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 <xw111lu...@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 <af...@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 <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/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_ >>>>>>>>> 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/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@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 >>> >> >> >> _______________________________________________ >> 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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