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
Thank you very much for your response and your detailed explanation !
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"
> 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:
>> Yiannis Georgiadis
>> UoA Computer Center Sys Admin
>> AMBER mailing list
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