Bug #2260

grompp running out of memory when excluded bonded neighbours is large

Added by Dallas Warren almost 3 years ago. Updated over 2 years ago.

preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:


Want to be able to exclude intramolecular contributions to RDFs for long linear molecules (38 united atoms long). When run grompp to exclude all atoms (nrexcl=37) within a molecule, memory gets used up and grompp is killed.

System comprises of 60 linear molecules containing 38 united atoms, with water and couple of toluene. Total atoms 64,875

Command using: gmx grompp -f md -c md_0 -t md_0 -p topol -o md_1

Attached tar includes .mdp .itp .top .gro .trr and ff files to enable generation of the tpr

C12E8.itp file currently has exclusion set to 37, which it runs out of memory with (36GB available).

My question to the emailing list about this:

exclusions_large.tar.gz (23 MB) exclusions_large.tar.gz Required files to run grompp with Dallas Warren, 10/05/2017 12:20 AM

Associated revisions

Revision b7d5d939 (diff)
Added by Erik Lindahl over 2 years ago

Fix complexity for large exclusion orders

To avoid exploding computational complexity
for highly connected molecules with large
values for excluded neighbors, avoid
adding a neighbor to the temporary nnb
structure if it is already present as a
lower-order neighbor.

Fixes #2260.

Change-Id: I30c27a281ddcbbac175f79ab9d5bba49f2f988ae


#1 Updated by Erik Lindahl over 2 years ago

  • Status changed from New to In Progress

#2 Updated by Erik Lindahl over 2 years ago

It seems like the algorithm we use to find all bonded neighbors up to N bonds away in do_gen() in gpp_nextnb.cpp behaves very badly for highly connected molecules. In this case we probably end up calculating something with close to N-faculty complexity...

#3 Updated by Gerrit Code Review Bot over 2 years ago

Gerrit received a related patchset '1' for Issue #2260.
Uploader: Erik Lindahl ()
Change-Id: gromacs~release-2018~I30c27a281ddcbbac175f79ab9d5bba49f2f988ae
Gerrit URL:

#4 Updated by Erik Lindahl over 2 years ago

  • Status changed from In Progress to Resolved

#5 Updated by Erik Lindahl over 2 years ago

  • Status changed from Resolved to Closed

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