Re: [AMBER] Problems during AMBER 10 compilation.

From: Zuzanna K. Ścigacz <>
Date: Tue, 6 Apr 2010 11:17:18 +0200

Dnia czwartek 01 kwiecień 2010, case napisał:
> On Thu, Apr 01, 2010, Zuzanna K. Scigacz wrote:
> > I am recently trying to install amber 10 on Xeon emt64t Linux machine
> > using gcc/gfortran compilers, and I am receiving a following error
> > message while linking sander:
> >
> > ../lmod/lmod.a(dsaupd.o): In function `dsaupd_':
> > _dsaupd.f:(.text+0x66): undefined reference to `ambsecond_'
> >
> > I have made sure that all serial amber build src is successfuly compiled,
> > and I have checked using nm command if ambsecond_ exists in any object
> > file and it is undefined in all of them.
> ambsecond_ should be in amber10/src/lib/sys.o.

nm shows that sys.o doesn't have such a symbol.

[r25] ~/amber10/src/lib > nm sys.o | grep ambsecond
[r25] ~/reef/amber10/src/lib >

> But your problem looks
> like you may be combining results from different compilers. Be sure you
> have run "make clean" (and "make -f Makefile_at clean" for good measure),
> before running trying build.
> ...hope this helps....dac

I tried on a absolutely fresh source, just patched using recommended patches
from AMBER website.

My build enviroment:
[r25] ~/amber10/src/lib > cat ~/
export AMBERHOME=$HOME/amber10


Zuzanna K. Ścigacz
HPC Systems Administrator
Poznan Supercomputing and Networking Center
Institute of Bioorganic Chemistry Polish Academy od Sciences
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Received on Tue Apr 06 2010 - 02:30:02 PDT
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