<br><br><div class="gmail_quote">On Thu, Nov 10, 2011 at 5:37 AM, Mr Bernard Ramos <span dir="ltr"><<a href="mailto:bgrquantum@yahoo.com">bgrquantum@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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<div><span>yes, I have also experience the same with Gromacs 4.5.5 and cygwin. I hope this issue will be addressed.Thanks<br></span></div></div></div></blockquote><div>The slow IO performance under cygwin is a known problem with the approach of cygwin and happens with any cygwin program and cannot be fixed by GROMACS. If you want decent IO performance you need to either use Visual C++ or Msys/MingW (see <a href="http://redmine.gromacs.org/issues/448">http://redmine.gromacs.org/issues/448</a>).</div>
<div><br></div><div>Roland</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt">
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<b><span style="font-weight:bold">From:</span></b> Roland Schulz <<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>><br>
<b><span style="font-weight:bold">To:</span></b> Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<b><span style="font-weight:bold">Sent:</span></b> Wednesday, November 9, 2011 11:03 AM<br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [gmx-users] CygWin and Gromacs 4.5.5<br>
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<div>On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham
<span dir="ltr"><<a rel="nofollow" href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
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<div>On 8/11/2011 11:35 PM, Szilárd Páll wrote:<br>
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<div>> Additionally, AFAIK you will get better performance if you compile<br>
> with MSVC which should be fairly easy if you use CMake - I'm not<br>
> entirely sure about this<br>
<br>
</div>
I'd be surprised. Why should MSVC outperform gcc?<br>
</blockquote>
<div>The file performance is horrible with cygwin (even much slower than a virtual machine). But this should only be important for analysis. For simulation I agree that the performance should be as good (I don't know about NUMA) .</div>
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<div>Roland</div>
<blockquote style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<font color="#888888"><br>
Mark<br>
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<div></div>
<div><br>
> though.<br>
> Cheers,<br>
> --<br>
> Szilárd<br>
><br>
><br>
><br>
> On Tue, Nov 8, 2011 at 12:41 PM,<<a rel="nofollow" href="mailto:bhf70@udsu.ru" target="_blank">bhf70@udsu.ru</a>> wrote:<br>
>> Help me.<br>
>> I want to install Gromacs 4.5.5 with usage CygWin.<br>
>> When I execute a command "make" I receive the error report:<br>
>><br>
>> numa_malloc.c:117: error: expected '> ' before ' Processor'<br>
>> numa_malloc.c:117: error: expected '> ' before ' ProcNumber'<br>
>> numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm '<br>
>> or.....................<br>
>> ...<br>
>> make [3]: *** [numa_malloc.lo] Error 1<br>
>> make [3]: leaving directory '/cygdrive/.....<br>
>> gromacs4.5.5/src/gmxlib/thread_mpi'<br>
>> make [3]: *** [install-recursive] Error 1<br>
>> make [3]: leaving directory '/cygdrive/..... gromacs4.5.5/src/gmxlib'<br>
>> make [3]: *** [install-recursive] Error 1<br>
>> make [3]: leaving directory '/cygdrive/..... gromacs4.5.5/src'<br>
>> make [3]: *** [install-recursive] Error 1<br>
>><br>
>> Where an error?<br>
>><br>
>><br>
>> CygWin it is installed with packets:<br>
>> Section "Devel"<br>
>> - autoconf: Wrapper scripts for autoconf commands<br>
>> - autoconf2.1: Stable version of the automatic configure script builder<br>
>> - autoconf2.5: Development version of the automatic configure script builder<br>
>> - automake1.9: a tool for generating GNU-compliant Makefiles<br>
>> - binutils: The GNU assembler, linker and binary utilites<br>
>> - gcc: A C compiler upgrade helper<br>
>> - gcc-core: A C compiler<br>
>> - gcc-g ++: A C ++ compiler<br>
>> - gcc-g77: Fortran compiler<br>
>> - gcc-mingw-core: Mingw32 support headers and libraries for GCC<br>
>> - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++<br>
>> - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran<br>
>> - libgcc1: GCC compiler support shared runtime<br>
>> - libgdbm-devel: GNU dbm database routines (development)<br>
>> - make: The GNU version of the ` make ` utility<br>
>> - mingw-runtime: MinGW Runtime<br>
>><br>
>> Section "Interpreters"<br>
>> - perl: Larry Wall ` s Practical Extracting and Report Language<br>
>><br>
>> Packet FFTW ver.3.2.2 is in addition compiled and installed<br>
>><br>
>> Trial setting Gromacs of 4.5.3 errors does not give.<br>
>><br>
>> The instruction on setting took here:<br>
>> <a href="http://lists.groma" target="_blank">http://lists.groma</a> <a rel="nofollow" href="http://cs.org/pipermail/gmx-users/2009-September/044792.html" target="_blank">
cs.org/pipermail/gmx-users/2009-September/044792.html</a><br>
>><br>
>> The error arises only for version Gromacs 4.5.5<br>
>><br>
>><br>
>> Igor<br>
>><br>
>><br>
>> --<br>
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