Bug #2947

mdrun segfaults when trying to use membed

Added by Paul Bauer 12 days ago. Updated 1 day ago.

Fix uploaded
Target version:
Affected version - extra info:
is present since 2019
Affected version:


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

index_before_gmembed.ndx (4.04 MB) index_before_gmembed.ndx Paul Bauer, 05/09/2019 03:47 PM
gmembed.tpr (11.5 MB) gmembed.tpr Paul Bauer, 05/09/2019 03:47 PM
gmembed.dat (902 Bytes) gmembed.dat Paul Bauer, 05/09/2019 04:25 PM


#2 Updated by Paul Bauer 12 days 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 12 days ago

#4 Updated by Joe Jordan 12 days ago

Is there a plan to introduce an integration test on membed once the bug is fixed?

#5 Updated by Paul Bauer 12 days ago

I think there should be one :)
This hid actually another bug introduced in d4f85b613049e141c44f505b49e28e8b706b76ae

#6 Updated by Paul Bauer 11 days ago

There is still another bug further on in the tree :(

#7 Updated by Paul Bauer 11 days ago

it seems like the next bug was introduced in the merge fb755982116311bee2d1f9770678d221112e1ddb

#8 Updated by Mark Abraham 11 days ago

pro tip, write commit:2w3scxc9 and you get a link to the git repo behind redmine

#9 Updated by Paul Bauer 1 day ago

  • Status changed from New to Fix uploaded

Also available in: Atom PDF