Many thanks for your replies
Triggering gc doesn't seem to help (though the object count goes down)
but reducing how much is processed at a time does. I actually didn't
have to go down to a molecule-at-a-time level but made due with inputs
half of the previous size. The RAM still fills up
On 6/26/2015 9:48 AM, az wrote:
Thanks Jean-Paul
You're right that I eat up a lot of memory with large files but I think
its not the whole story. If it were, my memory should come back each
time a new file is being read (jobs=[]), no ?
No. It's a feature of garbage collection: your memory
On Jun 27, 2015, at 6:05 AM, Dmitri Maziuk dmaz...@bmrb.wisc.edu wrote:
On 6/26/2015 9:48 AM, az wrote:
Thanks Jean-Paul
You're right that I eat up a lot of memory with large files but I think
its not the whole story. If it were, my memory should come back each
time a new file is being
I apologize that I haven't had a chance to look at this in detail yet, but
I can at least give a quick answer to the below:
Python uses a deterministic scheme for doing garbage collection based on
reference counting, so memory should be freed as soon as you do jobs=[].
That's assuming that the
On 6/27/2015 5:45 AM, Greg Landrum wrote:
...
That's assuming that the futures code (which I don't know) isn't doing
anything odd behind the scenes to hold onto references.
Or every mol in supplier holds a pointer to c++ dll that python vm
doesn't quite know how to garbage-collect, which keeps
Thanks Jean-Paul
You're right that I eat up a lot of memory with large files but I think
its not the whole story. If it were, my memory should come back each
time a new file is being read (jobs=[]), no ? Instead I hit my limit
after 8-10 very similar input files, even though the usage after
Hi
Using the cookbook code as basis (apologies if I should have posted in
the corresponding topic), I've put together a script to generate
conformers for my smiles library. Works like a charm too, aside from the
fact that after 10-20 hours, I'm out of RAM and swap (the memory
consumption
Isn't the problem here that you are keeping an array (jobs) and you keep
adding molecules to it never letting the garbage collector collect/clear
any memory ? If your file has a million molecules, you will have an array
of a million molecules in memory...
Why dont you process each single
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