Task #2947
make an end to end test for membed
Description
When using the membed functionality in mdrun, a segfault occurs after selecting the relevant groups.
The issue seems to be present since at least the original 2019 release and is still present at release-2019^HEAD.
Commands to reproduce
gmx mdrun -nt 1 -s gmembed.tpr -membed gmembed.dat -c pi_pH70_popc_further_solvate.pdb -mn index_before_gmembed.ndx -v select group 1 for protein select group 13 for POPC
Associated revisions
History
#1 Updated by Paul Bauer over 1 year ago
- File gmembed.tpr gmembed.tpr added
- File index_before_gmembed.ndx index_before_gmembed.ndx added
#2 Updated by Paul Bauer over 1 year ago
- Affected version - extra info changed from is present since 2018 to is present since 2019
Bisect shows that the bug got introduced in 8dd3c9ae88004054b3b112c23f747d27a19d8d29
#3 Updated by Paul Bauer over 1 year ago
- File gmembed.dat gmembed.dat added
#4 Updated by Joe Jordan over 1 year ago
Is there a plan to introduce an integration test on membed once the bug is fixed?
#5 Updated by Paul Bauer over 1 year ago
I think there should be one :)
This hid actually another bug introduced in d4f85b613049e141c44f505b49e28e8b706b76ae
#6 Updated by Paul Bauer over 1 year ago
There is still another bug further on in the tree :(
#7 Updated by Paul Bauer over 1 year ago
it seems like the next bug was introduced in the merge fb755982116311bee2d1f9770678d221112e1ddb
#8 Updated by Mark Abraham over 1 year ago
pro tip, write commit:2w3scxc9
and you get a link to the git repo behind redmine
#9 Updated by Paul Bauer over 1 year ago
- Status changed from New to Fix uploaded
#10 Updated by Paul Bauer over 1 year ago
- Status changed from Fix uploaded to Resolved
Applied in changeset 63b3d45c6f6f46b3c5843cae514819daea8f5ee4.
#11 Updated by Mark Abraham over 1 year ago
- Tracker changed from Bug to Task
- Subject changed from mdrun segfaults when trying to use membed to make an end to end test for membed
- Category set to testing
- Status changed from Resolved to Accepted
- Assignee deleted (
Paul Bauer) - Target version changed from 2019.3 to 2020-beta1
- Affected version - extra info deleted (
is present since 2019) - Affected version deleted (
2019.2)
membed will keep getting broken if nothing tests it
#12 Updated by Paul Bauer over 1 year ago
- Target version changed from 2020-beta1 to future
membed is currently disabled because it relied on the group scheme that has been removed for now
Fix membrane embedding
Refactoring forgot to allocate some data, causing a segmentation fault.
More refactoring used wrong data, causing a crash further on.
Even more refactoring lead to invalid memory access.
Fixes #2947
Change-Id: I61ad3125102b50c0338e0935a75cd7b1de95bc3f