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_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_libraries >>>>>>>>>>>>>>> _2018.3.222/linux/mpi/mic/lib:/opt/intel/compilers_and_libra >>>>>>>>>>>>>>> ries_2018.3.222/linux/compiler/lib/intel64_lin:/opt/intel/co >>>>>>>>>>>>>>> mpilers_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/intel >>>>>>>>>>>>>>> 64:/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 >>>>> >>>> >>>> >>> >>> _______________________________________________ >>> 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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