[petsc-users] Petsc+Chombo problem

Matthew Knepley knepley at gmail.com
Thu Dec 22 12:23:54 CST 2016 

On Thu, Dec 22, 2016 at 12:14 PM, Sharp Stone <thronesf at gmail.com> wrote:

> Thanks, Matt! Both libraries are the latest, and I guess they are
> compatible except for the path setups. I'm waiting for their reply.
>

No they are clearly not compatible.


> You are right. There's another file that needs to be modified. But the
> error can't go away "PetscCompGrid.H:19:34: error: petsc/private/pcimpl.h:
> No such file or directory". If you guys have any ideas, please let me know.
>

1) CLEARLY, you must replace all instances of this in Chombo in order to
get rid of this error

2) EVEN if you do that, it won't matter at all. If Chombo is including
those headers, it is using a different interface, and if
    you include the current headers, you will get type mismatches.

2) The ONLY solution here is to talk to the Chombo people and see which
version is compatible.

If the Chombo people do not respond, you should really think about whether
it is a piece of software you want to be using.

   Matt


> Thank you very much!
>
> On Thu, Dec 22, 2016 at 1:07 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> 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
>>
>
>
>
> --
> 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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