AMBER Archive (2008)

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

From: David A. Case (
Date: Fri Apr 18 2008 - 15:44:36 CDT

On Fri, Apr 18, 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.
> 1. The "configure_at icc" finished fine except for the g77 part(since we
> don't have g77/gfortran installed yet), which says " We will be unable to
> compile mopac or resp", since we are not going to use those two for now,
> we assume that we can ignore it for now, is it right? Or do we have to have
> it compiled for everything to work?

If you don't need mopac or resp, you are fine.

> So we assume it compiled successfully. Although one strange thing, I
> specified the complier as 'icc' as you can see in first step, but some
> progames still used 'gcc' and 'g++' as compilers (like Makefile in
> gleap/freelib/readline), is this normal? Do those programs have to be
> compiled by 'gcc'?

Yes: sleap has only been tested with gcc, so that is hard-wireds.

> 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 <

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

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.

....good luck...dac

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