[petsc-dev] Fwd: [petsc-maint #56111] petsc4py does not work with complex numbers?
Satish Balay
balay at mcs.anl.gov
Tue Nov 16 13:59:26 CST 2010
We pushed a fix for this to petsc-dev.
Satish
On Tue, 16 Nov 2010, Satish Balay wrote:
> Barry,
>
> I'm getting the following in the debugger:
>
> Breakpoint 1, KSPSolve_BCGSL (ksp=0x2cde280) at bcgsl.c:144
> 144 if (ksp->reason) {
> (gdb) p ksp->reason
> $2 = KSP_DIVERGED_DTOL
>
> And the following change fixes it for me. Does this look ok?
>
> Satish
>
> ------------
>
> asterix:/home/balay/tmp/petsc-dev>hg diff
> diff -r 9773839bae8f src/ksp/ksp/impls/bcgsl/bcgsl.c
> --- a/src/ksp/ksp/impls/bcgsl/bcgsl.c Tue Nov 16 08:39:10 2010 -0600
> +++ b/src/ksp/ksp/impls/bcgsl/bcgsl.c Tue Nov 16 12:41:10 2010 -0600
> @@ -146,6 +146,7 @@
> ksp->its = k+j;
> ksp->rnorm = nrm0;
> ierr = PetscObjectGrantAccess(ksp);CHKERRQ(ierr);
> + if (ksp->reason <0) bBombed = PETSC_TRUE;
> break;
> }
> }
> asterix:/home/balay/tmp/petsc-dev>
>
>
> On Tue, 16 Nov 2010, Barry Smith wrote:
>
> >
> > Satish,
> >
> > Check the values in the part of the code:
> >
> > /* Symmetrize MZa */
> > for(i = 0; i <= bcgsl->ell; ++i) {
> > for(j = i+1; j <= bcgsl->ell; ++j) {
> > MZa[i*ldMZ+j] = MZa[j*ldMZ+i] = PetscConj(MZa[j*ldMZ+i]);
> > }
> > }
> >
> > Are all the inputs and outputs to this chunk of code reasonable?
> >
> > Thanks
> >
> > Barry
> >
> >
> > On Nov 16, 2010, at 8:23 AM, Satish Balay wrote:
> >
> > > Yes - valgrind doesn't show anything with this code.. [it shows a
> > > bunch of python stuff - before PetscInitialize() - so I'm guessing
> > > this is unreleated python stuff..]
> > >
> > > And suprisingly fp_trap isn't catching the SIGFPE - when run inside
> > > valgrind..
> > >
> > > BTW: due to the SIGFPE - there is a Nan in the var - so this check
> > > [-(-var)==var] and it fails and gives the following message -
> > > eventhough its sequential run.
> > >
> > >>>> [0] Scalar value must be same on all processes, argument # 3
> > >
> > > Satish
> > >
> > >
> > > On Tue, 16 Nov 2010, Barry Smith wrote:
> > >
> > >>
> > >> Satish,
> > >>
> > >> Valgrind ok?
> > >>
> > >> Barry
> > >>
> > >> On Nov 16, 2010, at 7:23 AM, Satish Balay wrote:
> > >>
> > >>> With '-fp_trap -start_in_debugger' in ~/.petscrc, I get a crash at:
> > >>>
> > >>>>>>>>>>>>
> > >>> Program received signal SIGFPE, Arithmetic exception.
> > >>> 0x00007f86e5ee17b4 in ATL_zreftrsmLLNN () from /usr/lib64/atlas/libatlas.so.3
> > >>> (gdb) where
> > >>> #0 0x00007f86e5ee17b4 in ATL_zreftrsmLLNN ()
> > >>> from /usr/lib64/atlas/libatlas.so.3
> > >>> #1 0x00007f86e5efc9fb in ATL_ztrsmLLNN () from /usr/lib64/atlas/libatlas.so.3
> > >>> #2 0x00007f86e5efc4e1 in ATL_ztrsm () from /usr/lib64/atlas/libatlas.so.3
> > >>> #3 0x000000394422ebbc in ATL_zpotrs () from /usr/lib64/atlas/liblapack.so.3
> > >>> #4 0x00000039446a69cb in zpotrs_ () from /usr/lib64/atlas/liblapack.so.3
> > >>> #5 0x00007f86e71df480 in KSPSolve_BCGSL (ksp=0x1372da0) at bcgsl.c:179
> > >>> #6 0x00007f86e74dbd1e in KSPSolve (ksp=0x1372da0, b=0x13a9c30, x=0x13a5b20)
> > >>> at itfunc.c:427
> > >>> #7 0x00007f86e7ef5898 in __pyx_pf_8petsc4py_5PETSc_3KSP_solve (
> > >>> __pyx_v_self=0xc8e090, __pyx_args=<value optimized out>,
> > >>> __pyx_kwds=<value optimized out>) at src/petsc4py.PETSc.c:89419
> > >>>
> > >>>
> > >>> #5 0x00007f86e71df480 in KSPSolve_BCGSL (ksp=0x1372da0) at bcgsl.c:179
> > >>> 179 LAPACKpotrs_("Lower", &bell, &ione, &MZa[1+ldMZ], &ldMZ, &AY0c[1], &ldMZ, &bierr);
> > >>> (gdb) p ldMZ
> > >>> $1 = 3
> > >>> (gdb) p ldMZ
> > >>> $2 = 3
> > >>> (gdb) p MZa[1+ldMZ]
> > >>> $3 = 2.1147927874194505e-14 + 0 * I
> > >>> (gdb) p MZa[1+ldMZ+1]
> > >>> $4 = 2.1147927874194505e-14 + 0 * I
> > >>> (gdb) p MZa[1+ldMZ+2]
> > >>> $5 = 4.472348533721329e-28 + -0 * I
> > >>> (gdb) p AY0c[1]
> > >>> $6 = 2.1147927874194505e-14 + 0 * I
> > >>> (gdb) p AY0c[2]
> > >>> $7 = 0 + 0 * I
> > >>> (gdb) p AY0c[3]
> > >>> $8 = 1.9966503766457982e-314 + 9.5700515599449456e-321 * I
> > >>> (gdb)
> > >>> <<<<<<<<<<<<<<<
> > >>>
> > >>> So - perhaps some of these values are garbage - generated in earler
> > >>> part of the code? I don't know where the bug is yet..
> > >>>
> > >>> [BTW: VecEqual fix is pushed to both petsc-31 and petsc-dev]
> > >>>
> > >>> Satish
> > >>>
> > >>> On Mon, 15 Nov 2010, Lisandro Dalcin wrote:
> > >>>
> > >>>> petsc-dev has a bug in VecEqual for the case of complex scalars. I've
> > >>>> mailed Satish about this with a single-line patch. After applying the
> > >>>> patch, almost all petsc4py tests pass.
> > >>>>
> > >>>> Still, there is a failure, but I doubt it is petsc4py's fault:
> > >>>>
> > >>>> ======================================================================
> > >>>> ERROR: testSolve (test_ksp.TestKSPBCGSL)
> > >>>> ----------------------------------------------------------------------
> > >>>> Traceback (most recent call last):
> > >>>> File "test/test_ksp.py", line 132, in testSolve
> > >>>> self.ksp.solve(b, x)
> > >>>> File "KSP.pyx", line 326, in petsc4py.PETSc.KSP.solve
> > >>>> (src/petsc4py.PETSc.c:89520)
> > >>>> Error: error code 62
> > >>>> [0] KSPSolve() line 427 in /usr/local/petsc/dev/src/ksp/ksp/interface/itfunc.c
> > >>>> [0] KSPSolve_BCGSL() line 241 in
> > >>>> /usr/local/petsc/dev/src/ksp/ksp/impls/bcgsl/bcgsl.c
> > >>>> [0] VecMAXPY() line 1202 in /usr/local/petsc/dev/src/vec/vec/interface/rvector.c
> > >>>> [0] Invalid argument
> > >>>> [0] Scalar value must be same on all processes, argument # 3
> > >>>>
> > >>>>
> > >>>> On 15 November 2010 20:05, Satish Balay <balay at mcs.anl.gov> wrote:
> > >>>>> Ok. For now - I've added complex=1 for petsc4py.py [and mpi4py.py]
> > >>>>>
> > >>>>> Satish
> > >>>>>
> > >>>>> On Mon, 15 Nov 2010, Lisandro Dalcin wrote:
> > >>>>>
> > >>>>>> On 15 November 2010 19:01, Satish Balay <balay at mcs.anl.gov> wrote:
> > >>>>>>> I get the following with complex enabled. Does this mean 'some tests
> > >>>>>>> run but others fail'?
> > >>>>>>>
> > >>>>>>> I guess we'll have to wait for Lisandro to reply..
> > >>>>>>>
> > >>>>>>
> > >>>>>> Complex numbers should work just fine, at least with 3.1, I'm going to
> > >>>>>> check against petsc-dev.
> > >>>>>>
> > >>>>>>>
> > >>>>>>> asterix:/home/balay/tmp/petsc-dev/externalpackages/petsc4py-dev>make test
> > >>>>>>> python test/runtests.py < /dev/null
> > >>>>>>> [0 at asterix] Python 2.7 (/usr/bin/python)
> > >>>>>>> [0 at asterix] PETSc 3.1.0-p5 development (conf: 'asterix64')
> > >>>>>>> [0 at asterix] petsc4py 1.1.2 (build/lib.linux-x86_64-2.7/petsc4py)
> > >>>>>>> .......................................................................................................................................................................................................................EE...................................................................................................F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F....
..
> ..
> > > F
> > >>> ...
> > >>>>> ....
> > >>>>>>> .F........F........F........F.........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F........F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F..F...................FE..........FF.FEF...........F.....................................................................................................................................................................................................................FFFF........FFFF................................................................F...F..F.......F...F..F.......F...F..F........
> > >>>>>>> ======================================================================
> > >>>>>>> ERROR: testSetMonitor (test_ksp.TestKSPBCGSL)
> > >>>>>>> ----------------------------------------------------------------------
> > >>>>>>> Traceback (most recent call last):
> > >>>>>>> File "test/test_ksp.py", line 154, in testSetMonitor
> > >>>>>>> self.testSolve()
> > >>>>>>> File "test/test_ksp.py", line 132, in testSolve
> > >>>>>>> self.ksp.solve(b, x)
> > >>>>>>> File "KSP.pyx", line 326, in petsc4py.PETSc.KSP.solve (src/petsc4py.PETSc.c:89419)
> > >>>>>>> Error: error code 62
> > >>>>>>> [0] KSPSolve() line 427 in src/ksp/ksp/interface/itfunc.c
> > >>>>>>> [0] KSPSolve_BCGSL() line 241 in src/ksp/ksp/impls/bcgsl/bcgsl.c
> > >>>>>>> [0] VecMAXPY() line 1202 in src/vec/vec/interface/rvector.c
> > >>>>>>> [0] Invalid argument
> > >>>>>>> [0] Scalar value must be same on all processes, argument # 3
> > >>>>>>>
> > >>>>>>> ======================================================================
> > >>>>>>> ERROR: testSolve (test_ksp.TestKSPBCGSL)
> > >>>>>>> ----------------------------------------------------------------------
> > >>>>>>> Traceback (most recent call last):
> > >>>>>>> File "test/test_ksp.py", line 132, in testSolve
> > >>>>>>> self.ksp.solve(b, x)
> > >>>>>>> File "KSP.pyx", line 326, in petsc4py.PETSc.KSP.solve (src/petsc4py.PETSc.c:89419)
> > >>>>>>> Error: error code 62
> > >>>>>>> [0] KSPSolve() line 427 in src/ksp/ksp/interface/itfunc.c
> > >>>>>>> [0] KSPSolve_BCGSL() line 241 in src/ksp/ksp/impls/bcgsl/bcgsl.c
> > >>>>>>> [0] VecMAXPY() line 1202 in src/vec/vec/interface/rvector.c
> > >>>>>>> [0] Invalid argument
> > >>>>>>> [0] Scalar value must be same on all processes, argument # 3
> > >>>>>>>
> > >>>>>>> ======================================================================
> > >>>>>>> ERROR: testCreateTranspose (test_mat_py.TestDiagonal)
> > >>>>>>> ----------------------------------------------------------------------
> > >>>>>>> Traceback (most recent call last):
> > >>>>>>> File "test/test_mat_py.py", line 100, in tearDown
> > >>>>>>> self.assertEqual(getrefcount(ctx), 2)
> > >>>>>>> AssertionError: 3 != 2
> > >>>>>>>
> > >>>>>>> ======================================================================
> > >>>>>>> ERROR: testMultTransposeNewMeth (test_mat_py.TestIdentity)
> > >>>>>>> ---------------------------
> > >>>>>>>
> > >>>>>>>
> > >>>>>>> On Mon, 15 Nov 2010, Barry Smith wrote:
> > >>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> Could someone who knows answer this? If it supports complex then we'll need to change the flag in petsc4py.py
> > >>>>>>>>>
> > >>>>>>>>> Barry
> > >>>>>>>>>
> > >>>>>>>>> *******************************************************************************
> > >>>>>>>>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
> > >>>>>>>>> -------------------------------------------------------------------------------
> > >>>>>>>>> Cannot use petsc4py with complex numbers it is not coded for this capability
> > >>>>>>>>> *******************************************************************************
> > >>>>>>>>> File "./config/configure.py", line 260, in petsc_configure
> > >>>>>>>>> framework.configure(out = sys.stdout)
> > >>>>>>>>> File "/Users/srinath/work/Packages/rev-packages/petsc-dev/config/BuildSystem/config/framework.py", line 977, in configure
> > >>>>>>>>> child.configure()
> > >>>>>>>>> File "/Users/srinath/work/Packages/rev-packages/petsc-dev/config/BuildSystem/config/package.py", line 488, in configure
> > >>>>>>>>> self.consistencyChecks()
> > >>>>>>>>> File "/Users/srinath/work/Packages/rev-packages/petsc-dev/config/PETSc/package.py", line 40, in consistencyChecks
> > >>>>>>>>> raise RuntimeError('Cannot use '+self.name+' with complex numbers it is not coded for this capability')
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> Begin forwarded message:
> > >>>>>>>>>
> > >>>>>>>>>> From: Srinath Vadlamani <srinath at txcorp.com>
> > >>>>>>>>>> Date: November 15, 2010 3:27:55 PM CST
> > >>>>>>>>>> To: petsc-maint <petsc-maint at mcs.anl.gov>
> > >>>>>>>>>> Subject: [petsc-maint #56111] petsc4py does not work with complex numbers?
> > >>>>>>>>>> Reply-To: petsc-maint at mcs.anl.gov, Srinath Vadlamani <srinath at txcorp.com>
> > >>>>>>>>>>
> > >>>>>>>>>> Is this true?
> > >>>>>>>>>>
> > >>>>>>>>>> --
> > >>>>>>>>>> =========================
> > >>>>>>>>>> Srinath Vadlamani, PhD.
> > >>>>>>>>>> Tech-X Corp. Research Scientist
> > >>>>>>>>>> 5621 Arapahoe Ave. Suite A
> > >>>>>>>>>> Boulder, CO 80303
> > >>>>>>>>>> 303-996-2034
> > >>>>>>>>>> =========================
> > >>>>>>>>>>
> > >>>>>>>>>> Is this true?
> > >>>>>>>>>>
> > >>>>>>>>>> --
> > >>>>>>>>>> =========================
> > >>>>>>>>>> Srinath Vadlamani, PhD.
> > >>>>>>>>>> Tech-X Corp. Research Scientist
> > >>>>>>>>>> 5621 Arapahoe Ave. Suite A
> > >>>>>>>>>> Boulder, CO 80303
> > >>>>>>>>>> 303-996-2034
> > >>>>>>>>>> =========================
> > >>>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>
> > >>
> > >
> >
> >
>
>
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