AMBER Archive (2008)

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

From: Yu Chen (chen_at_hhmi.umbc.edu)
Date: Mon Apr 21 2008 - 09:30:10 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 < 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.

>
> 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?

Thanks,

CY

> ....good luck...dac
>
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===========================================
Yu Chen
Howard Hughes Medical Institute
Chemistry Building, Rm 182
University of Maryland at Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250

phone: (410)455-1728 (primary)
         (410)455-6347 (secondary)
fax: (410)455-1174
email: chen_at_hhmi.umbc.edu
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