Topics

1

General Questions and Answers / "dapl async_event" error

« on: May 6, 2023, 05:49 »

Dear Dr. Blom,

I had contacted you earlier regarding a peculiar "dapl async_event" error that I was getting while submitting jobs on HPC.
We were receiving these kind of notifications (shown below) in the log after which the simulation paused and did not proceed any further:
hm010:UCM:dec1:1f7d2700: 781258369 us(781258369 us!!!): dapl async_event CQ (0x1fdb8e0) ERR 0
hm010:UCM:dec1:1f7d2700: 781258411 us(42 us): -- dapl_evd_cq_async_error_callback (0x1f7d700, 0x18171f0, 0x2b351f7d1d30, 0x1fdb8e0)
hm010:UCM:dec1:1f7d2700: 781258429 us(18 us): dapl async_event QP (0x55c0cf0) Event 1

After reinstalling QATK I thought that the problem was mitigated. However, I found that it was not so. Jobs ran fine only when the size of the simulations were small, but as the simulation size was increased, the same problem started reappearing. Then I searched for this issue on internet I found someone also facing the exact same error while running MPI jobs on an HPC (posted on an intel forum, with link: https://community.intel.com/t5/Intel-oneAPI-HPC-Toolkit/dapl-async-event-QP/td-p/1133391). Here it was suggested that the error was occuring because of a CQ overrun (completion queue is not large enough for data queue processing). IBV_EVENT_CQ_ERR CQ is in error (CQ overrun), IBV_EVENT_QP_FATAL Error occurred on a QP and it transitioned to error state; and that it could be solved by increasing the default CQ (EVD) size.

I also contacted the intel community and came to know that this problem could also be occurring due to incompatibility between centos 7 and latest version of mpiexec.hydra, but I am unsure if QATK 2019.12 uses the latest version of mpiexec.

Based on the above, I feel that this problem could probably be resolved by tuning some internal MPI parameters but being a novice, I have absolutely no idea how to proceed any further. My research is virtually halted as I am unable run any computationally heavy simulations and I would be completely obliged to you if you could kindly guide me in resolving this problem.     

Eagerly awaiting your reply.

Sincerely,
Ambika

2

General Questions and Answers / Symmetry in band structure calculation

« on: April 17, 2023, 09:26 »

Respected Sir/madam
 I am trying to calculate banstructure of graphene. As per Quantumatk tutorial we  can take symmetry point [G, K, M,G].
But as we take these symmetry point for graphene structure it showing error.
For reference we have attached log file.  Kindly help

Thank you

3

General Questions and Answers / MPI batch script error

« on: March 17, 2023, 09:09 »

Respected Authority,

I  am trying to run QuantumATK on an HPC using slurm job manager (I have a perpetual license for version QuantumATK Q-2019.12-SP1). For running the simulation I am specifying the number of CPU to 240 (we have licence of  256), but I find that the simulation is failing every time. However instead of specifying the number of CPU when I specify the number of nodes=6  (1 node=40 CPU) the simulation does not show any error.  The super computer that we are using, has incorporated certain rules that will allow us to run simulation only by specifying the number of CPUs instead of number of nodes. Can you please provide any help or support regarding this matter?  As it will only be possible for us to run simulations by specifying the number of CPUs.
The batch script that we used to run the simulation is based on the one that was available from QuantumATK which is attached herewith for your reference.
I have also attached the log file showing the error that we faced.

Thanking you in advance.

4

General Questions and Answers / Error in optimization of device

« on: July 18, 2022, 15:36 »

Dear Admin
I am getting this error. What does it mean.

Calculating Eigenvalues    : cn113:UCM:22f42:cd0b2700: 686464132 us(686464132 us!!!): dapl async_event CQ (0x1de4450) ERR 0
cn113:UCM:22f42:cd0b2700: 686464166 us(34 us):  -- dapl_evd_cq_async_error_callback (0x1d85f40, 0x1829490, 0x2b2acd0b1d30, 0x1de4450)
cn113:UCM:22f42:cd0b2700: 686464308 us(142 us): dapl async_event QP (0x1f2d5a0) Event 1

Kindly reply

5

General Questions and Answers / Problem in optimization of device

« on: July 15, 2022, 08:26 »

Dear Admin
What if I optimize my device using LCAO without considering SCF. Will this device work? If i optimize my device using LCAO with SCF it rarely converge.
K is 1*15*120 and mesh cutoff=65 Hatree.
Kindly reply as soon as possible

6

General Questions and Answers / convergence problem

« on: June 17, 2022, 13:39 »

After putting gas molecule in device configuration, does simulation converge?
I put multiple gas molecule in device configuration and running in super computer by using 240 core but from yesterday it has not calculated i-v curve for a single point, it seems nothing is happening.

7

General Questions and Answers / job manager is not working

« on: June 9, 2022, 16:20 »

On opening job manager showing this error.
Traceback (most recent call last):
  File "zipdir\NL\GUI\MainWindow\MainWindow.py", line 1011, in jobManager
  File "zipdir\NL\GUI\MainWindow\MainWindow.py", line 1026, in jobManagerReference
  File "zipdir\NL\GUI\MainWindow\MainWindow.py", line 1043, in singletonTool
  File "zipdir\NL\GUI\Tools\JobManager\JobManager.py", line 271, in __init__
  File "zipdir\NL\GUI\Tools\JobManager\JobManager.py", line 421, in loadSettings
  File "zipdir\NL\GUI\Tools\JobManager\JobManager.py", line 390, in settings
  File "zipdir\NL\IO\NLSaveUtilities.py", line 902, in nlread
  File "zipdir\NL\IO\HDF5.py", line 541, in readHDF5
  File "zipdir\NL\IO\HDF5.py", line 984, in inspectHDF5
  File "zipdir\NL\IO\HDF5.py", line 235, in contents
  File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "build\lib\site-packages\h5py-2.7.1-py3.6-win-amd64.egg\h5py\_hl\group.py", line 167, in __getitem__
  File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py\h5o.pyx", line 190, in h5py.h5o.open
KeyError: 'Unable to open object (bad heap free list)'

8

General Questions and Answers / charge transfer calculation

« on: June 7, 2022, 13:36 »

How to calculate charge transfer. I calculated mulliken population. How to analyse it, what amount of charge is transfered to/from gas? I am sensing carbon monoxide on OH terminated graphene nanoribbon .I am attaching file here please help,.
If there is other way to calculate the charge transfer,then guide me.

9

General Questions and Answers / how to calculate atomic charge

« on: May 25, 2022, 09:59 »

How to calculate atomic charge by using mulliken population and bader analysis.
 I calculated DOS, transmission spectrum, band structure. all are fine but in dos its  blank. How to correct it.
After adsorption of gas there are not any changes observed in mulliken population, what it shows, but changes in transmission spectrum and band structure are visible?

10

General Questions and Answers / Error in running the program

« on: May 17, 2022, 13:58 »

 I have attached script below. I am not able to calculate transmission spectrum . kindly help me