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_ > libraries_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/ >>>>>>>> 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/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/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 >>>>>>>> [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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