Yambo Community Forum

Hi all,

I am using Yambo GPL Version 4.0.4 Revision 107 build with MPI+OpenMP.

When I was calcuating a SiO2 quartz, NaNs appeared in [06] BSE solver(s).

<31s> P0008: [06] BSE solver(s)
<34s> P0008: [06.01] Haydock solver
<37s> P0008: [Haydock] Iteration 1
<39s> P0008: [Haydock] Iteration 2
<41s> P0008: [Haydock] Iteration 3 Accuracy : NaN| -0.02000
<42s> P0008: [Haydock] Iteration 4 Accuracy : -NaN| -0.02000
<43s> P0008: [Haydock] Iteration 5 Accuracy : NaN| -0.02000
<44s> P0008: [Haydock] Iteration 6 Accuracy : -NaN| -0.02000
<45s> P0008: [Haydock] Iteration 7 Accuracy : NaN| -0.02000
<46s> P0008: [Haydock] Iteration 8 Accuracy : -NaN| -0.02000
<47s> P0008: [Haydock] Iteration 9 Accuracy : NaN| -0.02000
<48s> P0008: [Haydock] Iteration 10 Accuracy : -NaN| -0.02000

All the input files are attached.

At first I chose (d)iagonalization as a BSE solver,
but the calculation was interruppted after
[05.04] Bethe-Salpeter block due to a memory problem.

Then I restarted the calculation with (h)aydock method and
the above error appeared.

It would be helpful if you had any advice.

Best regards.

Kousuke Nakano

Dear Kosuke,
please note files are not attached. Please post input/reports and standard outputs.
The forum complains when fails have not specific suffixes, but you can tar/zip as this is allowed.

Best,
Daniele

Dear Daniele

I am sorry.

I failed to attach the files.

Best regards.

Kousuke.

Dear Kosuke,
at first glance I can't see anything wrong.
Can you post also the qe input files, and eventually pseudos if they are not in the qe website, as we can reproduce the error?

Best,
Daniele

Dear Daniele

I am sorry for my late reply.

I attached the qe_input, the pseudo potentials and the list of SAVE directory.

Best regards.

Kousuke

Dear Kosuke,
I had a look to your input files.

Unfortunately the run is quite big and "computer demanding".
Whcih means for us it is not easy to reproduce.

I can propose the following:
1) To have an idea where the problem comes from, you could inspect the ndb file produced by yambo.
ndb.* are databases produced with netcdf library. Thus you can visualize their content with the command "ncump $filename"
Can you try: "ncdump $filename | grep NaN > $filename.dat "
to see whether any of the databases generated by yambo has some NaN inside ?
In case, which one ?

2) To spot the source of the problem the best thing would be to have it in a small run.
Can you try to reduce the parameters to minimal values and see if you still get NaN ?
If not can you identify at which point you would get the NaN ?

Best,
D.

Dear Davide,

1) NaN appeared in [06] BSE solver(s)
-----------------------------------------------------------------------------------------------------

1) To have an idea where the problem comes from, you could inspect the ndb file produced by yambo.
ndb.* are databases produced with netcdf library. Thus you can visualize their content with the command "ncump $filename"
Can you try: "ncdump $filename | grep NaN > $filename.dat "
to see whether any of the databases generated by yambo has some NaN inside ?
In case, which one ?

2) To spot the source of the problem the best thing would be to have it in a small run.
Can you try to reduce the parameters to minimal values and see if you still get NaN ?
If not can you identify at which point you would get the NaN ?

Thank you for your advise, I solved the error!!

NaN appeared in ndb.BS_Q1_CPU_XXX.

Finally, I found the reason of the error is OpenMP failure.
NaN did not appear when I used flat-mpi.

I am cheking the compiler options again.

-----------------------------------------------------------------------------------------------------
2) BSE solver stops after 117 iterations

Although the BSK problems were solved with flatmpi, I encountered a strange error in BSE solver.

The BSE solver suddenly stopped after 117 iterations and the problem was not solved even when I restarted the calculation.

I did not find any error messages.

Do you have any suggestions?

I attached the input and output files.

Best regards

Kousuke.

Dear Davide,

I tried other options such as

BSHayTrs= 0.02000 # [BSS] [o/o] Haydock treshold. Strict(>0)/Average(<0)
BSHayTer # [BSS] Terminate Haydock continuos fraction

but I have not solved the problems yet...

I used 288 nodes (2304 cores) for the BSK (and BSS) calculations.

Any information would be helpful.

Best regards.

Kousuke Nakano.