And to have cleaner list - specify the (appropriate) compiler libraries via LIBS option
balay@pj01:~/petsc$ mpif90 -show gfortran -I/software/mpich-4.1.1/include -I/software/mpich-4.1.1/include -L/software/mpich-4.1.1/lib -lmpifort -Wl,-rpath -Wl,/software/mpich-4.1.1/lib -Wl,--enable-new-dtags -lmpi balay@pj01:~/petsc$ ./configure --download-fblaslapack --download-hdf5 --with-hdf5-fortran-bindings --download-metis --download-parmetis COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --with-debugging=0 LIBS="-lmpifort -lmpi -lgfortran -lstdc++" balay@pj01:~/petsc$ grep ^PETSC_EXTERNAL_LIB_BASIC arch-linux-c-opt/lib/petsc/conf/petscvariables PETSC_EXTERNAL_LIB_BASIC = -Wl,-rpath,/home/balay/petsc/arch-linux-c-opt/lib -L/home/balay/petsc/arch-linux-c-opt/lib -lflapack -lfblas -lparmetis -lmetis -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lm -lX11 -lquadmath -lmpifort -lmpi -lgfortran -lstdc++ Satish On Tue, 14 May 2024, Satish Balay via petsc-users wrote: > You can try using latest petsc version [3.21] - the list should be a bit more > cleaner with it. > > balay@pj01:~/petsc$ ./configure --download-mpich --download-fblaslapack > --download-hdf5 --with-hdf5-fortran-bindings --download-metis > --download-parmetis COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > --with-debugging=0 > > balay@pj01:~/petsc$ grep ^PETSC_EXTERNAL_LIB_BASIC > arch-linux-c-opt/lib/petsc/conf/petscvariables > PETSC_EXTERNAL_LIB_BASIC = -Wl,-rpath,/home/balay/petsc/arch-linux-c-opt/lib > -L/home/balay/petsc/arch-linux-c-opt/lib > -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/13 > -L/usr/lib/gcc/x86_64-redhat-linux/13 -lflapack -lfblas -lparmetis -lmetis > -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lm -lX11 -lmpifort -lmpi > -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ > > Satish > > On Tue, 14 May 2024, Runjian Wu wrote: > > > First clarification, NO issues happened. I am just curious about the > > duplicated libraries while I compile PFLOTRAN with PETSc. > > > > PETSc version: 3.16.2 > > > > Configure Options: --configModules=PETSc.Configure > > --optionsModule=config.compilerOptions --with-make-np=4 --with-cc=mpicc > > --with-cxx=mpicxx --with-fc=mpif90 --download-fblaslapack=yes > > --download-hdf5=/home/wurunjian/petsc_pkg/hdf5-1.12.1.tar.bz2 > > --download-hdf5-fortran-bindings=yes --download-metis=yes > > --download-parmetis=yes --CFLAGS=-O3 --CXXFLAGS=-O3 --FFLAGS=-O3 > > --with-debugging=0 > > > > PETSC_EXTERNAL_LIB_BASIC = > > -Wl,-rpath,/home/wurunjian/petsc/arch-linux2-c-opt/lib > > -L/home/wurunjian/petsc/arch-linux2-c-opt/lib > > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 > > -L/usr/lib/gcc/x86_64-linux-gnu/11 -lflapack -lfblas -lhdf5hl_fortran > > -lhdf5_fortran -lhdf5_hl -lhdf5 -lparmetis -lmetis -lm -lstdc++ -ldl > > -lmpichfort -lmpich -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath > > -lstdc++ -ldl > > > > On Mon, May 13, 2024 at 9:34 PM Satish Balay <ba...@mcs.anl.gov> wrote: > > > > > what version of PETSc? What configure command? What do you have for > > > PETSC_EXTERNAL_LIB_BASIC? > > > > > > You can send configure.log for your build to petsc-maint > > > > > > Generally duplicates should not cause grief. [as one needs them to > > > overcome circular dependencies]. > > > > > > What issues are you seeing? [send relevant logs] > > > > > > If the duplicates are coming form "compiler library" detection part of > > > configure - you can skip this part by listing the correct "compiler > > > libraries" > > > > > > for ex: with gcc/gfortran: > > > > > > LIBS="-lgfortran -lstdc++" > > > > > > However -lgfortran could be required for gcc - but a duplicate for > > > gfortran. > > > > > > Satish > > > > > > On Mon, 13 May 2024, Runjian Wu wrote: > > > > > > > Hi all, > > > > > > > > After I compiled PETSc, I found some duplicated libs in the variable > > > > PETSC_EXTERNAL_LIB_BASIC, e.g., -lm, -lgfortran -lstdc++. I am curious > > > how > > > > it happened and how to remove the duplicates? > > > > > > > > Thanks, > > > > > > > > Runjian Wu > > > > > > > > > > > > >
