BSE calculation stopped

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Daniele Varsano
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Re: BSE calculation stopped

Post by Daniele Varsano » Tue Feb 16, 2021 2:31 pm

Dear Ezekiel,
alpha it is not plotted because even if the system is 2D yambo cannot define the non periodic length of the cell needed for the refactor of alpha.
The condition is that there must be one cell unit vector _|_ to the 2D non periodic plane that must contain both the other two cell vectors.
Please see the warning in the report:

Code: Select all

[code] [WARNING]Non periodic geometry and unit cell are incompatible
[/code]

This is due because your A3 cell unit vector cell has small numbers n the first two component.

Code: Select all

Direct Lattice(DL) unit cell [iru  /  cc(a.u.)]
  A1 = 1.000000 -.1873E-6 -.3338E-7      5.940704 -.9638E-6 -.1429E-5
  A2 =-0.500000  1.000000 0.4477E-7     -2.970353  5.144801 0.1916E-5
  A3 =-.2374E-5 0.3449E-5  1.000000     -.1410E-4 0.1774E-4  42.79823
In order to have the alpha you should consider to repeat the calculation using A3=(0,0,1).
Or as the vector is "nearly" orthogonal, you can just multiply the eps spectrum for the correct factor, note they are proportional.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

ezekiel
Posts: 9
Joined: Fri Oct 02, 2020 11:01 pm

Re: BSE calculation stopped

Post by ezekiel » Wed Feb 17, 2021 12:56 pm

Dear Daniele,
I repeated the calculation using A3=(0,0,1) and I have the expected output files including that of alpha. I thank you for your time and the fruitful discussions.
Oyeniyi Ezekiel,
Theoretical Physicist,
Department of Physics,
University of Ibadan, Nigeria

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Daniele Varsano
Posts: 3354
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Re: BSE calculation stopped

Post by Daniele Varsano » Wed Feb 17, 2021 2:02 pm

Dear Ezekiel,

Great it worked!
Don't hesitate to post in the forum in the future if you need clarifications.
Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

ezekiel
Posts: 9
Joined: Fri Oct 02, 2020 11:01 pm

BSE calculation stopped

Post by ezekiel » Thu Jun 16, 2022 10:46 am

Hi,
I ran a BSE calculation on Marconi HPC. The calculation stopped with no output. My log file is attached. Please assist me on the way forward. Thank you.

Ezekiel Oyeniyi
University of Ibadan
Nigeria
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Oyeniyi Ezekiel,
Theoretical Physicist,
Department of Physics,
University of Ibadan, Nigeria

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Daniele Varsano
Posts: 3354
Joined: Tue Mar 17, 2009 2:23 pm
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Re: BSE calculation stopped

Post by Daniele Varsano » Thu Jun 16, 2022 12:29 pm

Dear Ezekiel,
it is not easy to spot the problem. It could be a memory issue.
Do you have any error messages from the queue system?
Another option would be to compile the code using the --enable-memory-profile option in the configure, in this way Yambo print the allocated memory before crashing.
Anyway, it seems the BS kernel has been computed (and hopefully stored), can you try to restart your calculation?
I've heard from some users having a similar problem in M100 (crashing when starting the solver section) that was solved by splitting the calculations into two runs: a first run to build the kernel (without bss runlevel) and a following run for the solver.
You can also try if this solve the problem.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

ezekiel
Posts: 9
Joined: Fri Oct 02, 2020 11:01 pm

Re: BSE calculation stopped

Post by ezekiel » Thu Jun 16, 2022 12:54 pm

Dear Daniele,
This is the message from the queue system:
OMP_NUM_THREADS=8
[r211n12:19477] *** Process received signal ***
[r211n12:19477] Signal: Segmentation fault (11)
[r211n12:19477] Signal code: (3)
[r211n12:19477] Failing at address: 0xffffffff8ded26a0
[r211n12:19477] [ 0] [r211n12:19474] *** Process received signal ***
[r211n12:19474] Signal: Segmentation fault (11)
[r211n12:19474] Signal code: (3)
[r211n12:19474] Failing at address: 0xffffffffa3eaec60
[r211n12:19474] [ 0] linux-vdso64.so.1(__kernel_sigtramp_rt64+0x0)[0x2000000504d8]
[r211n12:19474] [ 1] yambo[0x1021d5e4]
[r211n12:19474] linux-vdso64.so.1(__kernel_sigtramp_rt64+0x0)[0x2000000504d8]
[r211n12:19477] [ 1] yambo[0x1021d5e4]
[r211n12:19477] [ 2] yambo[0x1021aee0]
[r211n12:19477] [ 3] yambo[0x1021aa40]
[r211n12:19477] [ 4] yambo[0x1020b464]
[r211n12:19477] [ 5] [ 2] yambo[0x1021aee0]
[r211n12:19474] [ 3] yambo[0x1021aa40]
[r211n12:19474] [ 4] yambo[0x1020b464]
yambo[0x10141814]
[r211n12:19477] [ 6] yambo[0x1002f650]
[r211n12:19477] [ 7] yambo[0x1002717c]
[r211n12:19477] [ 8] yambo[0x10010a9c]
[r211n12:19477] [ 9] yambo[0x1000d2a4]
[r211n12:19477] [10] yambo[0x102c8ec0]
[r211n12:19477] [11] yambo[0x1000ca90]
[r211n12:19477] [12] /lib64/power9/libc.so.6(+0x241f8)[0x2000254741f8]
[r211n12:19477] [13] /lib64/power9/libc.so.6(__libc_start_main+0xb4)[0x2000254743e4]
[r211n12:19477] *** End of error message ***
[r211n12:19474] [ 5] yambo[0x10141814]
[r211n12:19474] [ 6] yambo[0x1002f650]
[r211n12:19474] [ 7] yambo[0x1002717c]
[r211n12:19474] [ 8] yambo[0x10010a9c]
[r211n12:19474] [ 9] yambo[0x1000d2a4]
[r211n12:19474] [10] yambo[0x102c8ec0]
[r246n20:20121] *** End of error message ***
yambo[0x1002717c]
[r214n12:117133] [10] yambo[0x10010a9c]
[r214n12:117133] [11] yambo[0x1000d2a4]
[r214n12:117133] [12] yambo[0x102c8ec0]
[r214n12:117133] [13] yambo[0x1000ca90]
[r214n12:117133] [14] /lib64/power9/libc.so.6(+0x241f8)[0x2000254741f8]
[r214n12:117133] [15] /lib64/power9/libc.so.6(__libc_start_main+0xb4)[0x2000254743e4]
[r214n12:117133] *** End of error message ***
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 28 with PID 108240 on node r255n10 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
5 total processes killed (some possibly by mpirun during cleanup)

[r211n12:19474] [11] yambo[0x1000ca90]
[r211n12:19474] [12] /lib64/power9/libc.so.6(+0x241f8)[0x2000254741f8]
[r211n12:19474] [13] /lib64/power9/libc.so.6(__libc_start_main+0xb4)[0x2000254743e4]
[r211n12:19474] *** End of error message ***
[r238n20:50123] *** Process received signal ***
[r238n20:50123] Signal: Segmentation fault (11)
Oyeniyi Ezekiel,
Theoretical Physicist,
Department of Physics,
University of Ibadan, Nigeria

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