<div dir="ltr">HI,<div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jul 9, 2014 at 6:37 AM, Mirco Wahab <span dir="ltr"><<a href="mailto:mirco.wahab@chemie.tu-freiberg.de" target="_blank">mirco.wahab@chemie.tu-freiberg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">After seeing some patches reaching gerrit, I tried to build it<br>
on Cygwin x64 w/recent gcc 4.8.3 (which comes ootb).<br>
<br>
three minor problems found:<br>
<br>
1) missing time.h in impl.h (inherited from 4.6.x), can be solved<br>
by hot-patching for now by:<br>
perl -i.bak -pe '$once||=s/\A/#define HAVE_SYS_TIME_H\n/'<br>
src/external/thread_mpi/src/impl.h<br></blockquote><div><br></div><div>That's weird I don't have that problem. I compiled using:</div><div>cmake .. -DGMX_GPU=no && make -j8 gmx</div><div>Using:</div><div>
latest 64bit Cygwin with gcc/g++ 4.8.3 and latest release-5-0 branch (a0043764d2aa) </div><div><br></div><div>I have #define HAVE_SYS_TIME_H in my config.h. Is this missing in yours? If so can you check why your cmake check failed?</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
2) in a recent patch (3764/5), set(CXX11_FLAG "-std=gnu++0x")<br>
has been added for Cygwin, but it also will work perfectly using<br>
"-std=gnu++11". In the 5.0-Release, this can eg. be written by hand<br>
into CMakeCache.txt:<br>
CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -std=gnu++11 -DNDEBUG<br></blockquote><div><br></div><div>This is has been submitted. </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br>
3) could not get gromacs w/shared fftw3 libs built for unknown reasons.<br>
Had to add -DBUILD_SHARED_LIBS=off, maybe this wont change anytime<br>
soon in the cygwin world.<br></blockquote><div><br></div><div>I uploaded a patch: <a href="https://gerrit.gromacs.org/#/c/3792">https://gerrit.gromacs.org/#/c/3792</a></div><div><br></div><div>Do you also get linker warnings? I get:</div>
<div><br></div><div> CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/options/options.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/options/options.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/selection/compiler.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/selection/compiler.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/selection/parser.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/selection/parser.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/selection/selelem.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div>CMakeFiles/libgromacs.dir/selection/selelem.cpp.o: duplicate section `.data$_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep[_ZGVZN5boost16exception_detail27get_static_exception_objectINS0_10bad_alloc_EEENS_13exception_ptrEvE2ep]' has different size</div>
<div><br></div><div>Anyone got an idea what could be going wrong there?</div><div><br></div><div>Roland</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br>
Voila, a working Gromacs-5-system can be built. The previous obligatory<br>
additional mdrun_mpi doesn't seem necessary any more but can be built<br>
too. Comparison using an old 1 Mio atom MARTINI membrane system<br>
(Phenom II X6, SSE2, RF electrostatics):<br>
<br>
Cygwin x64:<br>
<br>
mdrun<br>
Using 6 MPI threads<br>
Using 1 OpenMP thread per tMPI thread<br>
22.273 ns/day<br>
<br>
mdrun_mpi<br>
Using 1 MPI process<br>
Using 6 OpenMP threads<br>
19.341 ns/day<br>
<br>
<br>
Comparison to the host system (Windows 8.1 x64, VS 2012 x64 native):<br>
<br>
gmx mdrun -nb cpu<br>
Using 6 MPI threads<br>
Using 1 OpenMP thread per tMPI thread<br>
20.546<br>
<br>
gmx mdrun (CUDA6, GTX-660Ti)<br>
Using 1 MPI thread<br>
Using 6 OpenMP threads<br>
33.594 ns/day<br>
<br>
<br>
Not bad so far!<br>
<br>
Regards<br>
<span class=""><font color="#888888"><br>
M.<br>
<br>
<br>
<br>
<br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309
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