[petsc-users] ld: cannot find -lpetsc error
Diana Valencia
valencia at astro.utoronto.ca
Tue Oct 13 21:36:42 CDT 2015
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
> On Oct 13, 2015, at 10:35 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>
>
> 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
>
> On Tue, 13 Oct 2015, Diana Valencia wrote:
>
>> Here is the error message:
>>
>> [valencia at 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
>>
>>> On Oct 13, 2015, at 10:17 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>>>
>>> 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
>>>
>>> On Tue, 13 Oct 2015, Diana Valencia wrote:
>>>
>>>> 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
>>>>
>>>>> On Oct 13, 2015, at 9:57 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>>>>>
>>>>> "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
>>>>>
>>>>> On Tue, 13 Oct 2015, Diana Valencia wrote:
>>>>>
>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>
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