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

Aziz Fall afall at umich.edu
Wed Aug 8 02:55:25 CEST 2018 

I noticed that after I reconfigured and I looked at my make.inc file, my
MPI_LIBS and LAPACK_LIPS paths that I specified beforehand were erased,
will this affect the pw.x program from running parallely after it finishes
compiling, I am asking now because it will take a while to finish compiling.

On Tue, Aug 7, 2018 at 8:41 PM, Aziz Fall <afall at umich.edu> wrote:

> 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_2018.3.22
>>>>>>>>>>>> 2/linux/tbb/lib/intel64/gcc4.7:/opt/intel/compilers_and_lib
>>>>>>>>>>>> raries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/opt/intel/
>>>>>>>>>>>> debugger_2018/iga/lib:/opt/intel/debugger_2018/libipt/int
>>>>>>>>>>>> el64/lib:/opt/intel/compilers_and_libraries_2018.3.222/linux
>>>>>>>>>>>> /daal/lib/intel64_lin:/opt/intel/compilers_and_libraries_201
>>>>>>>>>>>> 8.3.222/linux/mpi/intel64/lib:/opt/intel/compilers_and_libra
>>>>>>>>>>>> ries_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
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
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