<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><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><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Roland Schulz <roland@utk.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><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></font><br>
<div id="yiv1258022376"><br><br><div class="yiv1258022376gmail_quote">On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham <span dir="ltr"><<a rel="nofollow" ymailto="mailto:Mark.Abraham@anu.edu.au" target="_blank" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="yiv1258022376gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="yiv1258022376im">On 8/11/2011 11:35 PM, Szilárd Páll wrote:<br></div><div class="yiv1258022376im">
> 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>
<div><br></div><div>Roland</div><blockquote class="yiv1258022376gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<font color="#888888"><br>
Mark<br>
</font><div><div></div><div class="yiv1258022376h5"><br>
> though.<br>
> Cheers,<br>
> --<br>
> Szilárd<br>
><br>
><br>
><br>
> On Tue, Nov 8, 2011 at 12:41 PM,<<a rel="nofollow" ymailto="mailto:bhf70@udsu.ru" target="_blank" href="mailto:bhf70@udsu.ru">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>
>> http://lists.groma <a rel="nofollow" target="_blank" href="http://cs.org/pipermail/gmx-users/2009-September/044792.html">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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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a rel="nofollow" target="_blank" href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>
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