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

Ye Luo xw111luoye at gmail.com
Wed Aug 8 03:37:11 CEST 2018 

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_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_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_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_librari
>>>>>>>>>>>>>> es_2018.3.222/linux/mpi/mic/lib:/opt/intel/compilers_and_lib
>>>>>>>>>>>>>> raries_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/compile
>>>>>>>>>>>>>> r/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/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/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
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>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
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