Re: [gmx-users] Fwd: lost particles while sorting

[Mark Abraham]

Hi,

If you think the software has a bug please open an issue at
https://redmine.gromacs.org and attach a full description and tpr. Multiple
people have observed this but the developers have not and can't fix it
until they have a way to reproduce it, please :-)

Mark

On Wed, Dec 6, 2017, 5:58 AM soumadwip ghosh 
wrote:

> ​​Hi,
>
> Sorry for reposting my query. I don't see a way to fix this software
> inconsistency issue.
>
> I am running NPT equilibration on gpu. After I finished the NVT I got an
> error saying
>
> Software Inconsistency Error:
>
> Lost particles while sorting (6 out of 8)
>
> Now I looked into the archive and it seems like a bug which was fixed in
> gromacs versions > 5.0. I am using gromacs-2016.4 and the error is
> sporadic. It means for a slightly different system (a mutation of the
> protein under consideration, almost identical in overall system size) the
> simulation runs fine on the same gpu using gromacs-2016.4. I have tried to
> run the buggy one by creating a tpr file using gromacs 5.1.0 but no luck
> yet. How do I fix this?
>
> I am uploading the .tpr (gromacs 2016.4) and .mdp file in the following
> link.
>
> I am looking forward to your help
>
> https://drive.google.com/file/d/1wfQdbTqkIEnfUE81IDb5iATkFyedP
> 2in/view?usp=sharing
>
> https://drive.google.com/file/d/1iFskowIggdFkNlJwkQJ_LbeumV-
> QtUZ2/view?usp=sharing
>
> Regards,
> Soumadwip Ghosh
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[gmx-users] Fwd: lost particles while sorting

[soumadwip ghosh]

​​Hi,

Sorry for reposting my query. I don't see a way to fix this software
inconsistency issue.

I am running NPT equilibration on gpu. After I finished the NVT I got an
error saying

Software Inconsistency Error:

Lost particles while sorting (6 out of 8)

Now I looked into the archive and it seems like a bug which was fixed in
gromacs versions > 5.0. I am using gromacs-2016.4 and the error is
sporadic. It means for a slightly different system (a mutation of the
protein under consideration, almost identical in overall system size) the
simulation runs fine on the same gpu using gromacs-2016.4. I have tried to
run the buggy one by creating a tpr file using gromacs 5.1.0 but no luck
yet. How do I fix this?

I am uploading the .tpr (gromacs 2016.4) and .mdp file in the following
link.

I am looking forward to your help

https://drive.google.com/file/d/1wfQdbTqkIEnfUE81IDb5iATkFyedP
2in/view?usp=sharing

https://drive.google.com/file/d/1iFskowIggdFkNlJwkQJ_LbeumV-
QtUZ2/view?usp=sharing

Regards,
Soumadwip Ghosh
-- 
Gromacs Users mailing list

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