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On Wed, Jun 07, 2006 at 10:31:30AM +0100, Charles Ballard wrote:
>
> CCP4 are pleased to announce the release of CCP4
> version 6.0.1. With respect to CCP4 6.0, this release
> contains a number of bug fixes (including an update of
> the refmac monomer dictionary), but no major change
> in functionality. In addition, CCP4mg has been updated
> to version 0.12.1 and Coot to version 0.1.1.
> Note that we expect to update the CCP4mg and Coot
> packages further after 6.0.1 as new versions become
> available.
>
I'm having trouble using refmac with the new release, built using
gfortran:
$ gfortran -v
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-libgcj-multifile
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada
--enable-java-awt=gtk --disable-dssi
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre
--with-cpu=generic --host=i386-redhat-linux
Thread model: posix
gcc version 4.1.0 20060304 (Red Hat 4.1.0-3)
and the relevant part of the output, traced with gdb (I can rebuild
with debugging symbols, if it will help):
N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663
0.5826 -11.5290
C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650
51.6512 0.2156
O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670
32.9089 0.2508
S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863
56.1720 0.8669
Number of reflections in file 133584
Number of reflection read 133584
Program received signal SIGSEGV, Segmentation fault.
0x08247941 in q3qd_tred_single_ ()
(gdb) where
#0 0x08247941 in q3qd_tred_single_ ()
#1 0x08247e48 in ssyev_mo_ ()
#2 0x081cc750 in aniso_eigens_ ()
#3 0x081cce8f in genpre_ ()
#4 0x08169e56 in MAIN__ ()
#5 0x08249577 in main ()
I built ccp4 using:
./configure --with-shared-libs --disable-lapack --with-fftw=/usr/lib
This also required me to edit the Makefile in the src/ subdir:
XLAPACK_LIB = -llapack
and also edit src/harvest_app_/pdb_extract/etc/make.platform.gnu4:
WARNINGS_AS_ERRORS=
in order to fully build.
-Tim
--
---------------------------------------------------------
Tim Fenn
[EMAIL PROTECTED]
Stanford University, School of Medicine
James H. Clark Center
318 Campus Drive, Room E300
Stanford, CA 94305-5432
Phone: (650) 736-1714
FAX: (650) 736-1961
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