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

Aziz Fall afall at umich.edu
Wed Aug 8 03:40:49 CEST 2018 

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_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_libraries
>>>>>>>>>>>>>>> _2018.3.222/linux/mpi/mic/lib:/opt/intel/compilers_and_libra
>>>>>>>>>>>>>>> ries_2018.3.222/linux/compiler/lib/intel64_lin:/opt/intel/co
>>>>>>>>>>>>>>> mpilers_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/intel
>>>>>>>>>>>>>>> 64:/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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>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
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