[petsc-users] ld: cannot find -lpetsc error

[Diana Valencia]

Dear Satish and all petsc users
Thank you for your email. Antoine Rozel also from the petsc community was able to help me (he also uses the same third party code I was trying to compile)
The version we use is old, because apparently is the one that works the best for the third party code.
I had to reinstall petsc, and somehow this fixed it.  The code compiled and is now running fine, however ex5 in the test examples failed.
Thanks for the input.
Diana

_______________________
Diana Valencia
Assistant Professor,  Physics & Astrophysics
Department of Physical and Environmental Sciences 
University of Toronto, Scarborough
1265 Military Trail, Toronto, ON, Canada, M1C 1A4
Voice 416 208-2986

> On Oct 8, 2015, at 4:31 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> 
> 1. Are you able to compile [using petsc makefile] and run PETSc examples?
> 
> 2. You are missing the link option -L/cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/lib
> 
> [you should verify the output from the example compile/link commands -
> and the compile/link command for this application.]
> 
> BTW: This is an old version of petsc.
> 
> Satish
> 
> On Thu, 8 Oct 2015, Diana Valencia wrote:
> 
>> Dear PETSc users,
>> 
>> In hopes that one of you can help me solve a compiling problem.
>> 
>> I am compiling a third party code (stagyy and stagyympi) on a cluster. I load the intel and open_mpi libraries to the cluster before compiling with petsc.
>> After compiling all the subroutines, I get an error building the code. Here is the stout:
>> 
>> I have set the PETSC_DIR and PETSC_ARCH in the .bashrc file, so I don’t think this is the problem.
>> 
>> Thank you in advance for all your help.
>> Diana
>> 
>> 
>> .
>> .
>> .
>> mpif90  -w -O2 -assume byterecl -r8 -I /cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/include -c main.f90
>> mpif90  -w -O2 -assume byterecl -r8 -I /cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/include -c advdif.f90
>> mpif90  -w -O2 -assume byterecl -r8 -I /cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/include -o stagyy main.o advdif.o communication.o continents.o evocore.o geometry.o init.o io.o iter.o melting.o miscellaneous.o MPDATA.o multi.o refstate.o phase_change.o poisson.o prolongate_restrict.o relax_all.o relax_cell.o relax_point.o residues.o tracers.o v_advection.o vee_cycle.o viscosity.o  crw.o geoid.o implicit_diffusion.o linpack.o plot.o wrtpng.o blas123.o lapack.o nxs_dummy.o  PETScimple_mod.o xdmf_hdf5_io_dummy.o bcs_mod.o composition_mod.o control_mod.o continents_mod.o vgrid_mod.o init_mod.o io_mod.o iter_mod.o melting_mod.o meltingfns_mod.o multi_mod.o phase_change_mod.o plot_mod.o precision_mod.o refstat_mod.o stencil_mod.o timestep_mod.o timing_mod.o tracers_mod.o viscosity_mod.o thermochem_mod.o platesLea_mod.o -lpng     -L/lib  -lpetsc -lX11 -lpthread -Wl,-rpath,/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs -lsuperlu_4.2 -lml -lmpi_cxx -lumfpack -lamd -lflapack -lfblas -ldl -L/cluster/apps/openmpi/1.6.5/x86_64/intel_15.0.0/lib -lmpi -lopen-rte -lopen-pal -lnuma -lrt -lnsl -lutil -L/cluster/apps/intel/composer_xe_2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64 -L/cluster/apps/intel/composer_xe_2015.0.090/composer_xe_2015.0.090/ipp/lib/intel64 -L/cluster/apps/intel/composer_xe_2015.0.090/composer_xe_2015.0.090/mkl/lib/intel64 -L/cluster/apps/intel/composer_xe_2015.0.090/composer_xe_2015.0.090/tbb/lib/intel64 -L/cluster/apps/gcc/4.8.2/lib/gcc/x86_64-unknown-linux-gnu/4.8.2 -L/cluster/apps/gcc/4.8.2/lib64 -L/cluster/apps/gcc/4.8.2/lib -limf -lsvml -lirng -lipgo -ldecimal -lcilkrts -lstdc++ -lgcc_s -lirc -lpthread -lirc_s -lmpi_f90 -lmpi_f77 -lm -lm -lifport -lifcore -lm -lm -lm -lmpi_cxx -ldl -lmpi -lopen-rte -lopen-pal -lnuma -lrt -lnsl -lutil -limf -lsvml -lirng -lipgo -ldecimal -lcilkrts -lstdc++ -lgcc_s -lirc -lpthread -lirc_s -ldl 
>> ld: cannot find -lpetsc
>> make: *** [stagyy] Error 1
>> mpif90  -w -O2 -assume byterecl -r8 -I /cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/include -o stagyympi main.o advdif.o communication.o continents.o evocore.o geometry.o init.o io.o iter.o melting.o miscellaneous.o MPDATA.o multi.o refstate.o phase_change.o poisson.o prolongate_restrict.o relax_all.o relax_cell.o relax_point.o residues.o tracers.o v_advection.o vee_cycle.o viscosity.o  crw.o geoid.o implicit_diffusion.o linpack.o plot.o wrtpng.o blas123.o lapack.o nxs_to_mpi.o PETScimple_mod.o xdmf_hdf5_io_dummy.o bcs_mod.o composition_mod.o control_mod.o continents_mod.o vgrid_mod.o init_mod.o io_mod.o iter_mod.o melting_mod.o meltingfns_mod.o multi_mod.o phase_change_mod.o plot_mod.o precision_mod.o refstat_mod.o stencil_mod.o timestep_mod.o timing_mod.o tracers_mod.o viscosity_mod.o thermochem_mod.o platesLea_mod.o -lpng     -L/lib  -lpetsc -lX11 -lpthread -Wl,-rpath,/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs -lsuperlu_4.2 -lml -lmpi_cxx -lumfpack -lamd -lflapack -lfblas -ldl -L/cluster/apps/openmpi/1.6.5/x86_64/intel_15.0.0/lib -lmpi -lopen-rte -lopen-pal -lnuma -lrt -lnsl -lutil -L/cluster/apps/intel/composer_xe_2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64 -L/cluster/apps/intel/composer_xe_2015.0.090/composer_xe_2015.0.090/ipp/lib/intel64 -L/cluster/apps/intel/composer_xe_2015.0.090/composer_xe_2015.0.090/mkl/lib/intel64 -L/cluster/apps/intel/composer_xe_2015.0.090/composer_xe_2015.0.090/tbb/lib/intel64 -L/cluster/apps/gcc/4.8.2/lib/gcc/x86_64-unknown-linux-gnu/4.8.2 -L/cluster/apps/gcc/4.8.2/lib64 -L/cluster/apps/gcc/4.8.2/lib -limf -lsvml -lirng -lipgo -ldecimal -lcilkrts -lstdc++ -lgcc_s -lirc -lpthread -lirc_s -lmpi_f90 -lmpi_f77 -lm -lm -lifport -lifcore -lm -lm -lm -lmpi_cxx -ldl -lmpi -lopen-rte -lopen-pal -lnuma -lrt -lnsl -lutil -limf -lsvml -lirng -lipgo -ldecimal -lcilkrts -lstdc++ -lgcc_s -lirc -lpthread -lirc_s -ldl 
>> ld: cannot find -lpetsc
>> make: *** [stagyympi] Error 1
>> make: Target `both' not remade because of errors.
>> 
>> _______________________
>> Diana Valencia
>> Assistant Professor,  Physics & Astrophysics
>> Department of Physical and Environmental Sciences 
>> University of Toronto, Scarborough
>> 1265 Military Trail, Toronto, ON, Canada, M1C 1A4
>> Voice 416 208-2986
>> 
>>