AMBER Archive (2006)

Subject: AMBER: Re: Problem in compiling sander with MMTSB

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Jun 15 2006 - 18:28:27 CDT

Hi,

On Wed, 14 Jun 2006, Honggao Liu wrote:

> I did a make clean after the patching. The output of nm -A mmtsb.o
> mmtsb_client.o | grep -i newtemp
> is:
> (/usr/local/packages/amber8/src/sander)# nm -A mmtsb.o mmtsb_client.o |
> grep -i newtemp
> mmtsb.o: .mmtsb_newtemp T 0
> mmtsb.o: .mmtsb_newtemp U -
> mmtsb.o: .newtemp U -
> mmtsb.o: .newtemp U -
> mmtsb.o: mmtsb_newtemp D 224 12
> mmtsb.o: mmtsb_newtemp d 208 4

There should be an entry for mmtsb_client.o.
For example, on linux:
% cd amber8/src
% ./configure -mmtsb ifort
% cd sander
% make clean; make
% nm -A mmtsb.o mmtsb_client.o | grep -i newtemp
mmtsb.o:00000b58 T mmtsb_newtemp_
mmtsb.o: U newtemp_
mmtsb_client.o:0000052c T newtemp_

I'll try to get access to an IBM.

Scott

> The mmtsb_client.c is attached.
>
> On Wed, 2006-06-14 at 20:29 -0700, Scott Brozell wrote:
>
> > On Wed, 14 Jun 2006, Honggao Liu wrote:
> >
> > > I am trying to compile Amber8 with -mmtsb option to build sander for
> > > MMTSB on our IBM AIX machines. I got the following message:
> > >
> > > /bin/true lmod.a
> > > xlf90 -qfree -o sander trace.o lmod.o decomp.o icosasurf.o
> > ...
> > > veclib.o mdm.o pb_init.o constantph.o prn_dipoles.o ../lmod/lmod.a
> > > -L/usr/lib -lmass -L/usr/lib -lblas -L/usr/lib
> > > -lessl ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a
> > > ld: 0711-317 ERROR: Undefined symbol: .newtemp
> > > ld: 0711-317 ERROR: Undefined symbol: .getbias
> > > ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
> > > information.
> > > make: The error code from the last command is 8.
> > >
> > > This is probably due to IBM XL Fortran external name mangling. Google
> > > searching this error and got your name. I patched all of the current bug
> > > fixes including bugfix.59 (Sander with MMTSB support may fail to
> > > compile), but the patching doe not help.
> >
> > Hmm, IBM usually mangles with CLINK_PLAIN; so those symbols look right.
> > Did you do a make clean after the patching ?
> >
> > If a fresh build fails then send the output of
> >
> > nm -A mmtsb.o mmtsb_client.o | grep -i newtemp
> >
> > The symbols between those files need to match.
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