Yambo 5 compilation error

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

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

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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
pyadav
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Re: Yambo 5 compilation error

Post by pyadav » Sat Nov 19, 2022 7:44 am

Dear Nicola,

Thank you for your response.

Please find the attached zip file, it contains the config/report file and the last file written in the log/ directory.
yambo_5.1_error.zip
Wishes,
Pushpendra
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Pushpendra Yadav
Ph.D. Research Scholar
Quantum Transport and Theory Group
Department of Physics
Indian Instittute of Technology Kanpur, India.

https://sites.google.com/site/amitkag1/

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Nicola Spallanzani
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Re: Yambo 5 compilation error

Post by Nicola Spallanzani » Wed Nov 23, 2022 5:14 pm

Dear Pushpendra,
this time I think that the issue is related to the old version of the hdf5 library used.
Try to let yambo to download and compile the library by itself. If you have not provided the library so try applying this patch:

Code: Select all

patch -u configure -i hdf5_v51_patch.txt
Best,
Nicola
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Nicola Spallanzani, PhD
S3 Centre, Istituto Nanoscienze CNR and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu

pyadav
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Re: Yambo 5 compilation error

Post by pyadav » Sun Nov 27, 2022 11:03 am

Dear Nicola,

Yes, last time I gave the path to pre installed hdf5. This time I did the configure without assigning it. After successful configure, when I 'make all' I receive the following error message-

Code: Select all

make[2]: *** [variables_BS.o] Error 1
variables_BS.f90(26): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [NETCDF]
	[interfaces/int_modules] int_modules (checking work to be done)
	[interfaces/int_modules] libint_modules.a (lib)
	[interfaces/p2y] p2y (checking work to be done)
p2y linking failed. Check log/compile_p2y.log
variables_BS.f90(26): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [NETCDF]
make[1]: *** [p2y] Error 1
p2y build failed



Here I also attach the log files in the attached zip file.
yambo_5.1.error2.zip
Thanking you,

Pushpendra
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Pushpendra Yadav
Ph.D. Research Scholar
Quantum Transport and Theory Group
Department of Physics
Indian Instittute of Technology Kanpur, India.

https://sites.google.com/site/amitkag1/

pyadav
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Re: Yambo 5 compilation error

Post by pyadav » Thu Dec 01, 2022 1:59 pm

Dear team yambo,

Can someone please help me with the above issue?

Thank you,
Pushpendra
Pushpendra Yadav
Ph.D. Research Scholar
Quantum Transport and Theory Group
Department of Physics
Indian Instittute of Technology Kanpur, India.

https://sites.google.com/site/amitkag1/

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Daniele Varsano
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Re: Yambo 5 compilation error

Post by Daniele Varsano » Wed Dec 07, 2022 10:54 am

Dera Pushendra,

did you make a make clean (all, distclean) before starting the procedure again?
If you already did that, hopefully Nicola can provide you more info.
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/

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Nicola Spallanzani
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Re: Yambo 5 compilation error

Post by Nicola Spallanzani » Wed Dec 07, 2022 11:29 am

Dear Pushpendra,
as said by Daniele you have to delete the previous compilation of the netcdf library. To do that you have to launch the command
make distclean
then run again the configure command.

About it, I see in the file config.log that there is a problem on how it is launched the configure command:

Code: Select all

$ ./configure CC=icc PFC=mpiifort FC=ifort MPIFC=mpiifort MPIF77=ifort MPICC=mpiicc F77=ifort --enable-dp F90=ifort --with-blas-libs=-Wl,--start-group /libmkl_intel_lp64.a /libmkl_sequential.a /libmkl_core.a -Wl,--end-group --with-lapack-libs=-Wl,--start-group /libmkl_intel_lp64.a /libmkl_sequential.a /libmkl_core.a -Wl,--end-group --with-blacs-libs=/libmkl_blacs_intelmpi_lp64.a --with-scalapack-libs=/libmkl_scalapack_lp64.a --with-fft-libs=-L/lib -lfftw3 --with-fft-path=
clearly some paths are missing in this line: maybe you are using some environment variables that are not defined.

Could you send me also the configure line that you are using?
Where are the mkl library installed?
Is the environment variable MKLROOT defined?
Where are the fftw libraries installed?

Best,
Nicola
Nicola Spallanzani, PhD
S3 Centre, Istituto Nanoscienze CNR and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu

pyadav
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Re: Yambo 5 compilation error

Post by pyadav » Thu Dec 22, 2022 12:51 pm

Dear Nicola,

I followed the 'make distclean' and started the installation fresh. This time I did not give any path while doing './configure'. It ended with the Yambo build failed.

The log files are attached herewith.
yambo_5.1.error3.zip
Thank you,
Pushpendra
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Pushpendra Yadav
Ph.D. Research Scholar
Quantum Transport and Theory Group
Department of Physics
Indian Instittute of Technology Kanpur, India.

https://sites.google.com/site/amitkag1/

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Nicola Spallanzani
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Re: Yambo 5 compilation error

Post by Nicola Spallanzani » Thu Dec 29, 2022 6:43 pm

Dear Pushpendra,
try simply with this command:

Code: Select all

make distclean
./configure CC=icc FC=ifort MPIFC=mpiifort MPIF77=ifort MPICC=mpiicc F77=ifort \
        --enable-mpi --enable-open-mp \
        --enable-msgs-comps \
        --enable-time-profile \
        --enable-memory-profile
Best,
Nicola

PS: if you continue to have problems send me also the config/report file.
Nicola Spallanzani, PhD
S3 Centre, Istituto Nanoscienze CNR and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu

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