# Fatal error when running on HPC through slrum

**URL:** <https://gromacs.bioexcel.eu/t/fatal-error-when-running-on-hpc-through-slrum/7945>\
**Category:** User discussions\
**Tags:** mdrun, simulation-setup, hpc\
**Created:** [December 30, 2023, 10:47pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-when-running-on-hpc-through-slrum/7945 "2023-12-30T22:47:09Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [December 30, 2023, 10:47pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-when-running-on-hpc-through-slrum/7945/1 "2023-12-30T22:47:09Z")

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GROMACS version:2018.1  
GROMACS modification: NO  
Here post your question

Hello everyone,

I’m trying to optimize a cluster for the best performance. I have used a .tpr file, which was simulated for 1 microsecond in another system. Now, when I run the .tpr in the current HPC, I’m getting an error as follows:

Fatal error:  
88 particles communicated to PME rank 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.

I have changed node 4 to 1 and altered other parameters in the SLURM script:

#SBATCH --nodes=1  
#SBATCH --ntasks=6  
#SBATCH --tasks-per-node=6

Now, I have created the simulation system from the HPC with the same structure and minimized to a maximum force of \<1000, and the simulation is equilibrated—all these on a single node. However, when I run the simulation without the SLURM script, on the single node, it runs without any issue. Nonetheless, even for a single node, the issue persists when I run it through SLURM.

Can someone have a look at this and provide any suggestions?

The relevant part of the SLURM script and log file is here:

> **[gromacs-log.txt](https://drive.google.com/file/d/1VdUwUydhrsTFBhQKkHH_7VujRTs04AVG/view?usp=sharing)**
>
> Google Drive file.

> **[script.txt](https://drive.google.com/file/d/1gNKW1ly3y8ynugs_MJzLWLlYin4oCebE/view?usp=sharing)**
>
> Google Drive file.

:

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**Author:** ![Carsten](https://avatars.discourse-cdn.com/v4/letter/c/f14d63/32.png) [@Carsten](https://gromacs.bioexcel.eu/u/Carsten)\
**Post date:** [January 2, 2024, 10:48am UTC](https://gromacs.bioexcel.eu/t/fatal-error-when-running-on-hpc-through-slrum/7945/2 "2024-01-02T10:48:23Z")

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Hi,

maybe you are running into a bug that was fixed in v. 2022.2 (but I am unsure about whether this bug was already there in 2018.1).

The issue is described here:

> **[Add clearing of LINCS indices (!2701) · Merge requests · GROMACS / GROMACS ·...](https://gitlab.com/gromacs/gromacs/-/merge_requests/2701)**
>
> The LINCS constraint indices in the second interdependent OpenMP task were not cleared. This could lead to corrections being applied to atoms with old indices on domains which...

You may want to upgrade to 2022.2 or later and see whether that solves your problem!

Best regards,  
Carsten