[CP2K-user] [CP2K:16544] QM/MM- out of memory

[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... at gmail.com şunları yazdı:

> 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
>
> On Wed, Feb 2, 2022 at 3:38 PM ışılay öztürk <isilay... at gmail.com> wrote:
>
>> 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
>>
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