Linking Problem

[bob]

Hi all,

I've been trying to compile yambo on a variety of systems and on one I receive errors which I'm not really sure what is going on.

Config.log is attached. Yambo is supposed to link against a system-wide netcdf but later seems to do something with a self-compiled one. And the first error about multiple mains I can't wrap my head around:

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>>>[Linking yambo]<<<
make[1]: Entering directory `/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/driver'
cd /oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/driver; /oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/sbin/moduledep.sh yambo_driver.o  > /oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/driver/make.dep
make[1]: Leaving directory `/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/driver'
make[1]: Entering directory `/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/driver'
yambo_driver.F
driver.o: In function `main':
/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/driver/driver.c:104: multiple definition of `main'
/opt/intel/2016.3.210/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/for_main.o:(.text+0x0): first defined here
/opt/intel/2016.3.210/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/for_main.o: In function `main':
(.text+0x2a): undefined reference to `MAIN__'
/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/lib/libpol_function.a(X_os.o): In function `x_os_':
X_os.f90:(.text+0x2e1a): undefined reference to `omp_set_lock_'
X_os.f90:(.text+0x3125): undefined reference to `omp_unset_lock_'
/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/lib/libmodules.a(mod_openmp.o): In function `openmp_mp_openmp_set_threads_':
mod_openmp.f90:(.text+0x53): undefined reference to `omp_set_num_threads_'
mod_openmp.f90:(.text+0x8e): undefined reference to `omp_set_num_threads_'
mod_openmp.f90:(.text+0xc1): undefined reference to `omp_set_num_threads_'
/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/lib/libmodules.a(mod_openmp.o): In function `openmp_mp_openmp_update_':
mod_openmp.f90:(.text+0x10c): undefined reference to `omp_get_thread_num_'
mod_openmp.f90:(.text+0x121): undefined reference to `omp_get_num_threads_'
/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/lib/libmodules.a(mod_openmp.o): In function `openmp_mp_openmp_locks_reset_':
mod_openmp.f90:(.text+0x1ca): undefined reference to `omp_destroy_lock_'
mod_openmp.f90:(.text+0x33f): undefined reference to `omp_init_lock_'
/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/lib/libmodules.a(mod_openmp.o): In function `openmp_mp_openmp_initialize_':
mod_openmp.f90:(.text+0x3b2): undefined reference to `omp_get_max_threads_'
mod_openmp.f90:(.text+0x3cd): undefined reference to `omp_get_thread_limit_'
mod_openmp.f90:(.text+0x3fa): undefined reference to `omp_set_dynamic_'
mod_openmp.f90:(.text+0x40c): undefined reference to `omp_set_nested_'
/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/lib/libnetcdf.a(libnetcdf5_la-nc5dispatch.o): In function `NC5_create':
(.text+0x6f): undefined reference to `ncmpi_create'
/oasis/projects/nsf/cob127/sneogi/timsteps/yambo-4.1.1-rev112/lib/libnetcdf.a(libnetcdf5_la-nc5dispatch.o): In function `NC5_open':
(.text+0x134): undefined reference to `ncmpi_open'

Appreciate any further insight into what I'm doing wrong.

Cheers,
Bjoern

[andrea.ferretti]

Dear Bjoern,

according to the error you report (and the config.log), i see two problems, one related to openmp support and one to netcdf.

* openmp: you are adding --enable-open-mp to the configure flags, thereby enabling amp support. Nevertheless, when coming
to the linking stage, openmp libs are not there... this is quite strange. Unless you configured with different options before and then
didn't do a full clean (make clean_all or make distclean), I am wondering whether the problem is related to your mvapich2 installation
(if I recall correctly, omg support needs to be activated)...
A quick and dirty solution to get a working executable is to drop the enable-open-mp, while for a full fledged mpi+omp version of yambo
further investigation is probably needed

* by the end of your error report, netcdf problems are also detected. My suspicion is that you are missing the hdf5 library (configure should
detect this but for some reasons it got tricked here, since your external netcdf library is properly detected)...
Solutions: if you have hdf5 installed, try to add it via configure using --with-hdf5-libs (or related flags), otherwise, if you drop the netcdf line
from configure flags yambo will resort to the internal netcdf lib which does not require hdf5

hope it helps
take care
Andrea

[bob]

It's rather weird. I have tried compiling without MPI - then there is an error that mpi_comm can't be found.

Compiling with MPI only still gives me errors when linking netcdf

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>>>[Linking yambo]<<<
make[1]: Entering directory `/pylon1/ct4s8ep/sneogi/timsteps/software/yambo-4.1.1-rev112/driver'
cd /pylon1/ct4s8ep/sneogi/timsteps/software/yambo-4.1.1-rev112/driver; /pylon1/ct4s8ep/sneogi/timsteps/software/yambo-4.1.1-rev112/sbin/moduledep.sh yambo_driver.o  > /pylon1/ct4s8ep/sneogi/timsteps/software/yambo-4.1.1-rev112/driver/make.dep
make[1]: Leaving directory `/pylon1/ct4s8ep/sneogi/timsteps/software/yambo-4.1.1-rev112/driver'
make[1]: Entering directory `/pylon1/ct4s8ep/sneogi/timsteps/software/yambo-4.1.1-rev112/driver'
yambo_driver.F
/pylon1/ct4s8ep/sneogi/timsteps/software/yambo-4.1.1-rev112/lib/libnetcdff.a(netcdf.o): In function `nf90_inq_libvers':
/pylon1/ct4s8ep/sneogi/timsteps/software/yambo-4.1.1-rev112/lib/netcdf/netcdf-y4.1.3/f90/netcdf_file.f90:12: undefined reference to `nf_inq_libvers_'

This *is* the self-compiled netcdf. This is how I configured it:

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./configure --with-blas-libs="-lmkl_intel_lp64  -lmkl_sequential -lmkl_core" --with-lapack-libs="-lmkl_intel_lp64  -lmkl_sequential -lmkl_core" FC=mpiifort F77=ifort CC=mpiicc MPICC=mpiicc

I'm confused. Is there maybe some detail that isn't passed to the netcdf compilation?

[Davide Sangalli]

Dear Bjoern,
for the parallel compilation what if you try setting:

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CC=icc FC=ifort F77=ifort PFC=mpiifort MPICC=mpiicc

(see configure --help)

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  CC          C compiler command
  FC          Fortran compiler command
  F77         Fortran 77 compiler command
  PFC         Parallel Fortran compiler command
  MPICC       Parallel C compiler command

For the serial compilation instead, open the source file src/modules/mod_parallel.F and replace

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   subroutine CREATE_the_COMM(WORLD, COMM, ID )
     integer       :: WORLD,ID,i_err
     type(MPI_comm):: COMM
     call MPI_COMM_SPLIT(WORLD,COMM%my_CHAIN,ID,COMM%COMM,i_err)
     call MPI_COMM_RANK(COMM%COMM,COMM%CPU_id,i_err)
     call MPI_COMM_SIZE(COMM%COMM,COMM%n_CPU ,i_err)
   end subroutine

with

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   subroutine CREATE_the_COMM(WORLD, COMM, ID )
     integer       :: WORLD,ID,i_err
     type(MPI_comm):: COMM
#if defined _MPI
     call MPI_COMM_SPLIT(WORLD,COMM%my_CHAIN,ID,COMM%COMM,i_err)
     call MPI_COMM_RANK(COMM%COMM,COMM%CPU_id,i_err)
     call MPI_COMM_SIZE(COMM%COMM,COMM%n_CPU ,i_err)
#endif
   end subroutine

[bob]

Thanks, that did it now. One system was weirdly configured with different compilers but not all with the compatible MPI libraries. Now it seems to go through.