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

[Aziz Fall]

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_
>>>>>>>>> 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
>>>>>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>>>>>>>
>>>>>>>>
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