QM/MM- out of memory

[ışılay öztürk]

Dear all,

I defined to memory but many times It has given to the problem as an out of memory and my calculation has not been able to complete.
I tried to so many things but I haven’t any idea what is wrong. I got this error with PBE, WB97X-D and BLYP.
It was only completed with PM3.

I am trying to apply QM/MM

Do you have any idea what I need to do about “out of memory”?

I have specified 1024MB (1GB) of memory. Is this per task, per core, for all the processes combined, or counted in yet some other way? I didn't understand. Also, how does CP2K handle memory? Is there a shared memory for all threads (like Gaussian, which has a single process), or does it actually run as a bunch of separate processes (Turbomole is built this way, for a different kind of example)? I need a deeper technical understanding of the memory requirements and architecture –from CP2K. Can you help me, please?

I was trying to apply this  tutorial

https://git.ecdf.ed.ac.uk/jsindt/practical_introduction_to_cp2k/-/tree/master/session_3_reaction_in_solution/exercises/3_monitorisation_qmmm
 with PBE.
I'm sure I'm doing something wrong, but I don't know which one. I am sharing with you my all files.

https://drive.google.com/drive/folders/1gPvJa6pqYX7xQhAWomiKOWyf2Bnyp7HL?usp=sharing


Thank you in advance.

Best regards

Işılay

[Fatih Ertinaz]

Hi Isilay,

You're basically requesting a memory space of 1 GB in your job script, however your job requires more than that as it fails oom error.

Simply remove the line where you ask for the memory. By doing that, you'll be able to consume the entire memory that is physically available in the node which is probably much larger than 1 GB.

Also, your job file looks like a Slurm file but you're using PBS environment variable in the script. I think you should change that to SLURM_SUBMIT_DIR.

That being said, there are some more confusions in your job script. For instance, you request 1 node and 4 tasks (--tasks-per-node=4), but in the srun you specify 24 processes. If I'm not wrong, a task in the Slurm world corresponds to an MPI rank, so you should be requesting 24 cores instead of 4. The cpus-per-task and omp_num_threads seemed a bit off as well. 

If I were you, I would allocate the entire node and avoid using the -n flag in the srun which should utilize the entire node by default.

Hope this helps

Fatih

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[ışılay öztürk]

Thank you so much! it is more clear for me now so Thanks! 

2 Şubat 2022 Çarşamba tarihinde saat 23:58:35 UTC+2 itibarıyla fert...@gmail.com şunları yazdı: