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Unexpected crush at the dipoles calculation with yambo5.2
Posted: Wed Sep 27, 2023 2:51 am
by jasonhan0710
Dear all,
I have updated the yambo to version 5.2. However, after I compiled it with Intel oneapi, it stopped every time and without any error information when calculating the dipole term in GW. Would you please help me figure out this problem? Thank you!
Best,
Jason
Re: Unexpected crush at the dipoles calculation with yambo5.2
Posted: Wed Sep 27, 2023 8:07 am
by Nicola Spallanzani
Dear Jason,
could you provide more information? For example sending the output and error files, the files "config.log", "config/report" and one of the log file that you can find in the LOG/ directory.
Best,
Nicola
Re: Unexpected crush at the dipoles calculation with yambo5.2
Posted: Wed Sep 27, 2023 9:21 am
by jasonhan0710
Hi Nicola,
Thanks for your reply.
The config.log file is attached.
I set
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./configure --enable-open-mp --enable-mpi \
--enable-time-profile --enable-memory-profile --enable-msgs-comps \
--enable-slepc-linalg \
--with-blas-libs="${MKL_LIBS}" --with-lapack-libs="${MKL_LIBS}" \
--with-fft-includedir="${MKLROOT}/include" --with-fft-libs="${MKL_LIBS}" \
--enable-dp
to compile the code.
The GW calculation stops at
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<02s> P1-c55: [DIP] Database not correct or missing. To be computed
<05s> P1-c55: [x,Vnl] computed using 130 projectors
<05s> P1-c55: [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
<05s> P1-c55: Dipoles: P, V and iR (T) | | [000%] --(E) --(X)
and the report files shows that
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[06] Dipoles
============
[RD./SAVE//ns.kb_pp_pwscf]------------------------------------------------------
Fragmentation : yes
- S/N 002730 ---------------------------------------------- v.05.01.00 r.22170 -
[WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
without and error information.
The slurm reports
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===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 2 PID 17140 RUNNING AT c56
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================
The same case can be calculated successfully with yambo-5.0.4.
Thank you!
Best,
Jason
Re: Unexpected crush at the dipoles calculation with yambo5.2
Posted: Wed Sep 27, 2023 10:32 am
by claudio
Dear Jason
you can try to compile with debug flags, just add --enable-debug-flags to the configure,
and see if you get more information about the crash
another advice: you may remove --enable-dp
usually double precision is not so important for the GW calculations
best
Claudio
Re: Unexpected crush at the dipoles calculation with yambo5.2
Posted: Thu Sep 28, 2023 9:09 am
by jasonhan0710
Dear Claudio and Nicola,
Thank you for your quick reply. I have recompiled yambo code with "--enable-debug-flags", however, it dose not give any error information in the report file and log file. The report file stops as previously and the log file shows that
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<---> [01] MPI/OPENMP structure, Files & I/O Directories
<---> MPI Cores-Threads : 1(CPU)-40(threads)
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] Reciprocal space
<---> [02.04] K-grid lattice
<---> Grid dimensions : 20 20
<---> [02.05] Energies & Occupations
<---> [03] Transferred momenta grid and indexing
<---> [04] Dipoles
<02s> [DIP] Database not correct or missing. To be computed
<03s> [x,Vnl] computed using 130 projectors
<03s> [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
<03s> Dipoles: P, V and iR (T) | | [000%] --(E) --(X)[1] 48147 segmentation fault
Do you have any thoughts on the problem?
Best,
Jason
Re: Unexpected crush at the dipoles calculation with yambo5.2
Posted: Thu Sep 28, 2023 10:50 am
by claudio
Dear Jason
it is difficult to day, where is the problem.
Another test you can do it is to remove the MKL libraries
./configure --enable-open-mp --enable-mpi --enable-slepc-linalg
and try to run it again
Claudio
Re: Unexpected crush at the dipoles calculation with yambo5.2
Posted: Sat Sep 30, 2023 6:22 am
by Daniele Varsano
Dear Jason,
besides what suggested by Claudio, it is useful to know the setup of your calculation. It is possible you are running out of memory.
You can add in the configure procedure the flag --enable-memory-profile and post your input and log file.
Best,
Daniele
Re: Unexpected crush at the dipoles calculation with yambo5.2
Posted: Sun Oct 01, 2023 4:03 am
by jasonhan0710
Hi Daniele and Claudio,
Thanks for helping me solve the problem. After I removed the MKL libraries, yambo can run normally. Thank you!
Best,
Jason