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...@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.zh...@gmail.com> > *Date: *Sunday, April 11, 2021 at 7:54 AM > *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 > > > > Thanks, Glad to know you have a workaround. > > --Junchao Zhang > > > > > > On Sat, Apr 10, 2021 at 10:06 PM Danyang Su <danyang...@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...@gmail.com> > *Date: *Saturday, April 10, 2021 at 4:08 PM > *To: *Junchao Zhang <junchao.zh...@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 > > > > 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.zh...@gmail.com> > *Date: *Saturday, April 10, 2021 at 3:57 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 > > > > 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...@gmail.com> wrote: > > > > Hi Junchao, > > > > Thanks for looking into this problem. The configuration log is attached. > > > > All the best, > > > > Danyang > > *From: *Junchao Zhang <junchao.zh...@gmail.com> > *Date: *Saturday, April 10, 2021 at 2:36 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 > > > > 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 > > > >
