Hi Junchao,
Thanks. I will test this branch and get back to you later.
All the best,
Danyang
From: Junchao Zhang <junchao.zh...@gmail.com>
Date: Saturday, April 10, 2021 at 3:32 PM
To: Danyang Su <danyang...@gmail.com>
Cc: Barry Smith <bsm...@petsc.dev>, "petsc-users@mcs.anl.gov"
<petsc-users@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.zh...@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...@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 <bsm...@petsc.dev>
Date: Saturday, April 10, 2021 at 10:31 AM
To: Danyang Su <danyang...@gmail.com>
Cc: "petsc-users@mcs.anl.gov" <petsc-users@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...@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
