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>
> >
> >
>
