This is happening because PETSc was configured to compile with the C compiler and use C complex numbers, meanwhile your main program is c++ so doesn’t appreciate the C version of complex numbers (yes, C and C++ are not as friendly as they should be).
I’ll try a build and see if I can fix this. You can run the same configure but use the additional ./configure option —with-clanguage=c++ (two dashes before the with) and it should work because then everything will get built with the C++ compiler and using C++ complex. Barry On Jul 19, 2014, at 5:16 PM, Francis Poulin <fpou...@uwaterloo.ca> wrote: > Hello again, > > My installation on my desktop seems to work well. > > I am having problems with my installation of petsc on my mac though. It > seems to go through the installation alright and even shows me the nice graph > of the performance. I used, > > ./configure --with-scalar-type=complex --with-cc=clang --with-cxx=clang++ > --with-fc=gfortran --with-c2html=0 --download-mpich > > However, when I try compiling the main.cpp I get an error, which I copied > below. I know this should work and wonder what my petsc installation is not > finding. Any suggestions? > > Cheers, Francis > > > TEST_MPI fpoulin$ make all -s > clang: warning: argument unused during compilation: > '-L/Users/fpoulin/software/petsc/lib' > clang: warning: argument unused during compilation: > '-L/Users/fpoulin/software/petsc/darwin10.6.0-c-debug/lib' > In file included from main.cpp:17: > In file included from /Users/fpoulin/software/petsc/include/petsc.h:5: > In file included from /Users/fpoulin/software/petsc/include/petscbag.h:4: > In file included from /Users/fpoulin/software/petsc/include/petscsys.h:366: > /Users/fpoulin/software/petsc/include/petscmath.h:562:10: error: use of > undeclared identifier 'cpow'; did you mean 'pow'? > return PetscPowScalar(base,cpower); > ^ > /Users/fpoulin/software/petsc/include/petscmath.h:252:31: note: expanded from > macro 'PetscPowScalar' > #define PetscPowScalar(a,b) PetscPowComplex(a,b) > ^ > /Users/fpoulin/software/petsc/include/petscmath.h:176:38: note: expanded from > macro 'PetscPowComplex' > #define PetscPowComplex(a,b) cpow(a,b) > ^ > /usr/include/math.h:443:15: note: 'pow' declared here > extern double pow(double, double); > ^ > 1 error generated. > make: *** [build/main.o] Error 1 > > > > ------------------ > Francis Poulin > Associate Professor > Associate Chair, Undergraduate Studies > Department of Applied Mathematics > University of Waterloo > > email: fpou...@uwaterloo.ca > Web: https://uwaterloo.ca/poulin-research-group/ > Telephone: +1 519 888 4567 x32637 > > > ________________________________________ > From: Francis Poulin > Sent: Saturday, July 19, 2014 2:09 PM > To: petsc-users > Subject: RE: [petsc-users] Question about PETSc installs and MPI > > Hello Satish, > > Thanks for the help on both counts. > > 1) I installed csh and petscmpiexec works, but I think I will stick to mpirun > > 2) Your modifications of the code make things work beautifully! > > Again, sorry to bug you but the help is greatly appreciated. > > Cheers, Francis > > ------------------ > Francis Poulin > Associate Professor > Associate Chair, Undergraduate Studies > Department of Applied Mathematics > University of Waterloo > > email: fpou...@uwaterloo.ca > Web: https://uwaterloo.ca/poulin-research-group/ > Telephone: +1 519 888 4567 x32637 > > > ________________________________________ > From: Satish Balay [ba...@mcs.anl.gov] > Sent: Saturday, July 19, 2014 11:52 AM > To: petsc-users > Cc: Francis Poulin > Subject: Re: [petsc-users] Question about PETSc installs and MPI > > And it appears the original code was tested with 'real' numbers and > petsc-3.4. It was > not really tested with complex numbers. I had to make the following changes > for > it to run with complex & petsc-3.5 > > Satish > > --------- > > balay@es^/scratch/balay/test $ ../petsc-3.5.0/arch-linux2-c-debug/bin/mpiexec > -n 8 valgrind --tool=memcheck -q ./main > Dot Product Check... > > Dot Product (should be 2*256) = 512.000000 > > Done. > > Derivative Check... > > Min (should be 0; if halos not defined properly, would be > -1.0/dDeltaX) = 0.000000 > Max (should be 0; if halos not defined properly, would be > +1.0/dDeltaX) = 0.000000 > > Done. > balay@es^/scratch/balay/test $ diff -Nru main.cpp.orig main.cpp > --- main.cpp.orig 2014-07-19 10:48:21.072486076 -0500 > +++ main.cpp 2014-07-19 10:47:26.977985006 -0500 > @@ -31,9 +31,9 @@ > // DMDA Environment > ////////////////////////////////////////////////////////////////////////// > // Boundary Conditions > - DMDABoundaryType bx = DMDA_BOUNDARY_GHOSTED; > - DMDABoundaryType by = DMDA_BOUNDARY_NONE; // no boundary points since nGx > = 1 > - DMDABoundaryType bz = DMDA_BOUNDARY_NONE; // no boundary points since nGz > = 1 > + DMBoundaryType bx = DM_BOUNDARY_GHOSTED; > + DMBoundaryType by = DM_BOUNDARY_NONE; // no boundary points since nGx = 1 > + DMBoundaryType bz = DM_BOUNDARY_NONE; // no boundary points since nGz = 1 > > > ////////////////////////////////////////////////////////////////////////// > // Stencil type > @@ -96,7 +96,7 @@ > DMDAGetCorners(m_3da, &si, 0, 0, &ei, 0, 0); > > // Access the elements of the local arrays as C++ multi-dim. array > structures > - double ***pvecA, ***pvecB; > + PetscScalar ***pvecA, ***pvecB; > DMDAVecGetArray(m_3da, m_vecA, &pvecA); > DMDAVecGetArray(m_3da, m_vecB, &pvecB); > > @@ -132,7 +132,7 @@ > VecAssemblyEnd(m_gTempB); > > // Take dot product > - double dDotProduct; > + PetscScalar dDotProduct; > VecDot(m_gTempA, m_gTempB, &dDotProduct); > > // Output dot product to check > @@ -163,7 +163,7 @@ > // Alternative (local vector): VecDuplicate(m_vecA, &m_vecDx); > > // Access the data in the vectors by using pointers > - double ***pDx; > + PetscScalar ***pDx; > DMDAVecGetArray(m_3da, m_vecA, &pvecA); > DMDAVecGetArray(m_3da, m_vecDx, &pDx); > > balay@es^/scratch/balay/test $ > > > > On Sat, 19 Jul 2014, Satish Balay wrote: > >> On Sat, 19 Jul 2014, Francis Poulin wrote: >> >>> Hello Barry, >>> >>> I was one of the two people that had difficulties with getting the correct >>> results with John's code. Previously, I didn't have valgrind installed so >>> I installed it using apt-get. Then I configured it using the following: >>> >>> ./configure --with-scalar-type=complex --with-cc=gcc -—with-cxx=c++ >>> --with-fc=gfortran --with-c2html=0 --download-mpich --download-scalapack >>> --download-hypre >>> >>> This is on ubuntu and is different from what I tried before in that now I >>> am downloading mpich, scalapack and hypre. I decided to download >>> scalapack since that seems like it could be useful. I was told that HYPRE >>> doesn't work with complex variables. Too bad, but not a big deal. >> >> PETSc does not use scalapack. Its useful only if you are using mumps.. >> >> --download-metis --download-parmetis --download-scalapack --download-mumps >> >>> >>> It completes the configure, make all and make test and even gives me the >>> figures of the parallel efficiency (or not quite efficiency maybe). I >>> didn't catch any errors, but there are possible errors in the log. When I >>> went to try making an example I found that I can't use petscmpiexec to run >>> anything in serial or parallel. >>> >>> fpoulin@vortex:~/software/petsc/src/ts/examples/tutorials$ >>> /home/fpoulin/software/petsc/bin/petscmpiexec -n 1 ./ex1 >>> -bash: /home/fpoulin/software/petsc/bin/petscmpiexec: /bin/csh: bad >>> interpreter: No such file or directory >> >> Perhaps you do not have csh installed on this machine. You can use mpiexec >> directly >> >> ./ex1 >> /home/fpoulin/software/petsc/arch-linux2-c-debug/bin/mpiexec -n 1 ./ex1 >> /home/fpoulin/software/petsc/arch-linux2-c-debug/bin/mpiexec -n 2 ./ex1 >> >> Satish >> >>> >>> I am sorry to bother you with this. I am also having issues with my >>> installation on my mac but I thought if i can figure this one out then >>> maybe I will have a better idea what's wrong with the other. >>> >>> Thank, >>> Francis >>> >>> >>> ------------------ >>> Francis Poulin >>> Associate Professor >>> Associate Chair, Undergraduate Studies >>> Department of Applied Mathematics >>> University of Waterloo >>> >>> email: fpou...@uwaterloo.ca >>> Web: https://uwaterloo.ca/poulin-research-group/ >>> Telephone: +1 519 888 4567 x32637 >>> >>> >>> ________________________________________ >>> From: Barry Smith [bsm...@mcs.anl.gov] >>> Sent: Friday, July 18, 2014 9:57 PM >>> To: John Yawney >>> Cc: petsc-users@mcs.anl.gov; Francis Poulin; Kim Usi >>> Subject: Re: [petsc-users] Question about PETSc installs and MPI >>> >>> I ran the program on linux with 1,2, 4 processes under valgrind for both >>> types of boundary conditions and it ran fine. >>> >>> Suggest your colleagues do a test configure of PETSc using >>> —download-mpich and see if they still get the problem or if it runs ok. >>> >>> The can also run with valgrind and see what it reports. >>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>> >>> Barry >>> >>> On Jul 18, 2014, at 8:16 PM, John Yawney <jyawney...@gmail.com> wrote: >>> >>>> Hello, >>>> >>>> I had a question about PETSc installations. On my local computer I >>>> configured PETSc (v 3.4.2) using the options: >>>> >>>> ./configure --with-cc=mpicc --with-cxx=mpic++ --download-f-blas-lapack >>>> --download-mpich --download-hypre >>>> >>>> I wrote a test program that defines a vector using DMDAs, computes a dot >>>> product, exchanges halo elements, and computes a low-order FD derivative >>>> of the vector. Under my installation of PETSc everything works fine. For >>>> some reason, when my colleagues run the program, they get segmentation >>>> fault errors. If they change the y and z boundary types to GHOSTED as >>>> well, they get the program to run until the end (seg faults at the end >>>> though) but they get a local value of the dot product. I've attached the >>>> main.cpp file for this script. >>>> >>>> When they installed their versions of PETSc they didn't use the >>>> --download-mpich option but instead used either: >>>> ./configure --download-f-blas-lapack --with-scalar-type=complex >>>> or with the option: >>>> --with-mpi-dir=/home/kim/anaconda/pkgs/mpich2-1.3-py27_0 >>>> >>>> Could this be causing a problem with the parallelization under PETSc? >>>> >>>> Thanks for the help and sorry for the long question. >>>> >>>> Best regards, >>>> John >>>> <main.cpp> >>> >>> >>
