCL only.
>>>
>>> That has to come later when I get up to speed, but carefully noted,
>>> thanks.
>>>
>>> > b) update the GROMACS CPU core in F at H because the one used in F at H is
>>> > several years behind and losing the benefit of the hard optimization
>>> work
>>> > that we've done in the meantime.
>>>
>>> Why would f at h not do this already??
>>>
>>
>> Limited resources and priorities for it. It's a science-driven project,
>> and if the people prepared to do the work want to use not-GROMACS for
>> their
>> science then that is that...
>>
>> But again, noted.
>>>
>>> > c) demonstrate that they can maintainably and usefully offer more than
>>> two
>>> > x86 builds of that GROMACS CPU core (GROMACS has lots of SIMD
>>> specialized
>>> > flavours, but F at H only offers SSE4.1 and basic AVX from those
>>> > flavours,
>>>
>>> Yes, thought this might be the case. Definitely worth it for newer
>>> chips.
>>> However, please note that SIMD performance for later chips do not
>>> always mix well with non-SIMD code and can overall *cost* performance
>>> <https://blog.cloudflare.com/on-the-dangers-of-intels-frequency-scaling/>
>>>
>>
>> Yes thanks, most of us know ;-) Just updating to add AVX2 would give a
>> clear win.
>>
>>
>>> > which leaves a lot of performance on the table on recent x86 CPUs. We
>>> > already have all the logic needed to work out which pre-built GROMACS
>>> > to
>>> > download and run, because we use it in containerized GROMACS builds
>>> also.)
>>> >
>>> > Unfortunately they've never open-sourced any of that, so finding out
>>> where
>>> > to start is the first challenge. But that way you'll have a lot more
>>> impact
>>> > sooner than you will from profiling GROMACS runs after 30 years of
>>> > optimization. ;-)
>>>
>>> I dunno yet. Model tuning is beyond me obviously, but I've seen some
>>> stuff in the code that I question WRT optimality. However if it's cold
>>> code or all memory bound then I'll be fixing the wrong thing. Time to
>>> profile, but need to get it to compile first.
>>>
>>
>> Memory? What's that? :-D GROMACS memory usage is typically measured in
>> megabytes, with sophisticated data-parallelism to keep the working set
>> for
>> each core down around cache sizes. Obviously you can scale up the problem
>> to get out of cache, but the problem sizes that suit interesting science
>> are comparable with the amount of L3 cache you get on a socket these
>> days.
>>
>> There's a big pile of code in the repo that warrants exhaustive
>> optimization, and a lot that is used by only a handful of people, which
>> generally doesn't. It's hard to make a valuable impact in either kind of
>> place, for different reasons.
>>
>> Mark
>>
>> Happy to take this offline and reduce mailing list clutter.
>>>
>>> cheers
>>>
>>> jan
>>>
>>> >
>>> > Mark
>>> >
>>> > On Mon, 23 Mar 2020 at 14:59, jan <rtm443x at googlemail.com> wrote:
>>> >
>>> >> Hi,
>>> >> I'm a general back-end dev.  Given the situation, and folding at home
>>> >> using gromacs, I thought I'd poke through the code. I noticed
>>> >> something unexpected, and was advised to email it here. in edsam.cpp,
>>> >> this:
>>> >>
>>> >>
>>> >> void do_linacc(rvec* xcoll, t_edpar* edi)
>>> >> {
>>> >>     /* loop over linacc vectors */
>>> >>     for (int i = 0; i < edi->vecs.linacc.neig; i++)
>>> >>     {
>>> >>         /* calculate the projection */
>>> >>         real proj = projectx(*edi, xcoll, edi->vecs.linacc.vec[i]);
>>> >>
>>> >>
>>> >>         /* calculate the correction */
>>> >>         real preFactor = 0.0;
>>> >>         if (edi->vecs.linacc.stpsz[i] > 0.0)
>>> >>         {
>>> >>             if ((proj - edi->vecs.linacc.refproj[i]) < 0.0)
>>> >>             {
>>> >>                 preFactor = edi->vecs.linacc.refproj[i] - proj;
>>> >>             }
>>> >>         }
>>> >>         if (edi->vecs.linacc.stpsz[i] < 0.0)
>>> >>         {
>>> >>             if ((proj - edi->vecs.linacc.refproj[i]) > 0.0)
>>> >>             {
>>> >>                 preFactor = edi->vecs.linacc.refproj[i] - proj;
>>> >>             }
>>> >>         }
>>> >>        [...]
>>> >>
>>> >>
>>> >> In both cases it reaches the same code
>>> >>
>>> >>   preFactor = edi->vecs.linacc.refproj[i] - proj
>>> >>
>>> >> That surprised me a bit, is it deliberate? If so it may be the code
>>> >> can be simplified anyway.
>>> >>
>>> >> That aside, if you're looking for performance I might be able to
>>> >> help.
>>> >> I don't know the high level stuff *at this point* and my C++ is so
>>> >> rusty it creaks, but I can brush that up, do profiling and whatnot.
>>> >> I'm pretty experience, just not in this area.  Speeding things up is
>>> >> something I've got a track record of (though I usually have a good
>>> >> feel for the problem domain first, which I don't here)
>>> >>
>>> >> Would it be of some value for me to try getting more speed? If so,
>>> >> first thing I'd need is to get this running under cygwin, which I'm
>>> >> struggling with.
>>> >>
>>> >> regards
>>> >>
>>> >> jan
>>> >> --
>>> >> Gromacs Developers mailing list
>>> >>
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>>> before
>>> >> posting!
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>>> >>
>>> >
>>> --
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