[gmx-developers] gmx_d nmeig command Not enough memory

[Erik Lindahl]

Seems like a bug - we should use a size_t to calculate the size of the matrix storage required.

However, before you get your hopes up: The reason why this happens is that you are asking the code to do a full diagonalization of a matrix that is 63255^2. That will take at least ~100GB of memory, and probably take several months. I would recommend that you use some cutoff-based electrostatics/VdW instead to enable sparse matrix diagonalization.

Cheers,

Erik




> On 05 Jul 2016, at 14:02, Adrien Nicolaï <adrien.nicolai at u-bourgogne.fr> wrote:
> 
> Dear GROMACS developers,
> 
> I’m performing a Normal mode analysis using the GROMACS 5.1 software. The system I study is a dimer of a protein surrounded by water molecules and is comprised of 21075 atoms (corresponding to 63225 modes). After a proper minimisation using the L-BFGS algorithm and a normal mode calculation in double precision, I tried to diagonalise the entire hessian matrix using the nmeig command.
> 
> The use of the gmx_d nmeig command leads to the following error:
> 
> Reading double precision matrix generated by GROMACS VERSION 5.1
> 
> -------------------------------------------------------
> Program gmx nmeig, VERSION 5.1
> Source code file: /tmp3/gromacs-5.1-20150825/gromacs-5.1/src/gromacs/utility/smalloc.c, line: 182
> 
> Fatal error:
> Not enough memory. Failed to calloc -297566671 elements of size 8 for eigenvectors
> (called from file /tmp3/gromacs-5.1-20150825/gromacs-5.1/src/gromacs/gmxana/gmx_nmeig.c, line 401)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors <http://www.gromacs.org/Documentation/Errors>
> -------------------------------------------------------
> : Cannot allocate memory
> Using begin = 1 and end = 63225
> Sparse matrix storage format, nrow=63225, ncols=63225
> Starter(339849): Return code=1
> Starter end(339849)
> 
> Could you help me with the meaning of this error? Is my system to big for NMA using GROMACS 5.1?
> 
> Thanks you in advance for your help
> 
> Best regards,
> 
> ************************************************************
> Adrien Nicolaï / Maître de conférences
> Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS
> Département NANO - Equipe Physique appliquée aux protéines
> Université de Bourgogne Franche-Comté / Faculté des Sciences et Techniques Mirande
> 9, Av. Savary - B.P. 47 870 21078. DIJON CEDEX - France
> Email : adrien.nicolai at u-bourgogne.fr <mailto:adrien.nicolai at u-bourgogne.fr>
> Tél: 03 80 39 60 93
> URL : https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html <https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html>
> ************************************************************
> 
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