Bug #2693
Several memory leaks in mdrun
Description
When trying to run simulations through the new API, several issues are reported on the ASAN build that point to severe memory leaks within mdrun.
I attached a log file for
valgrind --leak-check=full bin/gmxapi-test
I have a patch that fixes some of the direct leaks, but I'm out of my depth for most of the stuff.
Associated revisions
Fix memory leaks in ns cleanup
Added some missing sfrees to cleanup function
refs #2693
Change-Id: I1e1455794778139d3a3866e00c05f4ed97aea07c
Change t_extmass pointers to std::vector
Using std::vector in t_extmass fixes a leak in do_md.
Used arrayRefs to view arrays in NHC_trotter
Refs #2693
Change-Id: I6bd84952fb7a470879ddd665183680c865e22fc2
History
#1 Updated by Mark Abraham over 2 years ago
Yes, that's one of about 50 reasons we're not able to support an API in a useful way in GROMACS 2019. :-)
I'm not sure whether we have blanket suppressions somewhere for ASAN (more particularly, LeakSanitizer), but we certainly could. But I doubt there's a good way to separate the leaks from mdrun from any caused by the memory management in gmxapi.
#2 Updated by Paul Bauer about 2 years ago
- Target version changed from 2019 to future
Those are not going be fixed in 2019.
#3 Updated by Gerrit Code Review Bot about 2 years ago
Gerrit received a related patchset '2' for Issue #2693.
Uploader: Kevin Boyd (kevin.boyd@uconn.edu)
Change-Id: gromacs~master~I2a74543c3d393fca2a8e44e02e00c5daa68df922
Gerrit URL: https://gerrit.gromacs.org/8830
#4 Updated by Gerrit Code Review Bot about 2 years ago
Gerrit received a related patchset '1' for Issue #2693.
Uploader: Kevin Boyd (kevin.boyd@uconn.edu)
Change-Id: gromacs~master~I1e1455794778139d3a3866e00c05f4ed97aea07c
Gerrit URL: https://gerrit.gromacs.org/8831
#5 Updated by Gerrit Code Review Bot about 2 years ago
Gerrit received a related patchset '3' for Issue #2693.
Uploader: Kevin Boyd (kevin.boyd@uconn.edu)
Change-Id: gromacs~master~I45d18c503a87832332868e7fb9b63720548f243c
Gerrit URL: https://gerrit.gromacs.org/8832
#6 Updated by Gerrit Code Review Bot about 2 years ago
Gerrit received a related patchset '1' for Issue #2693.
Uploader: Kevin Boyd (kevin.boyd@uconn.edu)
Change-Id: gromacs~master~I6bd84952fb7a470879ddd665183680c865e22fc2
Gerrit URL: https://gerrit.gromacs.org/8847
Fix memory leak at end of do_md
Without domain decomposition, the atomtypes field of localtop is
dynamically allocated and needs freeing after mdrun
Refs #2693
Change-Id: I45d18c503a87832332868e7fb9b63720548f243c