MPICH error when using petsc-3.0.0-p4
Wee-Beng TAY
zonexo at gmail.com
Mon Apr 13 19:53:06 CDT 2009
Hi,
So when must I use PetscScalar, and when can I just use real(8)? This is
because most of my variables are in real(8), except for the Mat, Vec,
required in the solving of the linear eqn. Is there a rule? I initially
thought they are the same and if I remember correctly, it seems to work
fine in PETSc2.3.3.
My v_ast is now defined as:
PetscScalar, allocatable :: u_ast(:,:), v_ast(:,:)
allocate (u_ast(0:size_x+1,jsta_ext:jend_ext), STAT=status(1));allocate
(v_ast(0:size_x+1,jsta_ext:jend_ext), STAT=status(2))
if (status(1)/=0 .or. status(2)/=0) STOP "Cannot allocate memory"
Thank you very much and have a nice day!
Yours sincerely,
Wee-Beng Tay
Satish Balay wrote:
> And if v_ast() is used with PETSc - then it should be defined 'PetscScalar'
>
> and then you use MPI_ISEND(....,MPIU_SCALAR,...)
>
> Satish
>
>
> On Mon, 13 Apr 2009, Barry Smith wrote:
>
>
>> Where is your implicit none that all sane programmers begin their Fortran
>> subroutines with?
>>
>>
>> On Apr 13, 2009, at 11:11 AM, Wee-Beng TAY wrote:
>>
>>
>>> Hi Satish,
>>>
>>> Compiling and building now worked without error. However, when I run, I get
>>> the error:
>>>
>>> 0 - MPI_ISEND : Datatype is MPI_TYPE_NULL
>>> [0] Aborting program !
>>> [0] Aborting program!
>>> Error 323, process 0, host GOTCHAMA-E73BB3:
>>>
>>> The problem lies in this subroutine:
>>>
>>> subroutine v_ast_row_copy
>>>
>>> #include "finclude/petsc.h"
>>> #include "finclude/petscvec.h"
>>> #include "finclude/petscmat.h"
>>> #include "finclude/petscksp.h"
>>> #include "finclude/petscpc.h"
>>> #include "finclude/petscsys.h"
>>>
>>> !to copy data of jend row to others
>>>
>>> integer :: inext,iprev,istatus(MPI_STATUS_SIZE),irecv1,ierr,isend1
>>>
>>> inext = myid + 1
>>> iprev = myid - 1
>>>
>>> if (myid == num_procs - 1) inext = MPI_PROC_NULL
>>>
>>> if (myid == 0) iprev = MPI_PROC_NULL
>>>
>>> CALL
>>> MPI_ISEND(v_ast(1,jend),size_x,MPI_REAL8,inext,1,MPI_COMM_WORLD,isend1,ierr)
>>> CALL
>>> MPI_IRECV(v_ast(1,jsta-1),size_x,MPI_REAL8,iprev,1,MPI_COMM_WORLD,irecv1,ierr)
>>> CALL MPI_WAIT(isend1, istatus, ierr)
>>> CALL MPI_WAIT(irecv1, istatus, ierr)
>>>
>>> end subroutine v_ast_row_copy
>>>
>>>
>>> I copied this subroutine from the RS6000 mpi manual and it used to work. I
>>> wonder if this is a MPI or PETSc problem? Strange because I already specify
>>> the type to be MPI_REAL8. However changing to MPI_REAL solves the problem.
>>>
>>> If this is a MPI problem, then you can just ignore it. I'll check it in some
>>> MPI forum.
>>>
>>>
>>> Thank you very much and have a nice day!
>>>
>>> Yours sincerely,
>>>
>>> Wee-Beng Tay
>>>
>>>
>>>
>>> Satish Balay wrote:
>>>
>>>> Yes - all includes statements in both the sourcefiles should start
>>>> with "finclude/..." [so that -Id:\cygwin\codes\petsc-3.0.0-p4 is not
>>>> needed]
>>>>
>>>> And where you needed PETSC_AVOID_DECLARATIONS - you need to use the
>>>> 'def.h' equivelent includes.. The def.h files have only the
>>>> declarations [so the PETSC_AVOID_DECLARATIONS flag is no longer
>>>> needed/used]. You need only the definitions in the datasection of
>>>> 'module flux_area'. [All subroutines should use the regular includes]
>>>>
>>>> Satish
>>>>
>>>>
>>>> On Mon, 13 Apr 2009, Wee-Beng TAY wrote:
>>>>
>>>>
>>>>
>>>>> Hi Satish,
>>>>>
>>>>> I now used
>>>>>
>>>>> #include "finclude/petsc.h"
>>>>> #include "finclude/petscvec.h"
>>>>> #include "finclude/petscmat.h"
>>>>> #include "finclude/petscksp.h"
>>>>> #include "finclude/petscpc.h"
>>>>> #include "finclude/petscsys.h"
>>>>>
>>>>> for global.F and
>>>>>
>>>>> #include "finclude/petscdef.h"
>>>>> #include "finclude/petscvecdef.h"
>>>>> #include "finclude/petscmatdef.h"
>>>>> #include "finclude/petsckspdef.h"
>>>>> #include "finclude/petscpcdef.h"
>>>>>
>>>>> for flux_area.f90 and it's working now. Can you explain what's
>>>>> happening? Is
>>>>> this the correct way then?
>>>>>
>>>>> Thank you very much and have a nice day!
>>>>>
>>>>> Yours sincerely,
>>>>>
>>>>> Wee-Beng Tay
>>>>>
>>>>>
>>>>>
>>>>> Satish Balay wrote:
>>>>>
>>>>>
>>>>>> 2 changes you have to make for 3.0.0
>>>>>>
>>>>>> 1. "include/finclude.. -> "finclude..."
>>>>>>
>>>>>> 2. PETSC_AVOID_DECLARATIONS should be removed - and use petscdef.h
>>>>>> equivalnet files.
>>>>>> i.e
>>>>>>
>>>>>> change:
>>>>>> #define PETSC_AVOID_DECLARATIONS
>>>>>> #include "include/finclude/petsc.h"
>>>>>> #include "include/finclude/petscvec.h"
>>>>>> #include "include/finclude/petscmat.h"
>>>>>> #include "include/finclude/petscksp.h"
>>>>>> #include "include/finclude/petscpc.h"
>>>>>> #undef PETSC_AVOID_DECLARATIONS
>>>>>>
>>>>>> to:
>>>>>> #include "finclude/petscdef.h"
>>>>>> #include "finclude/petscvecdef.h"
>>>>>> #include "finclude/petscmatdef.h"
>>>>>> #include "finclude/petsckspdef.h"
>>>>>> #include "finclude/petscpcdef.h"
>>>>>>
>>>>>> Satish
>>>>>>
>>>>>> On Sun, 12 Apr 2009, Wee-Beng TAY wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi Satish,
>>>>>>>
>>>>>>> I am now using the PETSc ex2f example. I tried "make ex2f" and
>>>>>>> manage to
>>>>>>> build
>>>>>>> and run the file. Then I used the options as a reference for my
>>>>>>> visual
>>>>>>> fortran
>>>>>>> and it worked.
>>>>>>>
>>>>>>> The options are:
>>>>>>>
>>>>>>> /compile_only /debug:full /include:"Debug/"
>>>>>>> /include:"d:\cygwin\codes\petsc-3.0.0-p4\win32_mpi_debug\include"
>>>>>>> /include:"d:\cygwin\codes\petsc-3.0.0-p4\include"
>>>>>>> /include:"E:\cygwin\codes\MPICH\SDK\include" /nologo /threads
>>>>>>> /warn:nofileopt
>>>>>>> /module:"Debug/" /object:"Debug/" /pdbfile:"Debug/DF60.PDB"
>>>>>>> /fpp:"/m"
>>>>>>>
>>>>>>> and
>>>>>>>
>>>>>>> ws2_32.lib kernel32.lib user32.lib gdi32.lib winspool.lib
>>>>>>> comdlg32.lib
>>>>>>> advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib
>>>>>>> odbccp32.lib libpetscts.lib libpetscsnes.lib libpetscksp.lib
>>>>>>> libpetscdm.lib
>>>>>>> libpetscmat.lib libpetscvec.lib libpetsc.lib mpich.lib libfblas.lib
>>>>>>> libflapack.lib /nologo /subsystem:console /incremental:yes
>>>>>>> /pdb:"Debug/ex2f.pdb" /debug /machine:I386 /out:"Debug/ex2f.exe"
>>>>>>> /pdbtype:sept
>>>>>>> /libpath:"d:\cygwin\codes\petsc-3.0.0-p4\win32_mpi_debug\lib"
>>>>>>> /libpath:"E:\cygwin\codes\MPICH\SDK\lib"
>>>>>>>
>>>>>>> Now I add my own file called global.F and tried to compile, using
>>>>>>> the same
>>>>>>> options.But now it failed. The error is:
>>>>>>>
>>>>>>> --------------------Configuration: ex2f - Win32
>>>>>>> Debug--------------------
>>>>>>> Compiling Fortran...
>>>>>>> ------------------------------------------------------------------------
>>>>>>> D:\cygwin\codes\petsc-3.0.0-p4\projects\fortran\ksp\ex2f\global.F:
>>>>>>> 7: #include "include/finclude/petsc.h"
>>>>>>> ^
>>>>>>> ** error on line 7 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified
>>>>>>> in include directive.
>>>>>>> 8: #include "include/finclude/petscvec.h"
>>>>>>> ^
>>>>>>> ** error on line 8 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified
>>>>>>> in include directive.
>>>>>>> 9: #include "include/finclude/petscmat.h"
>>>>>>> ^
>>>>>>> ** error on line 9 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified
>>>>>>> in include directive.
>>>>>>> 10: #include "include/finclude/petscksp.h"
>>>>>>> ^
>>>>>>> ** error on line 10 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified in include directive.
>>>>>>> 11: #include "include/finclude/petscpc.h"
>>>>>>> ^
>>>>>>> ** error on line 11 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified in include directive.
>>>>>>> 12: #include "include/finclude/petscsys.h"
>>>>>>> ^
>>>>>>> ** error on line 12 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified in include directive.
>>>>>>> 97: #include "include/finclude/petsc.h"
>>>>>>> ^
>>>>>>> ** error on line 97 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified in include directive.
>>>>>>> 98: #include "include/finclude/petscvec.h"
>>>>>>> ^
>>>>>>> ** error on line 98 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified in include directive.
>>>>>>> 99: #include "include/finclude/petscmat.h"
>>>>>>> ^
>>>>>>> ** error on line 99 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified in include directive.
>>>>>>> 100: #include "include/finclude/petscksp.h"
>>>>>>> ^
>>>>>>> ** error on line 100 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified in include directive.
>>>>>>> 101: #include "include/finclude/petscpc.h"
>>>>>>> ^
>>>>>>> ** error on line 101 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified in include directive.
>>>>>>> 102: #include "include/finclude/petscsys.h"
>>>>>>> ^
>>>>>>> ** error on line 102 in D:\cygwin\codes\pets: cannot find file
>>>>>>> specified in include directive.
>>>>>>> global.i
>>>>>>> D:\cygwin\codes\petsc-3.0.0-p4\projects\fortran\ksp\ex2f\global.F(65)
>>>>>>> :
>>>>>>> Error:
>>>>>>> Syntax error, found ',' when expecting one of: ( : % . = =>
>>>>>>> Vec xx,b_rhs,xx_uv,b_rhs_uv
>>>>>>> -----------------^
>>>>>>> D:\cygwin\codes\petsc-3.0.0-p4\projects\fortran\ksp\ex2f\global.F(67)
>>>>>>> :
>>>>>>> Error:
>>>>>>> Syntax error, found ',' when expecting one of: ( : % . = =>
>>>>>>> Mat A_mat,A_mat_uv ! /* sparse matrix */
>>>>>>> --------------------^
>>>>>>> D:\cygwin\codes\petsc-3.0.0-p4\projects\fortran\ksp\ex2f\global.F(69)
>>>>>>> :
>>>>>>> Error:
>>>>>>> Syntax error, found ',' when expecting one of: ( : % . = =>
>>>>>>> KSP ksp,ksp_uv !/* linear solver context */
>>>>>>> -----------------^
>>>>>>> D:\cygwin\codes\petsc-3.0.0-p4\projects\fortran\ksp\ex2f\global.F(71)
>>>>>>> :
>>>>>>> Error:
>>>>>>> Syntax error, found ',' when expecting one of: ( : % . = =>
>>>>>>> PC pc,pc_uv
>>>>>>> ------------------^
>>>>>>> D:\cygwin\codes\petsc-3.0.0-p4\projects\fortran\ksp\ex2f\global.F(73)
>>>>>>> :
>>>>>>> Error:
>>>>>>> Syntax error, found END-OF-STATEMENT when expecting one of: ( : % .
>>>>>>> = =>
>>>>>>> PCType ptype
>>>>>>> -------------------------^
>>>>>>> D:\cygwin\codes\petsc-3.0.0-p4\projects\fortran\ksp\ex2f\global.F(75)
>>>>>>> :
>>>>>>> Error:
>>>>>>> Syntax error, found END-OF-STATEMENT when expecting one of: ( : % .
>>>>>>> = =>
>>>>>>> KSPType ksptype....
>>>>>>>
>>>>>>>
>>>>>>> I can get it to compile if I use :
>>>>>>>
>>>>>>> Debug/;d:\cygwin\codes\petsc-3.0.0-p4;d:\cygwin\codes\petsc-3.0.0-p4\include;d:\cygwin\codes\petsc-3.0.0-p4\win32_mpi_debug\include;E:\cygwin\codes\MPICH\SDK\include
>>>>>>>
>>>>>>> Compared to the original one above which is:
>>>>>>>
>>>>>>> Debug/;d:\cygwin\codes\petsc-3.0.0-p4\win32_mpi_debug\include;d:\cygwin\codes\petsc-3.0.0-p4\include;E:\cygwin\codes\MPICH\SDK\include
>>>>>>>
>>>>>>> Hence, there is an additional "d:\cygwin\codes\petsc-3.0.0-p4"
>>>>>>>
>>>>>>> I have attached my global.F. I wonder if this is the cause of the
>>>>>>> MPICH
>>>>>>> error.
>>>>>>>
>>>>>>> Currently, I have removed all other f90 files, except for global.F
>>>>>>> and
>>>>>>> flux_area.f90. It's when I 'm compiling flux_area.f90 that I got the
>>>>>>> MPI
>>>>>>> error
>>>>>>> stated below. I got the same error if I compile under cygwin using
>>>>>>> the
>>>>>>> same
>>>>>>> parameters.
>>>>>>>
>>>>>>> Hope you can help.
>>>>>>>
>>>>>>> Thank you very much and have a nice day!
>>>>>>>
>>>>>>> Yours sincerely,
>>>>>>>
>>>>>>> Wee-Beng Tay
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Satish Balay wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Do you get these errors with PETSc f90 examples?
>>>>>>>>
>>>>>>>> what 'USE statement' do you have in your code?
>>>>>>>>
>>>>>>>> I guess you'll have to check your code to see how you are using
>>>>>>>> f90
>>>>>>>> modules/includes.
>>>>>>>>
>>>>>>>> If you can get a minimal compileable code that can reproduce this
>>>>>>>> error - send us the code so that we can reproduce the issue
>>>>>>>>
>>>>>>>> Satish
>>>>>>>>
>>>>>>>> On Thu, 9 Apr 2009, Wee-Beng TAY wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I just built petsc-3.0.0-p4 with mpich and after that, I
>>>>>>>>> reinstalled
>>>>>>>>> my
>>>>>>>>> windows xp and installed mpich in the same directory. I'm using
>>>>>>>>> CVF
>>>>>>>>>
>>>>>>>>> Now, I found that when I'm trying to compile my code, I got the
>>>>>>>>> error:
>>>>>>>>>
>>>>>>>>> :\cygwin\codes\MPICH\SDK\include\mpif.h(105) : Error: The
>>>>>>>>> attributes
>>>>>>>>> of
>>>>>>>>> this
>>>>>>>>> name conflict with those made accessible by a USE statement.
>>>>>>>>> [MPI_STATUS_SIZE]
>>>>>>>>> INTEGER MPI_STATUS_IGNORE(MPI_STATUS_SIZE)
>>>>>>>>> --------------------------------^
>>>>>>>>> E:\cygwin\codes\MPICH\SDK\include\mpif.h(106) : Error: The
>>>>>>>>> attributes
>>>>>>>>> of
>>>>>>>>> this
>>>>>>>>> name conflict with those made accessible by a USE statement.
>>>>>>>>> [MPI_STATUS_SIZE]
>>>>>>>>> INTEGER MPI_STATUSES_IGNORE(MPI_STATUS_SIZE)
>>>>>>>>> ----------------------------------^
>>>>>>>>> E:\cygwin\codes\petsc-3.0.0-p4\include/finclude/petsc.h(154) :
>>>>>>>>> Error:
>>>>>>>>> The
>>>>>>>>> attributes of this name conflict with those made accessible by a
>>>>>>>>> USE
>>>>>>>>> statement. [MPI_DOUBLE_PRECISION]
>>>>>>>>> parameter(MPIU_SCALAR = MPI_DOUBLE_PRECISION)
>>>>>>>>> ------------------------------^
>>>>>>>>> Error executing df.exe.
>>>>>>>>>
>>>>>>>>> flux_area.obj - 3 error(s), 0 warning(s)
>>>>>>>>>
>>>>>>>>> My include option is :
>>>>>>>>>
>>>>>>>>> Debug/;$(PETSC_DIR);$(PETSC_DIR)\$(PETSC_ARCH)\;$(PETSC_DIR)\$(PETSC_ARCH)\include;$(PETSC_DIR)\include;E:\cygwin\codes\MPICH\SDK\include
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Interestingly, when I change my PETSC_DIR to petsc-dev, which
>>>>>>>>> correspond
>>>>>>>>> to an
>>>>>>>>> old build of petsc-2.3.3-p13, there is no problem.
>>>>>>>>>
>>>>>>>>> May I know what's wrong? Btw, I've converted my mpif.h from
>>>>>>>>> using "C"
>>>>>>>>> as
>>>>>>>>> comments to "!".
>>>>>>>>>
>>>>>>>>> Thank you very much and have a nice day!
>>>>>>>>>
>>>>>>>>> Yours sincerely,
>>>>>>>>>
>>>>>>>>> Wee-Beng Tay
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>
>>>>
>
>
>
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