[petsc-users] Undefined reference in PETSc 3.13+ with old MPI version

Sun Apr 11 20:20:08 CDT 2021

Danyang,
  I pushed another commit to the same branch jczhang/fix-mpi3-win to guard
uses of MPI_Iallreduce.

  Satish, it seems we need an MPI-2.2 CI to say petsc does not need MPI-3.0?

--Junchao Zhang

On Sun, Apr 11, 2021 at 1:45 PM Danyang Su <danyang.su at gmail.com> wrote:

> Hi Junchao,
>
>
>
> I also ported the changes you have made to PETSc 3.13.6 and configured
> with Intel 14.0 and OpenMPI 1.6.5, it works too.
>
> There is a similar problem in PETSc 3.14+ version as MPI_Iallreduce is
> only available in OpenMPI V1.7+. I would not say this is a bug, it just
> requires a newer MPI version.
>
>
>
> /home/danyangs/soft/petsc/petsc-3.14.6/intel-14.0.2-openmpi-1.6.5/lib/libpetsc.so:
> undefined reference to `MPI_Iallreduce'
>
>
>
> Thanks again for all your help,
>
>
>
> Danyang
>
> *From: *Junchao Zhang <junchao.zhang at gmail.com>
> *Date: *Sunday, April 11, 2021 at 7:54 AM
> *To: *Danyang Su <danyang.su at gmail.com>
> *Cc: *Barry Smith <bsmith at petsc.dev>, "petsc-users at mcs.anl.gov" <
> petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Undefined reference in PETSc 3.13+ with old
> MPI version
>
>
>
> Thanks, Glad to know you have a workaround.
>
> --Junchao Zhang
>
>
>
>
>
> On Sat, Apr 10, 2021 at 10:06 PM Danyang Su <danyang.su at gmail.com> wrote:
>
> Hi Junchao,
>
>
>
> I cannot configure your branch with same options due to the error in
> sowing. I had similar error before on other clusters with very old openmpi
> version. Problem was solved when openmpi was updated to a newer one.
>
>
>
> At this moment, I configured a PETSc version with Openmpi 2.1.6 version
> and it seems working properly.
>
>
>
> Thanks and have a good rest of the weekend,
>
>
>
> Danyang
>
>
>
> *From: *Danyang Su <danyang.su at gmail.com>
> *Date: *Saturday, April 10, 2021 at 4:08 PM
> *To: *Junchao Zhang <junchao.zhang at gmail.com>
> *Cc: *Barry Smith <bsmith at petsc.dev>, "petsc-users at mcs.anl.gov" <
> petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Undefined reference in PETSc 3.13+ with old
> MPI version
>
>
>
> Hi Junchao,
>
>
>
> The configuration is successful. The error comes from the last step when I
> run
>
>
>
> make PETSC_DIR=/home/danyangs/soft/petsc/petsc-3.13.6
> PETSC_ARCH=linux-intel-openmpi check
>
>
>
> ********************Error detected during compile or
> link!********************
>
> *See http://www.mcs.anl.gov/petsc/documentation/faq.html
> <http://www.mcs.anl.gov/petsc/documentation/faq.html>*
>
> */home/danyangs/soft/petsc/petsc-3.13.6/src/snes/tutorials ex5f*
>
> ***********************************************************
>
> mpif90 -fPIC -O3 -march=native -mtune=nativels
> -I/home/danyangs/soft/petsc/petsc-3.13.6/include
> -I/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/include
> ex5f.F90
> -Wl,-rpath,/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib
> -L/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib
> -Wl,-rpath,/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib
> -L/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib
> -Wl,-rpath,/global/software/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64
> -L/global/software/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64
> -Wl,-rpath,/global/software/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64
> -L/global/software/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64
> -Wl,-rpath,/global/software/openmpi-1.6.5/intel/lib64
> -L/global/software/openmpi-1.6.5/intel/lib64
> -Wl,-rpath,/global/software/intel/composerxe/mkl/lib/intel64
> -L/global/software/intel/composerxe/mkl/lib/intel64
> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.4.7
> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7
> -Wl,-rpath,/global/software/intel/composerxe/lib/intel64 -lpetsc -lHYPRE
> -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack
> -lsuperlu -lflapack -lfblas -lX11 -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl
> -lhdf5 -lparmetis -lmetis -lstdc++ -ldl -lmpi_f90 -lmpi_f77 -lmpi -lm
> -lnuma -lrt -lnsl -lutil -limf -lifport -lifcore -lsvml -lipgo -lintlc
> -lpthread -lgcc_s -lirc_s -lstdc++ -ldl -o ex5f
>
> ifort: command line warning #10159: invalid argument for option '-m'
>
> /home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib/libpetsc.so:
> undefined reference to `MPI_Win_allocate'
>
> /home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib/libpetsc.so:
> undefined reference to `MPI_Win_attach'
>
> /home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib/libpetsc.so:
> undefined reference to `MPI_Win_create_dynamic'
>
> gmake[4]: *** [ex5f] Error 1
>
>
>
> Thanks,
>
>
>
> Danyang
>
>
>
> *From: *Junchao Zhang <junchao.zhang at gmail.com>
> *Date: *Saturday, April 10, 2021 at 3:57 PM
> *To: *Danyang Su <danyang.su at gmail.com>
> *Cc: *Barry Smith <bsmith at petsc.dev>, "petsc-users at mcs.anl.gov" <
> petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Undefined reference in PETSc 3.13+ with old
> MPI version
>
>
>
> You sent a wrong one. This configure.log was from a successful
> configuration. Note FOPTFLAGS="-O3 -march=native -mtune=nativels" looks
> suspicious.
>
>
>
> --Junchao Zhang
>
>
>
>
>
> On Sat, Apr 10, 2021 at 5:32 PM Danyang Su <danyang.su at gmail.com> wrote:
>
>
>
> Hi Junchao,
>
>
>
> Thanks for looking into this problem. The configuration log is attached.
>
>
>
> All the best,
>
>
>
> Danyang
>
> *From: *Junchao Zhang <junchao.zhang at gmail.com>
> *Date: *Saturday, April 10, 2021 at 2:36 PM
> *To: *Danyang Su <danyang.su at gmail.com>
> *Cc: *Barry Smith <bsmith at petsc.dev>, "petsc-users at mcs.anl.gov" <
> petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Undefined reference in PETSc 3.13+ with old
> MPI version
>
>
>
> Hi, Danyang,
>
>
>
> Send the configure.log.  Also, PETSc does not need MPI_Win_allocate etc to
> work. I will have a look.
>
>
> --Junchao Zhang
>
>
>
>
>
> On Sat, Apr 10, 2021 at 2:47 PM Danyang Su <danyang.su at gmail.com> wrote:
>
> Hi Barry,
>
>
>
> I tried this option before but get ‘Error running configure on OpenMPI’
>
>
>
>
> *******************************************************************************
>
>          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for
> details):
>
>
> -------------------------------------------------------------------------------
>
> Error running configure on OPENMPI
>
>
> *******************************************************************************
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/configure.py", line
> 456, in petsc_configure
>
>     framework.configure(out = sys.stdout)
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/framework.py",
> line 1253, in configure
>
>     self.processChildren()
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/framework.py",
> line 1242, in processChildren
>
>     self.serialEvaluation(self.childGraph)
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/framework.py",
> line 1217, in serialEvaluation
>
>     child.configure()
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py",
> line 1144, in configure
>
>     self.executeTest(self.configureLibrary)
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/base.py",
> line 140, in executeTest
>
>     ret = test(*args,**kargs)
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py",
> line 902, in configureLibrary
>
>     for location, directory, lib, incl in self.generateGuesses():
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py",
> line 476, in generateGuesses
>
>     d = self.checkDownload()
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/packages/OpenMPI.py",
> line 56, in checkDownload
>
>     return self.getInstallDir()
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py",
> line 365, in getInstallDir
>
>     installDir = self.Install()
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/packages/OpenMPI.py",
> line 63, in Install
>
>     installDir = config.package.GNUPackage.Install(self)
>
>   File
> "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py",
> line 1667, in Install
>
>     raise RuntimeError('Error running configure on ' + self.PACKAGE)
>
>
> ================================================================================
>
> Finishing configure run at Sat, 10 Apr 2021 11:57:20 -0700
>
>
> ================================================================================
>
>
>
> Thanks,
>
>
>
> Danyang
>
>
>
> *From: *Barry Smith <bsmith at petsc.dev>
> *Date: *Saturday, April 10, 2021 at 10:31 AM
> *To: *Danyang Su <danyang.su at gmail.com>
> *Cc: *"petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Undefined reference in PETSc 3.13+ with old
> MPI version
>
>
>
>
>
>   Depending on the network you can remove the ./configure
> options --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90  and use instead
> --with-cc=icc --with-cxx=icpc and--with-fc=ifort --download-openmpi
>
>
>
>   Barry
>
>
>
>
>
> On Apr 10, 2021, at 12:18 PM, Danyang Su <danyang.su at gmail.com> wrote:
>
>
>
> Dear PETSc developers and users,
>
>
>
> I am trying to install the latest PETSc version on an ancient cluster. The
> OpenMPI version is 1.6.5 and Compiler is Intel 14.0, which are the newest
> on that cluster. I have no problem to install PETSc up to version 3.12.5.
> However, if I try to use PETSc 3.13+, there are three undefined reference
> errors in MPI_Win_allocate, MPI_Win_attach and MPI_Win_create_dynamic. I
> know these three functions are available from OpenMPI 2.0+. Because the
> cluster is not in technical support anymore, there is no way I can install
> new OpenMPI version or do some update. Is it possible to disable these
> three functions in PETSc 3.13+ version?
>
>
>
> The errors occur in ‘make check’ step:
>
> /home/dsu/soft/petsc/petsc-3.13.0/linux-intel-openmpi/lib/libpetsc.so:
> undefined reference to `MPI_Win_allocate'
>
> /home/dsu/soft/petsc/petsc-3.13.0/linux-intel-openmpi/lib/libpetsc.so:
> undefined reference to `MPI_Win_attach'
>
> /home/dsu/soft/petsc/petsc-3.13.0/linux-intel-openmpi/lib/libpetsc.so:
> undefined reference to `MPI_Win_create_dynamic'
>
>
>
> The configuration used is shown below:
>
> ./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90
> --download-mumps --download-scalapack --download-parmetis --download-metis
> --download-fblaslapack --download-hypre --download-superlu
> --download-hdf5=yes --with-debugging=0 COPTFLAGS="-O3 -march=native
> -mtune=native" CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3
> -march=native -mtune=nativels"
>
>
>
> Thanks,
>
>
>
> Danyang
>
>
>
>
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