[petsc-users] arkimex rejecting all dt in petsc 3.6.0
Italo Tasso
italo at tasso.com.br
Thu Jun 18 16:10:28 CDT 2015
Thank you Barry and Emil.
It works, but it takes twice as many steps than before.
Was it wrong before? Should I have been using this option all along?
I am solving the Navier-Stokes equations, full implicit and non-linear.
I also noticed two things:
In the 3.6.0 output, ts_monitor skips timestep #1.
If I use the equation type in 3.5.4, I get segmentation fault.
I attached the outputs.
On Thu, Jun 18, 2015 at 1:24 PM, Emil Constantinescu <emconsta at mcs.anl.gov>
wrote:
> No, I'm not sure if it should. It belongs to the same category as
> "problem_type" == TS_LINEAR / == TS_NONLINEAR.
>
> Emil
>
>
> On 6/18/15 11:15 AM, Abhyankar, Shrirang G. wrote:
>
>> Can the DAE equation type be supplied via a run-time option?
>>
>> Shri
>>
>> -----Original Message-----
>> From: barry smith <bsmith at mcs.anl.gov>
>> Date: Thursday, June 18, 2015 at 11:08 AM
>> To: Italo Tasso <italo at tasso.com.br>, "Constantinescu, Emil M."
>> <emconsta at mcs.anl.gov>
>> Cc: "petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
>> Subject: Re: [petsc-users] arkimex rejecting all dt in petsc 3.6.0
>>
>>
>>> Here is the response from Emil who made the changes to the code
>>>
>>> If you are solving a DAE then in the new version, we introduced a new
>>> flag that distinguishes between ODEs and DAEs leading to different
>>> semantics. For DAEs this is needed b/c it may not have consistent initial
>>> conditions.
>>>
>>> If solving DAEs, the user has to set the EquationType appropriately:
>>> e.g.,
>>> ierr = TSSetEquationType(ts,TS_EQ_DAE_IMPLICIT_INDEX1);CHKERRQ(ierr);
>>>
>>> This is documented in the doc, but I didn't add it to the changelog (Jed
>>> pointed it out to me).
>>>
>>> Currently it only affects -ts_type arkimex. I'll work with Satish to add
>>> it to the changelog.
>>>
>>> *If that's not the case:* let me know and we can dig deeper.
>>>
>>> Emil
>>>
>>> On Jun 18, 2015, at 5:48 AM, Italo Tasso <italo at tasso.com.br> wrote:
>>>>
>>>> I just upgraded to 3.6.0 and my code stopped working. All dt are
>>>> rejected. I used the same configure line, same code, same everything.
>>>>
>>>> With 3.5.4 I get:
>>>>
>>>> 0 TS dt 1e-06 time 0
>>>> 0 SNES Function norm 2.549981005316e+05
>>>> 1 SNES Function norm 6.107056905987e-03
>>>> 2 SNES Function norm 1.483881932064e-10
>>>> 3 SNES Function norm 9.122873794272e-11
>>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 3
>>>> 0 SNES Function norm 7.790429171165e+04
>>>> 1 SNES Function norm 7.289068747803e-04
>>>> 2 SNES Function norm 8.227639633330e-11
>>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
>>>> 0 SNES Function norm 1.154356516184e+05
>>>> 1 SNES Function norm 2.309925413255e-03
>>>> 2 SNES Function norm 6.382141981406e-11
>>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
>>>> TSAdapt 'basic': step 0 accepted t=0 + 1.000e-06
>>>> wlte=0.000654 family='arkimex' scheme=0:'3' dt=1.000e-05
>>>>
>>>> With 3.6.0 I get:
>>>>
>>>> 0 TS dt 1e-06 time 0
>>>> 0 SNES Function norm 2.549981005316e+05
>>>> 1 SNES Function norm 6.107056925316e-03
>>>> 2 SNES Function norm 1.519319591792e-10
>>>> 3 SNES Function norm 9.070104116945e-11
>>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 3
>>>> 0 SNES Function norm 7.790429171165e+04
>>>> 1 SNES Function norm 6.942541792651e-04
>>>> 2 SNES Function norm 8.458781909516e-11
>>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
>>>> 0 SNES Function norm 1.154356516184e+05
>>>> 1 SNES Function norm 2.287202942961e-03
>>>> 2 SNES Function norm 6.585201377573e-11
>>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
>>>> TSAdapt 'basic': step 0 rejected t=0 + 1.000e-06 wlte=
>>>> 324 family='arkimex' scheme=0:'3' dt=1.311e-07
>>>>
>>>> Any ideas? I attached the full output.
>>>>
>>>> Options I use:
>>>>
>>>> -ts_view -ts_type arkimex -ts_arkimex_fully_implicit -ts_adapt_monitor
>>>> -ts_monitor -snes_monitor -snes_converged_reason -ksp_type preonly
>>>> -pc_type lu -pc_factor_mat_solver_package mumps -snes_rtol 0 -snes_atol
>>>> 1e-10 -snes_stol 0
>>>>
>>>> <petsc354.txt><petsc360.txt>
>>>>
>>>
>>>
>>
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0 TS dt 1e-06 time 0
TSAdapt 'basic': step 0 accepted t=0 + 1.000e-06 wlte=0.723 family='arkimex' scheme=0:'1bee' dt=1.059e-06
TSAdapt 'basic': step 1 accepted t=1e-06 + 1.059e-06 wlte=0.000706 family='arkimex' scheme=0:'3' dt=1.059e-05
2 TS dt 1.05853e-05 time 2.05853e-06
TSAdapt 'basic': step 2 accepted t=2.05853e-06+ 1.059e-05 wlte=0.548 family='arkimex' scheme=0:'3' dt=1.164e-05
3 TS dt 1.16435e-05 time 1.26438e-05
TSAdapt 'basic': step 3 accepted t=1.26438e-05+ 1.164e-05 wlte=0.579 family='arkimex' scheme=0:'3' dt=1.257e-05
4 TS dt 1.25697e-05 time 2.42873e-05
TSAdapt 'basic': step 4 accepted t=2.42873e-05+ 1.257e-05 wlte=0.559 family='arkimex' scheme=0:'3' dt=1.373e-05
5 TS dt 1.37332e-05 time 3.6857e-05
TSAdapt 'basic': step 5 accepted t=3.6857e-05 + 1.373e-05 wlte=0.536 family='arkimex' scheme=0:'3' dt=1.522e-05
6 TS dt 1.52176e-05 time 5.05902e-05
TSAdapt 'basic': step 6 accepted t=5.05902e-05+ 1.522e-05 wlte=0.511 family='arkimex' scheme=0:'3' dt=1.713e-05
7 TS dt 1.71336e-05 time 6.58078e-05
TSAdapt 'basic': step 7 accepted t=6.58078e-05+ 1.713e-05 wlte=0.484 family='arkimex' scheme=0:'3' dt=1.964e-05
8 TS dt 1.96364e-05 time 8.29414e-05
TSAdapt 'basic': step 8 accepted t=8.29414e-05+ 1.964e-05 wlte=0.456 family='arkimex' scheme=0:'3' dt=2.295e-05
9 TS dt 2.29535e-05 time 0.000102578
TSAdapt 'basic': step 9 accepted t=0.000102578+ 2.295e-05 wlte=0.429 family='arkimex' scheme=0:'3' dt=2.740e-05
10 TS dt 2.7397e-05 time 0.000125531
TSAdapt 'basic': step 10 accepted t=0.000125531+ 2.740e-05 wlte=0.403 family='arkimex' scheme=0:'3' dt=3.339e-05
11 TS dt 3.33874e-05 time 0.000152928
TSAdapt 'basic': step 11 accepted t=0.000152928+ 3.339e-05 wlte=0.382 family='arkimex' scheme=0:'3' dt=4.142e-05
12 TS dt 4.14194e-05 time 0.000186316
TSAdapt 'basic': step 12 accepted t=0.000186316+ 4.142e-05 wlte=0.369 family='arkimex' scheme=0:'3' dt=5.199e-05
13 TS dt 5.19872e-05 time 0.000227735
TSAdapt 'basic': step 13 accepted t=0.000227735+ 5.199e-05 wlte=0.364 family='arkimex' scheme=0:'3' dt=6.553e-05
14 TS dt 6.55288e-05 time 0.000279722
TSAdapt 'basic': step 14 accepted t=0.000279722+ 6.553e-05 wlte=0.365 family='arkimex' scheme=0:'3' dt=8.254e-05
15 TS dt 8.25371e-05 time 0.000345251
TSAdapt 'basic': step 15 accepted t=0.000345251+ 8.254e-05 wlte=0.367 family='arkimex' scheme=0:'3' dt=1.037e-04
16 TS dt 0.00010372 time 0.000427788
TSAdapt 'basic': step 16 accepted t=0.000427788+ 1.037e-04 wlte=0.369 family='arkimex' scheme=0:'3' dt=1.301e-04
17 TS dt 0.000130137 time 0.000531508
TSAdapt 'basic': step 17 accepted t=0.000531508+ 1.301e-04 wlte= 0.37 family='arkimex' scheme=0:'3' dt=1.631e-04
18 TS dt 0.000163074 time 0.000661645
TSAdapt 'basic': step 18 accepted t=0.000661645+ 1.631e-04 wlte=0.372 family='arkimex' scheme=0:'3' dt=2.040e-04
19 TS dt 0.000204046 time 0.00082472
TSAdapt 'basic': step 19 accepted t=0.00082472 + 2.040e-04 wlte=0.374 family='arkimex' scheme=0:'3' dt=2.548e-04
20 TS dt 0.000254802 time 0.00102877
TSAdapt 'basic': step 20 accepted t=0.00102877 + 2.548e-04 wlte=0.377 family='arkimex' scheme=0:'3' dt=3.174e-04
21 TS dt 0.000317385 time 0.00128357
TSAdapt 'basic': step 21 accepted t=0.00128357 + 3.174e-04 wlte=0.381 family='arkimex' scheme=0:'3' dt=3.940e-04
22 TS dt 0.000394007 time 0.00160095
TSAdapt 'basic': step 22 accepted t=0.00160095 + 3.940e-04 wlte=0.386 family='arkimex' scheme=0:'3' dt=4.870e-04
23 TS dt 0.000486973 time 0.00199496
TSAdapt 'basic': step 23 accepted t=0.00199496 + 4.870e-04 wlte=0.393 family='arkimex' scheme=0:'3' dt=5.985e-04
24 TS dt 0.000598494 time 0.00248193
TSAdapt 'basic': step 24 accepted t=0.00248193 + 5.985e-04 wlte=0.401 family='arkimex' scheme=0:'3' dt=7.306e-04
25 TS dt 0.000730558 time 0.00308043
TSAdapt 'basic': step 25 accepted t=0.00308043 + 7.306e-04 wlte=0.409 family='arkimex' scheme=0:'3' dt=8.854e-04
26 TS dt 0.000885429 time 0.00381099
TSAdapt 'basic': step 26 accepted t=0.00381099 + 8.854e-04 wlte=0.408 family='arkimex' scheme=0:'3' dt=1.075e-03
27 TS dt 0.00107468 time 0.00469641
TSAdapt 'basic': step 27 accepted t=0.00469641 + 1.075e-03 wlte=0.347 family='arkimex' scheme=0:'3' dt=1.376e-03
28 TS dt 0.00137622 time 0.0057711
TSAdapt 'basic': step 28 accepted t=0.0057711 + 1.376e-03 wlte=0.326 family='arkimex' scheme=0:'3' dt=1.799e-03
29 TS dt 0.00179877 time 0.00714732
TSAdapt 'basic': step 29 accepted t=0.00714732 + 1.799e-03 wlte=0.313 family='arkimex' scheme=0:'3' dt=2.384e-03
30 TS dt 0.00238444 time 0.00894608
TSAdapt 'basic': step 30 accepted t=0.00894608 + 2.384e-03 wlte=0.307 family='arkimex' scheme=0:'3' dt=3.182e-03
31 TS dt 0.00318229 time 0.0113305
TSAdapt 'basic': step 31 accepted t=0.0113305 + 3.182e-03 wlte=0.301 family='arkimex' scheme=0:'3' dt=4.273e-03
32 TS dt 0.00427274 time 0.0145128
TSAdapt 'basic': step 32 accepted t=0.0145128 + 4.273e-03 wlte=0.296 family='arkimex' scheme=0:'3' dt=5.771e-03
33 TS dt 0.00577055 time 0.0187856
TSAdapt 'basic': step 33 accepted t=0.0187856 + 5.771e-03 wlte=0.291 family='arkimex' scheme=0:'3' dt=7.840e-03
34 TS dt 0.00784028 time 0.0245561
TSAdapt 'basic': step 34 accepted t=0.0245561 + 7.840e-03 wlte=0.286 family='arkimex' scheme=0:'3' dt=1.071e-02
35 TS dt 0.0107123 time 0.0323964
TSAdapt 'basic': step 35 accepted t=0.0323964 + 1.071e-02 wlte=0.269 family='arkimex' scheme=0:'3' dt=1.493e-02
36 TS dt 0.0149302 time 0.0431087
TSAdapt 'basic': step 36 accepted t=0.0431087 + 1.493e-02 wlte= 0.23 family='arkimex' scheme=0:'3' dt=2.193e-02
37 TS dt 0.0219264 time 0.0580389
TSAdapt 'basic': step 37 accepted t=0.0580389 + 2.193e-02 wlte= 0.19 family='arkimex' scheme=0:'3' dt=3.435e-02
38 TS dt 0.0343516 time 0.0799653
TSAdapt 'basic': step 38 accepted t=0.0799653 + 3.435e-02 wlte=0.132 family='arkimex' scheme=0:'3' dt=6.071e-02
39 TS dt 0.060712 time 0.114317
TSAdapt 'basic': step 39 accepted t=0.114317 + 6.071e-02 wlte=0.0437 family='arkimex' scheme=0:'3' dt=1.551e-01
40 TS dt 0.155117 time 0.175029
TSAdapt 'basic': step 40 accepted t=0.175029 + 1.551e-01 wlte=0.00333 family='arkimex' scheme=0:'3' dt=9.351e-01
41 TS dt 0.935113 time 0.330146
TSAdapt 'basic': step 41 accepted t=0.330146 + 9.351e-01 wlte=0.000792 family='arkimex' scheme=0:'3' dt=8.735e+00
42 TS dt 8.73474 time 1.26526
TSAdapt 'basic': step 42 accepted t=1.26526 + 8.735e+00 wlte=4.42e-05 family='arkimex' scheme=0:'3' dt=8.735e+01
43 TS dt 87.3474 time 10
CONVERGED_TIME at time 10 after 43 steps
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0 TS dt 1e-06 time 0
TSAdapt 'basic': step 0 accepted t=0 + 1.000e-06 wlte=4.64e-05 family='arkimex' scheme=0:'3' dt=1.000e-05
1 TS dt 1e-05 time 1e-06
TSAdapt 'basic': step 1 accepted t=1e-06 + 1.000e-05 wlte=0.0274 family='arkimex' scheme=0:'3' dt=2.984e-05
2 TS dt 2.98427e-05 time 1.1e-05
TSAdapt 'basic': step 2 accepted t=1.1e-05 + 2.984e-05 wlte=0.214 family='arkimex' scheme=0:'3' dt=4.489e-05
3 TS dt 4.48912e-05 time 4.08427e-05
TSAdapt 'basic': step 3 accepted t=4.08427e-05+ 4.489e-05 wlte= 0.16 family='arkimex' scheme=0:'3' dt=7.443e-05
4 TS dt 7.44292e-05 time 8.57339e-05
TSAdapt 'basic': step 4 accepted t=8.57339e-05+ 7.443e-05 wlte=0.128 family='arkimex' scheme=0:'3' dt=1.331e-04
5 TS dt 0.000133086 time 0.000160163
TSAdapt 'basic': step 5 accepted t=0.000160163+ 1.331e-04 wlte=0.132 family='arkimex' scheme=0:'3' dt=2.350e-04
6 TS dt 0.000234956 time 0.000293249
TSAdapt 'basic': step 6 accepted t=0.000293249+ 2.350e-04 wlte=0.143 family='arkimex' scheme=0:'3' dt=4.047e-04
7 TS dt 0.000404705 time 0.000528205
TSAdapt 'basic': step 7 accepted t=0.000528205+ 4.047e-04 wlte=0.152 family='arkimex' scheme=0:'3' dt=6.819e-04
8 TS dt 0.00068193 time 0.000932909
TSAdapt 'basic': step 8 accepted t=0.000932909+ 6.819e-04 wlte=0.162 family='arkimex' scheme=0:'3' dt=1.126e-03
9 TS dt 0.0011258 time 0.00161484
TSAdapt 'basic': step 9 accepted t=0.00161484 + 1.126e-03 wlte=0.172 family='arkimex' scheme=0:'3' dt=1.822e-03
10 TS dt 0.00182154 time 0.00274064
TSAdapt 'basic': step 10 accepted t=0.00274064 + 1.822e-03 wlte=0.183 family='arkimex' scheme=0:'3' dt=2.889e-03
11 TS dt 0.0028885 time 0.00456217
TSAdapt 'basic': step 11 accepted t=0.00456217 + 2.889e-03 wlte=0.195 family='arkimex' scheme=0:'3' dt=4.485e-03
12 TS dt 0.00448532 time 0.00745068
TSAdapt 'basic': step 12 accepted t=0.00745068 + 4.485e-03 wlte=0.209 family='arkimex' scheme=0:'3' dt=6.800e-03
13 TS dt 0.00679993 time 0.011936
TSAdapt 'basic': step 13 accepted t=0.011936 + 6.800e-03 wlte=0.229 family='arkimex' scheme=0:'3' dt=1.001e-02
14 TS dt 0.0100082 time 0.0187359
TSAdapt 'basic': step 14 accepted t=0.0187359 + 1.001e-02 wlte=0.251 family='arkimex' scheme=0:'3' dt=1.428e-02
15 TS dt 0.0142831 time 0.0287441
TSAdapt 'basic': step 15 accepted t=0.0287441 + 1.428e-02 wlte=0.253 family='arkimex' scheme=0:'3' dt=2.031e-02
16 TS dt 0.0203146 time 0.0430273
TSAdapt 'basic': step 16 accepted t=0.0430273 + 2.031e-02 wlte=0.222 family='arkimex' scheme=0:'3' dt=3.020e-02
17 TS dt 0.0301966 time 0.0633418
TSAdapt 'basic': step 17 accepted t=0.0633418 + 3.020e-02 wlte=0.155 family='arkimex' scheme=0:'3' dt=5.059e-02
18 TS dt 0.0505899 time 0.0935385
TSAdapt 'basic': step 18 accepted t=0.0935385 + 5.059e-02 wlte=0.0653 family='arkimex' scheme=0:'3' dt=1.131e-01
19 TS dt 0.113076 time 0.144128
TSAdapt 'basic': step 19 accepted t=0.144128 + 1.131e-01 wlte=0.00237 family='arkimex' scheme=0:'3' dt=7.635e-01
20 TS dt 0.763492 time 0.257205
TSAdapt 'basic': step 20 accepted t=0.257205 + 7.635e-01 wlte=0.000642 family='arkimex' scheme=0:'3' dt=7.635e+00
21 TS dt 7.63492 time 1.0207
TSAdapt 'basic': step 21 accepted t=1.0207 + 7.635e+00 wlte=4.38e-05 family='arkimex' scheme=0:'3' dt=1.344e+00
22 TS dt 1.34439 time 8.65561
TSAdapt 'basic': step 22 accepted t=8.65561 + 1.344e+00 wlte=2.85e-07 family='arkimex' scheme=0:'3' dt=1.344e+01
23 TS dt 13.4439 time 10
CONVERGED_TIME at time 10 after 23 steps
-------------- next part --------------
0 TS dt 1e-06 time 0
TSAdapt 'basic': step 0 accepted t=0 + 1.000e-06 wlte=0.723 family='arkimex' scheme=0:'1bee' dt=1.059e-06
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.5.4, May, 23, 2015
[0]PETSC ERROR: ./planb on a arch-linux2-c-opt named localhost.localdomain by root Thu Jun 18 17:53:30 2015
[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack --download-mpich --download-mumps --download-scalapack --download-parmetis --download-metis --with-debugging=0 COPTFLAGS="-Ofast -march=native -mtune=native" CXXOPTFLAGS="-Ofast -march=native -mtune=native" FOPTFLAGS="-Ofast -march=native -mtune=native"
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 29812 RUNNING AT localhost.localdomain
= EXIT CODE: 59
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
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