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 - 15:15:29 CDT

Hi,

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

> >> 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
cd test; ...

Scott

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