[gmx-developers] gmx_d nmeig command Not enough memory

Tue Jul 5 14:36:26 CEST 2016

Hi Adrien,

As Berk pointed out, the output already said you were using the sparse setting (it’s automatic). Switch is equivalent to cutoff in the sense that most elements of the Hessian will be zero.

For sparse matrix diagonalization it will be fine; there memory requirements will scale roughly as N, and the time required as N^2.

For full matrix diagonalization (which you’ll get e.g. with PME), memory scales as N^2, and the time required as N^3. That would completely kill you.

Cheers,

Erik

> On 05 Jul 2016, at 14:27, Adrien Nicolaï <adrien.nicolai at u-bourgogne.fr> wrote:
> 
> 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 <mailto: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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