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

Discussion:

Diana Valencia

2015-10-08 20:26:56 UTC

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 donât 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

Satish Balay

2015-10-08 20:31:30 UTC

Permalink

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

Post by Diana Valencia
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.
I have set the PETSC_DIR and PETSC_ARCH in the .bashrc file, so I donât 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

Diana Valencia

2015-10-13 20:14:17 UTC

Permalink

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

Post by Satish Balay
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

Post by Diana Valencia
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.
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

Satish Balay

2015-10-14 01:57:28 UTC

Permalink

"however ex5 in the test examples failed"

Sorry - this message is a bit confusing. Is petsc working fine for
your - or are you still having issues?

Satish

Post by 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

Diana Valencia

2015-10-14 02:04:35 UTC

Permalink

I meant to say that the code is working with PETSC despite the fact that when I tested, petsc did not pass the ex5 test.
cheers
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

Post by Satish Balay
"however ex5 in the test examples failed"
Sorry - this message is a bit confusing. Is petsc working fine for
your - or are you still having issues?
Satish

Post by Diana Valencia
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.
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

Satish Balay

2015-10-14 02:17:29 UTC

Permalink

thats wierd..

perhaps there were warnings in 'make test'? [warnings can be ignored]

alternatively - configure pickedup the wrong mpiexec but you are using
the correct one with your app?

Satish

Post by Diana Valencia
I meant to say that the code is working with PETSC despite the fact that when I tested, petsc did not pass the ex5 test.
cheers
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

Post by Satish Balay
"however ex5 in the test examples failed"
Sorry - this message is a bit confusing. Is petsc working fine for
your - or are you still having issues?
Satish

Diana Valencia

2015-10-14 02:21:13 UTC

Permalink

Here is the error message:

[***@euler01 petsc-3.2-p7]$ make test
Running test examples to verify correct installation
Using PETSC_DIR=/cluster/home/valencia/PETSC/petsc-3.2-p7 and PETSC_ARCH=arch-linux2-c-opt
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes
--------------Error detected during compile or link!-----------------------
See http://www.mcs.anl.gov/petsc/petsc-2/documentation/faq.html
mpif90 -c -O3 -I/cluster/home/valencia/PETSC/petsc-3.2-p7/include -I/cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/include -o ex5f.o ex5f.F
./ex5f.h(60): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: ( % [ : . = =>
DM da
----------------^
ex5f.F(56): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: ( % [ : . = =>
SNES snes
---------------------------------^
ex5f.F(57): error #5082: Syntax error, found ',' when expecting one of: ( % [ : . = =>
Vec x,r
------------------------------^
ex5f.F(58): error #5082: Syntax error, found ',' when expecting one of: ( % [ : . = =>
Mat J,A
------------------------------^
./ex5f.h(60): error #6218: This statement is positioned incorrectly and/or has syntax errors.
DM da
----------------^
ex5f.F(59): error #6236: A specification statement cannot appear in the executable section.
integer(kind=selected_int_kind(5)) its,i1,i4
------^
ex5f.F(60): error #6236: A specification statement cannot appear in the executable section.
integer(kind=selected_int_kind(5)) ierr
------^
ex5f.F(61): error #6236: A specification statement cannot appear in the executable section.
real(kind=selected_real_kind(10)) lambda_max,lambda_min
------^
ex5f.F(62): error #6236: A specification statement cannot appear in the executable section.
logical(kind=4) flg
------^
ex5f.F(71): error #6236: A specification statement cannot appear in the executable section.
external FormInitialGuess
------^
ex5f.F(72): error #6236: A specification statement cannot appear in the executable section.
external FormFunctionLocal,FormJacobianLocal
------^
ex5f.F(57): error #6404: This name does not have a type, and must have an explicit type. [VECX]
Vec x,r
------^
ex5f.F(57): error #6404: This name does not have a type, and must have an explicit type. [R]
Vec x,r
-------------------------------^
ex5f.F(58): error #6404: This name does not have a type, and must have an explicit type. [MATJ]
Mat J,A
------^
ex5f.F(58): error #6404: This name does not have a type, and must have an explicit type. [A]
Mat J,A
-------------------------------^
ex5f.F(81): error #6404: This name does not have a type, and must have an explicit type. [IERR]
call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
------------------------------------------------^
ex5f.F(87): error #6404: This name does not have a type, and must have an explicit type. [I1]
i1 = 1
------^
ex5f.F(88): error #6404: This name does not have a type, and must have an explicit type. [I4]
i4 = -4
------^
ex5f.F(89): error #6404: This name does not have a type, and must have an explicit type. [LAMBDA_MAX]
lambda_max = 6.81
------^
ex5f.F(90): error #6404: This name does not have a type, and must have an explicit type. [LAMBDA_MIN]
lambda_min = 0.0
------^
ex5f.F(93): error #6404: This name does not have a type, and must have an explicit type. [FLG]
& flg,ierr)
---------------------------------^
ex5f.F(103): error #6404: This name does not have a type, and must have an explicit type. [SNES]
call SNESCreate(PETSC_COMM_WORLD,snes,ierr)
---------------------------------------^
ex5f.F(116): error #6404: This name does not have a type, and must have an explicit type. [DA]
& PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,da,ierr)
-------------------------------------------------^
ex5f.F(121): error #6404: This name does not have a type, and must have an explicit type. [X]
call DMCreateGlobalVector(da,x,ierr)
-----------------------------------^
ex5f.F(152): error #6404: This name does not have a type, and must have an explicit type. [FORMFUNCTIONLOCAL]
call DMDASetLocalFunction(da,FormFunctionLocal,ierr)
-----------------------------------^
ex5f.F(153): error #6404: This name does not have a type, and must have an explicit type. [FORMJACOBIANLOCAL]
call DMDASetLocalJacobian(da,FormJacobianLocal,ierr)
-----------------------------------^
ex5f.F(173): error #6404: This name does not have a type, and must have an explicit type. [J]
call DMGetMatrix(da,'aij',J,ierr)
--------------------------------^
ex5f.F(226): error #6404: This name does not have a type, and must have an explicit type. [ITS]
call SNESGetIterationNumber(snes,its,ierr)
---------------------------------------^
./ex5f.h(60): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: ( % [ : . = =>
DM da
----------------^
ex5f.F(271): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: ( % [ : . = =>
Vec X
----------------^
/tmp/ifortGXVttY.i(6051): catastrophic error: Too many errors, exiting
compilation aborted for ex5f.F (code 1)
make[3]: [ex5f.o] Error 1 (ignored)
mpif90 -O3 -o ex5f ex5f.o -L/cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/lib -lpetsc -lX11 -lpthread -Wl,-rpath,/cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/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
ifort: error #10236: File not found: 'ex5f.o'
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
make[3]: [ex5f] Error 1 (ignored)
/bin/rm -f ex5f.o
Completed test examples

_______________________
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

Post by Satish Balay
thats wierd..
perhaps there were warnings in 'make test'? [warnings can be ignored]
alternatively - configure pickedup the wrong mpiexec but you are using
the correct one with your app?
Satish

Post by Satish Balay
"however ex5 in the test examples failed"
Sorry - this message is a bit confusing. Is petsc working fine for
your - or are you still having issues?
Satish

Satish Balay

2015-10-14 02:35:28 UTC

Permalink

The c examples ran fine - so the libraries are good.

Did you configure PETSc with --with-fortran-datatypes=1

[this is one reason why this compile will fail - esp for old version].

Alternatively - it wold be fixed form vs free form isssue [renaming
the file to ex5.F90 would get the compile going]

Since the libraries are fine - and your app works - you cold ignore this issue.

Satish

Post by Diana Valencia
Running test examples to verify correct installation
Using PETSC_DIR=/cluster/home/valencia/PETSC/petsc-3.2-p7 and PETSC_ARCH=arch-linux2-c-opt
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes
--------------Error detected during compile or link!-----------------------
See http://www.mcs.anl.gov/petsc/petsc-2/documentation/faq.html
mpif90 -c -O3 -I/cluster/home/valencia/PETSC/petsc-3.2-p7/include -I/cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/include -o ex5f.o ex5f.F
./ex5f.h(60): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: ( % [ : . = =>
DM da
----------------^
ex5f.F(56): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: ( % [ : . = =>
SNES snes
---------------------------------^
ex5f.F(57): error #5082: Syntax error, found ',' when expecting one of: ( % [ : . = =>
Vec x,r
------------------------------^
ex5f.F(58): error #5082: Syntax error, found ',' when expecting one of: ( % [ : . = =>
Mat J,A
------------------------------^
./ex5f.h(60): error #6218: This statement is positioned incorrectly and/or has syntax errors.
DM da
----------------^
ex5f.F(59): error #6236: A specification statement cannot appear in the executable section.
integer(kind=selected_int_kind(5)) its,i1,i4
------^
ex5f.F(60): error #6236: A specification statement cannot appear in the executable section.
integer(kind=selected_int_kind(5)) ierr
------^
ex5f.F(61): error #6236: A specification statement cannot appear in the executable section.
real(kind=selected_real_kind(10)) lambda_max,lambda_min
------^
ex5f.F(62): error #6236: A specification statement cannot appear in the executable section.
logical(kind=4) flg
------^
ex5f.F(71): error #6236: A specification statement cannot appear in the executable section.
external FormInitialGuess
------^
ex5f.F(72): error #6236: A specification statement cannot appear in the executable section.
external FormFunctionLocal,FormJacobianLocal
------^
ex5f.F(57): error #6404: This name does not have a type, and must have an explicit type. [VECX]
Vec x,r
------^
ex5f.F(57): error #6404: This name does not have a type, and must have an explicit type. [R]
Vec x,r
-------------------------------^
ex5f.F(58): error #6404: This name does not have a type, and must have an explicit type. [MATJ]
Mat J,A
------^
ex5f.F(58): error #6404: This name does not have a type, and must have an explicit type. [A]
Mat J,A
-------------------------------^
ex5f.F(81): error #6404: This name does not have a type, and must have an explicit type. [IERR]
call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
------------------------------------------------^
ex5f.F(87): error #6404: This name does not have a type, and must have an explicit type. [I1]
i1 = 1
------^
ex5f.F(88): error #6404: This name does not have a type, and must have an explicit type. [I4]
i4 = -4
------^
ex5f.F(89): error #6404: This name does not have a type, and must have an explicit type. [LAMBDA_MAX]
lambda_max = 6.81
------^
ex5f.F(90): error #6404: This name does not have a type, and must have an explicit type. [LAMBDA_MIN]
lambda_min = 0.0
------^
ex5f.F(93): error #6404: This name does not have a type, and must have an explicit type. [FLG]
& flg,ierr)
---------------------------------^
ex5f.F(103): error #6404: This name does not have a type, and must have an explicit type. [SNES]
call SNESCreate(PETSC_COMM_WORLD,snes,ierr)
---------------------------------------^
ex5f.F(116): error #6404: This name does not have a type, and must have an explicit type. [DA]
& PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,da,ierr)
-------------------------------------------------^
ex5f.F(121): error #6404: This name does not have a type, and must have an explicit type. [X]
call DMCreateGlobalVector(da,x,ierr)
-----------------------------------^
ex5f.F(152): error #6404: This name does not have a type, and must have an explicit type. [FORMFUNCTIONLOCAL]
call DMDASetLocalFunction(da,FormFunctionLocal,ierr)
-----------------------------------^
ex5f.F(153): error #6404: This name does not have a type, and must have an explicit type. [FORMJACOBIANLOCAL]
call DMDASetLocalJacobian(da,FormJacobianLocal,ierr)
-----------------------------------^
ex5f.F(173): error #6404: This name does not have a type, and must have an explicit type. [J]
call DMGetMatrix(da,'aij',J,ierr)
--------------------------------^
ex5f.F(226): error #6404: This name does not have a type, and must have an explicit type. [ITS]
call SNESGetIterationNumber(snes,its,ierr)
---------------------------------------^
./ex5f.h(60): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: ( % [ : . = =>
DM da
----------------^
ex5f.F(271): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: ( % [ : . = =>
Vec X
----------------^
/tmp/ifortGXVttY.i(6051): catastrophic error: Too many errors, exiting
compilation aborted for ex5f.F (code 1)
make[3]: [ex5f.o] Error 1 (ignored)
mpif90 -O3 -o ex5f ex5f.o -L/cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/lib -lpetsc -lX11 -lpthread -Wl,-rpath,/cluster/home/valencia/PETSC/petsc-3.2-p7/arch-linux2-c-opt/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
ifort: error #10236: File not found: 'ex5f.o'
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
ifort: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
make[3]: [ex5f] Error 1 (ignored)
/bin/rm -f ex5f.o
Completed test examples
_______________________
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

Post by Satish Balay
"however ex5 in the test examples failed"
Sorry - this message is a bit confusing. Is petsc working fine for
your - or are you still having issues?
Satish

Post by Diana Valencia
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.
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

Diana Valencia

2015-10-14 02:36:42 UTC

Permalink

I think for now, I’ll ignore it. Thank you for all your help
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

Post by Satish Balay
The c examples ran fine - so the libraries are good.
Did you configure PETSc with --with-fortran-datatypes=1
[this is one reason why this compile will fail - esp for old version].
Alternatively - it wold be fixed form vs free form isssue [renaming
the file to ex5.F90 would get the compile going]
Since the libraries are fine - and your app works - you cold ignore this issue.
Satish

Post by Satish Balay
"however ex5 in the test examples failed"
Sorry - this message is a bit confusing. Is petsc working fine for
your - or are you still having issues?
Satish

Post by Diana Valencia
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.
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