[gmx-users] CygWin and Gromacs 4.5.5

[Szilárd Páll]

On Tue, Nov 8, 2011 at 11:59 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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?


That statement was based on my previous experience which, admittedly, might
be outdated. I don't remember the exact details, but from what I recall,
the I had to fiddle quite a lot with gcc optimizations to get the
performance close to MSVC. One detail might be important: the code I was
working on is C/C++ mix which quite a lot of ++ in it.

Anyway, to get a better picture, it would be nice if people running GROMACS
on Windows could share their experience/performance numbers.

--
Szilárd



> 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<http://cs.org/pipermail/gmx-users/2009-September/044792.html>
>>>
>>> The error arises only for version Gromacs 4.5.5
>>>
>>>
>>> Igor
>>>
>>>
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>>>
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