AMBER Archive (2008)

Subject: Re: AMBER: AmberTools on OS X Leopard with Intel compilers

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Mon Apr 21 2008 - 15:33:49 CDT

Hi,

On Mon, 21 Apr 2008, Scott Brozell wrote:

> On Mon, 21 Apr 2008, Yu Chen wrote:
>
> > >>> We are tring to compile/test/install AmberTools as the first step in Amber
> > >>> 10 installation on a xserver with Leopard with Intel compiler (10.1.014).
> > >>
> > >> You may be the first to use icc on Leopard ... if someone else on the list
> > >> has tried that, they may chime in here.
>
> > >>> 3. After the 'make', we did 'make -f Makefile_at test' in the 'test'
> > >>> directory, but it gave out error right away with these:
> > >>> #######################################
> > >>> ( cd nab; make test )
> > >>> =====================================================
> > >>> Running test to make dna duplex:
> > >>>
> > >>> /bin/sh: line 1: 43282 Segmentation fault ./duplex < duplex.in
> > >>
> > >> Pretty serious. We know icc works on linux (x86_64 and ia64), but is not
> > >> working for you for some reason. And, as far as I know, we have only
> > >> tested
> > >> up to icc version 10.0.023. [You already reported off-line that icc 10.1
> > >> fails on the netcdf configure step, whereas 10.0.023 has no such problem.]
> > >>
> > >> The obvious workaround is to use gcc. It's not clear that icc is actually
> > >> faster, and it is clearly much less well tested. Unless you end up running
> > >> NAB for days on end, you would probably never notice the difference between
> > >> gcc and icc. The other programs in AmberTools are setup and analysis
> > >> routines, where it doesn't make sense to try to squeeze out the last bit of
> > >> performance.
> > >
> > > Thank you, Dr. Case for detailed explaination. I will try gcc. The reason we
> > > used icc is that the Apple software tech told us that Intel compiler used on
> > > Intel architecture is much faster than gcc.
> >
> > I tried both Apple stock gcc (4.0) and latest gcc (4.3) on AmberTools,
> > both failed compiling with the following: wondering if anybody can help
> >
> > =======================
> > ld: warning in /mfslab/software/amber/v10/lib/libpdb.a, file is not of
> > required architecture
> > Undefined symbols:
> > "_pdb_read_record", referenced from:
> > _loadPdb in trajectory.o
> > _checkCoordinates in ptraj.o
> > _ptrajInitializeState in ptraj.o
> > "_pdb_read_string", referenced from:
> > _checkCoordinates in ptraj.o
> > _checkCoordinates in ptraj.o
> > "_pdb_write_record", referenced from:
> > _savePdb in trajectory.o
> > _savePdbHigh in trajectory.o
> > collect2: ld returned 1 exit status
> > make[1]: *** [rdparm] Error 1
>
> Did you clean before rebuilding ?
> cd src; make clean

This one should be
cd src; make -f Makefile_at clean
because src now has two makefiles.

> > >> Of course, it you want, please go ahead and compile a debug version and try
> > >> to get a traceback on the seg fault.
> > >> That program is a trivial one, so the error
> > >> is probably generic somewhere. As a start, specify -static in
> > >> configure_at,
> > >> and modify the config.h file to turn of optimization and turn on debugging.
> > >
> > > I am not sure how to do this. I am not good at debugging. Could you give a
> > > little bit more detail on how to do this?
>
> cd src; cd nab; make clean; make AMBERBUILDFLAGS='-O0 -g' install

This one is correct because src/nab still has one makefile.

> cd test; ...
 
Scott

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