question about SRS5.0

Martin Hilbers mph at dl.ac.uk
Mon Dec 16 08:28:33 EST 1996


Thure wrote:
> 

> I found the bug, in fact there were two:
> 
> 1) edit file src/icarus.c
> 
> after line 670 you find
> 
>     if (!IcaCursorIsInput (job->inCursor, job->cursor)) {
> /*      CursorDelete (&job->cursor); */
>       job->cursor = NULL;
> 
>     }
> 
> remove the comments and rebuild srsbuild:
> 
> srsmake srsbuild
> 
> 2) edit icarus/db/embl.is
> 
> around line 55 you find
> 
>   seq:       ~ (/.*2BIT *Len:/ /[0-9]+/ {$len=$Ct} ln ln
>                {$s=$SeqGet2Bit:[$s file:$File len:$len]} ('>>>>'{$Not} ln)*|
>                /.*ASCII/ ln ln ('>>>>' {$Not} /.*/ {$SeqApp:[$s
> s:$Ct]})+) ~
> 
> change '$s=$SeqGet2Bit' to '$SeqGet2Bit'
> 
> regards
> thure


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"

I retried, but now tracked memory usage during srsbuild, and it
appears that after writing a subindex (*_1.inx etc), memory usage
hardly decreases, and continues to increase when srsbuild works
further through the database. I would expect that a significant 
amount of memory would be freed after writing an index file, or
that memory usage almost stops growing after writing the first one.

Is it possible there is a problem with freeing/reallocating memory
after a subindexfile has been written ?

This was with gcg formatted embl. I also made changes to the
embl.i and embl.is files, but I don't really think that causes the
problem (Ofcourse I might be completely wrong with that :-))

Cheers,

Martin

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