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Dear Nobuo:

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,

Bill


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott



On Jan 22, 2009, at 10:32 PM, Nobuo OKAZAKI wrote:

> Dear all,
>
> I tried to build CCP4 6.1 with Intel Compiler & Intel Math Kernel
> Library(MKL) on Fedora 8. I used MKL as LAPACK and FFTW libraries. The
> building processes have been completed successfully, but all tests
> passed except cbuccaneer.exam (core dumped).
>
> Log: ---
> % ./cbuccaneer.exam or "make runtest"
> (snip.)
> Cycle: 1
>
> C-alphas after finding:    5
> C-alphas after growing:    5
> ./cbuccaneer.exam: line 12: 23479 Aborted                 cbuccaneer  
> -mtzin-ref $CLIBD/reference_structures/reference-1tqw.mtz -pdbin-ref  
> $CLIBD/reference_structures/reference-1tqw.pdb -mtzin-wrk $CCP4_SCR/ 
> toxd_phase_mir_pirate1.mtz -pdbout-wrk $CCP4_SCR/toxd_phase_mir.pdb - 
> colin-wrk-fo '/NATIVE/NATIVE/[FTOXD3,SIGFTOXD3]' -colin-wrk-hl '/*/*/ 
> [pirate.ABCD.A,pirate.ABCD.B,pirate.ABCD.C,pirate.ABCD.D]' -find - 
> grow -join -link -prune
> (core dumped)
> -------------
>
> In case of compiling with Intel Compiler and default fftw libraries
> (bundled by CCP4), building and all test processes passed.
>
> Building process:
> % mkdir ccp4-intel
> % cd ccp4-intel
> % tar xvf CCP4-6.1.0.src.tar   (CCP4 core source package)
> % setenv XLDFLAGS "-lmkl -liomp5 -lguide"
> % setenv COPTIM "-O -ip"
> % setenv FFTW_LIBS "-lfftw2xc_intel -lmkl -liomp5 -lguide -lpthread"
> % setenv FFTW_CXXFLAGS "-I/opt/intel/Compiler/11.0/074/mkl/include/ 
> fftw"
> % ./install.sh
>   (building x-windows programs - no)
>   (building fftw library - no)
>
> Any suggestions?
> Thanks,
>
> Nobuo OKAZAKI