ok I'll try that and let you know On Tue, Aug 7, 2018 at 8:28 PM, Ye Luo <xw111lu...@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 <af...@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 <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_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 <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/in >>>>>>>>>>> tel/debugger_2018/iga/lib:/opt/intel/debugger_2018/libipt/ >>>>>>>>>>> intel64/lib:/opt/intel/compilers_and_libraries_2018.3.222/li >>>>>>>>>>> nux/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/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 >>> >> >> >> _______________________________________________ >> 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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