[gmx-developers] gmx_d nmeig command Not enough memory

[Adrien Nicolaï]

Dear Erik,

Thank you very much for your quick reply. I did the same calculation using another protein having 45000 modes and it took only a week to get the full diagonalization. That’s why I was quite optimistic with this calculation.

I will try to follow your suggestion. Right now I’m using shift for both Coulomb and vdW with a radius of 1.2 nm and a switch radius of 1.0 nm, as suggested in the GROMACS website for NMA. Do you think I should go for cutoff instead of switch?

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>
************************************************************

> On 05 Jul 2016, at 14:21, Erik Lindahl <erik.lindahl at gmail.com> wrote:
> 
> 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 <mailto: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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