[CIG-SHORT] Rate and State and Initial Traction
Romain Jolivet
rjolivet at caltech.edu
Mon Sep 3 15:25:09 PDT 2012
Thanks Brad,
I just saw your email. I thought the state-variable had a default value given by the expression you just sent me.
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 3:51 PM, cig-short-request at geodynamics.org wrote:
> Send CIG-SHORT mailing list submissions to
> cig-short at geodynamics.org
>
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> or, via email, send a message with subject or body 'help' to
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>
> Today's Topics:
>
> 1. Re: Rate and State and Initial Traction (Brad Aagaard)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 30 Aug 2012 15:51:45 -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: <503FEE81.504 at usgs.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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 --------------
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>>>>>> End of CIG-SHORT Digest, Vol 72, Issue 21
>>>>>> *****************************************
>>>>>
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>>>>
>>>>
>>>>
>>>> --
>>>> 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
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>>> *****************************************
>>
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>
>
>
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