AMBER Archive (2005)

Subject: RE: AMBER: Leap compilation issues

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 12 2005 - 11:47:05 CDT

Dear Justin,

Can you successfully compile other codes on your machine using ifort and gcc
4? E.g. lam or mpich and then run their tests. I've never tried Intel's
compilers on a machine with GCC 4 installed. Perhaps there is some
incompatibility here. Does Intel have any info on their site?

I'd be surprised if this is just a problem with compiling Amber.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be ready every day, and should not be used for urgent or sensitive issues.

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of justin litchfield
> Sent: Monday, July 11, 2005 18:25
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Leap compilation issues
>
>
> On Jul 11, 2005, at 10:05 AM, Ross Walker wrote:
>
> > Is the path /opt/intel/ifc/lib the correct compiler version? The
> > reason I
> > ask is that Intel switched to the name ifort for version 8 and
> > later. Hence
> > I suspect you may be setting LD_LIBRARY_PATH to a different
> > compiler version
> > to the one you compiled with.
> yes, that's the right compiler version, i checked it with which,
> etc. i had named it something non-standard on the install.
>
> > There are two options:
> >
> > 1. Re-run amber's configure script with the -static option and then
> > recompile.
> this fails on recompile, with the most applicable error message
> similar to this one appearing several times:
> /opt/intel/ifc/lib/libifcore.a(for_open_proc.o)(.text+0x3826): In
> function `for__compute_filename':
> ./src/libfor/for_open_proc.c: warning: Using 'getpwnam' in
> statically
> linked applications requires at runtime the shared libraries
> from the
> glibc version used for linking
>
> complete log in serial_p4_ifort.txt
>
>
> > 2. Make sure you source /opt/intel_fc_80/bin/ifortvars.sh -> Or
> > the correct
> > path for your compiler version. BEFORE you compile and
> BEFORE you run
> > Amber... Alternatively add this to your .bashrc file.
> sourcing this before compiling then running sander gives the same
> error. make test.leap works (until it gets to the sander
> parts), and
> xleap works, but antechamber (divcon) fails, as does sander.
> attached are the antechamber/sander failures. also, note
> that in the
> compilation there are tons of warnings like this:
> "xaAtomTable.c:636: warning: cast to pointer from integer of
> different size"
>
> a third attachment has my compilers/versions. andreas, you had
> suggested using maybe a different compiler or something with FC4,
> does anyone have specific suggestions for what to use/how to do
> this? i saw that forcing it to compile in 32 bit mode should be
> possible, but does anyone have specific directions? thank you,
>
> justin
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu