Yambo5.1.1 Tddft ALDA run error

Deals with issues related to computation of optical spectra in reciprocal space: RPA, TDDFT, local field effects.

Moderators: Davide Sangalli, andrea.ferretti, myrta gruning, andrea marini, Daniele Varsano, Conor Hogan

hongtang2023
Posts: 45
Joined: Thu Mar 16, 2023 7:02 am

Yambo5.1.1 Tddft ALDA run error

Post by hongtang2023 » Thu Apr 13, 2023 5:55 pm

Dear Yambo team,

I recently installed Yambo5.1.1 on 2 clusters. When I run TDDFT ALDA,I got error:

Code: Select all

 [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
 [WF-Oscillators/G space/Transverse up loader] Normalization (few states)  min/max  :  0.000000  0.999392


 [ERROR] STOP signal received while in[04] Dipoles

 [ERROR] Writing File ./alda_q100//ndb.dipoles; Variable  NOT DEFINED; Permission denied
This is really puzzling me. I am not sure if this is related to compilation.
I also attached log files of the compilations.
Please help.

Best,
Hong
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Dr. Hong Tang
Tulane University
New Orleans, LA
70118, USA

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Davide Sangalli
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Re: Yambo5.1.1 Tddft ALDA run error

Post by Davide Sangalli » Thu Apr 13, 2023 10:36 pm

Dear Hong,
thank you for joining the yamob forum.

Can you attach also the input, the report, and the log file of the run ?

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

hongtang2023
Posts: 45
Joined: Thu Mar 16, 2023 7:02 am

Re: Yambo5.1.1 Tddft ALDA run error

Post by hongtang2023 » Thu Apr 13, 2023 11:16 pm

Dear Davide,

Thanks for helping!

Please see attached all files in attachment.

Best,
Hong
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Dr. Hong Tang
Tulane University
New Orleans, LA
70118, USA

hongtang2023
Posts: 45
Joined: Thu Mar 16, 2023 7:02 am

Re: Yambo5.1.1 Tddft ALDA run error

Post by hongtang2023 » Thu Apr 13, 2023 11:38 pm

Dear Davide,

I don't know to save the messages showing on the screen when running Yambo.
I tried "yambo -F input_file -J q100 > output.out "

But it turns out that output.out file is empty.


Please let me know how to save the messages showing on the screen when running Yambo into an .out file.

Thanks!

Best,
Hong
Dr. Hong Tang
Tulane University
New Orleans, LA
70118, USA

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Davide Sangalli
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Re: Yambo5.1.1 Tddft ALDA run error

Post by Davide Sangalli » Fri Apr 14, 2023 9:42 am

Code: Select all

nohup yambo -F input_file -J q100
Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

hongtang2023
Posts: 45
Joined: Thu Mar 16, 2023 7:02 am

Re: Yambo5.1.1 Tddft ALDA run error

Post by hongtang2023 » Fri Apr 14, 2023 7:41 pm

Dear Davide,

Did you find the solution for the error I met?

Code: Select all

 [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
 [WF-Oscillators/G space/Transverse up loader] Normalization (few states)  min/max  :  0.000000  0.999392


 [ERROR] STOP signal received while in[04] Dipoles

 [ERROR] Writing File ./alda_q100//ndb.dipoles; Variable  NOT DEFINED; Permission denied
Thank you so much for helping!

Best,
Hong
Dr. Hong Tang
Tulane University
New Orleans, LA
70118, USA

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Daniele Varsano
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Re: Yambo5.1.1 Tddft ALDA run error

Post by Daniele Varsano » Mon Apr 17, 2023 7:50 am

Dear Hong Tang,
it seems you have I/O problem related to the netcdf library. It could be a problem of. miscompilation.
1) Can you attach your config.log file?

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/

hongtang2023
Posts: 45
Joined: Thu Mar 16, 2023 7:02 am

Re: Yambo5.1.1 Tddft ALDA run error

Post by hongtang2023 » Mon Apr 17, 2023 5:03 pm

Dear Daniele,

Please see attached log files and other related files.

Best,
Hong
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Dr. Hong Tang
Tulane University
New Orleans, LA
70118, USA

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Davide Sangalli
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Re: Yambo5.1.1 Tddft ALDA run error

Post by Davide Sangalli » Tue Apr 18, 2023 6:54 am

Dear Hong Tang,
the config.log attached seems to have failed

Code: Select all

configure: caught signal 2
configure: exit 1
Can you do a

Code: Select all

make clean_all
recompile

Code: Select all

./configure CC=gcc FC=gfortran MPIFC=mpifort --enable-mpi --enable-open-mp --enable-time-profile --enable-memory-profile --with-libxc-libs=/home/hongtang/LIBXC515_gcc/libxc-5.1.5/installed_dir/lib --with-libxc-path=/home/hongtang/LIBXC515_gcc/libxc-5.1.5/installed_dir
and attach the config.log.

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

hongtang2023
Posts: 45
Joined: Thu Mar 16, 2023 7:02 am

Re: Yambo5.1.1 Tddft ALDA run error

Post by hongtang2023 » Wed Apr 19, 2023 1:08 am

Dear Daniele and Davide,

Our local team found that Yambo5.1.1 needs high version gcc (for example gcc 11.2.0) and higher version mpi/openmp, which also should be compiled with gcc.11.2.0. With those setting, my installation of Yambo5.1.1 is ok now.

However, I tried to install Yambo 5.1.1 on Nersc cluster. It shows the same errors when run it.

Could you please help me how to install it on Nersc Cori cluster?
I cannot find mpicc, mpifort, mpiifort or mpif90.
I only find icc, ifort, gcc (7.5.0), gfortran. I also find ftn, which is for cray.

Nersc clusters use "srun" for submit jobs, instead of "mpirun".

The setting right now on Cori is:

Code: Select all

$ module list
Currently Loaded Modulefiles:
  1) modules/3.2.11.4
  2) darshan/3.4.0
  3) craype-network-aries
  4) intel/19.1.2.254
  5) craype/2.7.10
  6) cray-libsci/20.09.1
  7) udreg/2.3.2-7.0.3.1_3.41__g5f0d670.ari
  8) ugni/6.0.14.0-7.0.3.1_6.23__g8101a58.ari
  9) pmi/5.0.17
 10) dmapp/7.1.1-7.0.3.1_3.42__g93a7e9f.ari
 11) gni-headers/5.0.12.0-7.0.3.1_3.25__gd0d73fe.ari
 12) xpmem/2.2.27-7.0.3.1_3.26__gada73ac.ari
 13) job/2.2.4-7.0.3.1_3.33__g36b56f4.ari
 14) dvs/2.12_2.2.224-7.0.3.1_3.32__gc77db2af
 15) alps/6.6.67-7.0.3.1_3.41__gb91cd181.ari
 16) rca/2.2.20-7.0.3.1_3.44__g8e3fb5b.ari
 17) atp/3.14.9
 18) perftools-base/21.12.0
 19) PrgEnv-intel/6.0.10
 20) craype-haswell
 21) cray-mpich/7.7.19
 22) craype-hugepages2M
Dr. Hong Tang
Tulane University
New Orleans, LA
70118, USA

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