Re: [ccp4bb] cbuccanner.exam failed with libFFTW generated by Intel MKL

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: cbuccanner.exam failed with libFFTW generated by Intel MKL
From: Nobuo OKAZAKI okazaki {- dot -} nobuo {- at -} JAEA {- dot -} GO {- dot -} JP
Date: 2009-01-23

Next message:
Subject: Re: cbuccanner.exam failed with libFFTW generated by Intel MKL
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-01-23

Subject: Re: cbuccanner.exam failed with libFFTW generated by Intel MKL
From: Charles Ballard charles {- dot -} ballard {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-01-23

Dear Okazaki-san

no idea why buccaneer fails. The best I can do is try to reproduce
the problem and take a look at the core dump to determine why. We
have just received a small update from Kevin, so it would be good to
see if this fixes the problem.

Can you send your config.status (global) and your compiler version
(off list obviously)

Thanks

Charles Ballard
CCP4

On 23 Jan 2009, at 08:06, Nobuo OKAZAKI wrote:

> Dear Bill,
>
> Yes, the first problem I faced was precision. In double precision,
> all of CLIPPER programs did not run. After that, I have used with
> single
> precision MKL's FFT. And CLIPPER programs except cbuccaneer.exam
> successfully ran.
>
> So, I wonder why only the BUCCANEER fails under this environment. :(
>
> Certainly, using pre-built package is easear and faster than
> building by
> myself. But I want to compare performance between pre-built and Intel
> MKL. :)
>
> In my trial, test(make runtest) under Intel Compiler with Intel MKL(as
> LAPACK without FFT) is 8% faster than pre-build package. I wornder how
> much contributes with MKL's FFT library.
>
> Nobuo OKAZAKI
>
> Bill wrote:
>> I should let the experts answer definitively, but I think this might
>> be because the clipper-related stuff (and coot) need single-precision
>> s[r]fftw libraries.
>>
>> I had to do something like this:
>>
>> LDFLAGS="-Wl,-dylib_file,/sw/lib/libsfftw.2.0.7.dylib:/sw/lib/
>> libsrfftw.2.0.7.dylib"
>>
>> It will probably be a bit different on Fedora (linux uses .so instead
>> of .dylib suffixes). The main point is to force-feed it the single-
>> precision libraries.
>>
>> In practice it is probably just easier just to let ccp4 build its
>> own,
>> unless you need the mpi versions. Single precision makes the
>> calculation go faster and you can't see the difference in the
>> maps, in
>> my experience.
>>
>> HTH,

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: cbuccanner.exam failed with libFFTW generated by Intel MKL
From: Nobuo OKAZAKI okazaki {- dot -} nobuo {- at -} JAEA {- dot -} GO {- dot -} JP
Date: 2009-01-23

Next message:
Subject: Re: cbuccanner.exam failed with libFFTW generated by Intel MKL
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-01-23