Dynamic Memory Allocation


#1

Dear Admin,

I have been a frequent user of the haddock webserver. However, recently I experienced the following error in a protein protein docking experiment.

HEAP: maximum use = 3912450952 current use = 96000 bytes
HEAP: maximum overhead = 3648 current overhead = 752 bytes
PRIEND: 1 levels not terminated
LEVEL= 1 KEY=CNSsolve> ACTION=GO
============================================================
Maximum dynamic memory allocation: 3912450952 bytes
Maximum dynamic memory overhead: 3648 bytes
Program started at: 10:39:23 on 26-Feb-2019
Program stopped at: 12:53:14 on 26-Feb-2019
CPU time used: 8025.1340 seconds
============================================================

I have tried on Guru as well as easy interface. Neither worked. The size of the 2 protein are ~800 residues in total. A few questions:

  • Are there ways to increase the dynamic memory allocation?
  • Are there ways to cut memory cost in the simulation?
  • Will using less active residues help?

P.s. The run document is in http://milou.science.uu.nl/serviceresults/HADDOCK2.2/4648668538/Easy_A20_CYLD/

Best,
Jordy


#2

The memory is not per se the problem. BUT defining all residues as active is a BAD idea…

Don’t you have some knowledge of the binding site?
And at least do filter for solvent accessible residues.

Check our various online tutorials at bonvinlab.org/eduction