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

Wed Aug 8 02:41:25 CEST 2018

ok I'll try that and let you know

On Tue, Aug 7, 2018 at 8:28 PM, Ye Luo <xw111luoye at gmail.com> wrote:

> 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_libraries_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/in
>>>>>>>>>>> tel/debugger_2018/iga/lib:/opt/intel/debugger_2018/libipt/
>>>>>>>>>>> intel64/lib:/opt/intel/compilers_and_libraries_2018.3.222/li
>>>>>>>>>>> nux/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/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
>>>>>>>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>>>>>>>>>
>>>>>>>>>>
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