Error in [Linking yambo] in 5.0.4

[yhypku]

Dear developers,
I'm getting an error in the [Linking yambo] step. First I configure with command "./configure CC=icc FC=ifort CPP=cpp MPIFC=mpiifort". I copy the "liblapack.a" and "libblas.a" from compiled lapack-3.9.0 to /yambo-5.0.4/lib/external/intel/mpiifort/lib/. Then during "make all", errors appear as follows.

>>>[Linking yambo]<<<
make[2]: Entering directory `/gpfs/share/home/1500012896/software/yambo-5.0.4/driver'

/gpfs/share/home/1500012896/software/yambo-5.0.4/lib/external/intel/mpiifort/lib/liblapack.a(dtrtri.f.o): In function `dtrtri_':
dtrtri.f:(.text+0x13d): undefined reference to `_gfortran_concat_string'
/gpfs/share/home/1500012896/software/yambo-5.0.4/lib/external/intel/mpiifort/lib/liblapack.a(cgesvd.f.o): In function `cgesvd_':
cgesvd.f:(.text+0x36c): undefined reference to `_gfortran_concat_string'
cgesvd.f:(.text+0x5a8): undefined reference to `_gfortran_concat_string'
cgesvd.f:(.text+0xd21): undefined reference to `_gfortran_concat_string'
/gpfs/share/home/1500012896/software/yambo-5.0.4/lib/external/intel/mpiifort/lib/liblapack.a(chseqr.f.o): In function `chseqr_':
chseqr.f:(.text+0x3bf): undefined reference to `_gfortran_concat_string'
/gpfs/share/home/1500012896/software/yambo-5.0.4/lib/external/intel/mpiifort/lib/liblapack.a(ctrevc3.f.o):ctrevc3.f:(.text+0x1a7): more undefined references to `_gfortran_concat_string' follow
/gpfs/share/home/1500012896/software/yambo-5.0.4/lib/external/intel/mpiifort/lib/liblapack.a(ilaenv.f.o): In function `ilaenv_':
ilaenv.f:(.text+0x59): undefined reference to `_gfortran_compare_string'
ilaenv.f:(.text+0x276): undefined reference to `_gfortran_compare_string'
ilaenv.f:(.text+0x29f): undefined reference to `_gfortran_compare_string'
ilaenv.f:(.text+0x2d9): undefined reference to `_gfortran_compare_string'
ilaenv.f:(.text+0x2fa): undefined reference to `_gfortran_compare_string'
/gpfs/share/home/1500012896/software/yambo-5.0.4/lib/external/intel/mpiifort/lib/liblapack.a(ilaenv.f.o):ilaenv.f:(.text+0x319): more undefined references to `_gfortran_compare_string' follow
/gpfs/share/home/1500012896/software/yambo-5.0.4/lib/external/intel/mpiifort/lib/liblapack.a(xerbla.f.o): In function `xerbla_':
xerbla.f:(.text+0x49): undefined reference to `_gfortran_st_write'
xerbla.f:(.text+0x54): undefined reference to `_gfortran_string_len_trim'
xerbla.f:(.text+0x66): undefined reference to `_gfortran_transfer_character_write'
xerbla.f:(.text+0x76): undefined reference to `_gfortran_transfer_integer_write'
xerbla.f:(.text+0x7e): undefined reference to `_gfortran_st_write_done'
xerbla.f:(.text+0x87): undefined reference to `_gfortran_stop_string'
make[2]: *** [yambo] Error 1
make[2]: Leaving directory `/gpfs/share/home/1500012896/software/yambo-5.0.4/driver'
make[1]: *** [yambo] Error 2
make[1]: Leaving directory `/gpfs/share/home/1500012896/software/yambo-5.0.4'
yambo build failed

Can you tell me how to fix it?
Best,
Huaiyuan

[andrea.ferretti]

Dear Huaiyuan,

it seems your bias and lapack libraries are compiled with gfortran, while you are using the intel compilers, which causes the problem.
I would avoid copying blas and lapack by hand, while I would specify the proper libraries when running configure, eg:

Code: Select all

MKLROOT=/opt/intel/compilers_and_libraries_2020.0.166/linux/mkl

./configure \
  FC=ifort \
  CC=icc \
  --with-fft-libs="-mkl" \
  --with-blas-libs="-L$MKLROOT -lmkl_intel_lp64  -lmkl_sequential -lmkl_core " \
  --with-lapack-libs="-L$MKLROOT -lmkl_intel_lp64  -lmkl_sequential -lmkl_core " \
  --with-scalapack-libs="-L$MKLROOT -lmkl_scalapack_lp64 " \
  --with-blacs-libs="-L$MKLROOT -lmkl_blacs_intelmpi_lp64 " \
[...]

hope it helps
Andrea

[burkzdemir]

Dear Yambo Community,

I also have a similar linking problem for Yambo-5.2.4 for blas and lapack. I attached my config.log. And below is the compile_yambo.log;

*************************
ar -r libbse.a K_observables.o
ar -r libbse.a K_multiply_by_V.o
ar -r libbse.a K_multiply_by_V_transpose.o
ar -r libbse.a K_dot_product.o
ar -r libbse.a K_components_folded_in_serial_arrays.o
ar -r libbse.a K_stored_in_a_big_matrix.o
ar -r libbse.a K_diago_kerr_residual.o
ar -r libbse.a K_diago_magnons_residual.o
ar -r libbse.a PL_diago_residual.o
ar -r libbse.a PL_via_perturbative_inversion.o
mv libbse.a /arf/home/mkamislioglu/burak/yambo-5.2.4/lib
gfortran -E -P -cpp -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_TIMING -D_linux -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/headers/common -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/headers/parser -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/yambo/Ydriver/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/driver -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/version -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/include/ -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/v4/parallel/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/v4/parallel/include -I/arf/sw/lib/hdf5/1.14.3-openmpi-5.0.0/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/include/ -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/yambo/Ydriver/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/driver -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/version /arf/home/mkamislioglu/burak/yambo-5.2.4/driver/yambo.F >> yambo.tmp_source
mpifort -c -O3 -g -mtune=native -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/headers/common -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/headers/parser -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/yambo/Ydriver/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/driver -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/version -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/include/ -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/v4/parallel/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/v4/parallel/include -I/arf/sw/lib/hdf5/1.14.3-openmpi-5.0.0/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/include/ -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/yambo/Ydriver/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/driver -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/version yambo.f90
mpicc -I/arf/sw/lib/hdf5/szip-2.1.1-openmpi-5.0.0/include -I/arf/sw/lib/hdf5/zlib-1.3-openmpi-5.0.0/include -I/arf/sw/lib/hdf5/1.14.3-openmpi-5.0.0/include -D_C_US -D_FORTRAN_US -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_TIMING -D_linux -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/headers/common -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/headers/parser -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/yambo/Ydriver/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/driver -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/version -L/arf/home/mkamislioglu/burak/yambo-5.2.4/lib -D_yambo -c /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/yambo/Ydriver/src/driver/driver.c
mpifort -O3 -g -mtune=native -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/headers/common -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/headers/parser -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/yambo/Ydriver/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/driver -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/version -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/include/ -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/v4/parallel/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/v4/parallel/include -I/arf/sw/lib/hdf5/1.14.3-openmpi-5.0.0/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/include/ -I/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/yambo/Ydriver/include -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/driver -I/arf/home/mkamislioglu/burak/yambo-5.2.4/include/version -o yambo driver.o yambo.o -L/arf/home/mkamislioglu/burak/yambo-5.2.4/lib -lbse -lacfdt -lqp -lpol_function -ldipoles -ltddft -lsetup -lqp_control -linterpolate -lcoulomb -lwf_and_fft -lstop_and_restart -linterface -lxc_functionals -lio_parallel -lio -lYio -ltiming -lcommon -loutput -lparser -lparallel -lbz_ops -llinear_algebra -lmatrices -lmodules -lcommunicate -lallocations -lmemory -ltools -lyambo_Ydriver_main -lyambo_Ydriver_interface -lyambo_Ydriver_options -ldriver -lqe_pseudo -lmath77 -lslatec -llocal /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/lib/liblapack.a /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/lib/libblas.a /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/lib/libiotk.a /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/v4/parallel/lib/libnetcdff.a /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/v4/parallel/lib/libnetcdf.a -L/arf/sw/lib/hdf5/1.14.3-openmpi-5.0.0/lib /arf/sw/lib/hdf5/1.14.3-openmpi-5.0.0/lib/libhdf5hl_fortran.a /arf/sw/lib/hdf5/1.14.3-openmpi-5.0.0/lib/libhdf5_hl.a /arf/sw/lib/hdf5/1.14.3-openmpi-5.0.0/lib/libhdf5_fortran.a /arf/sw/lib/hdf5/1.14.3-openmpi-5.0.0/lib/libhdf5.a -L/arf/sw/lib/hdf5/zlib-1.3-openmpi-5.0.0/lib -L/arf/sw/lib/hdf5/szip-2.1.1-openmpi-5.0.0/lib -L/arf/sw/lib/openmpi/5.0.0/lib -lsz -lz -ldl -lm -Wl,-rpath -Wl,/arf/sw/lib/hdf5/1.14.3-openmpi-5.0.0/lib /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/lib/libxcf90.a /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/lib/libxcf03.a /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/lib/libxc.a /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/lib/libfftw3.a -lm
/usr/bin/ld: cannot find /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/lib/liblapack.a: No such file or directory
/usr/bin/ld: cannot find /arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/lib/libblas.a: No such file or directory

[Daniele Varsano]

Dear Burak,
it seems that lapack and blas libs are not present in the indicated directory.
/arf/home/mkamislioglu/burak/yambo-5.2.4/lib/external/gfortran/mpifort/lib/

So most probably either they have not be compiled or there was a previous error in the compilation.
I suggest you to recompile from scratch:

make distclean
./configure ...
make yambo

and check what happen when blas and lapack are compiled.

Best,

Daniele

[burkzdemir]

I checked and it seems they that they are installed. But, libblas.a and liblapack.a files are in /lib64 and not in /lib and the compilation is searching for these files in /lib. How can I solve this problem?

[Daniele Varsano]

Dear Burak,
you can redirect the path of the libraries with the configure command line:

Code: Select all

./configure 
--with-blas-libs="-L$PATH/lib64 -lblas" \
--with-lapack-libs="-L$PATH/lib64 -llapack" \

where you insert the full path where the libs are located.

Best,

Daniele

[burkzdemir]

Dear Daniele,

I compiled successfully with your suggestion. But, now I can only run serially. If I run parallel, then I get the following error;

/yambo-5.2.4/bin/yambo: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory

[burkzdemir]

I only get this error if I submit with job scheduler. If I directly submit from command line with mpirun then it runs successfully. I don't understand why I am getting this error when submit the job with sbatch.

Error: /yambo-5.2.4/bin/yambo: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory

[Daniele Varsano]

Dear Burak,

most probably, you need to set up the right environment inside the sbatch script, either loading the appropriate modules or setting the path by hand.
Something like:
EXPORT LD_LIBRARY_PATH=path_to_lapack_libs:$LD_LIBRARY_PATH

Best,
Daniele