*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Hi Tim,
I have not seen this with 4.0.3. Debug information would be
appreciated.
We are talking about a 32-bit intel box?
Charles Ballard
CCP4
On Wednesday, June 7, 2006, at 11:50 PM, Tim Fenn wrote:
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
---------------------------------------------------------
