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Yambo5.1.1 Tddft ALDA run error
Posted: Thu Apr 13, 2023 5:55 pm
by hongtang2023
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
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Thu Apr 13, 2023 10:36 pm
by Davide Sangalli
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.
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Thu Apr 13, 2023 11:16 pm
by hongtang2023
Dear Davide,
Thanks for helping!
Please see attached all files in attachment.
Best,
Hong
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Thu Apr 13, 2023 11:38 pm
by hongtang2023
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
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Fri Apr 14, 2023 9:42 am
by Davide Sangalli
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Fri Apr 14, 2023 7:41 pm
by hongtang2023
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
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Mon Apr 17, 2023 7:50 am
by Daniele Varsano
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
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Mon Apr 17, 2023 5:03 pm
by hongtang2023
Dear Daniele,
Please see attached log files and other related files.
Best,
Hong
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Tue Apr 18, 2023 6:54 am
by Davide Sangalli
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
recompile
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./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.
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Wed Apr 19, 2023 1:08 am
by hongtang2023
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