On Sep 11, 2008, at 4:19 AM, Namshin Kim wrote:
> First thing is maxlen and maxint is not working in > cnestedlist.NLMSA. I calculated and set the max idb size to be 1GB, > but it grows upto 4GB and stopped due to a memory error. Memory > error is caused by excessive memory usage in Collection. > seqdb.AnnotationDB.clear() function does not exist any more. I > reported this excessive memory usage in shelve and AFAIK > writeback=False option would prevent excessive memory usage. Please > let me know if I made a mistake. Hi Namshin, I think we need to disentangle the several possibilities that you mentioned: - maxlen, maxint size control of the NLMSA idb. Nothing has changed in this code and I doubt that this is the cause of your problem. Is the idb file actually growing above the max size you specified, or was your 4GB number simply a measure of RAM usage? Your report didn't make that clear. - Collection, which is just a shelve interface. Since you're using writeback=False it seems Collection is probably not the problem. Once again, nothing has changed in this code. - seqdb.AnnotationDB.clear(): as Titus said, he removed this recently. But we don't know whether you tested this with that most recent version. Actually, since your code example uses the clear() method, that implies you must be using an earlier version of Pygr. Please give us the git commit ID of the code that suffers the problem you reported. Please file this as a bug report in the issue tracker. See my recent email on what information I would like included in the report... It would also be helpful if you could re-test this problem with different pygr versions: - the latest git repository code: AnnotationDB by default now has a new option autoGC=True which automatically frees any annotation objects that the user is not currently using. Hopefully this will solve your problem. - if that doesn't solve the problem, please report to us the most recent version that does NOT have the memory usage problem you are reporting. Thanks!!! -- Chris --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
