[petsc-users] MatPermuteSparsify hanging

[Barry Smith]

  Ok, Then the problem is not a fundamental bug but a performance bug (that makes the routine unusable). It is not properly preallocating the new compressed matrix so setting values into it is taking FOREVER (hence the routine is unusable) so who wrote this routine and who is going to fix it.

  Kelly,

    What are you using this routine for? It is a pretty obscure that is hardly ever used. Do you need it?

   Barry

On Nov 29, 2010, at 4:23 PM, Kelly Fermoyle wrote:

> This is what I got on a desktop. It looks a lot more reasonable. I stopped
> it after a while and it appears to be in MatSetValues.
> 
> 
> 
> [Thread 0x40200940 (LWP 26776) exited]
> 
> Program received signal SIGINT, Interrupt.
> 0x0000000000accb16 in PetscMemcpy (a=0x2aaab7b499b0, b=0x2aaab6de4938,
> n=1796808) at memc.c:104
> 104	    memcpy((char*)(a),(char*)(b),n);
> (gdb) backtrace full
> #0  0x0000000000accb16 in PetscMemcpy (a=0x2aaab7b499b0, b=0x2aaab6de4938,
> n=1796808) at memc.c:104
>        al = 46912714873264
>        bl = 46912700827960
>        nl = 1796808
> #1  0x000000000069b8f9 in MatSetValues_SeqAIJ (A=0x1430490, m=1,
> im=0x7fffffffd270, n=21, in=0x2aaab2c76200, v=0x2aaab2d9a200,
>    is=INSERT_VALUES) at aij.c:225
>        len = 224601
>        new_j = 0x2aaab7d01200
>        Ain = 0x1431620
>        new_nz = 1755215
>        new_i = 0x2aaab83b4200
>        new_a = 0x2aaab6f9c200
>        a = 0x1431620
>        rp = 0x2aaab89c5d48
>        k = 0
>        low = 18
>        high = 21
>        t = 18
>        ii = 59410
>        row = 52376
>        nrow = 21
>        i = 21
>        col = 52922
>        l = 0
>        rmax = 21
>        N = 37
>        imax = 0x2aaab2e0f200
>        ai = 0x2aaab8aa2200
>        ailen = 0x2aaab2e4a200
>        ierr = 0
>        aj = 0x2aaab83ef200
>        nonew = 0
>        lastcol = 52922
>        ap = 0x2aaab6de4890
>        value = 25472.555765646161
>        aa = 0x2aaab6237200
>        ignorezeroentries = PETSC_FALSE
>        roworiented = PETSC_TRUE
> #2  0x000000000061c324 in MatSetValues (mat=0x1430490, m=1,
> idxm=0x7fffffffd270, n=21, idxn=0x2aaab2c76200, v=0x2aaab2d9a200,
>    addv=INSERT_VALUES) at matrix.c:921
>        ierr = 0
> #3  0x00000000006426d7 in MatPermuteSparsify (A=0x141a1a0, band=-1,
> frac=0, tol=0.001, rowp=0x13fde70, colp=0x142e630,
>    B=0x7fffffffd678) at matrix.c:4157
>        irowp = 0x142f050
>        icolp = 0x142fa70
>        rows = 0x2aaab2cb1200
>        cols = 0x2aaab2cec200
>        M = 59409
>        N = 59409
>        locRowStart = 0
>        locRowEnd = 59409
>        nz = 21
>        newNz = 21
>        cwork = 0x2aaab5271a24
>        cnew = 0x2aaab2c76200
>        vwork = 0x2aaab4bdd248
>        vnew = 0x2aaab2d9a200
>        bw = 2970
>        issize = 59409
>        row = 27126
>        locRow = 27126
>        newRow = 52376
>        col = 21
>        newCol = 52382
>        ierr = 0
> #4  0x000000000043822f in main (argc=17, argv=0x7fffffffd7a8) at
> SolveTest.cpp:54
>        ksp = 0x7fff00000001
>        colp = 0x142e630
> ---Type <return> to continue, or q <return> to quit---
>        vec_file =
> "/gpfs/home/kjf198/group/kjf198/SYMMETRIC_MATRICES/20-0.vec\000\000\000\000\000\000\200\325\377\377\377\177\000\000i4\271\255\252*\000\000\250\065\062\001\000\000\000\000\023\000\000\000\252*\000\000\300\065\062\001\000\000\000\000\001\000\000\000\000\000\000\000\250\065\062\001\000\000\000\000\221
> \226\256\252*\000\000\303\312\363\000\000\000\000\000\340,\226\256\252*\000\000\250\335\037\001\000\000\000\000\303\312\363\000\000\000\000\000\060\326\377\377\377\177\000\000\000\260\036\001\000\000\000\000\070\330\377\377\377\177\000\000b.\226\256\252*\000\000\000\330\377\377\377\177\000\000\000\260\036\001\000\000\000\000@\326\377\377\377\177\000\000\201\065\343M4\000\000\000\000\260\036\001\000\000\000\000@\326\377\377\377\177\000\000\000\260\036\001\000\000\000\000\t\204C\000\000\000\000"
>        mat_file =
> "/gpfs/home/kjf198/group/kjf198/SYMMETRIC_MATRICES/20-0.mat\000\377\377\177\000\000\000\020\214\256\252*\000\000>\340\215\256\252*\000\000`\023\214\256\252*\000\000\260\325\377\377\377\177\000\000\000\020\214\256\000\000\000\000\300®\257\252*\000\000`\263\252\252\252*\000\000\320\325\377\377\377\177\000\000\000\260\252\252\252*\000\000\023\246A\000\000\000\000\000`\263\252\252\252*\000\000\360\325\377\377\377\177\000\000\020\224\214\256\252*\000\000\000\020\214\256\252*\000\000\360\233\340M4\000\000\000\340\024\214\256\252*\000\000`\020\273\256\000\000\000\000y:<\a\000\000\000\000\000\260\036\001\000\000\000\000H[/\000\000\000\000\000\b(2\001\000\000\000\000\021\000\000\000\000\000\000\000\250\327\377\377\377\177\000\000\070\330\377\377\377\177\000"
>        reordering = "rcm", '\000' <repeats 252 times>
>        b = 0x13f6e30
>        rowp = 0x13fde70
>        ierr = 0
>        timestep = 20
>        x = 0x13fb6c0
>        start = 1.1098831058709664e-312
>        type = 0xecbb5a "rcm"
>        iters = 15513927
>        A = 0x141a1a0
>        P = 0x1430490
>        residual = 2.1861090613857222e-317
>        threshold = 0.001
>        mat_view = 0x13fb6c0
>        vec_view = 0x13fb6c0
>        iteration = 0
>        end = 7.6648711891784312e-317
> 
> 
> 
>> On Mon, Nov 29, 2010 at 20:28, Kelly Fermoyle <kjf198 at cse.psu.edu> wrote:
>> 
>>> I am using a Cray machine and it requires that I call as aprun -n 1
>>> ./prog_name, which does not seem to work with -start_in_debugger.
>>> 
>> 
>> Can you reproduce with the same code on a local machine (e.g.
>> desktop/laptop) where you can get a proper debugging session?
>> 
>> 
>>> Below is the output of the full backtrace:
>>> 
>> 
>> This trace is not even in your code
>> 
>>> #2  0x0000000000403be7 in main (argc=20, argv=0x7fffe2814538) at
>> aprun.c:225
>> 
>> Jed
>> 
>