Messages

1

General Questions and Answers / Re: Job suddenly stop and Segmentation fault

« on: Today at 05:06 »

Thanks for reply!
I am the only user of the server
If the license server cannot be connected due to network instability, will jobs suddenly stop?
But I remember that when encountering network conditions before, , the word "heartbeat" would appear in the log file.
Finally, I hope ATK can add the function of automatic restarting calculation, because I encountered many times that jobs suddenly stopped while I was sleeping, which was very frustrating.
Anyway, thank you very much for the help!
Thanks!

2

General Questions and Answers / Re: Job suddenly stop and Segmentation fault

« on: Yesterday at 09:44 »

Hello!
My jobs suddenly crashed again
When I use the "coredumpctl list" command, the following line appears:
Fri 2024-12-06 15:38:51 CST  396269 1000 1000 SIGSEGV present  /cad/synopsys/qatk/2023.12-sp1/atkpython/bin/python3.11   1.0G
Then I used "gdb /cad/synopsys/qatk/2023.12-sp1/atkpython/bin/python3.11 core"
It appears in the following line:
gdb: symbol lookup error: /lib/x86_64-linux-gnu/libpython3.12.so.1.0: undefined symbol: XML_SetReparseDeferralEnabled

I'm pretty sure the ram is enough during the calculation
My server has 500g of ram. The peak ram usage during calculation is about 200g.
Sometimes the calculation can be stable for 2 to 3 days, but sometimes the calculation stops after 4 hours.
I still don't know why jobs stopped suddenly.
Attached is my script below
Thanks!

3

General Questions and Answers / Re: Can the Electron Density (or Converged State) Calculated from IV Characteristic

« on: November 29, 2024, 04:11 »

Thanks for reply!
but,I still don’t understand
1.
I added configuration = nlread("file.hdf5", DeviceConfiguration)[-1] to the script.
If the metallic region in the DeviceConfiguration of file.hdf5 is at 0V, does that mean the calculated Veff result will be the "effective potential of the metallic region at 0V"?
But if I want to use the "DeviceConfiguration of the metallic region at 0V" as the initial state for calculating the "effective potential of the metallic region at -1V," is that possible?
2.
Also, where exactly should configuration = nlread("file.hdf5", DeviceConfiguration)[-1] be added in the script?
I tried adding it to both DeviceLCAOCalculator and DeviceConfiguration, but neither worked.
Thanks!
=======================================================
Thanks!
I already know how to import the initial state!

Just place the following:
job.setCalculator(
    calculator=calculator, initial_state=nlread("file.hdf5", DeviceConfiguration)[0]
)
before job.update()

4

General Questions and Answers / Re: Can the Electron Density (or Converged State) Calculated from IV Characteristic

« on: November 27, 2024, 05:33 »

Thanks for reply!
I have a few questions:
1.How do I use the nlread command?
potential_calculate = nlread(
    'iv_calculate.hdf5',
    DeviceConfiguration_0
)
Should I replace the DeviceConfiguration part of the original script with the text above?

2.Is there a strict requirement for reading DeviceConfiguration_0? For example, if I want to calculate the effective potential of gate (metallic region) at -1V, do I necessarily need to read the DeviceConfiguration at gate (metallic region) -1V? If I read DeviceConfiguration at gate (metallic region) 0V, will it restart the calculation, or will it take this converged state as the initial state and continue from there?

Thank you!

5

General Questions and Answers / Can the Electron Density (or Converged State) Calculated from IV Characteristic

« on: November 26, 2024, 13:51 »

Hello everyone!

Currently, I need to calculate three properties: IV characteristics, current density, and effective potential.
Each time, I have to restart the SCF calculation from scratch.

I would like to ask: is it possible to use the electron density obtained from the IV characteristics calculation for the effective potential calculation?
Would it work if I directly use nlread to read the HDF5 file generated from the IV characteristics?

Or are there other ways to improve the efficiency?

Thank you all!

6

General Questions and Answers / Re: How to Initialize from a converged state

« on: November 21, 2024, 06:01 »

[16547.681714] quantumatk[113938]: segfault at 100000009 ip 000079a194d08280 sp 00007fff5bf16218 error 4 in libQt5Gui.so.5.15.12[79a1948e5000+466000] likely on CPU 91 (core 43, socket 1)
Hello!
I found the crash report of coredump
Is there any solution to this?
The QATK version I use is 2024.09 and the OS version is ubuntu24.04.
The coredump occurs when SCF has completed its convergence when calculating IVCharacteristics. When entering Calculating Transmission, it suddenly crashes. My MPI setting is 24 and the threads setting is 8. What causes the coredump?
My CPU is amd epyc7k62 x2 total is 96cores and
Ram is 512g
Thanks

7

General Questions and Answers / How to Initialize from a converged state

« on: November 20, 2024, 13:43 »

Hi everyone!
Because coredump happens frequently on my server.
I confirm that my memory usage is sufficient (but I'm not sure if my ram is damaged)
I am calculating the IV of a 2-lead device. My plan is that I want my job to first converge to dE and dH 1e-2, then use this as the Initial state to calculate 1e-3, and finally converge to 1e- 4 or less, can this be done? If it can be done, how should it be done? If not, is there a similar method?
thank you

8

General Questions and Answers / Re: Job suddenly stop and Segmentation fault

« on: October 31, 2024, 05:06 »

OK
I would try lowering the MPI
Thanks for the reply!

 

9

General Questions and Answers / Job suddenly stop and Segmentation fault

« on: October 30, 2024, 09:55 »

Hi everyone,
My JOB has encountered Segmentation fault frequently recently.
I'm pretty sure there is enough ram during the calculation,
When doing SCF operation, the first few steps can be calculated stably, but it will stop when calculating the Calculating Density Matrix at a certain step.
The log file look like this at the end:
+------------------------------------------------------------------------------+
| Total Density Report                    DM           DD           dQ         |
+------------------------------------------------------------------------------+
| Left Electrode Extension            64.85281    -25.14719    -25.14719       |
| Right Electrode Extension           64.42974    -25.57026    -25.57026       |
| Central Region                    1532.77422    -33.22578    -33.22578       |
+------------------------------------------------------------------------------+
|  15 E = -509.293 dE =  2.042577e+00 dH =  4.867394e-01                       |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Density Matrix : ===========================

mobaxterm will display:
===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 58 PID 27109 RUNNING AT 512.lab.nycu.edu.tw
=   KILLED BY SIGNAL: 9 (Killed)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 59 PID 27123 RUNNING AT 512.lab.nycu.edu.tw
=   KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================
My ATK version is 2023.12-sp1 and operating system is CentOS 8
I only calculate the system of 240 atoms-noncollinear-FHI-DZP basis
I want to know how to solve the problem, or why the problem occurs.
Thanks!

10

General Questions and Answers / Re: How to reduce memory usage

« on: October 18, 2024, 06:17 »

229 atoms is not a lot, but when you use MPI parallelization the memory duplication can be quite large. So the main suggestion is to reduce MPI and use more threading.

It works!
Thanks for reply!

11

General Questions and Answers / How to reduce memory usage

« on: October 2, 2024, 14:44 »

Hello!
I am currently calculating a structure with 229 atoms in the central region with spin orbit coupling.
My server have 96 cores 512G ram
The MPI setting number of  processors is 64.
When atk calculates the central region, the memory usage will be insufficient.
Besides turning off SOC, is there any other way to reduce memory usage?
Thanks!

12

Installation and License Questions / Re: Error in open quantumatk

« on: September 27, 2024, 10:14 »

Thanks!
TSRI give me wrong file .
After I try symbolic link /uesr and /usr , I can open quantumatk!
Thanks again!

13

Installation and License Questions / Error in open quantumatk

« on: September 25, 2024, 15:56 »

Hello,
I am have some problem on opening quantumatk.
My linux version is Centos8 and the python version is 3.6.8
I get atk file from TSRI website
I can source the file which is /usr/cad/synopsys/CIC/qatk.cshrc
But open quantumatk , it have some error, it is like:
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""'
[root@512 synopsys]# quantumatk
/usr/cad/synopsys/qatk/cur/bin/quantumatk: /cad/synopsys/qatk/2023.12/atkpython/ bin/quantumatk: /user/cad/synopsys/qatk/2023.12/quantumatk/V-2023.12/atkpython/bin/python3.11 :bad interpreter: no such file or directory
/usr/cad/synopsys/qatk/cur/bin/quantumatk:line 66: /cad/synopsys/qatk/2023.12/atk python/bin/quantumatk:success
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""'
So,Need I upgrade the python version? , or need I delete all the atk file and install atk again?
Thanks!

14

General Questions and Answers / Re: How to Restart a stopped calculation(iv_characteristics)

« on: August 2, 2024, 04:58 »

Thank yuo!
I got it

15

General Questions and Answers / Re: How to Restart a stopped calculation(iv_characteristics)

« on: July 30, 2024, 05:16 »

Thanks for your helping!
My situation is a bit complicated.
My iv_characteristics just set one voltage point(vds_-0.05_vgs_0.00)
The voltage point is running SCF(200steps),it is not converged.
I have used checkpoint handler.
So i rerun the script,will it restarts from 200steps or starting a new calculation?
Thanks!