[gmx-developers] gmx_d nmeig command Not enough memory

[Adrien Nicolaï]

Dear Berk,

Yes I changed the default value from 50 to 3N because I need all the modes for further analyses. And it looks like it’s still taking “forever” to get the 50 first modes diagonalised...

Best,

************************************************************
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 14:26, Berk Hess <hess at kth.se> wrote:
> 
> 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 < <mailto:adrien.nicolai at u-bourgogne.fr>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>
>>> ************************************************************
>>> 
>>> -- 
>>> Gromacs Developers mailing list
>>> 
>>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List <http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List> before posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists>
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers> or send a mail to gmx-developers-request at gromacs.org <mailto:gmx-developers-request at gromacs.org>.
>> 
>> 
>> 
> 
> -- 
> Gromacs Developers mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers or send a mail to gmx-developers-request at gromacs.org.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20160705/56433c51/attachment.html>