On Wed, Oct 5, 2011 at 5:56 PM, Rongliang Chen <span dir="ltr"><<a href="mailto:rongliang.chan@gmail.com">rongliang.chan@gmail.com</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hello Everyone,<br><br>I am testing a non-linear problem using the snessolve(). The degree of freedoms of my test case is about 1 Million, which means the Jacobian matrix in the snessolve() is an 1 million by 1 million matrix and it should be a sparse matrix.<br>
And my question is that in the "-log_summary" output file I find a strange massage: "Matrix 39 39 18446744074642894848 0". Does this message mean that the matrix's memory usage is 1.8x10^20? I have no idea why an one million by one million matrix use so much memory. Is this possible? The output of the "-log_summary" followed. Thanks.<br>
</blockquote><div><br></div><div>That is an overflow somewhere. You can probably get the right answer by using -snes_view. I will try and track down this overflow.</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Best,<br>Rongliang<br><br>-------------------------------------------------------------------------------------------------------------------------<br>Starting to load grid...<br> Nodes on moving boundary: coarse 199, fine 799, Gridratio 0.250000.<br>
Setupping Interpolation matrix......<br>Interpolation matrix done......Time spent: 0.405431 <br>finished.<br>Grid has 32000 elements, 1096658 degrees of freedom.<br>Coarse grid has 2000 elements, 70170 degrees of freedom.<br>
[0] has 35380 degrees of freedom (matrix), 35380 degrees of freedom (including shared points).<br> [0] coarse grid has 2194 degrees of freedom (matrix), 2194 degrees of freedom (including shared points).<br> [31] has 32466 degrees of freedom (matrix), 34428 degrees of freedom (including shared points).<br>
[31] coarse grid has 2250 degrees of freedom (matrix), 2826 degrees of freedom (including shared points).<br>Time spend on the load grid and create matrix etc.: 3.577862.<br>Solving fixed mesh (steady-state problem)<br>
Solving coarse problem......<br> 0 SNES norm 3.1224989992e+01, 0 KSP its last norm 0.0000000000e+00.<br> 1 SNES norm 1.3987219837e+00, 25 KSP its last norm 2.4915963656e-01.<br> 2 SNES norm 5.1898321541e-01, 59 KSP its last norm 1.3451744761e-02.<br>
3 SNES norm 4.0024228221e-02, 56 KSP its last norm 4.9036146089e-03.<br> 4 SNES norm 6.7641787439e-04, 59 KSP its last norm 3.6925683196e-04.<br>Coarse solver done......<br>Initial value of object function (Energy dissipation) (Coarse): 38.9341108701<br>
0 SNES norm 7.4575110699e+00, 0 KSP its last norm 0.0000000000e+00.<br> 1 SNES norm 6.4497565921e-02, 51 KSP its last norm 7.4277453141e-03.<br> 2 SNES norm 9.2093642958e-04, 90 KSP its last norm 5.4331380112e-05.<br>
3 SNES norm 8.1283574549e-07, 103 KSP its last norm 7.5974191049e-07.<br>Initial value of object function (Energy dissipation) (Fine): 42.5134271399<br>Solution time of 17.180358 sec.<br>Fixed mesh (Steady-state) solver done.<br>
Total number of nonlinear iterations = 3<br>Total number of linear iterations = 244<br>Average number of linear iterations = 81.333336<br>Time computing: 17.180358 sec, Time outputting: 0.000000 sec.<br>Time spent in coarse nonlinear solve: 0.793436 sec, 0.046183 fraction of total compute time.<br>
Solving Shape Optimization problem (steady-state problem) <br>Solving coarse problem......<br> 0 SNES norm 4.1963166116e+01, 0 KSP its last norm 0.0000000000e+00.<br> 1 SNES norm 3.2749386875e+01, 132 KSP its last norm 4.0966334477e-01.<br>
2 SNES norm 2.2874504408e+01, 130 KSP its last norm 3.2526355310e-01.<br> 3 SNES norm 1.4327187891e+01, 132 KSP its last norm 2.1213029400e-01.<br> 4 SNES norm 1.7283643754e+00, 81 KSP its last norm 1.4233338128e-01.<br>
5 SNES norm 3.6703566918e-01, 133 KSP its last norm 1.6069896349e-02.<br> 6 SNES norm 3.6554528686e-03, 77 KSP its last norm 3.5379167356e-03.<br>Coarse solver done......<br>Optimized value of object function (Energy dissipation) (Coarse): 29.9743062939<br>
The reduction of the energy dissipation (Coarse): 23.012737% <br>The optimized curve (Coarse):<br> a = (4.500000, -0.042893, -0.002030, 0.043721, -0.018798, 0.001824) <br>Solving moving mesh equation......<br> KSP norm 2.3040219081e-07, KSP its. 741. Time spent 8.481956 <br>
Moving mesh solver done.<br> 0 SNES norm 4.7843968670e+02, 0 KSP its last norm 0.0000000000e+00.<br> 1 SNES norm 1.0148854085e+02, 49 KSP its last norm 4.7373180511e-01.<br> 2 SNES norm 1.8312214030e+00, 46 KSP its last norm 1.0133332840e-01.<br>
3 SNES norm 3.3101970861e-03, 212 KSP its last norm 1.7753271069e-03.<br> 4 SNES norm 4.9552614008e-06, 249 KSP its last norm 3.2293284103e-06.<br>Optimized value of object function (Energy dissipation) (Fine): 33.2754372645<br>
Solution time of <a href="tel:4053.227456" value="+14053227456" target="_blank">4053.227456</a> sec.<br>Number of unknowns = 1096658<br>Parameters: kinematic viscosity = 0.01<br> inlet velocity: u = 5, v = 0 <br>
Total number of nonlinear iterations = 4<br>Total number of linear iterations = 556<br>
Average number of linear iterations = 139.000000<br>Time computing: <a href="tel:4053.227456" value="+14053227456" target="_blank">4053.227456</a> sec, Time outputting: 0.000001 sec.<br>Time spent in coarse nonlinear solve: 24.239526 sec, 0.005980 fraction of total compute time.<br>
The optimized curve (fine):<br>
a = (4.500000, -0.046468, -0.001963, 0.045736, -0.019141, 0.001789) <br>The reduction of the energy dissipation (Fine): 21.729582% <br>Time spend on fixed mesh solving: 17.296872 <br>Time spend on shape opt. solving: <a href="tel:4053.250126" value="+14053250126" target="_blank">4053.250126</a> <br>
Latex command line: <br> np Newton GMRES Time(Total) Time(Coarse) Ratio <br> 32 & 4 & 139.00 & 4053.23 & 24.24 & 0.6\% <br><br>Running finished on: Wed Oct 5 11:32:04 2011<br>
Total running time: 4070.644329 <br>************************************************************************************************************************<br>*** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***<br>
************************************************************************************************************************<br><br>---------------------------------------------- PETSc Performance Summary: ----------------------------------------------<br>
<br>./joab on a Janus-nod named node1751 with 32 processors, by ronglian Wed Oct 5 11:32:04 2011<br>Using Petsc Release Version 3.2.0, Patch 1, Mon Sep 12 16:01:51 CDT 2011 <br><br> Max Max/Min Avg Total <br>
Time (sec): 4.074e+03 1.00000 4.074e+03<br>Objects: 1.011e+03 1.00000 1.011e+03<br>Flops: 2.255e+11 2.27275 1.471e+11 4.706e+12<br>Flops/sec: 5.535e+07 2.27275 3.609e+07 1.155e+09<br>
MPI Messages: 1.103e+05 5.41392 3.665e+04 1.173e+06<br>MPI Message Lengths: 1.326e+09 2.60531 2.416e+04 2.833e+10<br>MPI Reductions: 5.969e+03 1.00000<br><br>Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract)<br>
e.g., VecAXPY() for real vectors of length N --> 2N flops<br> and VecAXPY() for complex vectors of length N --> 8N flops<br><br>Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages --- -- Message Lengths -- -- Reductions --<br>
Avg %Total Avg %Total counts %Total Avg %Total counts %Total <br> 0: Main Stage: 4.0743e+03 100.0% 4.7058e+12 100.0% 1.173e+06 100.0% 2.416e+04 100.0% 5.968e+03 100.0% <br>
<br>------------------------------------------------------------------------------------------------------------------------<br>See the 'Profiling' chapter of the users' manual for details on interpreting output.<br>
Phase summary info:<br> Count: number of times phase was executed<br> Time and Flops: Max - maximum over all processors<br> Ratio - ratio of maximum to minimum over all processors<br> Mess: number of messages sent<br>
Avg. len: average message length<br> Reduct: number of global reductions<br> Global: entire computation<br> Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop().<br> %T - percent time in this phase %F - percent flops in this phase<br>
%M - percent messages in this phase %L - percent message lengths in this phase<br> %R - percent reductions in this phase<br> Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time over all processors)<br>
------------------------------------------------------------------------------------------------------------------------<br>Event Count Time (sec) Flops --- Global --- --- Stage --- Total<br>
Max Ratio Max Ratio Max Ratio Mess Avg len Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s<br>------------------------------------------------------------------------------------------------------------------------<br>
<br>--- Event Stage 0: Main Stage<br><br>MatMult 2493 1.0 1.2225e+0218.4 4.37e+09 1.1 3.9e+05 2.2e+03 0.0e+00 2 3 33 3 0 2 3 33 3 0 1084<br>MatMultTranspose 6 1.0 3.3590e-02 2.2 7.38e+06 1.1 8.0e+02 1.5e+03 0.0e+00 0 0 0 0 0 0 0 0 0 0 6727<br>
MatSolve 2467 1.0 1.1270e+02 1.7 5.95e+10 1.7 0.0e+00 0.0e+00 0.0e+00 2 33 0 0 0 2 33 0 0 0 13775<br>MatLUFactorSym 4 1.0 3.4774e+00 3.1 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 0 0 0 0 0 0 0 0 0 0 0<br>
MatLUFactorNum 18 1.0 2.0832e+02 3.7 1.55e+11 3.2 0.0e+00 0.0e+00 0.0e+00 2 56 0 0 0 2 56 0 0 0 12746<br>MatILUFactorSym 1 1.0 8.3280e-03 2.2 0.00e+00 0.0 0.0e+00 0.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0<br>
MatAssemblyBegin 103 1.0 7.6879e+0215.4 0.00e+00 0.0 1.6e+04 6.2e+04 1.7e+02 <a href="tel:7%C2%A0%200%C2%A0%201%C2%A0%204%C2%A0%203%C2%A0%C2%A0%207%C2%A0%200%C2%A0%201%C2%A0%204%C2%A0%203" value="+17014370143" target="_blank">7 0 1 4 3 7 0 1 4 3</a> 0<br>
MatAssemblyEnd 103 1.0 3.7818e+01 1.0 0.00e+00 0.0 3.0e+03 5.3e+02 1.6e+02 1 0 0 0 3 1 0 0 0 3 0<br>
MatGetRowIJ 5 1.0 4.8716e-02 2.6 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0<br>MatGetSubMatrice 18 1.0 4.3095e+00 2.5 0.00e+00 0.0 1.6e+04 3.5e+05 7.4e+01 0 0 1 20 1 0 0 1 20 1 0<br>
MatGetOrdering 5 1.0 1.4656e+00 2.8 0.00e+00 0.0 0.0e+00 0.0e+00 1.4e+01 0 0 0 0 0 0 0 0 0 0 0<br>MatPartitioning 1 1.0 1.4356e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0<br>
MatZeroEntries 42 1.0 2.0939e-01 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0<br>VecDot 17 1.0 1.2719e-02 6.8 5.47e+05 1.1 0.0e+00 0.0e+00 1.7e+01 0 0 0 0 0 0 0 0 0 0 1317<br>
VecMDot 2425 1.0 1.7196e+01 2.2 5.82e+09 1.1 0.0e+00 0.0e+00 2.4e+03 0 4 0 0 41 0 4 0 0 41 10353<br>VecNorm 2503 1.0 2.7923e+00 3.4 1.18e+08 1.1 0.0e+00 0.0e+00 2.5e+03 0 0 0 0 42 0 0 0 0 42 1293<br>
VecScale 2467 1.0 7.3112e-02 1.7 5.84e+07 1.1 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 24453<br>VecCopy 153 1.0 1.1636e-02 1.8 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0<br>
VecSet 5031 1.0 6.0423e-01 2.2 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0<br>VecAXPY 137 1.0 1.1462e-02 1.5 6.33e+06 1.1 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 16902<br>
VecWAXPY 19 1.0 1.7784e-03 1.4 2.83e+05 1.1 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 4869<br>VecMAXPY 2467 1.0 8.5820e+00 1.3 5.93e+09 1.1 0.0e+00 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 21153<br>
VecAssemblyBegin 69 1.0 1.0341e+0018.2 0.00e+00 0.0 4.9e+03 5.4e+02 2.1e+02 0 0 0 0 3 0 0 0 0 3 0<br>VecAssemblyEnd 69 1.0 2.4939e-04 2.8 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0<br>
VecScatterBegin 7491 1.0 1.3734e+00 1.7 0.00e+00 0.0 1.1e+06 1.9e+04 0.0e+00 0 0 96 76 0 0 0 96 76 0 0<br>VecScatterEnd 7491 1.0 2.0055e+02 8.7 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 3 0 0 0 0 3 0 0 0 0 0<br>
VecReduceArith 8 1.0 1.4977e-03 2.0 3.05e+05 1.1 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 6232<br>VecReduceComm 4 1.0 8.9908e-0412.2 0.00e+00 0.0 0.0e+00 0.0e+00 4.0e+00 0 0 0 0 0 0 0 0 0 0 0<br>
VecNormalize 2467 1.0 2.8067e+00 3.4 1.75e+08 1.1 0.0e+00 0.0e+00 2.4e+03 0 0 0 0 41 0 0 0 0 41 1905<br>SNESSolve 4 1.0 4.0619e+03 1.0 2.23e+11 2.3 9.4e+05 2.3e+04 4.1e+03100 98 80 77 68 100 98 80 77 68 1136<br>
SNESLineSearch 17 1.0 1.1423e+01 1.0 5.23e+07 1.1 1.8e+04 1.7e+04 3.3e+02 0 0 2 1 6 0 0 2 1 6 140<br>SNESFunctionEval 23 1.0 2.9742e+01 1.0 2.60e+07 1.1 1.9e+04 1.9e+04 3.5e+02 1 0 2 1 6 1 0 2 1 6 27<br>
SNESJacobianEval 17 1.0 3.6786e+03 1.0 0.00e+00 0.0 9.8e+03 6.4e+04 1.4e+02 90 0 1 2 2 90 0 1 2 2 0<br>KSPGMRESOrthog 2425 1.0 2.5150e+01 1.6 1.16e+10 1.1 0.0e+00 0.0e+00 2.4e+03 0 8 0 0 41 0 8 0 0 41 14157<br>
KSPSetup 36 1.0 2.5388e-02 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0<br>KSPSolve 18 1.0 3.6141e+02 1.0 2.25e+11 2.3 1.1e+06 2.4e+04 5.0e+03 9100 97 96 84 9100 97 96 84 13015<br>
PCSetUp 36 1.0 2.1635e+02 3.6 1.55e+11 3.2 1.8e+04 3.2e+05 1.5e+02 3 56 2 20 3 3 56 2 20 3 12274<br>PCSetUpOnBlocks 18 1.0 2.1293e+02 3.7 1.55e+11 3.2 0.0e+00 0.0e+00 2.7e+01 2 56 0 0 0 2 56 0 0 0 12471<br>
PCApply 2467 1.0 2.5616e+02 2.5 5.95e+10 1.7 7.3e+05 2.8e+04 0.0e+00 4 33 62 73 0 4 33 62 73 0 6060<br>------------------------------------------------------------------------------------------------------------------------<br>
<br>Memory usage is given in bytes:<br><br>Object Type Creations Destructions Memory Descendants' Mem.<br>Reports information only for process 0.<br><br>--- Event Stage 0: Main Stage<br><br> Matrix 39 39 18446744074642894848 0<br>
Matrix Partitioning 1 1 640 0<br> Index Set 184 184 2589512 0<br> IS L to G Mapping 2 2 301720 0<br> Vector 729 729 133662888 0<br>
Vector Scatter 29 29 30508 0<br> Application Order 2 2 9335968 0<br> SNES 4 4 5088 0<br> Krylov Solver 10 10 32264320 0<br>
Preconditioner 10 10 9088 0<br> Viewer 1 0 0 0<br>========================================================================================================================<br>
Average time to get PetscTime(): 1.19209e-07<br>Average time for MPI_Barrier(): 1.20163e-05<br>Average time for zero size MPI_Send(): 2.49594e-06<br>......................................<br>-----------------------------------------<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<br>