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
nlist<s><span style="text-align:right;">jjnr,
nlist</span></s>>jjnr=0x2b5cb01c9010
Or, after using 2016.6:
Fatal error:
Not enough memory. Failed to realloc <s>8589934592 bytes for
nlist</s>>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 5c4b41ed47094d0bff2c04874a637c992ead885d 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](/uploads/69833ad0889b2be0f97e088a1aa0b053/em.log) Energy minimisation .log-file
* [em.tpr](/uploads/9bd128513f0d5fe76bb9e3949d8d937f/em.tpr) Energy minimisation .tpr-file
* [stnv.pdb](/uploads/32b4fec80be1a74f75417e1531c53a0f/stnv.pdb)
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