Messages

16

General Questions and Answers / Re: Error on Cluster

« on: February 9, 2024, 04:51 »

Dear Filipr,
Thanks for responding.

GPU Response:
1. When I run on single GPU core, it runs very well and gives output nicely. (See attached Au_MoS2.py file)
2. When I run on multiple GPU cores, it shows an error (See attached file Error.txt).
3. Also see the attached Au_MoS2.log file.
4. Also see attached cpuinfoo.txt

CPU Response:
1. When I run on single or  multiple CPU cores, the output file shows this:
[0] MPI startup(): Intel(R) MPI Library, Version 2021.8  Build 20221129 (id: 339ec755a1)

• MPI startup(): Copyright (C) 2003-2022 Intel Corporation.  All rights reserved.
[0] MPI startup(): library kind: release

• MPI startup(): libfabric version: 1.13.2rc1-impi

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 805 RUNNING AT ssdnode2
=   KILLED BY SIGNAL: 4 (Illegal instruction)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 1 PID 806 RUNNING AT ssdnode2
=   KILLED BY SIGNAL: 4 (Illegal instruction)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 2 PID 807 RUNNING AT ssdnode2
=   KILLED BY SIGNAL: 4 (Illegal instruction)
===================================================================================

17

General Questions and Answers / Re: Using MTP forcefield that has more than required elements

« on: February 5, 2024, 19:03 »

Hi,
One approach is to test and verify it for your application as:
1. Optimize your material using this MTP and DFT and compare bond lengths, angles etc.
2. Run a small one atom movement NEB using MTP and DFT and compare results.

After verification, if you are using it for molecular dynamics make sure you verify/optimize all states of interest with DFT to check consistency.

18

General Questions and Answers / Re: Transmission with Different electrodes

« on: February 4, 2024, 05:55 »

Thanks for your response.

I am facing a convergence issue in non-zero bias transmission. I tried reducing pulay mixing, history steps but nothng is helping.
Can I have your email ID so that I can share my file?

19

General Questions and Answers / Error on Cluster

« on: February 2, 2024, 13:51 »

Dear Admin,

Any idea what is causing this error? QuantumATK version is latest one released in december 2023.V12.

I do not face any issue on previous version of QATK on same cluster.

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 181758 RUNNING AT node10
=   KILLED BY SIGNAL: 4 (Illegal instruction)
===================================================================================

20

General Questions and Answers / Re: M3GNET

« on: January 30, 2024, 11:37 »

Dear  Julian Schneider,
Thanks for your response.
Yes I got the speedup.
Earlier I was mistakenly using mpiexec.hydra instead of mpiexec.

Also, Thanks for the vdW code

21

General Questions and Answers / Re: M3GNET

« on: January 29, 2024, 08:11 »

Dear  Julian Schneider,

Can you please answer this?

22

General Questions and Answers / Re: MD Final configuration is different from the last image of trajectory movie

« on: January 19, 2024, 10:13 »

Hi,

Check tick on wrap atoms.

23

General Questions and Answers / Re: Mulliken Charge for each optimization step

« on: January 16, 2024, 13:11 »

Dear Jalmeida,
While you know your research problem well than what I understand. However, I believe this won't be of any use as optimization depends on algorithm used. Instead, a more better approach would be to use AIMD for your system and then track Milliken charge for each step.

Best regards

24

General Questions and Answers / Re: M3GNET

« on: January 16, 2024, 13:08 »

Dear  Julian Schneider,

Thanks for your great quick support.

I have a doubt, so when you say we can use OMP threading, does it mean the simulation will run on single core with multithreading or multi-cores with multi-threading?

Would it effectively increase the speed similar to when using MPI?

Also, In running an MD using M3GNET for bilayer MoS2 ,I have observed M3GNET does not account vdW forces. The two layers separated very far away during MD run. I tried fixing Center of Mass but it didn't help. Have you faced any such problem?

As a remedy, I was thinking to use LJ between two layers but I worry it should not introduce any artificial or additional forces in system. Please provide your comments.

UPDATE: I tested simulations of a structure with ~3000 atoms using:

OMP_NUM_THREADS=46 and MKL_NUM_THREADS=46 (Simulation time for 150 ps = 3 min)
OMP_NUM_THREADS=1 and MKL_NUM_THREADS=1 (Simulation time for 150 ps = 3 min)

but it shows no speedup.

Thanks a lot once again.
Regards

25

General Questions and Answers / Re: M3GNET

« on: January 13, 2024, 10:52 »

Dear Julian Schneider,

Thanks for your response.
The M3GNet Molecular Dynamics is running fine on single CPU core, but when I tried running it on multiple CPU cores (using mpiexec.hydra) with ~3100 atoms in a system.

I got the following error:

File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 780, in __run_atkpython File "AuMoS2Au.py", line 418, in <module> Exception: Non trivial MPI calculation with more than one process is not supported as errorOnMPI is True for the Calculator. Exception: Non trivial MPI calculation with more than one process is not supported as errorOnMPI is True for the Calculator. File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 305, in __init__ File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 251, in wrapper File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 402, in _setParallelOptions Exception: Non trivial MPI calculation with more than one process is not supported as errorOnMPI is True for the Calculator. Traceback (most recent call last): File "/home/Asif/QATK_V2023_12/quantumatk/V-2023.12/atkpython/bin/atkpython", line 8, in <module> sys.exit(__run_atkpython())


How do I run it on multiple CPU cores?
Do I need to change something in code?

Thanks

26

General Questions and Answers / Re: Settings LJ for Tags

« on: January 13, 2024, 08:57 »

Thanks.

27

General Questions and Answers / Re: M3GNET

« on: January 12, 2024, 14:26 »

Dear Julian Schneider,

Yes, I observed that calculations are running fine. Log file has all the details.

Thanks for your help.

28

General Questions and Answers / Re: M3GNET

« on: January 10, 2024, 10:46 »

Dear Admin,

Thanks for responding.
I tried the second method (Attached file) and then run the program using atkpython MoS2_M3GNet.py > logfile.log

But I am getting the following error:
"Initialising the GPUs failed: CUDA driver version is insufficient for CUDA runtime version."

Kindly help in this regard.

29

General Questions and Answers / Re: M3GNET

« on: January 9, 2024, 02:58 »

Dear QATK team,

Could you please answer this? I am not able to find M3GNET in ATK latest release?

30

General Questions and Answers / Settings LJ for Tags

« on: January 9, 2024, 02:54 »

Dear Admin,

I have an LJ potential curve for an interface with two materials (Tagged as 'L' and 'R'). I want to implement it in QuantumATK but it requires atom by atom interaction.

Is there a way to implement LJ potential for tags?