[petsc-dev] Fwd: [petsc-maint #56111] petsc4py does not work with complex numbers?
Barry Smith
bsmith at mcs.anl.gov
Tue Nov 16 11:28:10 CST 2010
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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