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

Ye Luo xw111luoye at gmail.com
Wed Aug 8 02:28:30 CEST 2018 

Your mpi wrapper mpif90 is using gfortran underneath from the ldd pw.x
output.
Could you add MPIF90=mpiifort in your configure line?
But I'm not sure if this is the real problem.
Ye


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

2018-08-07 19:24 GMT-05:00 Aziz Fall <afall at umich.edu>:

> no I am using the same machine for the build and run, its a workstation
> with 32 cores
>
> On Tue, Aug 7, 2018 at 8:22 PM, Ye Luo <xw111luoye at gmail.com> wrote:
>
>> 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_l
>>> ibraries_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/co
>>>>>>>>>> mpilers_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/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/daal/../tbb/lib/intel64_lin/gcc4.4
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> any help will be highly appreciated. Thanks in advanced
>>>>>>>>>>
>>>>>>>>>> Sincerely Aziz Fall
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> users mailing list
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>>>>>>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>>>>>>>>
>>>>>>>>>
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