AMBER Archive (2009)

Subject: Re: [AMBER] Problem build pmemd

From: Yiannis Georgiadis (giannis_at_cc.uoa.gr)
Date: Wed Mar 18 2009 - 19:57:44 CDT

It worked
Thank you very much for your response and your detailed explanation !

Yiannis Georgiadis

Robert Duke wrote:
> This is a simple matter of name mangling conventions between c and
> fortran, and you have some combination of c and fortran compilers that
> are not agreeing with each other. To figure out what you need to do,
> try the following in the pmemd directory after the compilation has
> been done (been linking has not succeeded):
>
> nm pmemd.o | grep unlimit_stack
> nm pmemd_clib.o | grep unlimit_stack
>
> Look at the outputs - they probably differ. You need to get the c
> compiler to be producing stuff from pmemd_clib.c that looks like what
> fortran is expecting (which is what you see in pmemd.o, related to a
> call from fortran to the c routine).
>
> So at the top of the pmemd_clib.c source file there is a manifest
> constants hack that handles this. Depending on which of the defined
> constants is defined by CFLAGS in config.h, the names of the pmemd c
> library routines will be mangled differently. The current choices for
> the defined constants are CLINK_CAPS, NO_C_UNDERSCORE,
> DBL_C_UNDERSCORE, and nothing.
> So do this in config.h by including the manifest constant in the
> config.h file - for example, you might use:
> CFLAGS = -DNO_C_UNDERSCORE
>
> For some compilers it is possible to change the name mangling expected
> by the fortran compiler by including a fortran compiler flag instead.
> Determining this requires reading the compiler manuals. I don't have
> a clue what compilers you have on this platform, but this covers all
> possible avenues. Presuming that the mpi routines are linking
> properly, you want to approach this problem by using the CFLAGS
> defined constant (if mpi is not linking either, then you have to get
> fortran to recognize the mpi names or recompile the mpi libraries in
> such a way that the exported mpi_* names are recognized).
>
> Regards - Bob Duke
>
> ----- Original Message ----- From: "Yiannis Georgiadis"
> <giannis_at_cc.uoa.gr>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Friday, March 13, 2009 8:14 PM
> Subject: [AMBER] Problem build pmemd
>
>
>>
>> Has anyone managed to build pmemd in hpux 11i platform ?
>> I am using hpf90 and gcc and I am getting at linking :
>>
>> /usr/ccs/bin/ld : Unsatisfied symbols:
>>
>> get_wall_time
>> unlimit_stack
>>
>> Yiannis Georgiadis
>> UoA Computer Center Sys Admin
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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