yambo 5.3.0 compilation error

[sitangshu]

Hi,

I am trying to install yambo 5.3.0 in my hpc. I found no issue with any library installations. The problem is appearing at these lines:
I am using:

Code: Select all

[sitangshub.iiita@login02 ~]$ module load spack/1.2.0

For better command line support, copy and paste the following:

. /home/apps/spack/share/spack/setup-env.sh

If using Spack to install to system area, set umask 0002

[sitangshub.iiita@login02 ~]$ module list

Currently Loaded Modules:
  1) spack/1.2.0

 

[sitangshub.iiita@login02 ~]$ source /home/apps/spack/share/spack/setup-env.sh

spack load /6asbh6t
spack load /ptyduiko
spack load /pmjv32t
[sitangshub.iiita@login02 ~]$ which ifort
which icx
which mpiifort
echo $MKLROOT
/home/apps/spack/opt/spack/linux-cascadelake/intel-oneapi-compilers-2024.2.1-6asbh6tb63mah6tb57zjkvsrmueeksxm/compiler/2024.2/bin/ifort
/home/apps/spack/opt/spack/linux-cascadelake/intel-oneapi-compilers-2024.2.1-6asbh6tb63mah6tb57zjkvsrmueeksxm/compiler/2024.2/bin/icx
/home/apps/spack/opt/spack/linux-cascadelake/intel-oneapi-mpi-2021.18.0-ptyduiko3g6jdoewrgpgeiawmxlxsnhf/mpi/2021.18/bin/mpiifort
/home/apps/spack/opt/spack/linux-cascadelake/intel-oneapi-mkl-2025.3.1-pmjv32twadyvr7s63hpcbszasbsobzau/mkl/2025.3

Code: Select all

\t[src/tools] lib_Y_tools.a (lib)
make[2]: warning: -j4 forced in submake: resetting jobserver mode.
\t[src/modules] mod_cufft
\t[src/modules] mod_openmp
\t[src/modules] mod_pars
\t[src/modules] mod_lexical_sort
\t[src/modules] mod_cudafor
\t[src/modules] mod_hip
\t[src/modules] mod_hipfft
\t[src/modules] mod_drivers
\t[src/modules] mod_OUTPUT
\t[src/modules] mod_cutoff_ws
\t[src/modules] mod_com_interfcs
\t[src/modules] mod_atom_proj
\t[src/modules] mod_ACFDT
\t[src/modules] mod_magnetic
\t[src/modules] mod_matrix_operate
\t[src/modules] mod_units
\t[src/modules] mod_wrapper
\t[src/modules] mod_cusolverdn_y
\t[src/modules] mod_descriptors
\t[src/modules] mod_wrapper_omp
\t[src/modules] mod_stderr
\t[src/modules] mod_logo
\t[src/modules] mod_memory
\t[src/modules] mod_frequency
\t[src/modules] mod_linear_algebra
\t[src/modules] mod_RT_occupations
\t[src/modules] mod_parallel
\t[src/modules] mod_SLK
\t[src/modules] mod_gpu
\t[src/modules] mod_electrons
\t[src/modules] mod_IO_interfaces
\t[src/modules] mod_DIPOLES
\t[src/modules] mod_LIVE_t
\t[src/modules] mod_mklfft_gpu
\t[src/modules] mod_matrix
\t[src/modules] mod_com
\t[src/modules] mod_FFT
\t[src/modules] mod_R_lattice
\t[src/modules] mod_IO
\t[src/modules] mod_timing
\t[src/modules] mod_debug
\t[src/modules] mod_collision_el
\t[src/modules] SET_logicals
\t[src/modules] mod_electric
\t[src/modules] mod_X
\t[src/modules] mod_xc_functionals
\t[src/modules] mod_D_lattice
\t[src/modules] mod_TDDFT
\t[src/modules] mod_BS
\t[src/modules] mod_global_XC
\t[src/modules] mod_wave_func
\t[src/modules] mod_functions
\t[src/modules] mod_MAGNONS
\t[src/modules] mod_parallel_interface
\t[src/modules] mod_DICHROISM
\t[src/modules] mod_BS_solvers
\t[src/modules] mod_collision_ext
\t[src/modules] mod_vec_operate
\t[src/modules] mod_RT_output
\t[src/modules] mod_POL_FIT
\t[src/modules] mod_ELPH
\t[src/modules] mod_RT_lifetimes
\t[src/modules] mod_plasma
\t[src/modules] mod_zeros
\t[src/modules] mod_PHOTOLUM
\t[src/modules] mod_pseudo
\t[src/modules] mod_ALLOC
\t[src/modules] mod_real_time
\t[src/modules] mod_QP
\t[src/modules] mod_EXCPH
\t[src/modules] mod_MPA
\t[src/modules] mod_QP_CTL
\t[src/modules] mod_RT_control
\t[src/modules] mod_COLL_interfaces
make[2]: *** [/home/nsmext/sitangshub.iiita/ondemand/data/software/yambo-phys-exc-ph/config/mk/local/rules.mk:15: mod_interfaces.o] Error 1
make[2]: *** Waiting for unfinished jobs....
\t[src/modules] mod_hamiltonian
\t[src/modules] mod_interpolate
\t[src/modules] mod_fields
f951: Fatal Error: Reading module ‘/home/nsmext/sitangshub.iiita/ondemand/data/software/yambo-phys-exc-ph/lib/external/gfortran/mpif90/double/include/petscmatdef.mod’ at line 1 column 2: Unexpected EOF
\t[driver] yambo (setup)
yambo linking failed. Check log/compile_yambo.log
f951: Fatal Error: Reading module ‘/home/nsmext/sitangshub.iiita/ondemand/data/software/yambo-phys-exc-ph/lib/external/gfortran/mpif90/double/include/petscmatdef.mod’ at line 1 column 2: Unexpected EOF
make[1]: *** [config/mk/global/actions/compile_yambo.mk:43: yambo] Error 1
yambo build failed
make: *** [Makefile:54: all] Error 1

[Nicola Spallanzani]

Dear Sitangshu,

Since the linking error in Yambo indicates that the problem is related to linking the PETSc library, I checked the PETSc log files. I noticed that PETSc was compiled using `mpicc` (a wrapper for GCC) as the C compiler and `mpiifort` (a wrapper for Intel Fortran) as the Fortran compiler. So there is a mix of compiler toolchains, which can often lead to unpredictable problems.

I also checked the Yambo compilation, and it seems that Yambo was compiled entirely using `mpicc` (GCC) and `mpif90` (GFortran). Therefore, if the PETSc libraries were built using `mpiifort` but you are trying to link them using `mpif90`, I can see how this could cause problems.

Moreover, as I understand it, your intention was to compile everything using the Intel compiler suite. In that case, I suggest adding the following variables to your `configure` command:

Code: Select all

./configure CC=icc FC=ifort MPICC=mpiicc MPIFC=mpiifort ...

Best,
Nicola

[sitangshu]

Oops!
I used intel mkl, but compiled with gcc
Working now.

Regards,
Sitangshu