I noticed that after I reconfigured and I looked at my make.inc file, my MPI_LIBS and LAPACK_LIPS paths that I specified beforehand were erased, will this affect the pw.x program from running parallely after it finishes compiling, I am asking now because it will take a while to finish compiling.
On Tue, Aug 7, 2018 at 8:41 PM, Aziz Fall <[email protected]> wrote: > ok I'll try that and let you know > > On Tue, Aug 7, 2018 at 8:28 PM, Ye Luo <[email protected]> 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 <[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_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 <[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_2018.3.22 >>>>>>>>>>>> 2/linux/tbb/lib/intel64/gcc4.7:/opt/intel/compilers_and_lib >>>>>>>>>>>> raries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/opt/intel/ >>>>>>>>>>>> debugger_2018/iga/lib:/opt/intel/debugger_2018/libipt/int >>>>>>>>>>>> el64/lib:/opt/intel/compilers_and_libraries_2018.3.222/linux >>>>>>>>>>>> /daal/lib/intel64_lin:/opt/intel/compilers_and_libraries_201 >>>>>>>>>>>> 8.3.222/linux/mpi/intel64/lib:/opt/intel/compilers_and_libra >>>>>>>>>>>> ries_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 >>>>>>>>>>>> [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 >>> >> >> >> _______________________________________________ >> users mailing list >> [email protected] >> https://lists.quantum-espresso.org/mailman/listinfo/users >> > >
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