re Problem with DM

Kevin Cowtan cowtan at
Tue Sep 19 09:35:45 EST 1995

In article <1995Sep14.225800.1576 at> jscarsdale at writes:
 >Y. W. Chen mentions a potential dm bug:
 >>I ran dm with skeletonisation but got an "bus error" and a core dump.  This
 >>  only happens at the last cycle.  I tried dm v.1.5 compiled with CCP4 2.11
 >> and dm v.1.6 compiled with CCP4 2.15, both give the same error message.  
 >>The machine I used is a SGI.  I tried running dm in IRIX 4 and IRIX 5.  Bot
 >>give the same error
 >We've seen this "problem" also, however, if you look at your HKLOUT file, I
 >think you'll find everything in order--it looks like this error, which I
 >believe means that something is trying to access non-existant memory, must
 >occur as the program is finishing, as the HKLOUT file appears to be complete.
 >From what I recall, the error seems to occur at about the time the xloggraph
 >records are being written to standard output; although I'm not sure as there 
 >is some buffering of standard output corresponding to 8192 byte chunks when
 >standard output is redirected to a file. 
 >We have been ignoring the error for as far as we can tell this appears to
 >simply be a nuisance error since it seems to be occurring after the skeleton-
 >isation calculation is complete since the records corresonding to the modified
 >phases and figures of merit have already been appended to HKLOUT.

I have been trying to track down a number of errors like this, but so
far I have had great difficulty reproducing the problems. The best
guess at the moment is that the problems are caused by compiling under
IRIX 5.x with optimisation flags. On alpha or HP there is no
problem. Other developers round this lab are reporting similar

So I suggest changing your makefile to compile the code with -g, -O0
or possibly -O1. If this still doesn't help, mail me, and I'll add you
to the list. Or find another machine!

Dr. Kevin D. Cowtan                                cowtan at
 +44 (0)1904 432565         
York University Protein Structure Research Group, Heslington, York, England

WWW Page: Crystallographic Fourier Picture Book, Silly Games, Silly Faces!!

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