[petsc-users] compiling petsc.h and cusp's headers

[Shiyuan]

*
*>*  Are you using the PETSc makefiles to compile it? Or did you make up that
*>* compile line yourself? Why not just use the PETSc makefile to compile it?



*Actually, the compiling command I usedd is generated by
PETSs's makefiles.* *But I am looking for something like "make
getincludedirs; make getpetscflags;
make getlinklibs" which can give me the compiling flags Petsc uses to
feed nvcc. Are there anything
like that?
*

*>*
*>*  Presumably cusp/thrust has some pattern for what include files need to be
*>* included in what order. If you do not know the pattern then why not start by
*>* copying what PETSc does, since that compiles? For example
*>* cuspvecimpl.h has
*>*
*>* #include <cublas.h>
*>* #include <cusp/blas.h>
*>* #include <thrust/device_vector.h>
*>* #include <thrust/iterator/constant_iterator.h>
*>* #include <thrust/transform.h>
*>* #include <thrust/iterator/permutation_iterator.h>
*>*
*>* while cuspmatimpl.h has
*>*
*>* #include <../src/vec/vec/impls/seq/seqcusp/cuspvecimpl.h>
*>* #include <cusp/csr_matrix.h>
*>* #include <cusp/multiply.h>
*>* /*for MatCreateSeqAIJCUSPFromTriple*/
*>* #include <cusp/coo_matrix.h>
*>*
*>* so start with at least those.   Generally just picking a couple of random
*>* include files from some C++ package (like cusp/thrust)  and including them
*>* won't work.


I did check the documentation of cusp, and I don't see a requirement about
**the order for including headers. It doesn't sound reasonable to
require programmers to enforce the order when the programmers
uses only functions from one library. Does it?( I think there is an
issue I don't see, please excuse me for my ignorance). And I did
try a few experiment where I picked some cusp examples and changed the
orders of including headers, and they do work.




*>I believe that your problem is the clash of VecType between CUSP and PETSc.
>In aijcusp.cu, we have

>#undef VecType
>#include "../src/mat/impls/aij/seq/seqcusp/cuspmatimpl.h"

 >   Matt

That explains it. But I still don't get the solution. If I want to
define a function where I call some functions provided by Petsc and
some functions  provided by cusp and thrust,
In what order should I include the headers? For example, if I want
Mat, Vec and cusp::krylov::cg.
 If I look at the aijcusp.cu where MatMult_SeqAIJCusp is defined, it
has a long list of headers,


#include "petscconf.h"
PETSC_CUDA_EXTERN_C_BEGIN
#include "../src/mat/impls/aij/seq/aij.h" /*I "petscmat.h" I*/
#include "petscbt.h"
#include "../src/vec/vec/impls/dvecimpl.h"
#include "private/vecimpl.h"
PETSC_CUDA_EXTERN_C_END
#undef VecType
#include "../src/mat/impls/aij/seq/seqcusp/cuspmatimpl.h"


#ifdef PETSC_HAVE_TXPETSCGPU

#include "csr_matrix_data.h"
#include "csr_matrix_data_gpu.h"
#include "csr_tri_solve_gpu.h"
#include "csr_tri_solve_gpu_level_scheduler.h"
#include "csr_spmv_inode.h"
#include <algorithm>
#include <vector>
#include <string>
#include <thrust/sort.h>
#include <thrust/fill.h>


But looking at this list of headers, I cannot see what files do I
really need and what else is missing if I only want Mat, Vec and
cusp::krylov::cg.
Is there a less painful way? Thanks.


Shiyuan
****

---------------------------------------------------------------------------------------------------------------------------------------------------------------------
**>* On Oct 4, 2011, at 2:07 PM, Shiyuan wrote:
*>*
*>* > Hi,
*>* >    I cannot compiling a source file with petsc.h and cusp headers like
*>* the following:
*>* >
*>* > #include"petsc.h"
*>* > #include<iostream>
*>* > #include "cusp/csr_matrix.h"
*>* > #include <cusp/krylov/cg.h>
*>* > int main(void){
*>* >     std::cout<<"Hello World!"<<std::endl;
*>* >     return 0;
*>* > }
*>* >
*>* > I use the following  to compile it:
*>* >
*>* > nvcc  -m64 -O -arch=sm_13  -c --compiler-options="-Wall -Wwrite-strings
*>* -Wno-strict-aliasing -Wno-unknown-pragmas -O
*>* -I/home/guest/sgu1/softwares/petsc-dev/include
*>* -I/home/guest/sgu1/softwares/petsc-dev/helena-cxx-nompi-os64-release/include
*>* -I/usr/local/cuda/include -I/home/guest/sgu1/softwares/cusp-library/
*>* -I/home/guest/sgu1/softwares/thrust/
*>* -I/home/guest/sgu1/softwares/petsc-dev/include/mpiuni  -DCUDA=1
*>* -I/home/guest/sgu1/softwares/slepc-dev
*>* -I/home/guest/sgu1/softwares/slepc-dev/helena-cxx-nompi-os64-release/include
*>* -I/home/guest/sgu1/softwares/slepc-dev/include
*>* -I/home/guest/sgu1/softwares/ImageMagick-6.7.2/include/ImageMagick
*>*  -D__INSDIR__= -I/home/guest/sgu1/softwares/slepc-dev
*>* -I/home/guest/sgu1/softwares/slepc-dev/helena-cxx-nompi-os64-release/include
*>* -I/home/guest/sgu1/softwares/slepc-dev/include" MyKspTmp4.cu -o MyKspTmp4.o
*>* >
*>* > and it gives me error:
*>* >
*>* /usr/local/cuda/include/thrust/detail/device/cuda/detail/b40c/vector_types.h(37):
*>* error: expected an identifier
*>* >
*>* > I think I did not do it in a correct way. I took a a look at some of
*>* petsc's .cu files, they usually include a  long list of headers. Can petsc.h
*>* directly included in a source code with cusp headers? What's the correct way
*>* to do it?  Does the makefile system in petsc provide the command or flags to
*>* do that? How can I obtain those flags?
*>* >
*>* > And after I compile it and obtain .o files, can I use g++ to link the .o
*>* files with petcs libs and other .o files as usual, i.e.,
*>* >     g++ -o $(BIN_DIR)/$@ $(CPPFLAGS) $@.s $(objects) $(PETSC_LIB)
*>* $(OTHERS)
*>* > or I need to do some extra steps and some specific linking flags to do
*>* that?
*>* > Thanks.
*>* >
*>* > Shiyuan
*>* >
*>* >
*>* >
*>*
*>*
*
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