Error in generating r_setup file

Concerns any physical issues arising during the setup step (-i option). This includes problems with symmetries, k/q-point sets, and so on. For technical problems (running in parallel, etc), refer to the Technical forum.

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el16yz
Posts: 23
Joined: Mon Sep 23, 2019 4:34 pm
Location: United Kingdom

Error in generating r_setup file

Post by el16yz » Tue Sep 24, 2019 10:11 am

Dear Yambo users,

The edition of Yambo I use is 4.4. I encountered a problem when I try to generate r_setup file. The error message is:
[ERROR] File ./SAVE//ns.db1; Variable G-VECTORS; NetCDF: Start+count exceeds dimension boundapplication called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor
And the information on my system:
[RD./SAVE//ns.db1]------------------------------------------
Bands : 320
K-points : 1
G-vectors [RL space]: 28363972
Components [wavefunctions]: 1676167
Symmetries [spatial+T-rev]: 2
Spinor components : 1
Spin polarizations : 2
Temperature [ev]: 0.02585
Electrons : 512.0000
WF G-vectors : 1676167
Max atoms/species : 96
No. of atom species : 5
Exact exchange fraction in XC : 0.000000
Exact exchange screening in XC : 0.000000
Magnetic symmetries : no
Is the problem dude to my G vector is too many to be transferred into yambo file? Is there any method can fix this problem? It will be very appreciated if you can help me.

Best wishes,
Yang

------
Yang Zhou
PhD student
University of Leeds
United Kingdom
Yang Zhou
PhD student
University of Leeds
United Kingdom

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Daniele Varsano
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Re: Error in generating r_setup file

Post by Daniele Varsano » Tue Sep 24, 2019 10:54 am

Dear Yang Zhou,
this is an error coming from the NETCDF libraries and yes, it is probably related to a large number of Gvectors needed for the density.
What you can to is to generate a setup input file adding verbosity for RL vectors:

Code: Select all

yambo -i -V RL
and lower the number of Gvectors in the MaXGvecs variable e.g. to the number of the WF G-vectors.

Anyway, if you do not have already done, probably the problem can be also overcome by linking the HDF5 library in the compilation.
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/

el16yz
Posts: 23
Joined: Mon Sep 23, 2019 4:34 pm
Location: United Kingdom

Re: Error in generating r_setup file

Post by el16yz » Wed Sep 25, 2019 12:31 pm

Dear Daniele,

Thanks for your suggestion.
What you can to is to generate a setup input file adding verbosity for RL vectors:

Code: Select all

yambo -i -V RL
[/quote]

I have tried this and still go error:
[ERROR] File ./SAVE//ns.db1; Variable G-VECTORS; NetCDF: Start+count exceeds dimension boundAttempting to use an MPI routine before initializing MPI
Now I am trying to link the HDF5 library. As the system I use is high-performance computing system, I have no idea how to complied Yambo with HDF5.

Best,
Yang

------
Yang Zhou
PhD student
University of Leeds
United Kingdom
Yang Zhou
PhD student
University of Leeds
United Kingdom

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Daniele Varsano
Posts: 3773
Joined: Tue Mar 17, 2009 2:23 pm
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Re: Error in generating r_setup file

Post by Daniele Varsano » Wed Sep 25, 2019 3:42 pm

Dear Yang,
in order to understand what is the source of the problem.
How much you lowered the MaXGvecs input variable?
You can try to reduce up to the wfs cutoff and see if it works.
As the system I use is high-performance computing system, I have no idea how to complied Yambo with HDF5.
I do not know it the code was already compiled linking with the HDF5 library, you should provide the config.log file. In any case, you should ask for help to your system administrator in order to know where the HDF5 libs are compiled and link them by using --enable-netcdf-hdf5 in the configure command line.
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/

el16yz
Posts: 23
Joined: Mon Sep 23, 2019 4:34 pm
Location: United Kingdom

Re: Error in generating r_setup file

Post by el16yz » Wed Sep 25, 2019 4:12 pm

Dear Daniele,

I cannot lower the MaXGvecs as it is failed to produce input file with yambo -i -V RL. Error message for that:
[ERROR] File ./SAVE//ns.db1; Variable G-VECTORS; NetCDF: Start+count exceeds dimension boundAttempting to use an MPI routine before initializing MPI
Best,
Yang

------
Yang Zhou
PhD student
University of Leeds
United Kingdom
Yang Zhou
PhD student
University of Leeds
United Kingdom

User avatar
Daniele Varsano
Posts: 3773
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: Error in generating r_setup file

Post by Daniele Varsano » Thu Sep 26, 2019 8:46 am

Dear Yang,

1) Did your p2y conversion finish correctly? I ask this because it is possible you have corrupted databases
2) You have 28363972 G vectors: This is a quite an unusual large number of G-vectors: I wonder if you are using a too large kinetic energy cutoff or a too large supercell.
Maybe you can try to lower one or both of these two parameters in your scf run.

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/

el16yz
Posts: 23
Joined: Mon Sep 23, 2019 4:34 pm
Location: United Kingdom

Re: Error in generating r_setup file

Post by el16yz » Thu Sep 26, 2019 10:26 am

Dear Daniele,
1) Did your p2y conversion finish correctly? I ask this because it is possible you have corrupted databases
Yes, there is no problem on finishing p2y.
2) You have 28363972 G vectors: This is a quite an unusual large number of G-vectors: I wonder if you are using a too large kinetic energy cutoff or a too large supercell.
The reason for the so many G vector is that the system I simulate is single molecule in Quantum Espresso. So I build a large cubic with large vacuum space, which leads too many G vectors. I will try to lower kinetic cut-off energy, but I cannot do more on super cell size as its minimum has been determined by convergence test. Thank you for your advices again.

Best,
Yang

------
Yang Zhou
PhD Student
University of Leeds
United Kingdom
Yang Zhou
PhD student
University of Leeds
United Kingdom

User avatar
Daniele Varsano
Posts: 3773
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: Error in generating r_setup file

Post by Daniele Varsano » Thu Sep 26, 2019 10:43 am

Dear Yang,
So I build a large cubic with large vacuum space, which leads too many G vectors. I will try to lower kinetic cut-off energy, but I cannot do more on super cell size as its minimum has been determined by convergence test.
I understand, if you do not have already done, you can use the Martyna-Tuckerman technique to isolate the system.
This is activated in QE input by using the assume_isolated="martyna-tuckerman" , and it accelerates a lot the convergence with respect the vacuum.
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/

el16yz
Posts: 23
Joined: Mon Sep 23, 2019 4:34 pm
Location: United Kingdom

Re: Error in generating r_setup file

Post by el16yz » Thu Sep 26, 2019 10:59 am

Dear Daniele,

Thanks for the advice. Actually, I have already used Martyna-Tuckerman method, but the super cell size is still large as 35 Angstrom.

Best,
Yang
Yang Zhou
PhD student
University of Leeds
United Kingdom

el16yz
Posts: 23
Joined: Mon Sep 23, 2019 4:34 pm
Location: United Kingdom

Re: Error in generating r_setup file

Post by el16yz » Mon Sep 30, 2019 1:32 pm

Dear Daniele,

I have tried to lower the kinetic energy cut-off in scf calculation. But the total G vector number doesn't vary with the kinetic energy cut-off. I think it should be only relative to the size of super cell. Besides, the HDF5 have been complied and Yambo should be able to handle big file. But the same error occurs when I run the yambo. Do you have any other suggestion to solve this large G-vector problem? Thank you.

Best wishes
Yang
Yang Zhou
PhD student
University of Leeds
United Kingdom

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