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