[Pw_forum] QE 5.0.2 compile problem and MKL problem

Mon Dec 9 12:32:29 CET 2013

On Mon, Dec 9, 2013 at 12:28 PM, Yue-Wen Fang <yuewen.fang at gmail.com> wrote:
> Dear axel,
>
> in fact, before conducting these complicated steps, I have followed the
> instructions from user's guide. However, all of them displayed several
> errors.

those are clearly in reference to OpenMPI, so the issue is in how you
are compiling and linking with the MPI library and not so much with
MKL.

you are best off to contact the support staff of the center where you
are trying to compile QE and work with them on the compilation, as
they would know best how to correctly compile parallel applications
and link with MKL on their machine.

axel.

> such as
>
> _sys2blacs_handle_.c:(.text+0x25): undefined reference to
> `ompi_mpi_comm_null'
> _sys2blacs_handle_.c:(.text+0x9f): undefined reference to
> `ompi_mpi_comm_null'
> _sys2blacs_handle_.c:(.text+0xc9): undefined reference to
> `ompi_mpi_comm_world'
> _sys2blacs_handle_.c:(.text+0x17d): undefined reference to
> `ompi_mpi_comm_null'
> _sys2blacs_handle_.c:(.text+0x1cb): undefined reference to
> `ompi_mpi_comm_world'
> /opt/intel/Compiler/11.1/059/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a(BI_MPI_F77_to_c_trans_comm.o):
> In function `BI_MPI_F77_to_c_trans_comm':
> _BI_MPI_F77_to_c_trans_comm.c:(.text+0x6): undefined reference to
> `MPI_Comm_f2c'
> make[2]: *** [pw.x] Error 1
> make[2]: Leaving directory `/vol-th/home/fyw/pwscf/espresso-5.0.2/PW/src'
> make[1]: *** [pw] Error 2
> make[1]: Leaving directory `/vol-th/home/fyw/pwscf/espresso-5.0.2/PW
>
>
>
>
> 2013/12/9 Axel Kohlmeyer <akohlmey at gmail.com>
>>
>> why so complicated? why not simply follow the installation
>> instructions in the User's Guide, set LIBDIRS accordingly to the
>> directory where you have MKL installed and let the configure script do
>> the rest for you.
>>
>> besides, the flags you provide are wrong. you should consult the MKL
>> documentation for a (detailed and precise) explanation of how to link
>> with MKL. if you insist on setting things yourself.
>>
>> axel.
>>
>> On Mon, Dec 9, 2013 at 9:58 AM, Yue-Wen Fang <yuewen.fang at gmail.com>
>> wrote:
>> > Dear QE users,
>> >
>> > In recent days, I'have compiled QE 5.0.2 for many times using different
>> > ways
>> > in several computing centers. Surprisingly, all gave me errors. The main
>> > problem is the MKL.
>> >
>> > The following is my steps.
>> >
>> > 1. I write a shell script named "fyw-configure" to proceed configure
>> >
>> > export CC=icc
>> > export F77=ifort
>> > export F90=ifort
>> > export MPIF90=mpif90
>> > export CFLAGS=-O2
>> > export FFLAGS=-O2
>> > export MKL_LIB="/vol-th/lib/mklem64t"
>> > ./configure BLACS_LIBS="-L$MKL_LIB -libmkl_blacs_lp64.a"
>> > LAPACK_LIBS="-L$MKL_LIB -libmkl_lapack95_ilp64.a"
>> > SCALAPACK_LIBS="-L$MKL_LIB -libmkl_scalapack_lp64.a"
>> > BLAS_LIBS="-L$MKL_LIB
>> > -libmkl_blas95_lp64.a -libmkl_core.a -libmkl_sequential.a"
>> >
>> > 2. conduct fyw-configure
>> >
>> > ./fyw-configure --enable-parallel
>> >
>> > The screen told me the following information.
>> >
>> > The following libraries have been found:
>> >   BLAS_LIBS=-L/vol-th/lib/mklem64t -libmkl_blas95_lp64.a -libmkl_core.a
>> > -libmkl_sequential.a
>> >   LAPACK_LIBS=-L/vol-th/lib/mklem64t -libmkl_lapack95_ilp64.a
>> >   SCALAPACK_LIBS=-L/vol-th/lib/mklem64t -libmkl_scalapack_lp64.a
>> >   FFT_LIBS=
>> > Please check if this is what you expect.
>> >
>> > I'am sure that these MKL files indeed exist in the directory of
>> > /vol-th/lib/mklem64t and they can be called by other computing softwares
>> > without errors.
>> >
>> > 3. make all
>> >
>> > make all error:
>> >            pwscf.o  libpw.a ../../Modules/libqemod.a ../../flib/ptools.a
>> > ../../flib/flib.a ../../clib/clib.a ../../iotk/src/libiotk.a
>> > -L/vol-th/lib/mklem64t -libmkl_scalapack_lp64.a -L/vol-th/lib/mklem64t
>> > -libmkl_lapack95_ilp64.a  -L/vol-th/lib/mklem64t -libmkl_blas95_lp64.a
>> > -libmkl_core.a -libmkl_sequential.a
>> > ld: cannot find -libmkl_scalapack_lp64.a
>> > make[2]: *** [pw.x] Error 1
>> > make[2]: Leaving directory
>> > `/vol-th/home/fyw/pwscf/espresso-5.0.2/PW/src'
>> > make[1]: *** [pw] Error 2
>> > make[1]: Leaving directory `/vol-th/home/fyw/pwscf/espresso-5.0.2/PW'
>> > make: *** [pw] Error 2
>> >
>> > It seems to be a pseudo link though this file indeed exist there.
>> >
>> > Maybe I hadn't compiled PWSCF for much time, some problems may be
>> > ignored by
>> > me during configure steps. I hope experienced experts here can help me
>> > to
>> > curb this problem.
>> >
>> > Thank you in advance!
>> >
>> > Regards！
>> > --
>> >
>> > ------------------------------------------------------------------------------------------------------------
>> > Yue-Wen FANG, PhD candidate
>> > Key Laboratory of Polar Materials and Devices, Ministry of Education
>> > East China Normal University
>> >
>> >
>> >
>> >
>> > _______________________________________________
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>> > Pw_forum at pwscf.org
>> > http://pwscf.org/mailman/listinfo/pw_forum
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
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>
>
>
>
> --
> ------------------------------------------------------------------------------------------------------------
> Yue-Wen FANG, PhD candidate
> Key Laboratory of Polar Materials and Devices, Ministry of Education
> East China Normal University
>
>
>
>
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-- 
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.