[QE-users] Problem when running the pw.x executable

Aziz Fall afall at umich.edu
Wed Aug 8 02:18:56 CEST 2018 

ok so regardless of whether I run pw.x with mpirun or not I get the same
error saying pw.x: symbol lookup error:
/usr/lib/libblacsCinit-openmpi.so.1: undefined symbol: ompi_mpi_comm_world

when I do which mpirun I
get /opt/intel/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpirun
so its very weird

On Tue, Aug 7, 2018 at 8:14 PM, Ye Luo <xw111luoye at gmail.com> wrote:

> Everything seems good. I'm wondering if it is the problem of your mpirun.
> Could you run pw.x directly without mpirun?
> If you type "which mpirun" on the machine your are running, is it from the
> intel parallel studio folder since you said you are using Intel MPI.
> Ye
>
> ===================
> Ye Luo, Ph.D.
> Leadership Computing Facility
> Argonne National Laboratory
>
> 2018-08-07 19:07 GMT-05:00 Aziz Fall <afall at umich.edu>:
>
>> yeah so when I type ldd pw.x I get the following
>>
>>         linux-vdso.so.1 =>  (0x00007ffffcb9e000)
>>         libmkl_scalapack_lp64.so => /opt/intel/compilers_and_libra
>> ries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_scalapack_lp64.so
>> (0x00007ffed7300000)
>>         libmkl_blacs_intelmpi_lp64.so => /opt/intel/compilers_and_libra
>> ries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_lp64.so
>> (0x00007ffed70b0000)
>>         libmkl_gf_lp64.so => /opt/intel/compilers_and_libra
>> ries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so
>> (0x00007ffed65a0000)
>>         libmkl_sequential.so => /opt/intel/compilers_and_libra
>> ries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_sequential.so
>> (0x00007ffed5130000)
>>         libmkl_core.so => /opt/intel/compilers_and_libra
>> ries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_core.so
>> (0x00007ffed10fe000)
>>         libmpifort.so.12 => /opt/intel/compilers_and_libra
>> ries_2018.3.222/linux/mpi/intel64/lib/libmpifort.so.12
>> (0x00007ffed0d40000)
>>         libmpi.so.12 => /opt/intel/compilers_and_libra
>> ries_2018.3.222/linux/mpi/intel64/lib/libmpi.so.12 (0x00007ffed00b0000)
>>         libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>> (0x00007ffecfe70000)
>>         libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3
>> (0x00007ffecfb40000)
>>         libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007ffecf830000)
>>         libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
>> (0x00007ffecf610000)
>>         libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ffecf240000)
>>         libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2
>> (0x00007ffecf020000)
>>         librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1
>> (0x00007ffecee10000)
>>         /lib64/ld-linux-x86-64.so.2 (0x00007ffed7e00000)
>>         libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0
>> (0x00007ffecebc0000)
>>
>> I am not sure I know what to make of this though, do you have an idea by
>> any chance?
>>
>> Sincerely Aziz Fall
>>
>> On Tue, Aug 7, 2018 at 7:48 PM, Ye Luo <xw111luoye at gmail.com> wrote:
>>
>>> $ldd pw.x.
>>> What prints out?
>>> It seems that /usr/lib/libblacsCinit-openmpi.so.1 get into your binary
>>> at a certain point. But it should not.
>>> This is the blacs from your OS used by scalapack but it is supposed to
>>> be the Intel one.
>>> Ye
>>>
>>> ===================
>>> Ye Luo, Ph.D.
>>> Leadership Computing Facility
>>> Argonne National Laboratory
>>>
>>> 2018-08-07 18:21 GMT-05:00 Aziz Fall <afall at umich.edu>:
>>>
>>>> so I changed the options in configure like you suggested with the
>>>> --with-scalapack=intel but I still get the same error after re-compiling.
>>>> Do you have any further suggestions?
>>>>
>>>> On Tue, Aug 7, 2018 at 6:22 PM, Aziz Fall <afall at umich.edu> wrote:
>>>>
>>>>> No, I did not add that configuration as part of configure but I did
>>>>> change the make.inc
>>>>>
>>>>> to have SCALAPACK_LIBS = -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64
>>>>> -lmkl_tbb_thread -lmkl_core -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
>>>>> -lpthread -ltbb -lstdc++ -lm -ldl  and
>>>>> MPI_LIBS       =  -L/opt/intel/impi/2018.3.222/lib64/ -lmpi, is that
>>>>> not enough or should I configure it again with the exact options
>>>>> --with-scalapack=intel?
>>>>>
>>>>> Thank You,
>>>>> Sincerely Aziz Fall
>>>>>
>>>>> On Tue, Aug 7, 2018 at 6:04 PM, Ye Luo <xw111luoye at gmail.com> wrote:
>>>>>
>>>>>> That seems for openmpi.
>>>>>> Did you put --with-scalapack=intel when you run configure?
>>>>>> Ye
>>>>>>
>>>>>> ===================
>>>>>> Ye Luo, Ph.D.
>>>>>> Leadership Computing Facility
>>>>>> Argonne National Laboratory
>>>>>>
>>>>>> 2018-08-07 16:42 GMT-05:00 Aziz Fall <afall at umich.edu>:
>>>>>>
>>>>>>> Dear Quantum espresso team,
>>>>>>>
>>>>>>> So recently I have been trying to run the executable pw.x on the bin
>>>>>>> directory. I pass in my input and output file appropriately, and I am using
>>>>>>> intel's Parallel studio compiler, with intel MPI. but when I run the
>>>>>>> program I get the following error
>>>>>>>
>>>>>>> pw.x: symbol lookup error: /usr/lib/libblacsCinit-openmpi.so.1:
>>>>>>> undefined symbol: ompi_mpi_comm_world
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> my LD_LIBRARY_PATH is the following
>>>>>>>
>>>>>>> LD_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2018.3.22
>>>>>>> 2/linux/mpi/intel64/lib:/opt/intel/compilers_and_libraries_2
>>>>>>> 018.3.222/linux/mpi/mic/lib:/opt/intel/compilers_and_librari
>>>>>>> es_2018.3.222/linux/compiler/lib/intel64_lin:/opt/intel/comp
>>>>>>> ilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin:/op
>>>>>>> t/intel/compilers_and_libraries_2018.3.222/linux/compiler/li
>>>>>>> b/intel64:/opt/intel/compilers_and_libraries_2018.3.222/linu
>>>>>>> x/compiler/lib/intel64_lin:/opt/intel/compilers_and_librarie
>>>>>>> s_2018.3.222/linux/mpi/intel64/lib:/opt/intel/compilers_and_
>>>>>>> libraries_2018.3.222/linux/mpi/mic/lib:/opt/intel/compile
>>>>>>> rs_and_libraries_2018.3.222/linux/ipp/lib/intel64:/opt/
>>>>>>> intel/compilers_and_libraries_2018.3.222/linux/compiler/lib/
>>>>>>> intel64_lin:/opt/intel/compilers_and_libraries_2018.
>>>>>>> 3.222/linux/mkl/lib/intel64_lin:/opt/intel/compilers_and_
>>>>>>> libraries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/opt/
>>>>>>> intel/compilers_and_libraries_2018.3.222/linux/tbb/lib/
>>>>>>> intel64/gcc4.7:/opt/intel/debugger_2018/iga/lib:/opt/
>>>>>>> intel/debugger_2018/libipt/intel64/lib:/opt/intel/compile
>>>>>>> rs_and_libraries_2018.3.222/linux/daal/lib/intel64_lin:/
>>>>>>> opt/intel/compilers_and_libraries_2018.3.222/linux/mpi/
>>>>>>> intel64/lib:/opt/intel/compilers_and_libraries_2018.3.222/
>>>>>>> linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2018.
>>>>>>> 3.222/linux/compiler/lib/intel64_lin:/opt/intel/compilers_
>>>>>>> and_libraries_2018.3.222/linux/mkl/lib/intel64_lin:/
>>>>>>> opt/intel/compilers_and_libraries_2018.3.222/linux/compiler/
>>>>>>> lib/intel64:/opt/intel/compilers_and_libraries_2018.
>>>>>>> 3.222/linux/compiler/lib/intel64_lin:/opt/intel/compilers_
>>>>>>> and_libraries_2018.3.222/linux/mpi/intel64/lib:/opt/
>>>>>>> intel/compilers_and_libraries_2018.3.222/linux/mpi/mic/lib:/
>>>>>>> opt/intel/compilers_and_libraries_2018.3.222/linux/
>>>>>>> ipp/lib/intel64:/opt/intel/compilers_and_libraries_2018.
>>>>>>> 3.222/linux/compiler/lib/intel64_lin:/opt/intel/
>>>>>>> compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_
>>>>>>> lin:/opt/intel/compilers_and_libraries_2018.3.222/linux/
>>>>>>> tbb/lib/intel64/gcc4.7:/opt/intel/compilers_and_libraries_
>>>>>>> 2018.3.222/linux/tbb/lib/intel64/gcc4.7:/opt/intel/
>>>>>>> debugger_2018/iga/lib:/opt/intel/debugger_2018/libipt/
>>>>>>> intel64/lib:/opt/intel/compilers_and_libraries_2018.3.222/
>>>>>>> linux/daal/lib/intel64_lin:/opt/intel/compilers_and_librar
>>>>>>> ies_2018.3.222/linux/mpi/intel64/lib:/opt/intel/compile
>>>>>>> rs_and_libraries_2018.3.222/linux/mpi/mic/lib:/opt/intel/
>>>>>>> compilers_and_libraries_2018.3.222/linux/compiler/lib/intel
>>>>>>> 64_lin:/opt/intel/compilers_and_libraries_2018.3.222/
>>>>>>> linux/mkl/lib/intel64_lin:/opt/intel/compilers_and_librar
>>>>>>> ies_2018.3.222/linux/compiler/lib/intel64:/opt/intel/
>>>>>>> compilers_and_libraries_2018.3.222/linux/compiler/lib/intel
>>>>>>> 64_lin:/opt/intel/compilers_and_libraries_2018.3.222/
>>>>>>> linux/mpi/intel64/lib:/opt/intel/compilers_and_libraries_
>>>>>>> 2018.3.222/linux/mpi/mic/lib:/opt/intel/compilers_and_
>>>>>>> libraries_2018.3.222/linux/ipp/lib/intel64:/opt/intel/
>>>>>>> compilers_and_libraries_2018.3.222/linux/compiler/lib/
>>>>>>> intel64_lin:/opt/intel/compilers_and_libraries_2018.
>>>>>>> 3.222/linux/mkl/lib/intel64_lin:/opt/intel/compilers_and_
>>>>>>> libraries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/opt/
>>>>>>> intel/compilers_and_libraries_2018.3.222/linux/tbb/lib/
>>>>>>> intel64/gcc4.7:/opt/intel/debugger_2018/iga/lib:/opt/
>>>>>>> intel/debugger_2018/libipt/intel64/lib:/opt/intel/compile
>>>>>>> rs_and_libraries_2018.3.222/linux/daal/lib/intel64_lin:/
>>>>>>> opt/intel/compilers_and_libraries_2018.3.222/linux/daal/../
>>>>>>> tbb/lib/intel64_lin/gcc4.4
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> any help will be highly appreciated. Thanks in advanced
>>>>>>>
>>>>>>> Sincerely Aziz Fall
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> users mailing list
>>>>>>> users at lists.quantum-espresso.org
>>>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>>>>>
>>>>>>
>>>>>>
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