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_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_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_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_librari >>>>>>>>>>>>>> es_2018.3.222/linux/mpi/mic/lib:/opt/intel/compilers_and_lib >>>>>>>>>>>>>> raries_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/compile >>>>>>>>>>>>>> r/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 >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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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