Hi Justin
is this a self compiled ccp4? Did you use gfortran? If so, it is a
known problem. From the online problems pages
CCP4i scripts fail due to parsing errors in log files
Date : 22/05/2006
CCP4 Version : 6.0.0 and others
System : Compilations that used gfortran
Level : Serious
Status : Workaround provided
Bugzilla number : #1687
Various ccp4i tasks which rely on the parsing of log files may fail
due to the lack of synchronisation between the fortran and C/C++
outputs, eg amore.
The workaround is to set GFORTRAN_UNBUFFERED_ALL to either 1 or Y at
runtime, to turn off buffering of output (there will be some
performance penalty for this).
(Thanks to Marian Szebenyi for reporting this)
Charles Ballard
CCP4
On 29 Oct 2007, at 12:33, Justin Schmitz wrote:
Hello All!
I have a problem with the output there from CCP4 into the log files
on a dual-Core Intel Mac with Os X Server 10.4 and CCP4 6.0.1.
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM13 Ano 0.147 -0.001 0.723 2.055 BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM14 Ano 0.347 0.519 0.895 0.939 BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM15 Ano 0.232 0.498 0.965 0.546 BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM16 Ano 0.031 0.124 0.022 -2.575 MLPHARE: Normal
termination
Times: User: 84.9s System: 0.3s Elapsed: 1:27
</pre>
</html>
<!--SUMMARY_END--></FONT></B>
BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM17 Ano 0.027 -0.001 0.859 2.450 BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM18 Ano 0.102 -0.002 0.870 3.247 BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM19 Ano 0.025 0.107 0.024 5.815 BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM20 Ano 0.024 0.072 0.069 5.565 BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
Many Programs do this e.g. refmac. The Termination message is
passed to the log file before all other data is in it. This breaks
of ploting or in case of mlphare of the whole process.
Does anybody know how to handle this? Is it related to the OS or to
CCP4?
Thanks for helping another time justin
