[CIG-SHORT] Rate and State and Initial Traction
Brad Aagaard
baagaard at usgs.gov
Thu Aug 30 15:51:45 PDT 2012
Romain,
Your initial state variable for rate-state friction is not set, so the
default value of 0.0 is used. As a result the friction coefficient is
infinite. I will change the default to something reasonable nonzero
value, which will show up in the next PyLith release along with a check
for this. In the meantime, set an initial value for the state variable
as is done in examples/3d/hex8/step14.cfg.
# Set spatial database for the initial value of the state variable.
db_initial_state = spatialdata.spatialdb.UniformDB
db_initial_state.label = Rate State Ageing State
db_initial_state.values = [state-variable]
# theta_ss = characteristic_slip_dist / reference_slip_rate
# ROMAIN: UPDATE THIS VALUE USING THE ABOVE EXPRESSION FOR THETA_SS
db_initial_state.data = [2.5e+9*s]
Brad
On 08/30/2012 02:29 PM, Romain Jolivet wrote:
> My relative tolerance is now 1e-20, and ksp_atol = 1e-12.
> zero_tolerance = 1e-10 , by default.
> PETSc says ksp converges due to atol (no funny stuff due to machine epsilon, then), and the ksp residual norm is 3 orders of magnitude smaller than zero_tolerance, but still the same crash.
>
> What worries me is that the exact same problem with SlipWeakening instead of RateStateAgeing runs fine, and converges quite fast.
>
> 227 KSP Residual norm 6.958904427869e-12
> 228 KSP Residual norm 6.691327759355e-12
> 229 KSP Residual norm 6.133784618340e-12
> 230 KSP Residual norm 5.231708553237e-12
> 231 KSP Residual norm 3.601477632037e-12
> 232 KSP Residual norm 2.240651195747e-12
> 233 KSP Residual norm 1.382256145050e-12
> 234 KSP Residual norm 1.051621131548e-12
> 235 KSP Residual norm 9.795463232997e-13
> Linear solve converged due to CONVERGED_ATOL iterations 235
> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> [0]PETSC ERROR: Floating point exception!
> [0]PETSC ERROR: Infinite or not-a-number generated in norm!
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development HG revision: 3bede28f1195e406d4257c9fbeebefe827793801 HG Date: Mon Jun 11 22:14:12 2012 -0400
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/mpinemesis on a pylith-da named dhcp-74-229.caltech.edu by jolivetinsar Thu Aug 30 14:22:49 2012
> [0]PETSC ERROR: Libraries linked from /Users/buildbot/install/pylith_darwin_10.6_binbot/lib
> [0]PETSC ERROR: Configure run at Tue Jun 12 06:09:00 2012
> [0]PETSC ERROR: Configure options --prefix=/Users/buildbot/install/pylith_darwin_10.6_binbot --download-f-blas-lapack=1 --with-sieve=1 --with-c2html=0 --CXXFLAGS=-DMPICH_IGNORE_CXX_SEEK --with-clanguage=C++ --with-mpicompilers=1 --with-debugging=0 --download-chaco=1 --download-boost=1 --download-ml=1 --with-hdf5=1 --with-hdf5-dir=/Users/buildbot/install/pylith_darwin_10.6_binbot --with-x=0 --with-shared-libraries=1
> [0]Fatal error. Calling MPI_Abort() to abort PyLith application.
> PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: VecNorm() line 169 in src/vec/vec/interface/rvector.c
> [0]PETSC ERROR: VecNormalize() line 263 in src/vec/vec/interface/rvector.c
> [0]PETSC ERROR: KSPGMRESCycle() line 127 in src/ksp/ksp/impls/gmres/gmres.c
> [0]PETSC ERROR: KSPSolve_GMRES() line 231 in src/ksp/ksp/impls/gmres/gmres.c
> [0]PETSC ERROR: KSPSolve() line 446 in src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: _sensitivitySolve() line 2172 in "unknowndirectory/"faults/FaultCohesiveDyn.cc
> Traceback (most recent call last):
> File "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 65, in onComputeNodes
> self.main(*args, **kwds)
> File "/Users/jolivetinsar/MYBIN/pylith/pylith-1/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/nemesis: mpirun: exit 255
> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/pylith: /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/nemesis: exit 1
>
>
> Romain Jolivet
> Postdoctoral Scholar
> Geological and Planetary Sciences
> California Institute of Technology, Pasadena, CA
> rjolivet at caltech.edu
> +1 (626) 560 6356
>
> On Aug 30, 2012, at 2:19 PM, cig-short-request at geodynamics.org wrote:
>
>> Send CIG-SHORT mailing list submissions to
>> cig-short at geodynamics.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> or, via email, send a message with subject or body 'help' to
>> cig-short-request at geodynamics.org
>>
>> You can reach the person managing the list at
>> cig-short-owner at geodynamics.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of CIG-SHORT digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Re: Rate and State and Initial Traction (Brad Aagaard)
>> 2. Re: Rate and State and Initial Traction (Matthew Knepley)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 30 Aug 2012 14:14:31 -0700
>> From: Brad Aagaard <baagaard at usgs.gov>
>> Subject: Re: [CIG-SHORT] Rate and State and Initial Traction
>> To: Matthew Knepley <knepley at mcs.anl.gov>
>> Cc: cig-short at geodynamics.org
>> Message-ID: <503FD7B7.3050102 at usgs.gov>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Matt,
>>
>> I suggested that Romain change ksp_rtol only, not ksp_atol. The relative
>> tolerance will be small enough so that the absolute tolerance (1.0e-12)
>> will be what stops the KSP solve.
>>
>> Brad
>>
>>
>> On 08/30/2012 02:08 PM, Matthew Knepley wrote:
>>> On Thu, Aug 30, 2012 at 4:04 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
>>>
>>>> Romain,
>>>>
>>>> The stacktrace shows which solve is encountering inf or nan. The routine
>>>> is _sensitivitySolve(). This is the solve associated with determining
>>>> how much to increment the slip to match the friction criterion.
>>>>
>>>> However, it looks like the problem is in the KSP solver tolerances. Note
>>>> that the solver stops with a residual of 2e-10 due to ksp_rtol being
>>>> met. However, the friction_tolerance is (by default) 1.0e-10. The error
>>>> in the solution is on the order of 2.0e-10 but the tolerance for
>>>> detecting whether a point is slipping is 1.0e-10. You want the error in
>>>> the linear solution to be smaller than the tolerance for detecting
>>>> sliding. This means you should reduce your ksp_rtol to something much
>>>> smaller, like 1.0e-20, to force ksp_atol to control convergence.
>>>> Usually, the starting residual is a few orders of magnitude smaller than
>>>> what you have so the tolerances I suggested work.
>>>>
>>>
>>> Okay, last time I told him not to use anything less than 1e-16 since there
>>> are funny effects below roundoff. Could you try 1e-15?
>>>
>>> We do need consistency checks in these nested iterations.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> Bottom line: Quasi-static friction solves generally require the linear
>>>> solves to converge due to the absolute tolerance, which *must* be
>>>> smaller than the zero_tolerance for friction.
>>>>
>>>> We will look into adding more consistency checking into the code to try
>>>> and catch these types of errors.
>>>>
>>>> Regards,
>>>> Brad
>>>>
>>>>
>>>> On 08/30/2012 01:38 PM, Romain Jolivet wrote:
>>>>> Thanks for the advice. I changed the preconditioner settings to what you
>>>> suggested. I don't see that jump in the linear norm anymore.
>>>>> However, I still have the floating point exception problem. This arise
>>>> after the first round of ksp.
>>>>>
>>>>> In the log file (attached), I see to messages saying the ksp solver for
>>>> friction does converge (twice), then the SNES residual norm is printed,
>>>> then KSP starts, and when it has to compute the new SNES residual norm, it
>>>> says that VecNorm() encoutered a Inf or NAN value:
>>>>>
>>>>> 141 KSP Residual norm 1.185626397065e-09
>>>>> 142 KSP Residual norm 8.558244459183e-10
>>>>> 143 KSP Residual norm 4.537120666370e-10
>>>>> 144 KSP Residual norm 2.695590025796e-10
>>>>> 145 KSP Residual norm 2.263153111449e-10
>>>>> 146 KSP Residual norm 2.156010427246e-10
>>>>> Linear solve converged due to CONVERGED_RTOL iterations 146
>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>> ------------------------------------
>>>>> [0]PETSC ERROR: Floating point exception!
>>>>> [0]PETSC ERROR: Infinite or not-a-number generated in norm!
>>>>> [0]PETSC ERROR:
>>>> ------------------------------------------------------------------------
>>>>> [0]PETSC ERROR: Petsc Development HG revision:
>>>> 3bede28f1195e406d4257c9fbeebefe827793801 HG Date: Mon Jun 11 22:14:12 2012
>>>> -0400
>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>> [0]PETSC ERROR:
>>>> ------------------------------------------------------------------------
>>>>> [0]PETSC ERROR:
>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/mpinemesis
>>>> on a pylith-da named dhcp-74-229.caltech.edu by jolivetinsar Thu Aug 30
>>>> 13:34:55 2012
>>>>> [0]PETSC ERROR: Libraries linked from
>>>> /Users/buildbot/install/pylith_darwin_10.6_binbot/lib
>>>>> [0]PETSC ERROR: Configure run at Tue Jun 12 06:09:00 2012
>>>>> [0]PETSC ERROR: Configure options
>>>> --prefix=/Users/buildbot/install/pylith_darwin_10.6_binbot
>>>> --download-f-blas-lapack=1 --with-sieve=1 --with-c2html=0
>>>> --CXXFLAGS=-DMPICH_IGNORE_CXX_SEEK --with-clanguage=C++
>>>> --with-mpicompilers=1 --with-debugging=0 --download-chaco=1
>>>> --download-boost=1 --download-ml=1 --with-hdf5=1
>>>> --with-hdf5-dir=/Users/buildbot/install/pylith_darwin_10.6_binbot
>>>> --with-x=0 --with-shared-libraries=1
>>>>> [0]PETSC ERROR:
>>>> ------------------------------------------------------------------------
>>>>> [0]PETSC ERROR: VecNorm() line 169 in src/vec/vec/interface/rvector.c
>>>>> [0]PETSC ERROR: VecNormalize() line 263 in
>>>> src/vec/vec/interface/rvector.c
>>>>> [0]PETSC ERROR: KSPGMRESCycle() line 127 in
>>>> src/ksp/ksp/impls/gmres/gmres.c
>>>>> [0]PETSC ERROR: KSPSolve_GMRES() line 231 in
>>>> src/ksp/ksp/impls/gmres/gmres.c
>>>>> [0]PETSC ERROR: KSPSolve() line 446 in src/ksp/ksp/interface/itfunc.c
>>>>> [0]PETSC ERROR: _sensitivitySolve() line 2172 in
>>>> "unknowndirectory/"faults/FaultCohesiveDyn.cc
>>>>> Traceback (most recent call last):
>>>>> File
>>>> "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PetscApplication.py",
>>>> line 65, in onComputeNodes
>>>>> Fatal error. Calling MPI_Abort() to abort PyLith application.
>>>>> self.main(*args, **kwds)
>>>>> File
>>>> "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PyLithApp.py",
>>>> line 119, in main
>>>>> self.problem.run(self)
>>>>> File
>>>> "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py",
>>>> line 154, in run
>>>>> self.formulation.step(t, dt)
>>>>> File
>>>> "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Implicit.py",
>>>> line 219, in step
>>>>> self.solver.solve(dispIncr, self.jacobian, residual)
>>>>> File
>>>> "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/problems.py",
>>>> line 180, in solve
>>>>> def solve(self, *args): return
>>>> _problems.SolverNonlinear_solve(self, *args)
>>>>> RuntimeError: std::exception
>>>>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/nemesis:
>>>> mpirun: exit 255
>>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/pylith:
>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/nemesis:
>>>> exit 1
>>>>>
>>>>> Any idea?
>>>>> Romain
>>>>>
>>>>>
>>>>>
>>>>> Romain Jolivet
>>>>> Postdoctoral Scholar
>>>>> Geological and Planetary Sciences
>>>>> California Institute of Technology, Pasadena, CA
>>>>> rjolivet at caltech.edu
>>>>> +1 (626) 560 6356
>>>>>
>>>>> On Aug 30, 2012, at 12:00 PM, cig-short-request at geodynamics.org wrote:
>>>>>
>>>>>> Send CIG-SHORT mailing list submissions to
>>>>>> cig-short at geodynamics.org
>>>>>>
>>>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>> or, via email, send a message with subject or body 'help' to
>>>>>> cig-short-request at geodynamics.org
>>>>>>
>>>>>> You can reach the person managing the list at
>>>>>> cig-short-owner at geodynamics.org
>>>>>>
>>>>>> When replying, please edit your Subject line so it is more specific
>>>>>> than "Re: Contents of CIG-SHORT digest..."
>>>>>>
>>>>>>
>>>>>> Today's Topics:
>>>>>>
>>>>>> 1. Re: Rate and State and Initial Traction (Brad Aagaard)
>>>>>> 2. Fwd: Rate and State and Initial Traction (Matthew Knepley)
>>>>>>
>>>>>>
>>>>>> ----------------------------------------------------------------------
>>>>>>
>>>>>> Message: 1
>>>>>> Date: Wed, 29 Aug 2012 12:36:08 -0700
>>>>>> From: Brad Aagaard <baagaard at usgs.gov>
>>>>>> Subject: Re: [CIG-SHORT] Rate and State and Initial Traction
>>>>>> To: cig-short at geodynamics.org
>>>>>> Message-ID: <503E6F28.6050001 at usgs.gov>
>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>>
>>>>>> Romain,
>>>>>>
>>>>>> It looks like you are using Schur complement preconditioner settings.
>>>>>> The jump in the KSP residual at iteration 10 is odd and suggests
>>>>>> something is not quite right in the linear solve (probably related to
>>>>>> the preconditioner). Try using the AMG preconditioner. It may not be
>>>>>> quite as fast but it is more robust. Matt can probably help you tune the
>>>>>> Schur complement solver conditions some more if necessary.
>>>>>>
>>>>>> Your SNES tolerances are quite large. I suggest using tolerances similar
>>>>>> to those in examples/3d/hex8/step14.cfg.
>>>>>>
>>>>>> SOLVER TOLERANCES
>>>>>>
>>>>>> ksp_rtol = 1.0e-16
>>>>>> ksp_atol = 1.0e-12
>>>>>>
>>>>>> snes_rtol = 1.0e-14
>>>>>> snes_atol = 1.0e-10
>>>>>>
>>>>>>
>>>>>> AMG PRECONDITIONER SETTINGS
>>>>>>
>>>>>> [pylithapp.timedependent.formulation]
>>>>>> split_fields = True
>>>>>> matrix_type = aij
>>>>>>
>>>>>> [pylithapp.petsc]
>>>>>> ksp_gmres_restart = 100
>>>>>> fs_pc_type = fieldsplit
>>>>>> fs_pc_fieldsplit_real_diagonal = true
>>>>>> fs_pc_fieldsplit_type = multiplicative
>>>>>> fs_fieldsplit_0_pc_type = ml
>>>>>> fs_fieldsplit_1_pc_type = jacobi
>>>>>> fs_fieldsplit_0_ksp_type = preonly
>>>>>> fs_fieldsplit_1_ksp_type = preonly
>>>>>>
>>>>>> Brad
>>>>>>
>>>>>>
>>>>>> On 08/29/2012 11:42 AM, Romain Jolivet wrote:
>>>>>>> Hello Brad, Matt, Charles and the pylith team,
>>>>>>>
>>>>>>> Following your advice from the other day, I am experimenting how to
>>>> create earthquakes on a frictional interface by applying a traction change
>>>> history. It works fine with the SlipWeakening law in 2D. I'm trying to move
>>>> on to the RateStateAgeing behavior and I have problems applying the initial
>>>> traction conditions:
>>>>>>>
>>>>>>> I use a SimpleDB to apply the frictional properties on the fault: one
>>>> domain is rate-strengthening, the other is rate-weakening with a linear
>>>> transition between the two domains. If I do not try to turn on any
>>>> traction_perturbation option, the code runs great, and I have a slow slip
>>>> all the along the fault at any time.
>>>>>>>
>>>>>>> As I want the rate-weakening domain to be stuck sometimes, I want to
>>>> turn on traction_perturbation.db_initial. I use a SimpleDB to put a
>>>> negative traction all along the fault, and a shear traction compatible with
>>>> the friction coefficients I impose. However, when I run this, I have the
>>>> following error message from PETSc (I attach the log):
>>>>>>>
>>>>>>>>>
>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Implicit.py:215:step
>>>>>>> -- implicit(info)
>>>>>>> -- Solving equations.
>>>>>>> 0 SNES Function norm 2.679589636063e+01
>>>>>>> 0 KSP Residual norm 9.637565795900e-01
>>>>>>> 1 KSP Residual norm 3.564937135471e-08
>>>>>>> 2 KSP Residual norm 4.313963401911e-16
>>>>>>> 3 KSP Residual norm 3.050427683646e-16
>>>>>>> 4 KSP Residual norm 2.490663081181e-16
>>>>>>> 5 KSP Residual norm 2.156976950523e-16
>>>>>>> 6 KSP Residual norm 1.929258577738e-16
>>>>>>> 7 KSP Residual norm 1.761163907914e-16
>>>>>>> 8 KSP Residual norm 1.630520838230e-16
>>>>>>> 9 KSP Residual norm 1.525212509706e-16
>>>>>>> 10 KSP Residual norm 1.833325155789e-11
>>>>>>> 11 KSP Residual norm 7.039784754868e-23
>>>>>>> Linear solve converged due to CONVERGED_ATOL iterations 11
>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>> ------------------------------------
>>>>>>> [0]PETSC ERROR: Floating point exception!
>>>>>>> [0]PETSC ERROR: Infinite or not-a-number generated in norm!
>>>>>>>
>>>>>>> If anyone has an idea about that error message....
>>>>>>>
>>>>>>> I think it has to do with some slip vector. If I set
>>>> friction.min_slip_rate=1e-1, this problem does not happen (the nonlinear
>>>> solver does not converge, but at least, no crash). If I set the normal
>>>> traction to be positive, it does not crash as well (and it does not
>>>> converge as well). I join to this message the cfg file I am using for that
>>>> experiment.
>>>>>>>
>>>>>>> Thank you
>>>>>>> Romain
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Romain Jolivet
>>>>>>> Postdoctoral Scholar
>>>>>>> Geological and Planetary Sciences
>>>>>>> California Institute of Technology, Pasadena, CA
>>>>>>> rjolivet at caltech.edu
>>>>>>> +1 (626) 560 6356
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> CIG-SHORT mailing list
>>>>>>> CIG-SHORT at geodynamics.org
>>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 2
>>>>>> Date: Wed, 29 Aug 2012 22:09:25 -0500
>>>>>> From: Matthew Knepley <knepley at mcs.anl.gov>
>>>>>> Subject: [CIG-SHORT] Fwd: Rate and State and Initial Traction
>>>>>> To: cig-short at geodynamics.org
>>>>>> Message-ID:
>>>>>> <CAMYG4GkMcUqRjhMaYZ8Ooj-x=
>>>> 06QKFrc7fiwW1dStmDSDO1qWA at mail.gmail.com>
>>>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>>>
>>>>>> On Wed, Aug 29, 2012 at 2:36 PM, Brad Aagaard <baagaard at usgs.gov>
>>>> wrote:
>>>>>>
>>>>>>> Romain,
>>>>>>>
>>>>>>> It looks like you are using Schur complement preconditioner settings.
>>>>>>> The jump in the KSP residual at iteration 10 is odd and suggests
>>>>>>> something is not quite right in the linear solve (probably related to
>>>>>>>
>>>>>>
>>>>>> Brad is right that the tolerances here will produce some garbage. Going
>>>>>> below
>>>>>> machine epsilon (about 10^-16) means you get randomness and ultimately
>>>>>> underflow which I think you got in a norm calculation since things get
>>>>>> squared.
>>>>>> The solver should have converged on iterate 2, and will with the
>>>> tolerances
>>>>>> that
>>>>>> Brad suggested.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Matt
>>>>>>
>>>>>>
>>>>>>> the preconditioner). Try using the AMG preconditioner. It may not be
>>>>>>> quite as fast but it is more robust. Matt can probably help you tune
>>>> the
>>>>>>> Schur complement solver conditions some more if necessary.
>>>>>>>
>>>>>>> Your SNES tolerances are quite large. I suggest using tolerances
>>>> similar
>>>>>>> to those in examples/3d/hex8/step14.cfg.
>>>>>>>
>>>>>>> SOLVER TOLERANCES
>>>>>>>
>>>>>>> ksp_rtol = 1.0e-16
>>>>>>> ksp_atol = 1.0e-12
>>>>>>>
>>>>>>> snes_rtol = 1.0e-14
>>>>>>> snes_atol = 1.0e-10
>>>>>>>
>>>>>>>
>>>>>>> AMG PRECONDITIONER SETTINGS
>>>>>>>
>>>>>>> [pylithapp.timedependent.formulation]
>>>>>>> split_fields = True
>>>>>>> matrix_type = aij
>>>>>>>
>>>>>>> [pylithapp.petsc]
>>>>>>> ksp_gmres_restart = 100
>>>>>>> fs_pc_type = fieldsplit
>>>>>>> fs_pc_fieldsplit_real_diagonal = true
>>>>>>> fs_pc_fieldsplit_type = multiplicative
>>>>>>> fs_fieldsplit_0_pc_type = ml
>>>>>>> fs_fieldsplit_1_pc_type = jacobi
>>>>>>> fs_fieldsplit_0_ksp_type = preonly
>>>>>>> fs_fieldsplit_1_ksp_type = preonly
>>>>>>>
>>>>>>> Brad
>>>>>>>
>>>>>>>
>>>>>>> On 08/29/2012 11:42 AM, Romain Jolivet wrote:
>>>>>>>> Hello Brad, Matt, Charles and the pylith team,
>>>>>>>>
>>>>>>>> Following your advice from the other day, I am experimenting how to
>>>>>>> create earthquakes on a frictional interface by applying a traction
>>>> change
>>>>>>> history. It works fine with the SlipWeakening law in 2D. I'm trying to
>>>> move
>>>>>>> on to the RateStateAgeing behavior and I have problems applying the
>>>> initial
>>>>>>> traction conditions:
>>>>>>>>
>>>>>>>> I use a SimpleDB to apply the frictional properties on the fault: one
>>>>>>> domain is rate-strengthening, the other is rate-weakening with a linear
>>>>>>> transition between the two domains. If I do not try to turn on any
>>>>>>> traction_perturbation option, the code runs great, and I have a slow
>>>> slip
>>>>>>> all the along the fault at any time.
>>>>>>>>
>>>>>>>> As I want the rate-weakening domain to be stuck sometimes, I want to
>>>>>>> turn on traction_perturbation.db_initial. I use a SimpleDB to put a
>>>>>>> negative traction all along the fault, and a shear traction compatible
>>>> with
>>>>>>> the friction coefficients I impose. However, when I run this, I have
>>>> the
>>>>>>> following error message from PETSc (I attach the log):
>>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Implicit.py:215:step
>>>>>>>> -- implicit(info)
>>>>>>>> -- Solving equations.
>>>>>>>> 0 SNES Function norm 2.679589636063e+01
>>>>>>>> 0 KSP Residual norm 9.637565795900e-01
>>>>>>>> 1 KSP Residual norm 3.564937135471e-08
>>>>>>>> 2 KSP Residual norm 4.313963401911e-16
>>>>>>>> 3 KSP Residual norm 3.050427683646e-16
>>>>>>>> 4 KSP Residual norm 2.490663081181e-16
>>>>>>>> 5 KSP Residual norm 2.156976950523e-16
>>>>>>>> 6 KSP Residual norm 1.929258577738e-16
>>>>>>>> 7 KSP Residual norm 1.761163907914e-16
>>>>>>>> 8 KSP Residual norm 1.630520838230e-16
>>>>>>>> 9 KSP Residual norm 1.525212509706e-16
>>>>>>>> 10 KSP Residual norm 1.833325155789e-11
>>>>>>>> 11 KSP Residual norm 7.039784754868e-23
>>>>>>>> Linear solve converged due to CONVERGED_ATOL iterations 11
>>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>>> ------------------------------------
>>>>>>>> [0]PETSC ERROR: Floating point exception!
>>>>>>>> [0]PETSC ERROR: Infinite or not-a-number generated in norm!
>>>>>>>>
>>>>>>>> If anyone has an idea about that error message....
>>>>>>>>
>>>>>>>> I think it has to do with some slip vector. If I set
>>>>>>> friction.min_slip_rate=1e-1, this problem does not happen (the
>>>> nonlinear
>>>>>>> solver does not converge, but at least, no crash). If I set the normal
>>>>>>> traction to be positive, it does not crash as well (and it does not
>>>>>>> converge as well). I join to this message the cfg file I am using for
>>>> that
>>>>>>> experiment.
>>>>>>>>
>>>>>>>> Thank you
>>>>>>>> Romain
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Romain Jolivet
>>>>>>>> Postdoctoral Scholar
>>>>>>>> Geological and Planetary Sciences
>>>>>>>> California Institute of Technology, Pasadena, CA
>>>>>>>> rjolivet at caltech.edu
>>>>>>>> +1 (626) 560 6356
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> CIG-SHORT mailing list
>>>>>>>> CIG-SHORT at geodynamics.org
>>>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> CIG-SHORT mailing list
>>>>>>> CIG-SHORT at geodynamics.org
>>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> URL:
>>>> http://geodynamics.org/pipermail/cig-short/attachments/20120829/9e91899c/attachment.html
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> CIG-SHORT mailing list
>>>>>> CIG-SHORT at geodynamics.org
>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>
>>>>>>
>>>>>> End of CIG-SHORT Digest, Vol 72, Issue 21
>>>>>> *****************************************
>>>>>
>>>>> _______________________________________________
>>>>> CIG-SHORT mailing list
>>>>> CIG-SHORT at geodynamics.org
>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>
>>>>
>>>> _______________________________________________
>>>> CIG-SHORT mailing list
>>>> CIG-SHORT at geodynamics.org
>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>
>>>
>>>
>>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 30 Aug 2012 16:19:45 -0500
>> From: Matthew Knepley <knepley at mcs.anl.gov>
>> Subject: Re: [CIG-SHORT] Rate and State and Initial Traction
>> To: Romain Jolivet <rjolivet at caltech.edu>
>> Cc: cig-short at geodynamics.org
>> Message-ID:
>> <CAMYG4GkacxPh4TMvcXeWu84bFdzqvVuaQcd7mvXQJGdtddzkMw at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> On Thu, Aug 30, 2012 at 4:11 PM, Romain Jolivet <rjolivet at caltech.edu>wrote:
>>
>>> I did just run:
>>>
>>> pylith step01.cfg --petsc.fp_trap=0
>>>
>>> Is that what you meant? If it is, I still have the same problem :-) and it
>>> does not change what I see on the screen. Should it change something?\
>>>
>>
>> Then it is not underflow.
>>
>>
>>> However, the norm computation problem does not appear when I set the
>>> zero_tolerance to 1.0 (it does not converge though, but I don't have this
>>> Floating point exception...)
>>>
>>
>> As Brad says, change the relative tolerance, but leave the absolute
>> tolerance intact.
>>
>> Matt
>>
>>
>>> Romain
>>>
>>>
>>> Romain Jolivet
>>> Postdoctoral Scholar
>>> Geological and Planetary Sciences
>>> California Institute of Technology, Pasadena, CA
>>> rjolivet at caltech.edu
>>> +1 (626) 560 6356
>>>
>>> On Aug 30, 2012, at 2:00 PM, Matthew Knepley wrote:
>>>
>>> On Thu, Aug 30, 2012 at 3:38 PM, Romain Jolivet <rjolivet at caltech.edu>wrote:
>>>
>>>> Thanks for the advice. I changed the preconditioner settings to what you
>>>> suggested. I don't see that jump in the linear norm anymore.
>>>> However, I still have the floating point exception problem. This arise
>>>> after the first round of ksp.
>>>>
>>>> In the log file (attached), I see to messages saying the ksp solver for
>>>> friction does converge (twice), then the SNES residual norm is printed,
>>>> then KSP starts, and when it has to compute the new SNES residual norm, it
>>>> says that VecNorm() encoutered a Inf or NAN value:
>>>>
>>>
>>> It could still be underflow. Try running with --petsc.fp_trap=0
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> 141 KSP Residual norm 1.185626397065e-09
>>>> 142 KSP Residual norm 8.558244459183e-10
>>>> 143 KSP Residual norm 4.537120666370e-10
>>>> 144 KSP Residual norm 2.695590025796e-10
>>>> 145 KSP Residual norm 2.263153111449e-10
>>>> 146 KSP Residual norm 2.156010427246e-10
>>>> Linear solve converged due to CONVERGED_RTOL iterations 146
>>>> [0]PETSC ERROR: --------------------- Error Message
>>>> ------------------------------------
>>>> [0]PETSC ERROR: Floating point exception!
>>>> [0]PETSC ERROR: Infinite or not-a-number generated in norm!
>>>> [0]PETSC ERROR:
>>>> ------------------------------------------------------------------------
>>>> [0]PETSC ERROR: Petsc Development HG revision:
>>>> 3bede28f1195e406d4257c9fbeebefe827793801 HG Date: Mon Jun 11 22:14:12 2012
>>>> -0400
>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>> [0]PETSC ERROR:
>>>> ------------------------------------------------------------------------
>>>> [0]PETSC ERROR:
>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/mpinemesis
>>>> on a pylith-da named dhcp-74-229.caltech.edu by jolivetinsar Thu Aug 30
>>>> 13:34:55 2012
>>>> [0]PETSC ERROR: Libraries linked from
>>>> /Users/buildbot/install/pylith_darwin_10.6_binbot/lib
>>>> [0]PETSC ERROR: Configure run at Tue Jun 12 06:09:00 2012
>>>> [0]PETSC ERROR: Configure options
>>>> --prefix=/Users/buildbot/install/pylith_darwin_10.6_binbot
>>>> --download-f-blas-lapack=1 --with-sieve=1 --with-c2html=0
>>>> --CXXFLAGS=-DMPICH_IGNORE_CXX_SEEK --with-clanguage=C++
>>>> --with-mpicompilers=1 --with-debugging=0 --download-chaco=1
>>>> --download-boost=1 --download-ml=1 --with-hdf5=1
>>>> --with-hdf5-dir=/Users/buildbot/install/pylith_darwin_10.6_binbot
>>>> --with-x=0 --with-shared-libraries=1
>>>> [0]PETSC ERROR:
>>>> ------------------------------------------------------------------------
>>>> [0]PETSC ERROR: VecNorm() line 169 in src/vec/vec/interface/rvector.c
>>>> [0]PETSC ERROR: VecNormalize() line 263 in src/vec/vec/interface/rvector.c
>>>> [0]PETSC ERROR: KSPGMRESCycle() line 127 in
>>>> src/ksp/ksp/impls/gmres/gmres.c
>>>> [0]PETSC ERROR: KSPSolve_GMRES() line 231 in
>>>> src/ksp/ksp/impls/gmres/gmres.c
>>>> [0]PETSC ERROR: KSPSolve() line 446 in src/ksp/ksp/interface/itfunc.c
>>>> [0]PETSC ERROR: _sensitivitySolve() line 2172 in
>>>> "unknowndirectory/"faults/FaultCohesiveDyn.cc
>>>> Traceback (most recent call last):
>>>> File
>>>> "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PetscApplication.py",
>>>> line 65, in onComputeNodes
>>>> Fatal error. Calling MPI_Abort() to abort PyLith application.
>>>> self.main(*args, **kwds)
>>>> File
>>>> "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PyLithApp.py",
>>>> line 119, in main
>>>> self.problem.run(self)
>>>> File
>>>> "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py",
>>>> line 154, in run
>>>> self.formulation.step(t, dt)
>>>> File
>>>> "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Implicit.py",
>>>> line 219, in step
>>>> self.solver.solve(dispIncr, self.jacobian, residual)
>>>> File
>>>> "/Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/problems.py",
>>>> line 180, in solve
>>>> def solve(self, *args): return _problems.SolverNonlinear_solve(self,
>>>> *args)
>>>> RuntimeError: std::exception
>>>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/nemesis:
>>>> mpirun: exit 255
>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/pylith:
>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/bin/nemesis:
>>>> exit 1
>>>>
>>>> Any idea?
>>>> Romain
>>>>
>>>>
>>>>
>>>> Romain Jolivet
>>>> Postdoctoral Scholar
>>>> Geological and Planetary Sciences
>>>> California Institute of Technology, Pasadena, CA
>>>> rjolivet at caltech.edu
>>>> +1 (626) 560 6356
>>>>
>>>> On Aug 30, 2012, at 12:00 PM, cig-short-request at geodynamics.org wrote:
>>>>
>>>>> Send CIG-SHORT mailing list submissions to
>>>>> cig-short at geodynamics.org
>>>>>
>>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>> or, via email, send a message with subject or body 'help' to
>>>>> cig-short-request at geodynamics.org
>>>>>
>>>>> You can reach the person managing the list at
>>>>> cig-short-owner at geodynamics.org
>>>>>
>>>>> When replying, please edit your Subject line so it is more specific
>>>>> than "Re: Contents of CIG-SHORT digest..."
>>>>>
>>>>>
>>>>> Today's Topics:
>>>>>
>>>>> 1. Re: Rate and State and Initial Traction (Brad Aagaard)
>>>>> 2. Fwd: Rate and State and Initial Traction (Matthew Knepley)
>>>>>
>>>>>
>>>>> ----------------------------------------------------------------------
>>>>>
>>>>> Message: 1
>>>>> Date: Wed, 29 Aug 2012 12:36:08 -0700
>>>>> From: Brad Aagaard <baagaard at usgs.gov>
>>>>> Subject: Re: [CIG-SHORT] Rate and State and Initial Traction
>>>>> To: cig-short at geodynamics.org
>>>>> Message-ID: <503E6F28.6050001 at usgs.gov>
>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>
>>>>> Romain,
>>>>>
>>>>> It looks like you are using Schur complement preconditioner settings.
>>>>> The jump in the KSP residual at iteration 10 is odd and suggests
>>>>> something is not quite right in the linear solve (probably related to
>>>>> the preconditioner). Try using the AMG preconditioner. It may not be
>>>>> quite as fast but it is more robust. Matt can probably help you tune the
>>>>> Schur complement solver conditions some more if necessary.
>>>>>
>>>>> Your SNES tolerances are quite large. I suggest using tolerances similar
>>>>> to those in examples/3d/hex8/step14.cfg.
>>>>>
>>>>> SOLVER TOLERANCES
>>>>>
>>>>> ksp_rtol = 1.0e-16
>>>>> ksp_atol = 1.0e-12
>>>>>
>>>>> snes_rtol = 1.0e-14
>>>>> snes_atol = 1.0e-10
>>>>>
>>>>>
>>>>> AMG PRECONDITIONER SETTINGS
>>>>>
>>>>> [pylithapp.timedependent.formulation]
>>>>> split_fields = True
>>>>> matrix_type = aij
>>>>>
>>>>> [pylithapp.petsc]
>>>>> ksp_gmres_restart = 100
>>>>> fs_pc_type = fieldsplit
>>>>> fs_pc_fieldsplit_real_diagonal = true
>>>>> fs_pc_fieldsplit_type = multiplicative
>>>>> fs_fieldsplit_0_pc_type = ml
>>>>> fs_fieldsplit_1_pc_type = jacobi
>>>>> fs_fieldsplit_0_ksp_type = preonly
>>>>> fs_fieldsplit_1_ksp_type = preonly
>>>>>
>>>>> Brad
>>>>>
>>>>>
>>>>> On 08/29/2012 11:42 AM, Romain Jolivet wrote:
>>>>>> Hello Brad, Matt, Charles and the pylith team,
>>>>>>
>>>>>> Following your advice from the other day, I am experimenting how to
>>>> create earthquakes on a frictional interface by applying a traction change
>>>> history. It works fine with the SlipWeakening law in 2D. I'm trying to move
>>>> on to the RateStateAgeing behavior and I have problems applying the initial
>>>> traction conditions:
>>>>>>
>>>>>> I use a SimpleDB to apply the frictional properties on the fault: one
>>>> domain is rate-strengthening, the other is rate-weakening with a linear
>>>> transition between the two domains. If I do not try to turn on any
>>>> traction_perturbation option, the code runs great, and I have a slow slip
>>>> all the along the fault at any time.
>>>>>>
>>>>>> As I want the rate-weakening domain to be stuck sometimes, I want to
>>>> turn on traction_perturbation.db_initial. I use a SimpleDB to put a
>>>> negative traction all along the fault, and a shear traction compatible with
>>>> the friction coefficients I impose. However, when I run this, I have the
>>>> following error message from PETSc (I attach the log):
>>>>>>
>>>>>>>>
>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Implicit.py:215:step
>>>>>> -- implicit(info)
>>>>>> -- Solving equations.
>>>>>> 0 SNES Function norm 2.679589636063e+01
>>>>>> 0 KSP Residual norm 9.637565795900e-01
>>>>>> 1 KSP Residual norm 3.564937135471e-08
>>>>>> 2 KSP Residual norm 4.313963401911e-16
>>>>>> 3 KSP Residual norm 3.050427683646e-16
>>>>>> 4 KSP Residual norm 2.490663081181e-16
>>>>>> 5 KSP Residual norm 2.156976950523e-16
>>>>>> 6 KSP Residual norm 1.929258577738e-16
>>>>>> 7 KSP Residual norm 1.761163907914e-16
>>>>>> 8 KSP Residual norm 1.630520838230e-16
>>>>>> 9 KSP Residual norm 1.525212509706e-16
>>>>>> 10 KSP Residual norm 1.833325155789e-11
>>>>>> 11 KSP Residual norm 7.039784754868e-23
>>>>>> Linear solve converged due to CONVERGED_ATOL iterations 11
>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>> ------------------------------------
>>>>>> [0]PETSC ERROR: Floating point exception!
>>>>>> [0]PETSC ERROR: Infinite or not-a-number generated in norm!
>>>>>>
>>>>>> If anyone has an idea about that error message....
>>>>>>
>>>>>> I think it has to do with some slip vector. If I set
>>>> friction.min_slip_rate=1e-1, this problem does not happen (the nonlinear
>>>> solver does not converge, but at least, no crash). If I set the normal
>>>> traction to be positive, it does not crash as well (and it does not
>>>> converge as well). I join to this message the cfg file I am using for that
>>>> experiment.
>>>>>>
>>>>>> Thank you
>>>>>> Romain
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Romain Jolivet
>>>>>> Postdoctoral Scholar
>>>>>> Geological and Planetary Sciences
>>>>>> California Institute of Technology, Pasadena, CA
>>>>>> rjolivet at caltech.edu
>>>>>> +1 (626) 560 6356
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> CIG-SHORT mailing list
>>>>>> CIG-SHORT at geodynamics.org
>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> Message: 2
>>>>> Date: Wed, 29 Aug 2012 22:09:25 -0500
>>>>> From: Matthew Knepley <knepley at mcs.anl.gov>
>>>>> Subject: [CIG-SHORT] Fwd: Rate and State and Initial Traction
>>>>> To: cig-short at geodynamics.org
>>>>> Message-ID:
>>>>> <CAMYG4GkMcUqRjhMaYZ8Ooj-x=
>>>> 06QKFrc7fiwW1dStmDSDO1qWA at mail.gmail.com>
>>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>>
>>>>> On Wed, Aug 29, 2012 at 2:36 PM, Brad Aagaard <baagaard at usgs.gov>
>>>> wrote:
>>>>>
>>>>>> Romain,
>>>>>>
>>>>>> It looks like you are using Schur complement preconditioner settings.
>>>>>> The jump in the KSP residual at iteration 10 is odd and suggests
>>>>>> something is not quite right in the linear solve (probably related to
>>>>>>
>>>>>
>>>>> Brad is right that the tolerances here will produce some garbage. Going
>>>>> below
>>>>> machine epsilon (about 10^-16) means you get randomness and ultimately
>>>>> underflow which I think you got in a norm calculation since things get
>>>>> squared.
>>>>> The solver should have converged on iterate 2, and will with the
>>>> tolerances
>>>>> that
>>>>> Brad suggested.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> the preconditioner). Try using the AMG preconditioner. It may not be
>>>>>> quite as fast but it is more robust. Matt can probably help you tune
>>>> the
>>>>>> Schur complement solver conditions some more if necessary.
>>>>>>
>>>>>> Your SNES tolerances are quite large. I suggest using tolerances
>>>> similar
>>>>>> to those in examples/3d/hex8/step14.cfg.
>>>>>>
>>>>>> SOLVER TOLERANCES
>>>>>>
>>>>>> ksp_rtol = 1.0e-16
>>>>>> ksp_atol = 1.0e-12
>>>>>>
>>>>>> snes_rtol = 1.0e-14
>>>>>> snes_atol = 1.0e-10
>>>>>>
>>>>>>
>>>>>> AMG PRECONDITIONER SETTINGS
>>>>>>
>>>>>> [pylithapp.timedependent.formulation]
>>>>>> split_fields = True
>>>>>> matrix_type = aij
>>>>>>
>>>>>> [pylithapp.petsc]
>>>>>> ksp_gmres_restart = 100
>>>>>> fs_pc_type = fieldsplit
>>>>>> fs_pc_fieldsplit_real_diagonal = true
>>>>>> fs_pc_fieldsplit_type = multiplicative
>>>>>> fs_fieldsplit_0_pc_type = ml
>>>>>> fs_fieldsplit_1_pc_type = jacobi
>>>>>> fs_fieldsplit_0_ksp_type = preonly
>>>>>> fs_fieldsplit_1_ksp_type = preonly
>>>>>>
>>>>>> Brad
>>>>>>
>>>>>>
>>>>>> On 08/29/2012 11:42 AM, Romain Jolivet wrote:
>>>>>>> Hello Brad, Matt, Charles and the pylith team,
>>>>>>>
>>>>>>> Following your advice from the other day, I am experimenting how to
>>>>>> create earthquakes on a frictional interface by applying a traction
>>>> change
>>>>>> history. It works fine with the SlipWeakening law in 2D. I'm trying to
>>>> move
>>>>>> on to the RateStateAgeing behavior and I have problems applying the
>>>> initial
>>>>>> traction conditions:
>>>>>>>
>>>>>>> I use a SimpleDB to apply the frictional properties on the fault: one
>>>>>> domain is rate-strengthening, the other is rate-weakening with a linear
>>>>>> transition between the two domains. If I do not try to turn on any
>>>>>> traction_perturbation option, the code runs great, and I have a slow
>>>> slip
>>>>>> all the along the fault at any time.
>>>>>>>
>>>>>>> As I want the rate-weakening domain to be stuck sometimes, I want to
>>>>>> turn on traction_perturbation.db_initial. I use a SimpleDB to put a
>>>>>> negative traction all along the fault, and a shear traction compatible
>>>> with
>>>>>> the friction coefficients I impose. However, when I run this, I have
>>>> the
>>>>>> following error message from PETSc (I attach the log):
>>>>>>>
>>>>>>>>>
>>>>>>
>>>> /Users/jolivetinsar/MYBIN/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Implicit.py:215:step
>>>>>>> -- implicit(info)
>>>>>>> -- Solving equations.
>>>>>>> 0 SNES Function norm 2.679589636063e+01
>>>>>>> 0 KSP Residual norm 9.637565795900e-01
>>>>>>> 1 KSP Residual norm 3.564937135471e-08
>>>>>>> 2 KSP Residual norm 4.313963401911e-16
>>>>>>> 3 KSP Residual norm 3.050427683646e-16
>>>>>>> 4 KSP Residual norm 2.490663081181e-16
>>>>>>> 5 KSP Residual norm 2.156976950523e-16
>>>>>>> 6 KSP Residual norm 1.929258577738e-16
>>>>>>> 7 KSP Residual norm 1.761163907914e-16
>>>>>>> 8 KSP Residual norm 1.630520838230e-16
>>>>>>> 9 KSP Residual norm 1.525212509706e-16
>>>>>>> 10 KSP Residual norm 1.833325155789e-11
>>>>>>> 11 KSP Residual norm 7.039784754868e-23
>>>>>>> Linear solve converged due to CONVERGED_ATOL iterations 11
>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>> ------------------------------------
>>>>>>> [0]PETSC ERROR: Floating point exception!
>>>>>>> [0]PETSC ERROR: Infinite or not-a-number generated in norm!
>>>>>>>
>>>>>>> If anyone has an idea about that error message....
>>>>>>>
>>>>>>> I think it has to do with some slip vector. If I set
>>>>>> friction.min_slip_rate=1e-1, this problem does not happen (the
>>>> nonlinear
>>>>>> solver does not converge, but at least, no crash). If I set the normal
>>>>>> traction to be positive, it does not crash as well (and it does not
>>>>>> converge as well). I join to this message the cfg file I am using for
>>>> that
>>>>>> experiment.
>>>>>>>
>>>>>>> Thank you
>>>>>>> Romain
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Romain Jolivet
>>>>>>> Postdoctoral Scholar
>>>>>>> Geological and Planetary Sciences
>>>>>>> California Institute of Technology, Pasadena, CA
>>>>>>> rjolivet at caltech.edu
>>>>>>> +1 (626) 560 6356
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> CIG-SHORT mailing list
>>>>>>> CIG-SHORT at geodynamics.org
>>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> CIG-SHORT mailing list
>>>>>> CIG-SHORT at geodynamics.org
>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>> -------------- next part --------------
>>>>> An HTML attachment was scrubbed...
>>>>> URL:
>>>> http://geodynamics.org/pipermail/cig-short/attachments/20120829/9e91899c/attachment.html
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> CIG-SHORT mailing list
>>>>> CIG-SHORT at geodynamics.org
>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>
>>>>>
>>>>> End of CIG-SHORT Digest, Vol 72, Issue 21
>>>>> *****************************************
>>>>
>>>> _______________________________________________
>>>> CIG-SHORT mailing list
>>>> CIG-SHORT at geodynamics.org
>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>>>
>>>
>>>
>>
>>
>> --
>> 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
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: http://geodynamics.org/pipermail/cig-short/attachments/20120830/964a474f/attachment.htm
>>
>> ------------------------------
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>>
>> End of CIG-SHORT Digest, Vol 72, Issue 25
>> *****************************************
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
More information about the CIG-SHORT
mailing list