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

Sat Apr 10 17:52:08 CDT 2021

Hi Junchao,

Thanks. I will test this branch and get back to you later.

All the best,

Danyang

From: Junchao Zhang <junchao.zhang at gmail.com>
Date: Saturday, April 10, 2021 at 3:32 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

Danyang,

  Could you try branch jczhang/fix-mpi3-win with your old configuration (i.e., use system mpicc)? Note the MR 3849 is based off latest petsc-3.15 release

  Thanks.

--Junchao Zhang

On Sat, Apr 10, 2021 at 4:36 PM Junchao Zhang <junchao.zhang at gmail.com> wrote:

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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