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

Ye Luo xw111luoye at gmail.com
Wed Aug 8 03:36:02 CEST 2018 

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/
>>>>>>>>>>>>> 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_librar
>>>>>>>>>>>>> ies_2018.3.222/linux/mpi/mic/lib:/opt/intel/compilers_and_li
>>>>>>>>>>>>> braries_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_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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>>>>>>>>>>>
>>>>>>>>>>
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