Re: [AMBER-Developers] Current build fail with amber11CVS

From: case <>
Date: Thu, 4 Mar 2010 08:58:28 -0500

On Thu, Mar 04, 2010, Mark Williamson wrote:

> Fresh checkout of the amber11 cvs tree as of Thu Mar 4 02:57:47 PST 2010
> ifort 10.1.018
> RHEL4.8 X86_64
> ./configure intel ; make -f Makefile_at
> <...snip....>
> icc -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o
> trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o rms.o
> display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o
> thermo.o pubfft.o cluster.o clusterLib.o
> /server-home/mjw/code/AMBER/amber11/lib/libpdb.a
> /server-home/mjw/code/AMBER/amber11/lib/arpack.a
> /server-home/mjw/code/AMBER/amber11/lib/lapack.a
> /server-home/mjw/code/AMBER/amber11/lib/blas.a -lifport -lifcore -lsvml
> ../netcdf/lib/libnetcdf.a -lm
> thermo.o(.text+0x475): In function `thermo_':
> : undefined reference to `for_write_seq_fmt'

Mark, it would be really helpful if you could spend some time to debug
this yourself, since only you seem to have a machine/compiler that is
showing this error. Or, maybe others on the list that have had this
happen can chime in here; it's never happened to me.

Some things to check:

Did you run the Intel scripts to set up your environment variables? Of
course, be sure that icc and ifort are both at the 10.1.018 level.

If you look above, icc is called with the flags "-lifport -lifcore" which
should be linking in the fortran functions like for_write_seq_fmt. Since
you are not getting any "can't find lifport" errors, it looks like icc is
finding these libraries.

If I go to intel's 10.1.018 libraries on *my* machine, (which is in
/opt/intel/fce/10.1.018/lib), I see the needed entry point:

casegroup% nm libifcore.a | grep for_write_seq_fmt
                 U for_write_seq_fmt
000000000000017c T for_write_seq_fmt
000000000000185a T for_write_seq_fmt_xmit

So, it is important to figure out what is different between your installation
than mine? Are compilers installed in a different way? Do you have a
different set of entries in libifcore.a?

The linker is in some sense a black box, but it operates on known principles;
It's hard to remotely debug such problems, however.

Finally, let us know if you figure it out. We need to get instructions in the
manual so that users' wont hit the same problems you are hitting.


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Received on Thu Mar 04 2010 - 06:00:04 PST
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