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

Ye Luo xw111luoye at gmail.com
Wed Aug 8 02:14:35 CEST 2018 

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_
> libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_scalapack_lp64.so
> (0x00007ffed7300000)
>         libmkl_blacs_intelmpi_lp64.so => /opt/intel/compilers_and_
> libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_lp64.so
> (0x00007ffed70b0000)
>         libmkl_gf_lp64.so => /opt/intel/compilers_and_
> libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so
> (0x00007ffed65a0000)
>         libmkl_sequential.so => /opt/intel/compilers_and_
> libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_sequential.so
> (0x00007ffed5130000)
>         libmkl_core.so => /opt/intel/compilers_and_
> libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_core.so
> (0x00007ffed10fe000)
>         libmpifort.so.12 => /opt/intel/compilers_and_
> libraries_2018.3.222/linux/mpi/intel64/lib/libmpifort.so.12
> (0x00007ffed0d40000)
>         libmpi.so.12 => /opt/intel/compilers_and_
> libraries_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_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/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/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/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/
>>>>>> 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
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>>>>>>
>>>>>
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