[petsc-users] SNESComputeJacobianDefaultColor use too much memory

[Rongliang Chen]

Dear Barry,

Many thanks for your reply.

I checked with the valgrind and did not obtain any outputs 
(|massif.out.<pid>|) because the job was killed before it reached the end.

Then I switch to a smaller case, it works well and one of the output is 
attached (I did not find any useful information in it). The output with 
the option -mat_coloring_view is followed, which shows that the number 
of colors is 65. Any ideas for this?

MatColoring Object: 480 MPI processes
   type: sl
   Weight type: RANDOM
   Distance 2, Max. Colors 65535
   Number of colors 65
   Number of total columns 1637350

Best regards,
Rongliang

On 02/17/2016 01:13 AM, Barry Smith wrote:
>    How many colors are needed?
>
>    You need to produce a breakdown of where all the memory is being used. For example valgrind with the http://valgrind.org/docs/manual/ms-manual.html
>
>    Barry
>
>> On Feb 16, 2016, at 6:45 AM, Rongliang Chen <rongliang.chan at gmail.com> wrote:
>>
>> Dear all,
>>
>> I am using the DMPlex to solve a PDE on a unstructured mesh and I use the SNESComputeJacobianDefaultColor to compute the Jacobian matrix.
>>
>> My code works well for small problems (such as problem with 3.3x10^5 cells using 120 cores) but when I increase the number of cells (2.6x10^6 cells using 1920 cores), I go out of memory in the function MatColoringApply. It shows that one of the cores uses over 11G memory. I think this is unreasonable. Do you have any suggestions for debugging this problem?
>>
>> Best regards,
>> Rongliang

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cmd: ./Nwtun -f /HOME/siat_crl_1/WORKSPACE/rlchen/meshes/FVM/3DNACA0012AIRFOIL_Hex75x25x50x40.exo -overlap 1 -options_file options.txt -ksp_monitor -time_integral_method 1 -initial_time 0.0 -final_time 1.0 -dt 1.e-3 -timestep 2 -max_time_its 0 -includeenergy -reconstruct -PressureFlux -testcase 3DNACA -output_solution -solutionfile /HOME/siat_crl_1/WORKSPACE/rlchen/results/FVM/3DNACA0012AIRFOIL_Hex150x50x100x80_imp -steps_output 100 -inflow_u 349.02 -viscosity 0.01 -k 0.026 -monitor_step_gap -R 287.02 -adiabatic 1.4 -Euler -Attack 10 -Mach 0.8 -fd_jacobian_color -limiter zero -RiemannSolver Rusanov -CFL 0.9 -reconstruct -second_order -parallel_csr -parallel_output -DiffFuncForJac -mat_coloring_view
time_unit: i
#-----------
snapshot=0
#-----------
time=0
mem_heap_B=0
mem_heap_extra_B=0
mem_stacks_B=0
heap_tree=empty