Re: [petsc-users] PETSc configuration error on macOS Monterey with Intel oneAPI
Hi Samar, Yes, with mpich, there is no such error. I will just use this configuration for now. Thanks, Danyang From: Samar Khatiwala Date: Thursday, January 13, 2022 at 1:16 AM To: Danyang Su Cc: PETSc Subject: Re: [petsc-users] PETSc configuration error on macOS Monterey with Intel oneAPI Hi Danyang, Just to reiterate, the presence of -Wl,-flat_namespace *is* the problem. I got rid of it by configuring mpich with --enable-two-level-namespace. I reported this problem to the PETSc folks a few weeks ago and they were going to patch MPICH.py (under config/BuildSystem/config/packages) to pass this flag. So you could try configuring with —download-mpich (or build your own mpich, which is pretty straightforward). If you’re wedded to openmpi, you could patch up OpenMPI.py yourself (maybe --enable-two-level-namespace is called something else for openmpi). Best, Samar On Jan 13, 2022, at 6:01 AM, Danyang Su wrote: Hi Samar, Thanks for your suggestion. Unfortunately, it does not work. I checked the mpif90 wrapper and the option "-Wl,-flat_namespace” is present. (base) ➜ bin ./mpif90 -show ifort -I/Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/include -Wl,-flat_namespace -Wl,-commons,use_dylibs -I/Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/lib -L/Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi Thanks anyway, Danyang From: Samar Khatiwala Date: Wednesday, January 12, 2022 at 2:01 PM To: Danyang Su Cc: PETSc Subject: Re: [petsc-users] PETSc configuration error on macOS Monterey with Intel oneAPI Hi Danyang, I had trouble configuring PETSc on MacOS Monterey with ifort when using mpich (which I was building myself). I tracked it down to an errant "-Wl,-flat_namespace” option in the mpif90 wrapper. I rebuilt mpich with the "--enable-two-level-namespace” configuration option and the problem went away. I don’t know if there’s a similar issue with openmpi but you could check the corresponding mpif90 wrapper (mpif90 -show) whether "-Wl,-flat_namespace” is present or not. If so, perhaps passing "--enable-two-level-namespace” to PETSc configure might fix the problem (although I don’t know how you would set this flag *just* for building openmpi). Samar On Jan 12, 2022, at 9:41 PM, Danyang Su wrote: Hi All, I got an error in PETSc configuration on macOS Monterey with Intel oneAPI using the following options: ./configure --with-cc=icc --with-cxx=icpc --with-fc=ifort --with-blas-lapack-dir=/opt/intel/oneapi/mkl/2022.0.0/lib/ --with-debugging=1 PETSC_ARCH=macos-intel-dbg --download-mumps --download-parmetis --download-metis --download-hypre --download-superlu --download-hdf5=yes --download-openmpi Error with downloaded OpenMPI: Cannot compile/link FC with /Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/bin/mpif90. Any suggestions for that? There is no problem if I use GNU compiler and MPICH. Thanks, Danyang
Re: [petsc-users] PETSc configuration error on macOS Monterey with Intel oneAPI
Hi Danyang, Just to reiterate, the presence of -Wl,-flat_namespace *is* the problem. I got rid of it by configuring mpich with --enable-two-level-namespace. I reported this problem to the PETSc folks a few weeks ago and they were going to patch MPICH.py (under config/BuildSystem/config/packages) to pass this flag. So you could try configuring with —download-mpich (or build your own mpich, which is pretty straightforward). If you’re wedded to openmpi, you could patch up OpenMPI.py yourself (maybe --enable-two-level-namespace is called something else for openmpi). Best, Samar > On Jan 13, 2022, at 6:01 AM, Danyang Su wrote: > > Hi Samar, > > Thanks for your suggestion. Unfortunately, it does not work. I checked the > mpif90 wrapper and the option "-Wl,-flat_namespace” is present. > > (base) ➜ bin ./mpif90 -show > ifort -I/Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/include > -Wl,-flat_namespace -Wl,-commons,use_dylibs > -I/Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/lib > -L/Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/lib > -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi > > Thanks anyway, > > Danyang > From: Samar Khatiwala > Date: Wednesday, January 12, 2022 at 2:01 PM > To: Danyang Su > Cc: PETSc > Subject: Re: [petsc-users] PETSc configuration error on macOS Monterey with > Intel oneAPI > > Hi Danyang, > > I had trouble configuring PETSc on MacOS Monterey with ifort when using mpich > (which I was building myself). I tracked it down to an errant > "-Wl,-flat_namespace” > option in the mpif90 wrapper. I rebuilt mpich with the > "--enable-two-level-namespace” configuration option and the problem went > away. I don’t know if there’s a similar > issue with openmpi but you could check the corresponding mpif90 wrapper > (mpif90 -show) whether "-Wl,-flat_namespace” is present or not. If so, > perhaps passing > "--enable-two-level-namespace” to PETSc configure might fix the problem > (although I don’t know how you would set this flag *just* for building > openmpi). > > Samar > > >> On Jan 12, 2022, at 9:41 PM, Danyang Su > <mailto:danyang...@gmail.com>> wrote: >> >> Hi All, >> >> I got an error in PETSc configuration on macOS Monterey with Intel oneAPI >> using the following options: >> >> >> ./configure --with-cc=icc --with-cxx=icpc --with-fc=ifort >> --with-blas-lapack-dir=/opt/intel/oneapi/mkl/2022.0.0/lib/ >> --with-debugging=1 PETSC_ARCH=macos-intel-dbg --download-mumps >> --download-parmetis --download-metis --download-hypre --download-superlu >> --download-hdf5=yes --download-openmpi >> >> >> Error with downloaded OpenMPI: Cannot compile/link FC with >> /Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/bin/mpif90. >> >> >> Any suggestions for that? >> >> >> There is no problem if I use GNU compiler and MPICH. >> >> >> Thanks, >> >> >> Danyang
Re: [petsc-users] PETSc configuration error on macOS Monterey with Intel oneAPI
Hi Samar, Thanks for your suggestion. Unfortunately, it does not work. I checked the mpif90 wrapper and the option "-Wl,-flat_namespace” is present. (base) ➜ bin ./mpif90 -show ifort -I/Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/include -Wl,-flat_namespace -Wl,-commons,use_dylibs -I/Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/lib -L/Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi Thanks anyway, Danyang From: Samar Khatiwala Date: Wednesday, January 12, 2022 at 2:01 PM To: Danyang Su Cc: PETSc Subject: Re: [petsc-users] PETSc configuration error on macOS Monterey with Intel oneAPI Hi Danyang, I had trouble configuring PETSc on MacOS Monterey with ifort when using mpich (which I was building myself). I tracked it down to an errant "-Wl,-flat_namespace” option in the mpif90 wrapper. I rebuilt mpich with the "--enable-two-level-namespace” configuration option and the problem went away. I don’t know if there’s a similar issue with openmpi but you could check the corresponding mpif90 wrapper (mpif90 -show) whether "-Wl,-flat_namespace” is present or not. If so, perhaps passing "--enable-two-level-namespace” to PETSc configure might fix the problem (although I don’t know how you would set this flag *just* for building openmpi). Samar On Jan 12, 2022, at 9:41 PM, Danyang Su wrote: Hi All, I got an error in PETSc configuration on macOS Monterey with Intel oneAPI using the following options: ./configure --with-cc=icc --with-cxx=icpc --with-fc=ifort --with-blas-lapack-dir=/opt/intel/oneapi/mkl/2022.0.0/lib/ --with-debugging=1 PETSC_ARCH=macos-intel-dbg --download-mumps --download-parmetis --download-metis --download-hypre --download-superlu --download-hdf5=yes --download-openmpi Error with downloaded OpenMPI: Cannot compile/link FC with /Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/bin/mpif90. Any suggestions for that? There is no problem if I use GNU compiler and MPICH. Thanks, Danyang
Re: [petsc-users] PETSc configuration error on macOS Monterey with Intel oneAPI
Hi Danyang, I had trouble configuring PETSc on MacOS Monterey with ifort when using mpich (which I was building myself). I tracked it down to an errant "-Wl,-flat_namespace” option in the mpif90 wrapper. I rebuilt mpich with the "--enable-two-level-namespace” configuration option and the problem went away. I don’t know if there’s a similar issue with openmpi but you could check the corresponding mpif90 wrapper (mpif90 -show) whether "-Wl,-flat_namespace” is present or not. If so, perhaps passing "--enable-two-level-namespace” to PETSc configure might fix the problem (although I don’t know how you would set this flag *just* for building openmpi). Samar > On Jan 12, 2022, at 9:41 PM, Danyang Su wrote: > > Hi All, > > I got an error in PETSc configuration on macOS Monterey with Intel oneAPI > using the following options: > > > ./configure --with-cc=icc --with-cxx=icpc --with-fc=ifort > --with-blas-lapack-dir=/opt/intel/oneapi/mkl/2022.0.0/lib/ --with-debugging=1 > PETSC_ARCH=macos-intel-dbg --download-mumps --download-parmetis > --download-metis --download-hypre --download-superlu --download-hdf5=yes > --download-openmpi > > > Error with downloaded OpenMPI: Cannot compile/link FC with > /Users/danyangsu/Soft/PETSc/petsc-3.16.3/macos-intel-dbg/bin/mpif90. > > > Any suggestions for that? > > > There is no problem if I use GNU compiler and MPICH. > > > Thanks, > > > Danyang
