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Hi,

I am runnung a phonon calculation with VASP via phononpy, e.g. same job with different positions of atoms, however, some of those jobs randomly cancelled. I tried to debug this with the people from the computing facility and according to them the result is not enough memory. However, once I rerun the same job it again randomly works. Other simulations with same settings having different atom positions works well. I am puzzelled with that. Would someone experience a similar issue or have an idea?

I attach the files and numstat data for the simulation.

Hi burakgurlek,

I've checked your POSCAR also wrt. symmetry and first thought: sometimes you'll have a symmetric structure, so it works, because of less memory requirements, mostly not: fail.

Another note: The attached POSCAR shows 96(!) f.u. of (C3H2)., where I found a P-1 structure with just 12 f.u., 8 times less atoms, also far less effort in later (frequency) analysis.
I'd suggest if you need phonopy, go for that 12 f.u. structure, make a P1 with no symmetry out of it and end up with 60 atoms(!) instead of 480. And see if this is sufficient for your purpose.

Cheers,

alex

Dear Alex,

thanks for the response. It could be the symmetry issue, but I have no experience how symmetry effects scf calculations. In addition, I did not get your second point. Yes I will use phonopy but this is for 2x2x2 unit-cell that is why it is 480 atoms. I do not see how you do reduce this number and expect the same accuracy.

Regards,
Burak

Hello Burak,

about your questions:
1) VASP exploits symmetry incertain ways, which leeds also to reduced resource requirement, hence less memory.
2) what I was suggesting(!) is to reconsider your approach, because there is the much smaller cell with symmetry P-1 (no memory issues later).

I do not understand why you want to calculate a cell containing 12 times the necessary atoms, when you can get along with the smaller set.

Best regards,

alex

Dear Alex,

thanks for your answer

1- I guess the symmetry is not the issue here as the simulation works in resubmission of the same files. There should be a problem mostly regarding the nodes I use but hpc guys cannot see other than memory error. I do not think something inherently wrong with symmetries
2- In the phonon calculation, the size of the unit-cell has certain effects. Thats why simulation via primitive-cell could be problematic.

Regards,
Burak