question about SRS5.0

Thure Etzold etzold at embl-heidelberg.de
Wed Dec 18 05:16:39 EST 1996

Martin Hilbers wrote:
> Despite the changes, I seem to have a memory problem. I tried to
> index the new EMBL release this weekend, and it crashed with this
> message:
> ...no. 720600, MJU67483
> SRSDB:embl.is:72: error: insufficient memory - error during malloc,
> could not allocate "sequence"

sorry for the long silence - I was sick for a couple of days. I found
the problem with index building for EMBL. It is not caused by a memory
leak but by memory fragmentation. Building the index chunks iteratively
requires large chunks of memory to be freed and allocated at each 
run and for some reason the program gets new memory from the system 
instead of
reclaiming freed blocks. This behaviour is much more pronounced on
irix than osf1. srsbuild does now the memory management for these
large chunks itself which seems to solve the problem. I managed to 
build EMBL with less than 50 mbyte virtual memory

Tao, since you have only 32mb you should really try to upgrade your
machine but in the meantime you could try to set the partition size
to 60000

EMBL_DB:$library:[EMBL group:@SEQUENCE_LIBS partSize:60000

We hope to create a new version with these changes by the end of the
day which will be announced.



Thure Etzold                                   | EMBL
E-mail: etzold at embl-heidelberg.de              | Postfach 10.2209
Tel: (49) 6221 387529                          | 69012 Heidelberg
Fax: (49) 6221 387517                          | Germany

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