Yambo Community Forum

Hi,
I have a problem with "make yambo interfaces" when I installed yambo.
error message:
make[1]: Entering directory `/home/yuan/yambo/yambo-3.2.0-r.315/interfaces/p2y'
gcc -g -O2 -D_C_US -D_FORTRAN_US -c /home/yuan/yambo/yambo-3.2.0-r.315/driver/getopt.c
ifort -assume bscc -O3 -tpp7 -nofor_main -I/home/yuan/yambo/yambo-3.2.0-r.315/include -I/home/yuan/espresso-3.2.3/iotk//src -o p2y driver.o getopt.o pw_errore.o mod_pw_data.o qexml_v3.2.o mod_p2y.o p2y_db1.o p2y_wf.o p2y_i.o -lint_modules -L/home/yuan/yambo/yambo-3.2.0-r.315/lib -lio -lcommon -lcommunicate -lparser -lmodules -lexternal_c -liotk -llapack -lblas -lfftw3 -lm
/home/yuan/yambo/yambo-3.2.0-r.315/lib/libiotk.a(iotk_error.o)(.text+0x414): In function `iotk_error_handler_x_':
: undefined reference to `mpi_abort_'
make[1]: *** [p2y] Error 1
make[1]: Leaving directory `/home/yuan/yambo/yambo-3.2.0-r.315/interfaces/p2y'
make: *** [interfaces] Error 2

before this, I configure yambo in this way:
./configure --with-iotk='/home/yuan/espresso-3.2.3/iotk/' --with-p2y=3.2.3 ( I also tried to add "--without-mpi" but the same error message)
In the end of configuration, it said:

# [ ] Double precision
# [X] Redundant compilation
# [ ] MPI
# [X] PW (3.2) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [ ] NETCDF/Large Files
# [XX] Built-in BLAS/LAPACK

It looks yambo already connected with PWSCF when I configure yambo, but the problem came out when I make inferface with pwscf. So how to solve this problem?
Thank you!
yuan ping
University of California, Davis

yping wrote:Hi,
I have a problem with "make yambo interfaces" when I installed yambo.
error message:
make[1]: Entering directory `/home/yuan/yambo/yambo-3.2.0-r.315/interfaces/p2y'
gcc -g -O2 -D_C_US -D_FORTRAN_US -c /home/yuan/yambo/yambo-3.2.0-r.315/driver/getopt.c
ifort -assume bscc -O3 -tpp7 -nofor_main -I/home/yuan/yambo/yambo-3.2.0-r.315/include -I/home/yuan/espresso-3.2.3/iotk//src -o p2y driver.o getopt.o pw_errore.o mod_pw_data.o qexml_v3.2.o mod_p2y.o p2y_db1.o p2y_wf.o p2y_i.o -lint_modules -L/home/yuan/yambo/yambo-3.2.0-r.315/lib -lio -lcommon -lcommunicate -lparser -lmodules -lexternal_c -liotk -llapack -lblas -lfftw3 -lm
/home/yuan/yambo/yambo-3.2.0-r.315/lib/libiotk.a(iotk_error.o)(.text+0x414): In function `iotk_error_handler_x_':
: undefined reference to `mpi_abort_'

It looks to me like PW is compiled with MPI suport while Yambo is not (they must be both serial or parallel). So when Yambo links to the IOTK library the `mpi_abort_' in IOTK is not resolved. So try either recompiling IOTK in serial or compiling Yambo in parallel.

Cheers

Andrea

Dear andrea marini,

I am a first user in yambo. I am calculating the absorption spectra of h-BN for 5*5 unit cell. Here I use the k-point mesh 3*3*1 about gamma point. According to the symmetry, there are five k-point in the pwscf output file. In the yambo.in file, I use X_finite_q_nCPU_invert=2 for matrix inversion. But in the report file, it always take 8 core for matrix inversion( X_finite_q_nCPU_invert= 8 # [PARALLEL] CPUs for matrix inversion). I don't understand the resign. Another question, yambo create individual electron elergy loss file corresponding to each k-point. Please tail me.

Thanking you.

Regards
Joydev De
PhD student
NISER,India

Dear Joydev
please respect the forum rules. You should open a new topic or reply to an existing post with a titlr related to your question and not reply to announcements and instructions of the forum. Coming to your question: you cam simply ignore the finite_cpu variable. If you are interested in absoprtion you need only q=0 limit and this is done by setring q pt indexes to 1 (1|1|).. In your input you are asking for the response for all the finite q.
1|5|
I invite you to take a look to the tutorials where input files and variae meanings are explained.
Anyway in general when asking for help please attach your input and report files.
Please do not reply to this post. If you need open a new one with the appropriate title.
Best

Daniele

Hi,

Can any one help me for calculating the spin polarised absorption spectra calculation using yambo?
For spin polarised calculation, first I have done the spin polarised scf and nscf using
pwscf. After that I want to calculate spin polarised spectra . But in the out put file, there is
no data for spin up and spin down separately. I thing for spin up and spin down, there are two different file.
Am I right ? Please help me !

I also attache my scf and nscf file.

Dear Joydev,
I asked you already different times to respect the forum rules.
Here, you are answering to a post called README first, which is meant to explain the rules of the forum to all the users, hence not related at all with your problem. Moreover, in this post, you can read 3 rules and you are not respecting two of them:

*Sign your posts with your complete name and affiliation.
*Check for the most appropriate subforum

This is because a well-organized forum is more useful as all the users can find solutions to their problem searching in the appropriate forum.

Now I can see nothing strange in your output, you performed a spin-polarized scf/nscf calculation: you can find in the output files.

What is exactly your problem?

Please do not answer to this post, but please visit the right subforum:
Spin-dependent and spinorial calculations
and open a new topic if you do not find answers to your doubts and need help.

Best,

Daniele

Hi!
Could you please explain me, how can I produce log file l_* for the process? Unfortunately I could not figure it out from the tutorial.
Also typing > ls -lsrtR > LIST_log tells me, that the command -lsrtR is not found. What can be wrong?
Best Regards,
Evgeniia

Dear Evgeniia,
the log files are in the LOG directory. Please post all the info you think is relevant to spot the problem.
Please note that this topic is a README with some instructions or the forum, as also wrote to the user in this thread this is not the right place to ask questions.

Best,
Daniele

Sorry about that, I will try to move these questions to technical issues.
Best regards,
Evgeniia

Dear YAMBO developer,

I have an issue in running Yambo with the version yambo-master.So, when I use p2y it runs successfully. However, if I try to run the second step using 'yambo' I get the following message error:

~> yambo
yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

Sorry to bother if there is already a reply in the forum I did not see.