Memory usage when reading 2019-beta2 .tpr-files with trjconv from version 2018.3
Trying to to use "gmx trjconv" in version 2018.3 and accidentally supplying a .tpr-file created with 2019-beta2 immediately consumed 15 gb of ram and swapped an additional 5 gb. Have only tried to recreate the issue with version 2018.3
echo 0 | gmx trjconv -f traj_comp.xtc -o traj_whole.xtc -pbc whole
.tpr- and xtc-files for recreation are quite large and can be supplied upon request
#2 Updated by Christian Wennberg almost 2 years ago
Looks like the issue doesn't recreate itself anymore for some reason, now it throws this error message and quits every time I test it out.
Not enough memory. Failed to calloc 1118727312 elements of size 4 for
(called from file
Example .tpr-file attached
#3 Updated by Paul Bauer almost 2 years ago
The error itself is caused because the tpr files in 2019 no longer support implicit solvent, leading to the sections in the file being offset and do_tpx reading garbage when passing through the do_cmap section that causes the memory exhaustion. Not sure how to fix this, as I don't think the formats from versions newer than the current one are supposed to be usable.
#7 Updated by Mark Abraham over 1 year ago
- Status changed from New to Feedback wanted
- Target version changed from 2019.1 to 2019.2
I can't reproduce anything. My 2018.3 install (and tcbs module 2018.4, and my release-2018 HEAD) all reject this .tpr (tested with
gmx dump -s topol.tpr), observing that the tpr format has version 116 which is higher than the program version 112. That's by design - we bump the version every time something is changed in an incompatible way.
release-2019 reads it as expected.
@Christian My only guess is that you may have had a gmx binary pick up a .so from another version, perhaps using a gmx from a build tree with another GMXRC already sourced.