Issues compiling yambo 5.0 on HPC

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? This is the place to look.

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

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If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message
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Davide Sangalli
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Re: Issues compiling yambo 5.0 on HPC

Post by Davide Sangalli » Mon Apr 05, 2021 10:12 pm

Dear Marzieh
Marzieh wrote:
Mon Mar 22, 2021 12:44 pm

Since I did not see these parts during run by yambo 5.0.0 (in both parallel and without parallel):

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[WF-HF/Rho] Performing Wave-Functions I/O from ./SAVE
[WF-GW] Performing Wave-Functions I/O from ./SAVE
It seems yambo 5.0.0 can not read files from ./SAVE.

Best,
Marzieh
yambo 5.0.0 is reading the WFs, just it is not writing the above lines in the report.
This is not the source of your issue.

Did you try compiling 5.0.1 ?
We fixed few bugs.

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
http://www.oldism.cnr.it/en/davide-sangalli-cv/
http://www.max-centre.eu/

Marzieh
Posts: 23
Joined: Sun Feb 28, 2021 8:46 pm

Re: Issues compiling yambo 5.0 on HPC

Post by Marzieh » Tue Apr 06, 2021 7:44 am

Dear Davide,
As I mentioned here (viewtopic.php?f=1&t=1935), I compiled yambo5.0.1,yambo5.0.0 and yambo4.5.3.
But that issue was not solved by yambo5.0.0 and yambo5.0.1.
I attached cofigure.log files here again.
I am looking forward to hearing from you to solve this issue.

Best,
Marzieh
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Marzieh Ghoohestani, PhD
Institute of Condensed Matter and Nanosciences,
Université Catholique de Louvain,
8 Chemin des étoiles, 1348 Louvain-la-Neuve, Belgium
https://uclouvain.be/en/directories/marzieh.ghoohestani

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Davide Sangalli
Posts: 376
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Re: Issues compiling yambo 5.0 on HPC

Post by Davide Sangalli » Tue Apr 06, 2021 10:02 am

Ok, sorry.
I replied under the other forum discussion, but indeed it is better if we proceed here.

I post again the suggested configuration options:

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./configure FC="ifort" MPIFC="mpiifort" F77="ifort" MPIF77="mpiifort" CC="icc" MPICC="mpiicc" CPP="gcc -E -P" FPP="gfortran -E -P -cpp"   \
--enable-hdf5-par-io \
--enable-mpi \
--enable-open-mp \
--enable-dp \
--with-blas-libs="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm" \
--with-lapack-libs="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm" \
--with-fft-includedir="-I${MKLROOT}/include/fftw" \
--with-fft-libs="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm" \
--with-blacs-libs="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_core -liomp5 -lpthread -lm" \
--with-scalapack-libs="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_core -liomp5 -lpthread -lm"
Which error do you get when also using

Code: Select all

--enable-int-linalg
?

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
http://www.oldism.cnr.it/en/davide-sangalli-cv/
http://www.max-centre.eu/

Marzieh
Posts: 23
Joined: Sun Feb 28, 2021 8:46 pm

Re: Issues compiling yambo 5.0 on HPC

Post by Marzieh » Tue Apr 06, 2021 12:11 pm

Dear Davide,

I compiled yambo5.0.1 with the suggested configuration options but the issue was not solved. (E-Eo and Sc|Eo for are still NaN).

I also compiled using --enable-int-linalg, yambo build failed because too many errors.
Ihave attached confif.log and errors.

Best,
Marzieh
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Marzieh Ghoohestani, PhD
Institute of Condensed Matter and Nanosciences,
Université Catholique de Louvain,
8 Chemin des étoiles, 1348 Louvain-la-Neuve, Belgium
https://uclouvain.be/en/directories/marzieh.ghoohestani

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Davide Sangalli
Posts: 376
Joined: Tue May 29, 2012 4:49 pm
Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
Contact:

Re: Issues compiling yambo 5.0 on HPC

Post by Davide Sangalli » Tue Apr 06, 2021 2:36 pm

For the issue with the compilation of the internal lapack you can open the file

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lib/lapack/make.inc_lib
comment this line

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#TIMER = INT_ETIME
and uncomment

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TIMER = NONE

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
http://www.oldism.cnr.it/en/davide-sangalli-cv/
http://www.max-centre.eu/

Marzieh
Posts: 23
Joined: Sun Feb 28, 2021 8:46 pm

Re: Issues compiling yambo 5.0 on HPC

Post by Marzieh » Tue Apr 06, 2021 4:42 pm

Dear Davide,

I did what you suggested.

Code: Select all

./configure FC="ifort" MPIFC="mpiifort" F77="ifort" MPIF77="mpiifort" CC="icc" MPICC="mpiicc" CPP="gcc -E -P" FPP="gfortran -E -P -cpp"   \
--enable-hdf5-par-io \
--enable-mpi \
--enable-open-mp \
--enable-dp \
--enable-int-linalg \
--with-blas-libs="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm" \
--with-lapack-libs="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm" \
--with-fft-includedir="-I${MKLROOT}/include/fftw" \
--with-fft-libs="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm" \
--with-blacs-libs="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_core -liomp5 -lpthread -lm" \
--with-scalapack-libs="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_core -liomp5 -lpthread -lm"
and

Code: Select all

vi lib/lapack/make.inc_lib

  #TIMER = INT_ETIME
  TIMER = NONE
  
  make all -j 8


But that issue is not solved (E-Eo and Sc|Eo for are still NaN).

I have attached config.log.

Best,
Marzieh
You do not have the required permissions to view the files attached to this post.
Marzieh Ghoohestani, PhD
Institute of Condensed Matter and Nanosciences,
Université Catholique de Louvain,
8 Chemin des étoiles, 1348 Louvain-la-Neuve, Belgium
https://uclouvain.be/en/directories/marzieh.ghoohestani

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