[gmx-users] CygWin and Gromacs 4.5.5

[Mark Abraham]

On 8/11/2011 11:35 PM, Szilárd Páll wrote:
> Hi,
>
> There have been quite some discussion on the topic of GROMACS on
> Cygwin so please search the mailing list for information.

Actually I don't think this issue has been addressed. Some NUMA-aware 
thread_mpi stuff does not work under Cygwin, and code added since 4.5.4 
assumes that it does. I can find no reason to support that assumption.

To work around, use configure --disable-threads.

>
> Some of that information might have not gone into the wiki
> (http://goo.gl/ALQuC) - especially that the page appears to be intact
> for the last 7 months. [Which is a pity and it would be really much
> appreciated if people in the future contribute back!!!]
>
> Additionally, AFAIK you will get better performance if you compile
> with MSVC which should be fairly easy if you use CMake - I'm not
> entirely sure about this

I'd be surprised. Why should MSVC outperform gcc?

Mark

> though.
> Cheers,
> --
> Szilárd
>
>
>
> On Tue, Nov 8, 2011 at 12:41 PM,<bhf70 at udsu.ru>  wrote:
>> Help me.
>> I want to install Gromacs 4.5.5 with usage CygWin.
>> When I execute a command "make" I receive the error report:
>>
>> numa_malloc.c:117: error: expected '>  ' before ' Processor'
>> numa_malloc.c:117: error: expected '>  ' before ' ProcNumber'
>> numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm '
>> or.....................
>> ...
>> make [3]: *** [numa_malloc.lo] Error 1
>> make [3]: leaving directory '/cygdrive/.....
>> gromacs4.5.5/src/gmxlib/thread_mpi'
>> make [3]: *** [install-recursive] Error 1
>> make [3]: leaving directory '/cygdrive/..... gromacs4.5.5/src/gmxlib'
>> make [3]: *** [install-recursive] Error 1
>> make [3]: leaving directory '/cygdrive/..... gromacs4.5.5/src'
>> make [3]: *** [install-recursive] Error 1
>>
>> Where an error?
>>
>>
>> CygWin it is installed with packets:
>> Section "Devel"
>> - autoconf: Wrapper scripts for autoconf commands
>> - autoconf2.1: Stable version of the automatic configure script builder
>> - autoconf2.5: Development version of the automatic configure script builder
>> - automake1.9: a tool for generating GNU-compliant Makefiles
>> - binutils: The GNU assembler, linker and binary utilites
>> - gcc: A C compiler upgrade helper
>> - gcc-core: A C compiler
>> - gcc-g ++: A C ++ compiler
>> - gcc-g77: Fortran compiler
>> - gcc-mingw-core: Mingw32 support headers and libraries for GCC
>> - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++
>> - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran
>> - libgcc1: GCC compiler support shared runtime
>> - libgdbm-devel: GNU dbm database routines (development)
>> - make: The GNU version of the ` make ` utility
>> - mingw-runtime: MinGW Runtime
>>
>> Section "Interpreters"
>> - perl: Larry Wall ` s Practical Extracting and Report Language
>>
>> Packet FFTW ver.3.2.2 is in addition compiled and installed
>>
>> Trial setting Gromacs of 4.5.3 errors does not give.
>>
>> The instruction on setting took here:
>> http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html
>>
>> The error arises only for version Gromacs 4.5.5
>>
>>
>> Igor
>>
>>
>> --
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