April 2012 - petsc-dev - mailman3.cels.anl.gov

nvcc -g3 error
by Ben Jamroz 12 Apr '12

12 Apr '12

Hi, I've had trouble building a debug version of petsc-dev with nvcc. At compile time I was getting the following error. =============================================================== libfast in: /scr_0/jamroz/petsc-dev-jamroz/src/vec/vec/impls/seq/seqcusp nvcc -O3 -g -g -arch=sm_20 -c --compiler-options=-g -O3 -g3 -fno-inline -O0 -I/scr_0/jamroz/petsc-dev-jamroz/include -I/scr_0/jamroz/petsc-dev-jamroz/arch-linux2-c-debug/include -I/usr/local/cuda/4.1/cuda/include -I/scr_0/jamroz/gpuPETSc/txpetscgpu/include -I/scr_0/jamroz/ -I/usr/local/cuda/4.1/cuda/include/ -I/usr/mpi/gcc/openmpi-1.4.3/include -D__INSDIR__=src/vec/vec/impls/seq/seqcusp/ veccusp.cu <built-in>(1): error: "__STDC_HOSTED__" is predefined; attempted redefinition ignored <built-in>(1): error: "__WCHAR_TYPE__" is predefined; attempted redefinition ignored <built-in>(1): error: "__x86_64" is predefined; attempted redefinition ignored <built-in>(1): error: "__x86_64__" is predefined; attempted redefinition ignored <built-in>(1): error: "__linux__" is predefined; attempted redefinition ignored <built-in>(1): error: "__unix__" is predefined; attempted redefinition ignored <built-in>(1): error: "unix" is predefined; attempted redefinition ignored 7 errors detected in the compilation of "/tmp/tmpxft_00006e29_00000000-7_veccusp.cpp3.i". /usr/bin/ar: veccusp.o: No such file or directory =============================================================== It turns out that -g3 (debug level) in the --compiler-options was causing the trouble. Commenting out this line in BuildSystem/config/compilerOptions.py (line 24) fixed this error. According to http://gcc.gnu.org/onlinedocs/gcc/Debugging-Options.html the default debug is level 2. Just a heads up. -Ben ps. My config script was: ./configure --with-debugging=1 --with-mpi=1 --with-thrust-dir=/usr/local/cuda/4.1/cuda/include/ --with-cusp-dir=/scr_0/jamroz/ --CFLAGS="-g -O3" --with-cuda=1 --with-cuda-dir=/usr/local/cuda/4.1/cuda --CUDAFLAGS="-O3 -g" --with-cudac=nvcc --with-cuda-arch=sm_20 --with-precision=double --with-txpetscgpu=1 --download-txpetscgpu=no --with-txpetscgpu-dir=/scr_0/jamroz/gpuPETSc/txpetscgpu -- Ben Jamroz jamroz(a)txcorp.com Tech-X Corporation 5621 Arapahoe Ave, Suite A Boulder, CO 80303 Phone: (720) 974-1853, Fax: (303) 448-7756

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Re: [petsc-dev] KKT MG
by Dmitry Karpeev 11 Apr '12

11 Apr '12

Are you thinking of using PCSetModifyMatrices()? Actually, this brings up another issue (now on petsc-dev). Should this callback be attached to a Mat, instead of a PC? Then MatGetSubMatrices() can use this callback on each of the extracted submatrices, if necessary. In the case of a KKT system, it would then set the nontrivial block size on the primal submatrix. Dmitry. On Wed, Apr 11, 2012 at 3:33 PM, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > The original matrix might not have blocks, but that does not mean that a > submatrix does not have blocks. > On Apr 11, 2012 3:30 PM, "Mark F. Adams" <mark.adams(a)columbia.edu> wrote: > >> >> On Apr 11, 2012, at 11:24 AM, Jed Brown wrote: >> >> On Wed, Apr 11, 2012 at 12:01, Mark F. Adams <mark.adams(a)columbia.edu>wrote: >> >>> eed to know the block size (eg, 4). I get this info by having the user >>> set the block size of the matrix. This is what you should do for the >>> non-contact test. This will not work with contact equations ... or at >>> least it does not make sense. How can I get this info? >>> >>> 1) hard wire it: if I see 7 vectors then bs=4. >>> >> >> Hell no. >> >> >>> >>> 2) have setNearNullSpace take a block size, and set the vector block >>> size, which I can get like I do from the matrix now. >>> >> >> No. >> >> When you call MatGetSubMatrix(), you will get back a matrix that has a >> near null space (and a block size if that happens to be relevant; there >> will not be a block size if deformation and thermodynamics are in different >> spaces). Don't worry about how that is done, just call MatGetSubMatrix(). >> >> >> OK, I don't see how you know that the block size is 4 ... do you call >> MatSetBlockSize even if there are constraints that are not blocked? >> >>

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Re: [petsc-dev] single-precision sdot_ in OS X Lion.
by Sean Farley 11 Apr '12

11 Apr '12

> > It seems that BLAS sdot_ in OX X Lion actually returns "double" > instead of "float". I'm using the attached patch with success. Of > course, it would need a proper configure test that I'm not in position > to provide but Matt volunteered to write. Can any of you (Sean?) > running Lion try to reproduce the issue using configure > --with-precision=single && make all && make test , and then try my > patch? Sure, I'll take a look at this today.

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single-precision sdot_ in OS X Lion.
by Lisandro Dalcin 11 Apr '12

11 Apr '12

It seems that BLAS sdot_ in OX X Lion actually returns "double" instead of "float". I'm using the attached patch with success. Of course, it would need a proper configure test that I'm not in position to provide but Matt volunteered to write. Can any of you (Sean?) running Lion try to reproduce the issue using configure --with-precision=single && make all && make test , and then try my patch? -- Lisandro Dalcin --------------- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169

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Re: [petsc-dev] What is this?
by Barry Smith 11 Apr '12

11 Apr '12

On Apr 11, 2012, at 6:38 AM, Matthew Knepley wrote: > https://bitbucket.org/petsc/petsc-dev/changeset/ee2a81f77333 > > I wanted all those braces. I have braces around every if clause, no exceptions. Why? They are confusing and serve no useful purpose. None of the rest of the code has them. Do you want them in all the code? And on the same line as the SETERRQ? Not indented on a separate line like all the other clauses? We really have to switch to use some programmable pretty printer so everyone can have their favorite styles in the Emacs buffer but there is a canonical version in the repository. Barry > > Matt > > -- > 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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What is this?
by Matthew Knepley 11 Apr '12

11 Apr '12

https://bitbucket.org/petsc/petsc-dev/changeset/ee2a81f77333 I wanted all those braces. I have braces around every if clause, no exceptions. Matt -- 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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Re: [petsc-dev] PCApplyTranspose in BiCG
by Alexander Grayver 11 Apr '12

11 Apr '12

On 10.04.2012 14:19, Jed Brown wrote: > > There is no space allocated at (44,44); note that counting is 0-based. > This consistency check has been in PETSc for many years, so I don't > know why you didn't trip it in earlier runs. Do you have some options > in PETSC_OPTIONS or .petscrc? Jed, This is not possible: >> A = PetscBinaryRead('A.dat','complex',true); >> find(diag(A)==0) ans = Empty matrix: 0-by-1 >> A(45,45) ans = (1,1) 7.999999999999997e+002 +6.316546778308559e-009i Sorry, I forgot to mention that this is double complex matrix and vector. Have you read it as real double? > > If it is of any help files are here: > http://dl.dropbox.com/u/60982984/A.dat > http://dl.dropbox.com/u/60982984/RHS.dat > > Is this possible to look up changes in one file only? > > > $ hg log src/ksp/ksp/impls/tfqmr/ > > But the problem was clearly not in that file. -- Regards, Alexander

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Re: [petsc-dev] make reconfigure
by Lisandro Dalcin 10 Apr '12

10 Apr '12

On 10 April 2012 22:00, Satish Balay <balay(a)mcs.anl.gov> wrote: > On Tue, 10 Apr 2012, Satish Balay wrote: > >> On Tue, 10 Apr 2012, Lisandro Dalcin wrote: >> >> > On 10 April 2012 21:12, Satish Balay <balay(a)mcs.anl.gov> wrote: >> > > Lisandro has commit access - so can push directly. [Lisandro - can you >> > > commit/push?] >> > > >> > >> > Yes, but I'm visiting KAUST, and while being at home, sometimes my ssh >> > connections randomly stop working for a random period of time. >> >> I can push your diffs - but perhaps you might want to test if ssh on >> port 443 [https port] works arround the difficulties you are having? >> >> hg pull -u ssh://[email protected]:443//hg/petsc/petsc-dev > > pushed now > Many thanks! PS: pulling is not an issue, as I can always use http. But for pushing, your tip may prove useful. Thanks. -- Lisandro Dalcin --------------- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169

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Re: [petsc-dev] make reconfigure
by Satish Balay 10 Apr '12

10 Apr '12

On Tue, 10 Apr 2012, Satish Balay wrote: > On Tue, 10 Apr 2012, Lisandro Dalcin wrote: > > > On 10 April 2012 21:12, Satish Balay <balay(a)mcs.anl.gov> wrote: > > > Lisandro has commit access - so can push directly. [Lisandro - can you > > > commit/push?] > > > > > > > Yes, but I'm visiting KAUST, and while being at home, sometimes my ssh > > connections randomly stop working for a random period of time. > > I can push your diffs - but perhaps you might want to test if ssh on > port 443 [https port] works arround the difficulties you are having? > > hg pull -u ssh://[email protected]:443//hg/petsc/petsc-dev pushed now satish

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Re: [petsc-dev] Fwd: A few remaining issues with Mat block sizes
by Satish Balay 10 Apr '12

10 Apr '12

pushed now. satish On Tue, 10 Apr 2012, Barry Smith wrote: > > Satish, > > Please add this patch. > > Thanks > > Barry > > > Begin forwarded message: > > > From: Lisandro Dalcin <dalcinl(a)gmail.com> > > Date: April 10, 2012 12:43:39 PM CDT > > To: For users of the development version of PETSc <petsc-dev(a)mcs.anl.gov> > > Subject: Re: [petsc-dev] A few remaining issues with Mat block sizes > > Reply-To: For users of the development version of PETSc <petsc-dev(a)mcs.anl.gov> > > > > On 10 April 2012 17:58, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > >> > >> Lisandro, > >> > >> Thanks, I have incorporated these and a few other blocksize fixes. > >> > > > > Many thanks, Barry! However, I still think you are missing this one (I > > found the issue after running petsc4py testsuite). Pasted below and > > also attached. Please review and push. > > > > > > diff -r 2d1c2b03ef3a src/mat/impls/aij/seq/aij.c > > --- a/src/mat/impls/aij/seq/aij.c Tue Apr 10 09:57:31 2012 -0500 > > +++ b/src/mat/impls/aij/seq/aij.c Tue Apr 10 20:36:48 2012 +0300 > > @@ -3477,9 +3477,12 @@ > > PetscErrorCode ierr; > > > > PetscFunctionBegin; > > + if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, > > "Ii[0] must be 0 it is %D", Ii[0]); > > + > > + ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); > > + ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); > > + > > ierr = MatGetSize(B, &m, &n);CHKERRQ(ierr); > > - > > - if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, > > "Ii[0] must be 0 it is %D", Ii[0]); > > ierr = PetscMalloc((m+1) * sizeof(PetscInt), &nnz);CHKERRQ(ierr); > > for(i = 0; i < m; i++) { > > nz = Ii[i+1]- Ii[i]; > > > > > > -- > > Lisandro Dalcin > > --------------- > > CIMEC (INTEC/CONICET-UNL) > > Predio CONICET-Santa Fe > > Colectora RN 168 Km 472, Paraje El Pozo > > 3000 Santa Fe, Argentina > > Tel: +54-342-4511594 (ext 1011) > > Tel/Fax: +54-342-4511169 > [see attached file: matblocksize-seqaij-csr.diff] >

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