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

Aziz Fall afall at umich.edu
Wed Aug 8 03:50:04 CEST 2018 

yeah unfortunately I get the same error again, sorry if this is taking up
your time

On Tue, Aug 7, 2018 at 9:40 PM, Aziz Fall <afall at umich.edu> wrote:

> ok thanks I will try it and let you know, hopefully I dont run into any
> issues this time
>
> On Tue, Aug 7, 2018 at 9:37 PM, Ye Luo <xw111luoye at gmail.com> wrote:
>
>> There was a typo mpiifort instead of mpif90 in your case.
>> ./configure MPIF90=mpiifort CC=icc --with-scalapack=intel
>>
>>
>> ===================
>> Ye Luo, Ph.D.
>> Leadership Computing Facility
>> Argonne National Laboratory
>>
>> 2018-08-07 20:36 GMT-05:00 Ye Luo <xw111luoye at gmail.com>:
>>
>>> Why don't you trust the configure? The configure can cover most
>>> scenarios.
>>> Most users should rely on the configure instead of modifying the
>>> make.inc by hand.
>>> Linux+OpenMP/IntelMPI+Intel compiler+MKL is very common and the
>>> configure can handle it very well.
>>> I can handle BG/Q or Cray machines without touch make.inc.
>>> In your case, if you sourced the intel parallel studio environment
>>> script, then only need
>>> ./configure MPIF90=mpif90 CC=icc --with-scalapack=intel
>>> MPI is enabled by default, if you want openmp just add --enable-openmp.
>>>
>>> To accelerate compilation, you can use -j with make. The parallel
>>> compilation is well maintained at least for pw.
>>> I never have issue with make -j 16 pw. For other target, you can try
>>> parallel compilation but may have some dependency not well maintained.
>>>
>>> Ye
>>>
>>> ===================
>>> Ye Luo, Ph.D.
>>> Leadership Computing Facility
>>> Argonne National Laboratory
>>>
>>> 2018-08-07 19:55 GMT-05:00 Aziz Fall <afall at umich.edu>:
>>>
>>>> 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_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_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/com
>>>>>>>>>>>>>>>> pilers_and_libraries_2018.3.22
>>>>>>>>>>>>>>>> 2/linux/mpi/intel64/lib:/opt/i
>>>>>>>>>>>>>>>> ntel/compilers_and_libraries_2
>>>>>>>>>>>>>>>> 018.3.222/linux/mpi/mic/lib:/o
>>>>>>>>>>>>>>>> pt/intel/compilers_and_librari
>>>>>>>>>>>>>>>> es_2018.3.222/linux/compiler/l
>>>>>>>>>>>>>>>> ib/intel64_lin:/opt/intel/comp
>>>>>>>>>>>>>>>> ilers_and_libraries_2018.3.222
>>>>>>>>>>>>>>>> /linux/mkl/lib/intel64_lin:/op
>>>>>>>>>>>>>>>> t/intel/compilers_and_librarie
>>>>>>>>>>>>>>>> s_2018.3.222/linux/compiler/li
>>>>>>>>>>>>>>>> b/intel64:/opt/intel/compilers
>>>>>>>>>>>>>>>> _and_libraries_2018.3.222/linu
>>>>>>>>>>>>>>>> x/compiler/lib/intel64_lin:/op
>>>>>>>>>>>>>>>> t/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_2018.3.2
>>>>>>>>>>>>>>>> 22/linux/compiler/lib/intel64_
>>>>>>>>>>>>>>>> lin:/opt/intel/compilers_and_l
>>>>>>>>>>>>>>>> ibraries_2018.3.222/linux/mkl/
>>>>>>>>>>>>>>>> lib/intel64_lin:/opt/intel/com
>>>>>>>>>>>>>>>> pilers_and_libraries_2018.3.22
>>>>>>>>>>>>>>>> 2/linux/tbb/lib/intel64/gcc4.7
>>>>>>>>>>>>>>>> :/opt/intel/compilers_and_libr
>>>>>>>>>>>>>>>> aries_2018.3.222/linux/tbb/lib
>>>>>>>>>>>>>>>> /intel64/gcc4.7:/opt/intel/deb
>>>>>>>>>>>>>>>> ugger_2018/iga/lib:/opt/intel/
>>>>>>>>>>>>>>>> debugger_2018/libipt/intel64/l
>>>>>>>>>>>>>>>> ib:/opt/intel/compilers_and_li
>>>>>>>>>>>>>>>> braries_2018.3.222/linux/daal/
>>>>>>>>>>>>>>>> lib/intel64_lin:/opt/intel/com
>>>>>>>>>>>>>>>> pilers_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_librar
>>>>>>>>>>>>>>>> ies_2018.3.222/linux/compiler/
>>>>>>>>>>>>>>>> lib/intel64_lin:/opt/intel/com
>>>>>>>>>>>>>>>> pilers_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/compile
>>>>>>>>>>>>>>>> rs_and_libraries_2018.3.222/li
>>>>>>>>>>>>>>>> nux/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_librar
>>>>>>>>>>>>>>>> ies_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/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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