April 2018 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] [petsc-users] PetscPrintf
by Rongliang Chen 16 Apr '18

16 Apr '18

Thanks Barry. I will update my petsc. By the way, I simply replaced the functions PetscFormatConvert() and PetscVFPrintfDefault() with those in petsc-3.6 and it works for me. Best, Rongliang On 04/17/2018 05:53 AM, Smith, Barry F. wrote: > Rongliang, > > I have prepared a fix for this in the branch barry/bugfix-petscformatconvert which comes from the master branch of PETSc. > > Unfortunately it requires many changes so cannot be back ported to previous releases. > > Thanks for reporting the problem, > > Barry > > >> On Apr 11, 2018, at 6:17 PM, Rongliang Chen <rongliang.chan(a)gmail.com> wrote: >> >> Dear All, >> >> >> When I tried to print a long string using PetscPrintf() I found that it truncated the string. Attached is a simple example for this (run with single processor). I used PetscPrintf() and printf() to print the same string and the printf() seems OK. I am using petsc-3.8.4. >> >> >> Best, >> >> Rongliang >> >> <ex111.c>

1 0

Re: [petsc-dev] Is mpich/master:a8a2b30fd21 tested with Petsc?
by Satish Balay 16 Apr '18

16 Apr '18

On Tue, 13 Mar 2018, Eric Chamberland wrote: > Hi, > > each night we are testing mpich/master with our petsc-based code.ï¿œ I don't > know if PETSc team is doing the same thing with mpich/master?ï¿œï¿œ (Maybe it is a > good idea?) > > Everything was fine (except the issue > https://github.com/pmodels/mpich/issues/2892) up to commit 7b8d64debd, but > since commit mpich:a8a2b30fd21), I have a segfault on a any parallel nightly > test. I attempted a bisect of the above range of commits - and narrowed down to: >>>>>>> db11d4c4a70e39a28be88ed32f00542301699e08 is the first bad commit <<<<<<< >>>>>>>> balay@asterix /home/balay/soft/build/mpich ((db11d4c4a...)|BISECTING) $ git show db11d4c4a70e39a28be88ed32f00542301699e08 commit db11d4c4a70e39a28be88ed32f00542301699e08 (HEAD, refs/bisect/bad) Author: Ken Raffenetti <raffenet(a)mcs.anl.gov> Date: Thu Feb 15 11:37:59 2018 -0600 init: Fix tag upper limit initialization The starting point for this value is equivalent to the usable tag bits macro. This value should be set before device initialization, otherwise devices will assume they have more bits than are actually available. Signed-off-by: Wesley Bland <wesley.bland(a)intel.com> diff --git a/src/mpi/init/initthread.c b/src/mpi/init/initthread.c index cbc41f4d5..b31ae2f07 100644 --- a/src/mpi/init/initthread.c +++ b/src/mpi/init/initthread.c @@ -403,7 +403,7 @@ int MPIR_Init_thread(int *argc, char ***argv, int required, int *provided) MPIR_Process.attrs.host = MPI_PROC_NULL; MPIR_Process.attrs.io = MPI_PROC_NULL; MPIR_Process.attrs.lastusedcode = MPI_ERR_LASTCODE; - MPIR_Process.attrs.tag_ub = 0; + MPIR_Process.attrs.tag_ub = MPIR_TAG_USABLE_BITS; MPIR_Process.attrs.universe = MPIR_UNIVERSE_SIZE_NOT_SET; MPIR_Process.attrs.wtime_is_global = 0; @@ -531,13 +531,6 @@ int MPIR_Init_thread(int *argc, char ***argv, int required, int *provided) MPIR_Assert(((unsigned) MPIR_Process. attrs.tag_ub & ((unsigned) MPIR_Process.attrs.tag_ub + 1)) == 0); - /* Set aside tag space for tagged collectives and failure notification */ -#ifdef HAVE_TAG_ERROR_BITS - MPIR_Process.attrs.tag_ub >>= 3; -#else - MPIR_Process.attrs.tag_ub >>= 1; -#endif - /* Assert: tag_ub is at least the minimum asked for in the MPI spec */ MPIR_Assert(MPIR_Process.attrs.tag_ub >= 32767); <<<<<<<<<<<<<<<<< Reverthing this patch gets mpich-3.3b2 working with petsc Satish

1 0

Re: [petsc-dev] [petsc-users] PetscPrintf
by Smith, Barry F. 16 Apr '18

16 Apr '18

Rongliang, I have prepared a fix for this in the branch barry/bugfix-petscformatconvert which comes from the master branch of PETSc. Unfortunately it requires many changes so cannot be back ported to previous releases. Thanks for reporting the problem, Barry > On Apr 11, 2018, at 6:17 PM, Rongliang Chen <rongliang.chan(a)gmail.com> wrote: > > Dear All, > > > When I tried to print a long string using PetscPrintf() I found that it truncated the string. Attached is a simple example for this (run with single processor). I used PetscPrintf() and printf() to print the same string and the printf() seems OK. I am using petsc-3.8.4. > > > Best, > > Rongliang > > <ex111.c>

1 0

Re: [petsc-dev] KSP accepts mismatched sizes between Mat and PC
by Alp Dener 16 Apr '18

16 Apr '18

Sounds good. The fact that it isn’t checking for size is helpful for my use case as well. I just wanted to make sure it wasn’t a bug. — Alp Dener On April 16, 2018 at 1:56:30 PM, Smith, Barry F. (bsmith(a)mcs.anl.gov) wrote: Normally they need to be the same, but not always. For KSPLSQR the A matrix may be rectangular but the B matrix is A^TA which is square. This special case is why we don't do error checking. Barry > On Apr 16, 2018, at 1:04 PM, Alp Dener <alp.dener(a)gmail.com> wrote: > > Hi Barry, > > While I was working on some active-set related stuff in TAO, I discovered that I can call KSPSetOperators() with differently sized Mat and PC objects without getting any errors or warnings about the size mismatch. Note that my Mat object is explicit, but the PC object is a MATSHELL. Is this intended behavior, or is it a bug? > > — > Alp Dener

1 0

Re: [petsc-dev] KSP accepts mismatched sizes between Mat and PC
by Smith, Barry F. 16 Apr '18

16 Apr '18

Normally they need to be the same, but not always. For KSPLSQR the A matrix may be rectangular but the B matrix is A^TA which is square. This special case is why we don't do error checking. Barry > On Apr 16, 2018, at 1:04 PM, Alp Dener <alp.dener(a)gmail.com> wrote: > > Hi Barry, > > While I was working on some active-set related stuff in TAO, I discovered that I can call KSPSetOperators() with differently sized Mat and PC objects without getting any errors or warnings about the size mismatch. Note that my Mat object is explicit, but the PC object is a MATSHELL. Is this intended behavior, or is it a bug? > > — > Alp Dener

1 0

Re: [petsc-dev] Matlab interface issue
by Smith, Barry F. 16 Apr '18

16 Apr '18

Hmm, I tried on my Mac and had the same problem. But then I upgraded from Matlab 2017A to 2018A and boom the problem went away and it was able to build the socket mex files without a problem. So my conclusion is that we shouldn't change anything in the PETSc makefiles? Barry > On Apr 16, 2018, at 6:41 AM, Vaclav Hapla <vaclav.hapla(a)erdw.ethz.ch> wrote: > > Hello > > I need to compile PETSc with MATLAB interface on Mac OS. > > First thing is that Mex supports only Xcode or Intel compilers, not GCC. So I compiled PETSc with Xcode, using options > --with-cc="/usr/bin/xcrun -sdk macosx10.13 clang" --with-matlab --with-matlab-arch=maci64 --with-matlab-engine --with-mpi=0 > > But the target "matlabcodes" (in src/sys/classes/viewer/impls/socket/matlab/makefile) was failing with > Undefined symbols for architecture x86_64: > "_main", referenced from: > implicit entry/start for main executable > ld: symbol(s) not found for architecture x86_64 > > After some investigation I found out the problem lies in specifying environment variables to the mex compiler. Mex has some predefined values of these variables and fails if we override them. According to MATLAB documentation, it should be possible to just append what we need, e.g. > LDFLAGS='${LDFLAGS} ${PETSC_EXTERNAL_LIB_BASIC}' > but this apparently does not work as excepted, some predefined options are removed this way. I was debugging that by adding -v to ${MATLAB_MEX} calls in the makefile. It seems the injected LDFLAGS is interpreted _after_ something more is added to LDFLAGS by MEX (stupid). > > What works for me is specifying the options directly do ${MATLAB_MEX}. This is also tricky, though, as ${MATLAB_MEX} does not accept all options, e.g. -Wl,-rpath. So I ended up with replacing > GCC='${CC}' CC='${PCC}' CFLAGS='${COPTFLAGS} ${CC_FLAGS} ${CCPPFLAGS}' LDFLAGS='${PETSC_EXTERNAL_LIB_BASIC}' > by > ${PETSC_CC_INCLUDES} -L${PETSC_DIR}/${PETSC_ARCH}/lib ${PETSC_LIB_BASIC} > in src/sys/classes/viewer/impls/socket/matlab/makefile. See the attached patch. This at least compiled. > > > Do you think this could break anything? Do you have some better idea? > > BTW It would be better if the matlabcodes target could be turned off by configure, if one is interested only in using MATLAB Engine and wants to avoid problems with the mex compiler. > > Thanks, > Vaclav > <patch>

1 0

KSP accepts mismatched sizes between Mat and PC
by Alp Dener 16 Apr '18

16 Apr '18

Hi Barry, While I was working on some active-set related stuff in TAO, I discovered that I can call KSPSetOperators() with differently sized Mat and PC objects without getting any errors or warnings about the size mismatch. Note that my Mat object is explicit, but the PC object is a MATSHELL. Is this intended behavior, or is it a bug? — Alp Dener

1 0

Re: [petsc-dev] Default dimension of a DM
by Smith, Barry F. 16 Apr '18

16 Apr '18

Seems ok to me. Barry > On Apr 16, 2018, at 9:03 AM, Matthew Knepley <knepley(a)gmail.com> wrote: > > I am fine with this change. > > Matt > > On Mon, Apr 16, 2018 at 9:19 AM, Stefano Zampini <stefano.zampini(a)gmail.com> wrote: > Maybe this is silly, but why the default dimenson of a DM is 0; why not -1? > A DM of dimension 0 is a point, while a DM of dimension -1 is a DM in a not yet complete setup state. > -- > Stefano > > > > -- > 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 > > https://www.cse.buffalo.edu/~knepley/

1 0

Re: [petsc-dev] Default dimension of a DM
by Matthew Knepley 16 Apr '18

16 Apr '18

I am fine with this change. Matt On Mon, Apr 16, 2018 at 9:19 AM, Stefano Zampini <stefano.zampini(a)gmail.com> wrote: > Maybe this is silly, but why the default dimenson of a DM is 0; why not -1? > A DM of dimension 0 is a point, while a DM of dimension -1 is a DM in a > not yet complete setup state. > -- > Stefano > -- 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 https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>

1 0

Default dimension of a DM
by Stefano Zampini 16 Apr '18

16 Apr '18

Maybe this is silly, but why the default dimenson of a DM is 0; why not -1? A DM of dimension 0 is a point, while a DM of dimension -1 is a DM in a not yet complete setup state. -- Stefano

1 0