[petsc-users] Petsc+Chombo problem

Thu Dec 22 12:07:34 CST 2016

On Thu, Dec 22, 2016 at 11:54 AM, Sharp Stone <thronesf at gmail.com> wrote:

> Mat and Satish,
>
> Thank you for your replies. I'm using Chombo-3.2 + Petsc-3.7.4. I have not
> yet received replies from Chombo. So I have to ask you guys to see if my
> paths have been correctly set up. When I changed the #include
> <petsc-private/pcimpl.h> to #include<petsc/private/pcimpl.h>, I still got
> the errors "PetscCompGrid.H:19:34: error: petsc-private/pcimpl.h: No such
> file or directory". Highly appreciate your help!
>

Clearly there was another include. Satish is right that you need to get the
right version for Chombo.

   Matt

> On Thu, Dec 22, 2016 at 12:05 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> On Thu, Dec 22, 2016 at 11:01 AM, Sharp Stone <thronesf at gmail.com> wrote:
>>
>>> Dear folks,
>>>
>>> I'm now using Chombo with Petsc solver. When compiling the Chombo
>>> examples of Petsc, I always got errors below. I wonder if anyone has such
>>> experience to get rid of these. Thanks very much in advance!
>>>
>>>
>>> In file included from PetscCompGrid.cpp:13:
>>> PetscCompGrid.H:19:34: error: petsc-private/pcimpl.h: No such file or
>>> directory
>>>
>>
>> You might have a version mismatch here. PETSc changed the directory
>> structure to conform better to the Linux standard
>>
>>   $PETSC_DIR/include/petsc-private
>>
>> became
>>
>>   $PETSC_DIR/include/petsc/private
>>
>>   Thanks,
>>
>>     Matt
>>
>>
>>> In file included from PetscCompGrid.cpp:13:
>>> PetscCompGrid.H:55: error: ‘Mat’ does not name a type
>>> PetscCompGrid.H:60: error: ‘PetscErrorCode’ does not name a type
>>> PetscCompGrid.H:62: error: ‘PetscErrorCode’ does not name a type
>>> PetscCompGrid.H:63: error: ‘PetscErrorCode’ does not name a type
>>> PetscCompGrid.H:66: error: ‘PetscInt’ was not declared in this scope
>>> PetscCompGrid.H:66: error: template argument 1 is invalid
>>> PetscCompGrid.H:76: error: ‘PetscErrorCode’ does not name a type
>>> PetscCompGrid.H:90: error: ‘PetscInt’ was not declared in this scope
>>> PetscCompGrid.H:90: error: template argument 1 is invalid
>>> PetscCompGrid.H:90: error: template argument 1 is invalid
>>> PetscCompGrid.H:90: error: template argument 1 is invalid
>>> PetscCompGrid.H:90: error: template argument 1 is invalid
>>> PetscCompGrid.H:92: error: ‘PetscInt’ was not declared in this scope
>>> PetscCompGrid.H:92: error: template argument 1 is invalid
>>> PetscCompGrid.H:92: error: template argument 1 is invalid
>>> PetscCompGrid.H:92: error: template argument 1 is invalid
>>> PetscCompGrid.H:92: error: template argument 1 is invalid
>>> PetscCompGrid.H:93: error: ‘PetscInt’ was not declared in this scope
>>> PetscCompGrid.H:93: error: template argument 1 is invalid
>>> PetscCompGrid.H:93: error: template argument 1 is invalid
>>> PetscCompGrid.H:93: error: template argument 1 is invalid
>>> PetscCompGrid.H:93: error: template argument 1 is invalid
>>> PetscCompGrid.H:97: error: ‘Mat’ does not name a type
>>> PetscCompGrid.H: In constructor ‘PetscCompGrid::PetscCompGrid(int)’:
>>> PetscCompGrid.H:35: error: class ‘PetscCompGrid’ does not have any field
>>> named ‘m_mat’
>>> PetscCompGrid.H: At global scope:
>>> PetscCompGrid.H:138: error: ‘PetscReal’ does not name a type
>>> PetscCompGrid.H:140: error: ISO C++ forbids declaration of ‘PetscReal’
>>> with no type
>>> PetscCompGrid.H:140: error: expected ‘;’ before ‘*’ token
>>> PetscCompGrid.cpp: In destructor ‘virtual CompBC::~CompBC()’:
>>> PetscCompGrid.cpp:38: error: ‘m_Rcoefs’ was not declared in this scope
>>> PetscCompGrid.cpp:38: error: ‘PetscFree’ was not declared in this scope
>>> PetscCompGrid.cpp: In constructor ‘CompBC::CompBC(int, IntVect)’:
>>> PetscCompGrid.cpp:41: error: class ‘CompBC’ does not have any field
>>> named ‘m_Rcoefs’
>>> PetscCompGrid.cpp: In member function ‘void CompBC::define(int,
>>> IntVect)’:
>>> PetscCompGrid.cpp:49: error: ‘m_Rcoefs’ was not declared in this scope
>>> PetscCompGrid.cpp:49: error: ‘PetscFree’ was not declared in this scope
>>> PetscCompGrid.cpp:54: error: ‘PetscReal’ was not declared in this scope
>>> PetscCompGrid.cpp:54: error: ‘m_Rcoefs’ was not declared in this scope
>>> PetscCompGrid.cpp:54: error: ‘PetscMalloc’ was not declared in this scope
>>> PetscCompGrid.cpp: At global scope:
>>> PetscCompGrid.cpp:59: error: ‘PetscReal’ does not name a type
>>> PetscCompGrid.cpp: In member function ‘virtual void
>>> ConstDiriBC::createCoefs()’:
>>> PetscCompGrid.cpp:72: error: ‘m_Rcoefs’ was not declared in this scope
>>> PetscCompGrid.cpp:77: error: ‘m_Rcoefs’ was not declared in this scope
>>> PetscCompGrid.cpp:85: error: ‘m_Rcoefs’ was not declared in this scope
>>> PetscCompGrid.cpp:93: error: ‘m_Rcoefs’ was not declared in this scope
>>> PetscCompGrid.cpp: In member function ‘virtual void
>>> ConstDiriBC::operator()(FArrayBox&, const Box&, const ProblemDomain&,
>>> Real, bool)’:
>>> PetscCompGrid.cpp:137: error: ‘m_Rcoefs’ was not declared in this scope
>>> PetscCompGrid.cpp: In member function ‘virtual void
>>> PetscCompGrid::clean()’:
>>> PetscCompGrid.cpp:154: error: ‘m_mat’ was not declared in this scope
>>> PetscCompGrid.cpp:156: error: ‘MatDestroy’ was not declared in this scope
>>> PetscCompGrid.cpp: In member function ‘virtual void
>>> PetscCompGrid::define(const ProblemDomain&, Vector<DisjointBoxLayout>&,
>>> Vector<int>&, BCHolder, const RealVect&, int, int)’:
>>> PetscCompGrid.cpp:218: error: request for member ‘resize’ in
>>> ‘((PetscCompGrid*)this)->PetscCompGrid::m_GIDs’, which is of non-class
>>> type ‘int’
>>> PetscCompGrid.cpp:219: error: request for member ‘resize’ in
>>> ‘((PetscCompGrid*)this)->PetscCompGrid::m_crsSupportGIDs’, which is of
>>> non-class type ‘int’
>>> PetscCompGrid.cpp:220: error: request for member ‘resize’ in
>>> ‘((PetscCompGrid*)this)->PetscCompGrid::m_fineCoverGIDs’, which is of
>>> non-class type ‘int’
>>> PetscCompGrid.cpp:249: error: ‘PetscInt’ was not declared in this scope
>>> PetscCompGrid.cpp:249: error: expected `;' before ‘my0’
>>> PetscCompGrid.cpp:256: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:256: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:256: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:256: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:256: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:257: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:257: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:257: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:257: error: new initializer expression list treated as
>>> compound expression
>>> PetscCompGrid.cpp:257: error: cannot convert ‘IntVect’ to ‘int’ in
>>> initialization
>>> PetscCompGrid.cpp:261: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:261: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:261: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:261: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:262: error: request for member ‘setVal’ in ‘gidfab’,
>>> which is of non-class type ‘int’
>>> PetscCompGrid.cpp:276: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:281: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:288: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:288: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:288: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:288: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:295: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:295: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:295: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:295: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:299: error: ‘gidfab’ cannot be used as a function
>>> PetscCompGrid.cpp:299: error: ‘my0’ was not declared in this scope
>>> PetscCompGrid.cpp:308: error: ‘MPI_Comm’ was not declared in this scope
>>> PetscCompGrid.cpp:308: error: expected `;' before ‘wcomm’
>>> PetscCompGrid.cpp:310: error: ‘wcomm’ was not declared in this scope
>>> PetscCompGrid.cpp:310: error: ‘m_mat’ was not declared in this scope
>>> PetscCompGrid.cpp:310: error: ‘MatCreate’ was not declared in this scope
>>> PetscCompGrid.cpp:311: error: ‘my0’ was not declared in this scope
>>> PetscCompGrid.cpp:311: error: ‘PETSC_DECIDE’ was not declared in this
>>> scope
>>> PetscCompGrid.cpp:311: error: ‘MatSetSizes’ was not declared in this
>>> scope
>>> PetscCompGrid.cpp:312: error: ‘MatSetBlockSize’ was not declared in this
>>> scope
>>> PetscCompGrid.cpp:313: error: ‘MATAIJ’ was not declared in this scope
>>> PetscCompGrid.cpp:313: error: ‘MatSetType’ was not declared in this scope
>>> PetscCompGrid.cpp:314: error: ‘MatSetFromOptions’ was not declared in
>>> this scope
>>> PetscCompGrid.cpp:334: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:334: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:334: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:334: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:338: error: ‘gidfab’ cannot be used as a function
>>> PetscCompGrid.cpp:338: error: ‘gidfab’ cannot be used as a function
>>> PetscCompGrid.cpp:339: error: ‘gidfab’ cannot be used as a function
>>> PetscCompGrid.cpp:342: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:348: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:350: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:350: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:350: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:350: error: invalid type in declaration before ‘;’
>>> token
>>> PetscCompGrid.cpp:358: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:358: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:358: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:358: error: new initializer expression list treated as
>>> compound expression
>>> PetscCompGrid.cpp:358: error: cannot convert ‘const IntVect’ to ‘int’ in
>>> initialization
>>> PetscCompGrid.cpp:359: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:359: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:359: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:359: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:359: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:363: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:363: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:363: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:363: error: no match for ‘operator[]’ in ‘* pl[dit]’
>>> PetscCompGrid.cpp:364: error: request for member ‘setVal’ in ‘gidfab’,
>>> which is of non-class type ‘int’
>>> PetscCompGrid.cpp:367: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:367: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:379: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:379: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:379: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:379: error: new initializer expression list treated as
>>> compound expression
>>> PetscCompGrid.cpp:379: error: cannot convert ‘const IntVect’ to ‘int’ in
>>> initialization
>>> PetscCompGrid.cpp:380: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:380: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:380: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:380: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:380: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:384: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:384: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:384: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:384: error: no match for ‘operator[]’ in ‘* pl[dit]’
>>> PetscCompGrid.cpp:385: error: request for member ‘setVal’ in ‘gidfab’,
>>> which is of non-class type ‘int’
>>> PetscCompGrid.cpp:388: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:388: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:394: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:394: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:394: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:394: error: no match for ‘operator[]’ in ‘* pl[dit]’
>>> PetscCompGrid.cpp:398: error: request for member ‘box’ in ‘gidfab’,
>>> which is of non-class type ‘int’
>>> PetscCompGrid.cpp: At global scope:
>>> PetscCompGrid.cpp:409: error: ‘PetscErrorCode’ does not name a type
>>> PetscCompGrid.cpp: In member function ‘virtual void
>>> PetscCompGrid::applyBCs(IntVect, int, const DataIndex&, Box,
>>> StencilTensor&)’:
>>> PetscCompGrid.cpp:611: error: ‘class ConstDiriBC’ has no member named
>>> ‘getCoef’
>>> PetscCompGrid.cpp: In member function ‘virtual void
>>> PetscCompGrid::InterpToCoarse(IntVect, int, const DataIndex&,
>>> StencilTensor&)’:
>>> PetscCompGrid.cpp:699: error: ‘PetscInt’ was not declared in this scope
>>> PetscCompGrid.cpp:699: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:699: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:699: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:700: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:700: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:700: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:700: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:709: error: ‘gidfab’ cannot be used as a function
>>> PetscCompGrid.cpp:720: error: expected `;' before ‘cidx’
>>> PetscCompGrid.cpp:720: error: ‘cidx’ was not declared in this scope
>>> PetscCompGrid.cpp:723: error: ‘kk’ was not declared in this scope
>>> PetscCompGrid.cpp:741: error: ‘supgidfab’ cannot be used as a function
>>> PetscCompGrid.cpp:743: error: ‘supgidfab’ cannot be used as a function
>>> PetscCompGrid.cpp: In member function ‘virtual void
>>> PetscCompGrid::InterpToFine(IntVect, int, const DataIndex&,
>>> StencilTensor&)’:
>>> PetscCompGrid.cpp:772: error: ‘PetscInt’ was not declared in this scope
>>> PetscCompGrid.cpp:772: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:772: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:772: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:773: error: ‘PetscInt’ cannot appear in a
>>> constant-expression
>>> PetscCompGrid.cpp:773: error: template argument 1 is invalid
>>> PetscCompGrid.cpp:773: error: invalid type in declaration before ‘=’
>>> token
>>> PetscCompGrid.cpp:773: error: invalid types ‘int[int]’ for array
>>> subscript
>>> PetscCompGrid.cpp:774: error: request for member ‘box’ in ‘covergidfab’,
>>> which is of non-class type ‘int’
>>> PetscCompGrid.cpp:783: error: ‘gidfab’ cannot be used as a function
>>> PetscCompGrid.cpp: At global scope:
>>> PetscCompGrid.cpp:812: error: ‘PetscErrorCode’ does not name a type
>>> PetscCompGrid.cpp:917: error: ‘PetscErrorCode’ does not name a type
>>> PetscCompGrid.cpp:964: error: ‘PetscErrorCode’ does not name a type
>>> make[3]: *** [o/2d.Linux.64.mpicxx.mpif90.DEBUG.PETSC/PetscCompGrid.o]
>>> Error 1
>>> make[2]: *** [AMRElliptic] Error 2
>>> make[1]: *** [AMRElliptic] Error 2
>>> make: *** [execPETSc] Error 2
>>>
>>> --
>>> Best regards,
>>>
>>> Feng
>>>
>>
>>
>>
>> --
>> 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
>>
>
>
>
> --
> Best regards,
>
> Feng
>

-- 
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
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