[gmx-users] CygWin and Gromacs 4.5.5

[Roland Schulz]

On Thu, Nov 10, 2011 at 5:37 AM, Mr Bernard Ramos <bgrquantum at yahoo.com>wrote:

>  yes, I have also experience the same with Gromacs 4.5.5 and cygwin. I
> hope this issue will be addressed.Thanks
>
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 http://redmine.gromacs.org/issues/448).

Roland

>
>   ------------------------------
> *From:* Roland Schulz <roland at utk.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Wednesday, November 9, 2011 11:03 AM
> *Subject:* Re: [gmx-users] CygWin and Gromacs 4.5.5
>
>
>
> On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
> On 8/11/2011 11:35 PM, Szilárd Páll wrote:
>  > 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?
>
> 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) .
>
>  Roland
>
>
> 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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>
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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