[petsc-users] Compiling program with program files dependencies (SLEPC )
Matthew Knepley
knepley at gmail.com
Fri Apr 25 09:55:17 CDT 2014
On Fri, Apr 25, 2014 at 9:45 AM, Steve Ndengue <steve.ndengue at gmail.com>wrote:
> Dear all,
>
> Sorry, I had a typo: I was still editing the .f90 program file instead of
> the .F90 file.
>
> However, now I am having troubles forming the matrice I would like to
> diagonalize.
> Presently the size is not yet huge and it could be held in a previously
> computed matrix of dimension N*N.
>
> I am using the following to build the matrix and the compiling from the
> example 1 and slightly modified:
>
> ***
> *!*
> * CALL SlepcInitialize(PETSC_NULL_CHARACTER,ierr)*
> * CALL MPI_Comm_rank(PETSC_COMM_WORLD,rank,ierr)*
> * nn = N*
> *! CALL PetscOptionsGetInt(PETSC_NULL_CHARACTER,'-n',n,flg,ierr)*
> *!*
>
> *!*
> *! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> *
> *! Compute the operator matrix that defines the eigensystem, Ax=kx*
> *! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> *
>
> * call MatCreate(PETSC_COMM_WORLD,A,ierr)*
> * call MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,nn,nn,ierr)*
> * call MatSetFromOptions(A,ierr)*
> * call MatSetUp(A,ierr)*
>
> * call MatGetOwnershipRange(A,Istart,Iend,ierr)*
> * do i=Istart,Iend-1*
> * do j=0,nn-1*
> * call MatSetValue(A,i,-1,j,-1,H_mat(i,j),INSERT_VALUES,ierr)*
> * enddo*
> * enddo*
> * call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr)*
> * call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr)! ** Create
> eigensolver context*
> * CALL EPSCreate(PETSC_COMM_WORLD,solver,ierr)*
> *!** ** Set operators. In this case, it is a standard eigenvalue
> problem*
> * CALL EPSSetOperators(solver,A,PETSC_NULL_OBJECT,ierr)*
> *print*,'here10,ierr',ierr*
> * CALL EPSSetProblemType(solver,EPS_HEP,ierr)*
> *! ** Set working dimensions*
> * CALL EPSSETDimensions(solver,nstates,10*nstates,2*nstates)*
> *! ** Set calculation of lowest eigenvalues*
> * CALL EPSSetWhichEigenpairs(solver,EPS_SMALLEST_REAL)*
>
> *! ** Set solver parameters at runtime*
> * CALL EPSSetFromOptions(solver,ierr)*
> *! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> *
> *! Solve the eigensystem*
> *! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> *
> * CALL EPSSolve(solver,ierr)*
> *print*,'here6'*
> *! ** Optional: Get some information from the solver and display it*
> * CALL EPSGetType(solver,tname,ierr)*
> * if (rank .eq. 0) then*
> * write(*,120) tname*
> * endif*
> * 120 format (' Solution method: ',A)*
> * CALL
> EPSGetDimensions(solver,nstates,PETSC_NULL_INTEGER, &*
> * & PETSC_NULL_INTEGER,ierr)*
> * if (rank .eq. 0) then*
> * write(*,130) nstates*
> * endif*
> * 130 format (' Number of requested eigenvalues:',I4)*
> *! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> *
> *! Display solution and clean up*
> *! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> *
> * CALL EPSPrintSolution(solver,PETSC_NULL_OBJECT,ierr)*
> * CALL EPSDestroy(solver,ierr)*
> *****
>
> I get the following error message when making the code:
>
Run in the debugger, -start_in_debugger, and get a stack trace for the
error.
Matt
> ***
> *[0]PETSC ERROR:
> ------------------------------------------------------------------------*
> *[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range*
> *[0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger*
> *[0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> <http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>[0]PETSC
> ERROR: or try http://valgrind.org <http://valgrind.org> on GNU/linux and
> Apple Mac OS X to find memory corruption errors*
> *[0]PETSC ERROR: likely location of problem given in stack below*
> *[0]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------*
> *[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,*
> *[0]PETSC ERROR: INSTEAD the line number of the start of the
> function*
> *[0]PETSC ERROR: is given.*
> *[0]PETSC ERROR: --------------------- Error Message
> ------------------------------------*
> *[0]PETSC ERROR: Signal received!*
> *[0]PETSC ERROR:
> ------------------------------------------------------------------------*
> *[0]PETSC ERROR: Petsc Release Version 3.4.4, Mar, 13, 2014 *
> *[0]PETSC ERROR: See docs/changes/index.html for recent updates.*
> *[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.*
> *[0]PETSC ERROR: See docs/index.html for manual pages.*
> *[0]PETSC ERROR:
> ------------------------------------------------------------------------*
> *[0]PETSC ERROR: ./**PgmPrincipal** on a arch-linux2-c-debug named
> r10dawesr by ndengues Fri Apr 25 09:36:59 2014*
> *[0]PETSC ERROR: Libraries linked from
> /usr/local/home/ndengues/Downloads/Libraries/petsc-3.4.4/arch-linux2-c-debug/lib*
> *[0]PETSC ERROR: Configure run at Thu Apr 24 20:35:39 2014*
> *[0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=gfortran
> --download-f-blas-lapack --download-mpich*
> *[0]PETSC ERROR:
> ------------------------------------------------------------------------*
> *[0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file*
> *application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0*
> *[cli_0]: aborting job:*
> *application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0*
> ***
>
>
>
> Once more, the program execute without troubles for all the examples in
> the package.
>
> Sincerely,
>
>
> On 04/24/2014 10:14 PM, Satish Balay wrote:
>
> petsc examples work fine.
>
> send us the code that breaks. Also copy/paste the *complete* output from 'make' when
> you attempt to compile this code.
>
> Satish
>
> On Thu, 24 Apr 2014, Barry Smith wrote:
>
>
> Try .F files instead of .F90 some Fortran compilers handle preprocessing in different ways for .F and .F90
>
> Please also send configure.log and make.log so we know what compilers etc you are using.
>
> Barry
>
> Note that we are using C pre processing directives,
>
> On Apr 24, 2014, at 7:57 PM, Steve Ndengue <steve.ndengue at gmail.com> <steve.ndengue at gmail.com> wrote:
>
>
> The results is the same with lower case letters...
>
>
> On 04/24/2014 07:39 PM, Matthew Knepley wrote:
>
> On Thu, Apr 24, 2014 at 8:36 PM, Steve Ndengue <steve.ndengue at gmail.com> <steve.ndengue at gmail.com> wrote:
> Thank you for the quick reply.
>
> It partly solved the problem; the PETSC and SLEPC files are now included in the compilation.
>
> However the Warning are now error messages!
> ***
> pgm_hatom_offaxis_cyl.F90:880:0: error: invalid preprocessing directive #INCLUDE
> pgm_hatom_offaxis_cyl.F90:887:0: error: invalid preprocessing directive #IF
> pgm_hatom_offaxis_cyl.F90:890:0: error: invalid preprocessing directive #ELSE
> pgm_hatom_offaxis_cyl.F90:893:0: error: invalid preprocessing directive #ENDIF
> ***
>
> These should not be capitalized.
>
> Matt
>
> And the corresponding code lines are:
> ***
> #INCLUDE <finclude/slepcepsdef.h>
> USE slepceps
>
> !
> IMPLICIT NONE
> !----------------------
> !
> #IF DEFINED(PETSC_USE_FORTRAN_DATATYPES)
> TYPE(Mat) A
> TYPE(EPS) solver
> #ELSE
> Mat A
> EPS solver
> #ENDIF
> ***
>
> Sincerely.
>
> On 04/24/2014 07:25 PM, Satish Balay wrote:
>
> On Thu, 24 Apr 2014, Steve Ndengue wrote:
>
>
>
> Dear all,
>
> I am having trouble compiling a code with some dependencies that shall call
> SLEPC.
> The compilation however goes perfectly for the various tutorials and tests in
> the package.
>
> A sample makefile looks like:
>
> ***
>
> /default: code//
> //routines: Rout1.o Rout2.o Rout3.o Module1.o//
> //code: PgmPrincipal//
> //sources=Rout1.f Rout2.f Rout3.f Module1.f90//
>
>
> Its best to rename your sourcefiles .F/.F90 [and not .f/.f90
> [this enables using default targets from petsc makefiles - and its
> the correct notation for preprocessing - which is required by petsc/slepc]
>
>
>
> //objets=Rout1.o Rout2.o Rout3.o Module1.o Pgm//Principal//.o//
> //
> //%.o: %.f//
> // -${FLINKER} -c $<//
>
>
> And you shouldn't need to create the above .o.f target.
>
> Satish
>
>
>
>
> //
> //Module1_mod.mod Module1.o: //Module1//.f90//
> // -${FLINKER} -c //Module1//.f90//
> //
> //include ${SLEPC_DIR}/conf/slepc_common//
> //
> //Pgm//Principal//: ${objets} chkopts//
> // -${FLINKER} -o $@ ${objets} ${SLEPC_LIB}//
> //
> //.PHONY: clean//
> // ${RM} *.o *.mod Pgm//Principal//
> /
> ***
>
> The code exits with Warning and error messages of the type:
>
> *Warning: Pgm**Principal**.f90:880: Illegal preprocessor directive**
> **Warning: Pgm**Principal**.f90:889: Illegal preprocessor directive**
> **Warning: Pgm**Principal**.f90:892: Illegal preprocessor directive**
> **Warning: Pgm**Principal**.f90:895: Illegal preprocessor directive*
>
> and
>
> *USE slepceps**
> ** 1**
> **Fatal Error: Can't open module file 'slepceps.mod' for reading at (1): No
> such file or directory
>
>
> *I do not get these errors with the tests and errors files.
>
>
> Sincerely,
>
>
>
>
> --
> Steve
>
>
>
>
> --
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
> -- Norbert Wiener
>
> --
> Steve
>
>
>
>
>
>
> --
> Steve
>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20140425/7d2c0e3b/attachment-0001.html>
More information about the petsc-users
mailing list