[gmx-developers] gmx_d nmeig command Not enough memory

[Berk Hess]

This is using the sparse matrix code. The default value for -last (end) 
is 50, which should work. I assume you increased it.

We should fix the code by casting the column and row size to size_t 
before multiplying them.

Cheers,

Berk

On 2016-07-05 14:21, Erik Lindahl 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*
>> *-------------------------------------------------------*
>> *: 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
>> ************************************************************
>>
>> -- 
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