Memory leak? Memory consumption rises quickly when using JD2 app(s)

[Anonymous]

Hey!

I don’t know if this is a known issue or not, but when I run score_jd2 with a -in:list:l I get increasing memory consumption, which passes 1.4g (RES column untop `top`) within a minute. Using score with same flags has constant memory usage. I did this check because a JD2 app I’m developing also showed increasingly high memory usage, so I suspect it’s a JD2 issue (?)

Command line is:
${DIR}/main/source/bin/score.linuxgccrelease
-out:nooutput
-in:file:l test-score.pdblist
-in:path pdb-clean > score-test.out 2> score-test.err

Tried weekly 2014.22 and weekly 2014.35. Both compiled and run on debian-flavor linux with scons, gcc4.7, x86_64, 8g RAM.

I can attach some log files.
Attached is the test-score.pdblist file (with a txt extension so I can upload; the PDBs themselves were stripped of all non-ATOM records, hence the -in:path pdb-clean; will check what happens with the raw PDBs).

Can anyone confirm this is an issue?
Is this an app issue or usage issue? Would appreciate any help!

Thanks,
Yuval

[Anonymous]

Apparently this stems from a feature which saves old poses so that they may be later reloaded. It is avoidable via the -jd2:delete_old_poses flag. Muy importante.

[Author]

Posts