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