Hi Garo,
We got close to getting everything working with XLF90 and AMBERTools
1.5/Amber11 for Power 7 but then IBM pulled out of the Blue Waters project.
I can try to dig out the notes and you can see if you can convert it over to
BlueGene/P. The last BlueGene I had access to was a BlueGene/L in AMBER 10
days and the performance was so bad it wasn't worth the effort to keep
trying to update all the configure scripts for the cross compiling needed
etc. Blue Gene was like IBM tried their hardest to break existing configure
/ build approaches so I pretty much gave up on it.
You can look for the PMEMD instructions for AMBER 9 here:
http://ambermd.org/config.bgl.html
One could probably hack up a PMEMD 11 build for BlueGene/P from these. Note
you would have to use the configure.advanced script in the PMEMD directory
rather than the AMBERTools configure script. Since PMEMD is the only code
worth running on BlueGene/P anyway, not building AMBERTools or sander should
be too much of an issue.
All the best
Ross
> -----Original Message-----
> From: Garo Garabedyan [mailto:g.a.garabedyan.gmail.com]
> Sent: Wednesday, September 14, 2011 11:33 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Compiling Amber11 on Blue Gene/P
>
> Hi,
> I would like to ask all here-Amber developers and users. Have someone
> built Amber11 with IBM XL compiler scripts? I have tried many times but
> with
> no success (errors look like due to Amber source code).
>
> *Garo Garabedyan*
>
> Telephone 089 59-59-703
> garabedyan.wordpress.com
>
> Sofia, Bulgaria
>
> *Гаро Гарабедян*
>
> Телефон 089 59-59-703
> garabedyan.wordpress.com
>
> София, България
>
>
>
> 2011/9/14 Garo Garabedyan <g.a.garabedyan.gmail.com>
>
> > Hi,
> > Thank you for your immediate help.
> > As I have wrote on my previous email I have tried to compile
> Amber11 with
> > XL compilers (both without and with AmberTools) but the errors seems
> to me
> > code specific according to the best of my knowledge. At
> >
> http://wiki.vlsci.unimelb.edu.au/foswiki/bin/view/Public/TamboApplicati
> ons seems
> > that someone have succeeded in building Amber with XL compiler
> scripts.
> >
> > *Garo Garabedyan*
> >
> > Telephone 089 59-59-703
> > garabedyan.wordpress.com
> >
> > Sofia, Bulgaria
> >
> > *Гаро Гарабедян*
> >
> > Телефон 089 59-59-703
> > garabedyan.wordpress.com
> >
> > София, България
> >
> >
> >
> > On Wed, Sep 14, 2011 at 00:09, Jed W Pitera <pitera.us.ibm.com>
> wrote:
> >
> >>
> >> Garo --
> >>
> >> 1. Many FORTRAN compilers add a trailing underscore to
> >> external
> >> names (e.g. functions & subroutines). This is a common issue when
> trying
> >> to call FORTRAN from C and vice versa. There is usually a compiler
> option
> >> to disable this feature. It is "-qnoextname" on IBM xlf compilers
> and
> >> "-fno-underscoring" for GCC/gfortran. On UNIX/Linux systems you can
> use
> >> "nm" to view the symbol tables in each object file to see what
> external
> >> names are actually being produced by the compiler.
> >>
> >> 2. It looks like you are trying to mix object files
> created by
> >> the
> >> GNU fortran compiler (wrapped by mpif90) with those built with
> mpxlf90.
> >> If
> >> you can, try building everything with mpxlf90.
> >>
> >> --Jed
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> _______________________________________________
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Received on Wed Sep 14 2011 - 12:30:02 PDT
