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

Ye Luo xw111luoye at gmail.com
Wed Aug 8 02:22:58 CEST 2018 

Did you build the code and run it on different machines? Ye

===================
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory

2018-08-07 19:18 GMT-05:00 Aziz Fall <afall at umich.edu>:

> 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/compilers_
>>>>>>>> and_libraries_2018.3.222/linux/ipp/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/mkl/lib/intel64_lin:/opt/intel/compilers_and_librar
>>>>>>>> ies_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_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_libraries_
>>>>>>>> 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/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_libraries_2018.3.222/linux/daal/../tbb/
>>>>>>>> lib/intel64_lin/gcc4.4
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> any help will be highly appreciated. Thanks in advanced
>>>>>>>>
>>>>>>>> Sincerely Aziz Fall
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>> users at lists.quantum-espresso.org
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>>>>>>>>
>>>>>>>
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>>>>>>
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