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 <[email protected]>: > 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 <[email protected]> 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 <[email protected]>: >> >>> 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 <[email protected]> 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 <[email protected]>: >>>> >>>>> 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_libra >>>>> ries_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 <[email protected]> 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 <[email protected]>: >>>>>> >>>>>>> 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 <[email protected]> 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 <[email protected]> >>>>>>>> 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 <[email protected]>: >>>>>>>>> >>>>>>>>>> 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. >>>>>>>>>> 3.222/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/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_librar >>>>>>>>>> ies_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 >>>>>>>>>> [email protected] >>>>>>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> users mailing list >>>>>>>>> [email protected] >>>>>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> users mailing list >>>>>>> [email protected] >>>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> users mailing list >>>>>> [email protected] >>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> users mailing list >>>>> [email protected] >>>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>>> >>>> >>>> >>>> _______________________________________________ >>>> users mailing list >>>> [email protected] >>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>> >>> >>> >>> _______________________________________________ >>> users mailing list >>> [email protected] >>> https://lists.quantum-espresso.org/mailman/listinfo/users >>> >> >> >> _______________________________________________ >> users mailing list >> [email protected] >> https://lists.quantum-espresso.org/mailman/listinfo/users >> > > > _______________________________________________ > users mailing list > [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users >
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