Yambo 4.3.2 compilation failed.

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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
Post Reply
sebastien.k.umons
Posts: 3
Joined: Tue May 14, 2019 2:10 pm

Yambo 4.3.2 compilation failed.

Post by sebastien.k.umons » Tue May 14, 2019 2:19 pm

Dear all,

I try to compile with intel 2017 compiler the Yambo 4.3.2 with interface with QE 6.4 but the build failed.

Here is my configure command:
./configure CC=icc FC=ifort F77=ifort --with-blas-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \
--with-lapack-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-fft-libs="-mkl" \
--with-scalapack-libs="-lmkl_scalapack_ilp64" --with-blacs-libs="-lmkl_blacs_intelmpi_ilp64 -liomp5 -lpthread -lm -ldl" \
--with-iotk-path="/opt/sw/arch/manual/q-e/q-e-qe-6.4.1/iotk/src" \
--with-hdf5-path="/opt/cecisw/arch/easybuild/2017b/software/HDF5/1.8.19-intel-2017b" \
--with-hdf5-includedir="/opt/cecisw/arch/easybuild/2017b/software/HDF5/1.8.19-intel-2017b/include" \
--with-hdf5-libdir="/opt/cecisw/arch/easybuild/2017b/software/HDF5/1.8.19-intel-2017b/lib" \
--with-netcdf-path="/opt/cecisw/arch/easybuild/2017b/software/netCDF/4.4.1.1-intel-2017b-HDF5-1.8.19" \
--with-netcdf-libdir="/opt/cecisw/arch/easybuild/2017b/software/netCDF/4.4.1.1-intel-2017b-HDF5-1.8.19/lib64" \
--with-netcdf-includedir="/opt/cecisw/arch/easybuild/2017b/software/netCDF/4.4.1.1-intel-2017b-HDF5-1.8.19/include" \
--with-netcdf-libs="-lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lcurl -lz" \
--with-netcdff-path="/opt/cecisw/arch/easybuild/2017b/software/netCDF-Fortran/4.4.4-intel-2017b-HDF5-1.8.19" \
--with-netcdff-libdir="/opt/cecisw/arch/easybuild/2017b/software/netCDF-Fortran/4.4.4-intel-2017b-HDF5-1.8.19/lib" \
--with-netcdff-includedir="/opt/cecisw/arch/easybuild/2017b/software/netCDF-Fortran/4.4.4-intel-2017b-HDF5-1.8.19/include" \
--with-libxc-path="/opt/cecisw/arch/easybuild/2017b/software/libxc/2.2.3-intel-2017b" \
--with-libxc-libdir="/opt/cecisw/arch/easybuild/2017b/software/libxc/2.2.3-intel-2017b/lib" \
--with-libxc-includedir="/opt/cecisw/arch/easybuild/2017b/software/libxc/2.2.3-intel-2017b/include" \
--enable-open-mp

And finally my last compilation log >>>[Linking p2y]

<<<
make[2]: Entering directory `/opt/sw/arch/manual/yambo/4.3.2/interfaces/p2y'
cd /opt/sw/arch/manual/yambo/4.3.2/interfaces/p2y; /opt/sw/arch/manual/yambo/4.3.2/sbin/moduledep.sh mod_pw_data.o qexml.o qexsd_p2y.o qeh5_module.o qexpt_p2y.o pw_pseudo_read.o mod_p2y.o numrec_kinds.o mod_numerical.o numrec_module.o numrec_locate.o numrec_polint.o numrec_polcof.o numrec_ddpoly.o num_interpolation_module.o pw_struct_module.o pw_basis_module.o pw_wfc_module.o pw_pseudo_module.o pw_atoms_module.o pw_setqf.o qe_pseudo_init.o PP_PWscf_driver.o PP_PWscf_comp.o PP_PWscf_comp_nlcc.o p2y_db1.o p2y_wf.o p2y_i.o > /opt/sw/arch/manual/yambo/4.3.2/interfaces/p2y/make.dep
make[2]: Leaving directory `/opt/sw/arch/manual/yambo/4.3.2/interfaces/p2y'
make[2]: Entering directory `/opt/sw/arch/manual/yambo/4.3.2/interfaces/p2y'
mod_pw_data.F qexml.F qeh5_module.f90(426): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DREAD_F]
CALL H5Dread_f( h5_dataset%id, h5_realdp_type, ptr, ierr, mem_hid, file_hid, H5P_DEFAULT_F )
---------^
qeh5_module.f90(445): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DREAD_F]
CALL H5Dread_f( h5_dataset%id, H5_REALDP_TYPE, ptr, ierr, mem_hid, file_hid, H5P_DEFAULT_F )
---------^
qeh5_module.f90(466): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DREAD_F]
CALL H5Dread_f( h5_dataset%id, H5T_NATIVE_INTEGER , ptr, ierr, mem_hid, file_hid, H5P_DEFAULT_F )
---------^
qeh5_module.f90(510): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5_REALDP_TYPE, buf , ierr, memspace_,&
---------^
qeh5_module.f90(530): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5_REALDP_TYPE, buf , ierr, memspace_,&
---------^
qeh5_module.f90(549): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5_REALDP_TYPE, buf , ierr, memspace_,&
---------^
qeh5_module.f90(569): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5_REALDP_TYPE, buf , ierr, memspace_,&
--------^
qeh5_module.f90(590): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5_REALDP_TYPE, buf , ierr, memspace_,&
--------^
qeh5_module.f90(610): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, h5_realdp_type, buf , ierr, memspace_,&
---------^
qeh5_module.f90(630): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5T_NATIVE_INTEGER , buf , ierr, memspace_,&
--------^
qeh5_module.f90(651): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5T_NATIVE_INTEGER , buf , ierr, memspace_,&
--------^
qeh5_module.f90(671): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5T_NATIVE_INTEGER , buf , ierr, memspace_,&
---------^
qeh5_module.f90(699): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5AWRITE_F]
call H5Awrite_f (attr_id, string_type, buf, ierr )
--------^
qeh5_module.f90(754): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5AWRITE_F]
CALL H5Awrite_f (attr_id, mem_type, buf , ierr )
----------^
qeh5_module.f90(808): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5AWRITE_F]
CALL H5Awrite_f (attr_id, mem_type, buf , ierr )
----------^
qeh5_module.f90(857): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5AREAD_F]
CALL H5Aread_f( attr_id, mem_type,

I already tried to compile with other settings but for me it's always stop on [Linking p2y]

I already have the bin/yambo !

HDF5 version problem ? Any idea ?

Thanks in advance,
Sébastien.
Sébastien Kozlowskyj
HPC System Administrator
Laboratory for Chemistry of Novel Materials
University of Mons
Place du Parc, 20 7000 Mons (Belgium)

http://www.umons.ac.be
http://morris.umons.ac.be
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User avatar
Daniele Varsano
Posts: 3816
Joined: Tue Mar 17, 2009 2:23 pm
Contact:
Contact Daniele Varsano

Re: Yambo 4.3.2 compilation failed.

Post by Daniele Varsano » Tue May 14, 2019 2:45 pm

Dear Sébastien,
please include your full name and affiliation in your signature, this is a rule of the forum and you can do once for all by filling the signature in your user profile.
I can see you have multiple definition of netcdf necdff path/lib/includedir, is it a possible source of confusion?
Probably people involved in the p2y interface coding can give you an advice on how to solve the problem.

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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sebastien.k.umons
Posts: 3
Joined: Tue May 14, 2019 2:10 pm

Re: Yambo 4.3.2 compilation failed.

Post by sebastien.k.umons » Wed May 15, 2019 9:52 am

Hi,

I recompiled with your first suggestion and modify the definition of netCDF and I get the same error:

/configure CC=icc FC=ifort F77=ifort --with-blas-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-lapack-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-fft-libs="-mkl" --with-scalapack-libs="-lmkl_scalapack_ilp64" --with-blacs-libs="-lmkl_blacs_intelmpi_ilp64 -liomp5 -lpthread -lm -ldl" --with-iotk-path="/opt/sw/arch/manual/q-e/q-e-qe-6.4.1/iotk/src" --with-hdf5-path="/opt/cecisw/arch/easybuild/2017b/software/HDF5/1.8.19-intel-2017b" --with-hdf5-includedir="/opt/cecisw/arch/easybuild/2017b/software/HDF5/1.8.19-intel-2017b/include" --with-hdf5-libdir="/opt/cecisw/arch/easybuild/2017b/software/HDF5/1.8.19-intel-2017b/lib" --with-netcdf-libs="-L/opt/cecisw/arch/easybuild/2017b/software/netCDF/4.4.1.1-intel-2017b-HDF5-1.8.19 -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lcurl -lz" --with-netcdff-path="/opt/cecisw/arch/easybuild/2017b/software/netCDF-Fortran/4.4.4-intel-2017b-HDF5-1.8.19" --with-libxc-path="/opt/cecisw/arch/easybuild/2017b/software/libxc/2.2.3-intel-2017b" --with-libxc-libdir="/opt/cecisw/arch/easybuild/2017b/software/libxc/2.2.3-intel-2017b/lib" --with-libxc-includedir="/opt/cecisw/arch/easybuild/2017b/software/libxc/2.2.3-intel-2017b/include" --enable-open-mp
...
..
ake[2]: Entering directory `/opt/sw/arch/manual/yambo/4.3.2/interfaces/p2y'
mod_pw_data.F qexml.F qeh5_module.f90(426): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DREAD_F]
CALL H5Dread_f( h5_dataset%id, h5_realdp_type, ptr, ierr, mem_hid, file_hid, H5P_DEFAULT_F )
---------^
qeh5_module.f90(445): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DREAD_F]
CALL H5Dread_f( h5_dataset%id, H5_REALDP_TYPE, ptr, ierr, mem_hid, file_hid, H5P_DEFAULT_F )
---------^
qeh5_module.f90(466): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DREAD_F]
CALL H5Dread_f( h5_dataset%id, H5T_NATIVE_INTEGER , ptr, ierr, mem_hid, file_hid, H5P_DEFAULT_F )
---------^
qeh5_module.f90(510): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5_REALDP_TYPE, buf , ierr, memspace_,&
---------^
qeh5_module.f90(530): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5_REALDP_TYPE, buf , ierr, memspace_,&
---------^
qeh5_module.f90(549): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5_REALDP_TYPE, buf , ierr, memspace_,&
---------^
qeh5_module.f90(569): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DWRITE_F]
CALL H5Dwrite_f ( h5_dataset%id, H5_REALDP_TYPE, buf , ierr, memspace_,&
--------^

Thanks in advance,
Sébastien.
Sébastien Kozlowskyj
HPC System Administrator
Laboratory for Chemistry of Novel Materials
University of Mons
Place du Parc, 20 7000 Mons (Belgium)

http://www.umons.ac.be
http://morris.umons.ac.be
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andrea.ferretti
Posts: 206
Joined: Fri Jan 31, 2014 11:13 am

Re: Yambo 4.3.2 compilation failed.

Post by andrea.ferretti » Wed May 15, 2019 11:08 am

Dear Sébastien,

some compilation issues may arise with HDF5 if the F2003 interfaces are not activated.
This is also compatible with the fact that yambo compiles, while p2y (the one using such interfaces) does not.

Until HDF5 v1.8.x you have to ask for both fortran and fortran-2003 interfaces at configuration time.
From HDF5-1.10.x on, I think that the fortran bindings automatically contain also F2003 interfaces
(so, the problem does not show up any longer).

if you don't have access to already-compiled libraries with this requirements, just let yambo compile
netcdf and hdf5 for you (drop the corresponding flags from your yambo configuration script)

hope it helps
Andrea
Andrea Ferretti, PhD
CNR-NANO-S3 and MaX Centre
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322; Skype: andrea_ferretti
URL: http://www.nano.cnr.it
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sebastien.k.umons
Posts: 3
Joined: Tue May 14, 2019 2:10 pm

Re: Yambo 4.3.2 compilation failed.

Post by sebastien.k.umons » Wed May 15, 2019 3:02 pm

HI,

First Thanks to Andrea for your suggestions !!!

I finally completed successfully the Yambo 4.3.3 code compilation by replacing the HDF5 version 1.8.9 by 1.10.1 and configure with the following lines:

./configure CC=icc FC=ifort F77=ifort --with-blas-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \
--with-lapack-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-fft-libs="-mkl" \
--with-scalapack-libs="-lmkl_scalapack_ilp64" --with-blacs-libs="-lmkl_blacs_intelmpi_ilp64 -liomp5 -lpthread -lm -ldl" \
--with-iotk-path="/opt/sw/arch/manual/q-e/q-e-qe-6.4.1/iotk/src" \
--with-hdf5-path="/opt/cecisw/arch/easybuild/2017b/software/HDF5/1.10.1-intel-2017b" \
--with-hdf5-includedir="/opt/cecisw/arch/easybuild/2017b/software/HDF5/1.10.1-intel-2017b/include" \
--with-hdf5-libdir="/opt/cecisw/arch/easybuild/2017b/software/HDF5/1.10.1-intel-2017b/lib" \
--with-netcdf-libs="-L/opt/cecisw/arch/easybuild/2017b/software/netCDF/4.4.1.1-intel-2017b/lib64 -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lcurl -lz" \
--with-netcdff-path="/opt/cecisw/arch/easybuild/2017b/software/netCDF-Fortran/4.4.4-intel-2017b" \
--with-libxc-path="/opt/cecisw/arch/easybuild/2017b/software/libxc/2.2.3-intel-2017b" \
--with-libxc-libdir="/opt/cecisw/arch/easybuild/2017b/software/libxc/2.2.3-intel-2017b/lib" \
--with-libxc-includedir="/opt/cecisw/arch/easybuild/2017b/software/libxc/2.2.3-intel-2017b/include" \
--enable-open-mp

To be tested now by my users...

Regards,
Sébastien.
Sébastien Kozlowskyj
HPC System Administrator
Laboratory for Chemistry of Novel Materials
University of Mons
Place du Parc, 20 7000 Mons (Belgium)

http://www.umons.ac.be
http://morris.umons.ac.be
Top
User avatar
Daniele Varsano
Posts: 3816
Joined: Tue Mar 17, 2009 2:23 pm
Contact:
Contact Daniele Varsano

Re: Yambo 4.3.2 compilation failed.

Post by Daniele Varsano » Wed May 15, 2019 3:10 pm

Dear Sébastien,
I'm glad to know the problem is solved!

Regards,
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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