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_libraries_2018.3.222/linux/mpi/intel64/bin/mpirun so its very weird On Tue, Aug 7, 2018 at 8:14 PM, Ye Luo <xw111lu...@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 <af...@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_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 <xw111lu...@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 <af...@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 <af...@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 <xw111lu...@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 <af...@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/compile >>>>>>> rs_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/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@lists.quantum-espresso.org >>>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> users mailing list >>>>>> users@lists.quantum-espresso.org >>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>>>> >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> users mailing list >>>> users@lists.quantum-espresso.org >>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>> >>> >>> >>> _______________________________________________ >>> users mailing list >>> users@lists.quantum-espresso.org >>> https://lists.quantum-espresso.org/mailman/listinfo/users >>> >> >> >> _______________________________________________ >> users mailing list >> users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users >> > > > _______________________________________________ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users >
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