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  • #2932
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Issue created Apr 25, 2019 by Paul Bauer@acmnpvMaintainer

Failed to realloc error - Redmine #2932

Archive from user: Maxim Brodmerkel

Hello,

I encountered an error while working on simulating the satellite tobacco necrosis virus, comprising 147960 atoms.

During the energy minimisation step using GROMACS version 2019.1 I encountered following error:

Fatal error:
Not enough memory. Failed to realloc 18446744065119617024 bytes for
nlistjjnr, nlist>jjnr=0x2b5cb01c9010

Or, after using 2016.6:

Fatal error:
Not enough memory. Failed to realloc 8589934592 bytes for nlist>jjnr,
nlist->jjnr=3eb9a010

Further informations:
The simulations are done in the gas phase, with all-to-all neighbourlist and no cut-offs.

I hope you could help me with fixing this error.

With kind regards,
Maxim Brodmerkel

(from redmine: issue id 2932, created on 2019-04-25 by gmxdefault, closed on 2019-05-23)

  • Changesets:
    • Revision 5c4b41ed by Paul Bauer on 2019-05-23T08:09:48Z:
Add check for allocating too many interactions

Also change argument to nbnxn reallocation function from int to
std::size_t to avoid signed integer overflow.

Fixes #2932

Change-Id: I97bdd825ba1e4d81b65b4e4c037f980164c571f2
  • Uploads:
    • em.log Energy minimisation .log-file
    • em.tpr Energy minimisation .tpr-file
    • stnv.pdb
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