yeah unfortunately I get the same error again, sorry if this is taking up your time
On Tue, Aug 7, 2018 at 9:40 PM, Aziz Fall <[email protected]> wrote: > ok thanks I will try it and let you know, hopefully I dont run into any > issues this time > > On Tue, Aug 7, 2018 at 9:37 PM, Ye Luo <[email protected]> wrote: > >> There was a typo mpiifort instead of mpif90 in your case. >> ./configure MPIF90=mpiifort CC=icc --with-scalapack=intel >> >> >> =================== >> Ye Luo, Ph.D. >> Leadership Computing Facility >> Argonne National Laboratory >> >> 2018-08-07 20:36 GMT-05:00 Ye Luo <[email protected]>: >> >>> Why don't you trust the configure? The configure can cover most >>> scenarios. >>> Most users should rely on the configure instead of modifying the >>> make.inc by hand. >>> Linux+OpenMP/IntelMPI+Intel compiler+MKL is very common and the >>> configure can handle it very well. >>> I can handle BG/Q or Cray machines without touch make.inc. >>> In your case, if you sourced the intel parallel studio environment >>> script, then only need >>> ./configure MPIF90=mpif90 CC=icc --with-scalapack=intel >>> MPI is enabled by default, if you want openmp just add --enable-openmp. >>> >>> To accelerate compilation, you can use -j with make. The parallel >>> compilation is well maintained at least for pw. >>> I never have issue with make -j 16 pw. For other target, you can try >>> parallel compilation but may have some dependency not well maintained. >>> >>> Ye >>> >>> =================== >>> Ye Luo, Ph.D. >>> Leadership Computing Facility >>> Argonne National Laboratory >>> >>> 2018-08-07 19:55 GMT-05:00 Aziz Fall <[email protected]>: >>> >>>> 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_libraries_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/com >>>>>>>>>>>>>>>> pilers_and_libraries_2018.3.22 >>>>>>>>>>>>>>>> 2/linux/mpi/intel64/lib:/opt/i >>>>>>>>>>>>>>>> ntel/compilers_and_libraries_2 >>>>>>>>>>>>>>>> 018.3.222/linux/mpi/mic/lib:/o >>>>>>>>>>>>>>>> pt/intel/compilers_and_librari >>>>>>>>>>>>>>>> es_2018.3.222/linux/compiler/l >>>>>>>>>>>>>>>> ib/intel64_lin:/opt/intel/comp >>>>>>>>>>>>>>>> ilers_and_libraries_2018.3.222 >>>>>>>>>>>>>>>> /linux/mkl/lib/intel64_lin:/op >>>>>>>>>>>>>>>> t/intel/compilers_and_librarie >>>>>>>>>>>>>>>> s_2018.3.222/linux/compiler/li >>>>>>>>>>>>>>>> b/intel64:/opt/intel/compilers >>>>>>>>>>>>>>>> _and_libraries_2018.3.222/linu >>>>>>>>>>>>>>>> x/compiler/lib/intel64_lin:/op >>>>>>>>>>>>>>>> t/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_2018.3.2 >>>>>>>>>>>>>>>> 22/linux/compiler/lib/intel64_ >>>>>>>>>>>>>>>> lin:/opt/intel/compilers_and_l >>>>>>>>>>>>>>>> ibraries_2018.3.222/linux/mkl/ >>>>>>>>>>>>>>>> lib/intel64_lin:/opt/intel/com >>>>>>>>>>>>>>>> pilers_and_libraries_2018.3.22 >>>>>>>>>>>>>>>> 2/linux/tbb/lib/intel64/gcc4.7 >>>>>>>>>>>>>>>> :/opt/intel/compilers_and_libr >>>>>>>>>>>>>>>> aries_2018.3.222/linux/tbb/lib >>>>>>>>>>>>>>>> /intel64/gcc4.7:/opt/intel/deb >>>>>>>>>>>>>>>> ugger_2018/iga/lib:/opt/intel/ >>>>>>>>>>>>>>>> debugger_2018/libipt/intel64/l >>>>>>>>>>>>>>>> ib:/opt/intel/compilers_and_li >>>>>>>>>>>>>>>> braries_2018.3.222/linux/daal/ >>>>>>>>>>>>>>>> lib/intel64_lin:/opt/intel/com >>>>>>>>>>>>>>>> pilers_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_librar >>>>>>>>>>>>>>>> ies_2018.3.222/linux/compiler/ >>>>>>>>>>>>>>>> lib/intel64_lin:/opt/intel/com >>>>>>>>>>>>>>>> pilers_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/compile >>>>>>>>>>>>>>>> rs_and_libraries_2018.3.222/li >>>>>>>>>>>>>>>> nux/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_librar >>>>>>>>>>>>>>>> ies_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 >>>>>>>>>>>>>>>> [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 >>>>>> >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> 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
