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Re: For Loop and NDSolve

  • To: mathgroup at smc.vnet.net
  • Subject: [mg85259] Re: For Loop and NDSolve
  • From: Jean-Marc Gulliet <jeanmarc.gulliet at gmail.com>
  • Date: Mon, 4 Feb 2008 03:17:29 -0500 (EST)
  • Organization: The Open University, Milton Keynes, UK
  • References: <fnuh4s$9ni$1@smc.vnet.net> <fo19o9$fu8$1@smc.vnet.net> <fo3g6g$b24$1@smc.vnet.net>

PV wrote:

> Hello Here is a stand alone version of my code, I have not got rid of
> the for loop as suggested by Szabolcs here but Iam trying something
> like that right now! I would be grateful to anybody who can give me a
> hint or two abot which part of this code is eating up excessive
> memory!

<snip>

Hi Prasanna,

You will find below a slightly modify version of the code you posted, so 
we can track the memory consumption and some possible memory leaks, as 
well as part of the results I got for N0 = 500. (Note that the program 
took about 13 hours of CPU time to complete the hundred iterations. I 
started it on Saturday night -- before leaving for a party -- and it was 
completed when I return to my iMac on Sunday afternoon.)

Glancing at the results, I suspect that the large memory consumption is 
due to the large size of the solution (called "soln" in the code) 
returned by NDSolve. NDSolve returns a solution in the form of an 
InterpolatingFunction object. The size of this object depends on the 
number of sampling points that are required to get a good fit. Roughly 
speaking, the size of the solution returned by NDSolve, an interpolating 
function, is proportional to the complexity of the system to be solved, 
say the number of non-trivial equations in your system.

My understanding -- or, at this stage, I should say, "A wild guess" -- 
is that the sparce matrix you build at each iteration becomes less dense 
(that is, holds more non-zero entries) depending on the original size of 
the problem (N0) and the number of iterations (j). Therefore the system 
to be solved becomes more complex and the solution (soln) becomes 
larger. As one can see below, soln starts at about 600 MB and ends at 
about 2 GB.

Hope this helps,
-- 
Jean-Marc

(* Beginning of the code *)

$HistoryLength = 0;

$Version (* "6.0 for Mac OS X x86 (64-bit) (June 19, 2007)" *)

c3 = 0.035896;
N0 = 500;
k0 = 1/40;
L = 80 \[Pi];
\[Eta] = 1.0485203*10^6;
\[Gamma] = 1.85353*^6;
\[Kappa] = 3.707*^6;
delt = 1/1000;

a = 0.26452763498582404;

V0[a_] := 79.06*Abs[a]^2

deltanew[n_] :=
  If[Mod[n, N0] == 0,
   N0*1/(Sqrt[L])*
    NIntegrate[
     E^(-I*n*k0*z)*MathieuC[-0.81399423, -1.383053249, z], {z, 0, Pi}],
    0]
list1 = 1/(L)*Chop[Table[deltanew[n], {n, -4*N0, 4*N0}]];

zeropad = Table[0, {l, 1, 16*N0}];
wavefn = Join[list1, zeropad];

fieldlist3 = {};
couplinglist = {};
normlist = {};

Print["\n-----------------"];
Print["Memory consumption for N0 = ", N0];
Print["Entering Loop - Memory Used: ", MemoryInUse[],
   ", Max Memory: ", MaxMemoryUsed[]];

cputime = First@Timing[
     For[j = 1, j <= 100, t = j*1/1000;

      Print["\nMemory Used: ", MemoryInUse[], ", Max Memory: ",
       MaxMemoryUsed[]];

      solnmatrix = -I/c3*
        SparseArray[{{i_,
            i_} -> (-V0[a]/2 + ((i - (4*N0 + 1))*k0 - 2*t)^2), {m_,
             n_} /; Abs[m - n] == N0 -> -V0[a]/4}, {24*N0 + 1,
          24*N0 + 1}];

      Print["solnmatrix size: ", ByteCount@solnmatrix];
      Print["Memory Used: ", MemoryInUse[], ", Max Memory: ",
       MaxMemoryUsed[]];

      soln =
       NDSolve[{u'[p] == solnmatrix.u[p], u[0] == wavefn},
        u, {p, 0, delt}];

      Print["soln size: ", ByteCount@soln];
      Print["Memory Used: ", MemoryInUse[], ", Max Memory: ",
       MaxMemoryUsed[]];

      wavefn = First[u[delt] /. soln];

      Print["wavefn size: ", ByteCount@wavefn];
      Print["Memory Used: ", MemoryInUse[], ", Max Memory: ",
       MaxMemoryUsed[]];

      C1 = (Tr[Abs[wavefn]^2/2] +
          0.25*Sum[
            Conjugate[wavefn[[n]]]*wavefn[[n + N0]], {n, 1,
             23*N0 + 1}] +
          0.25*Sum[
            Conjugate[wavefn[[n]]]*wavefn[[n - N0]], {n, N0 + 1,
             24*N0 + 1}])*L;

      Print["C1 size: ", ByteCount@C1];
      Print["Memory Used: ", MemoryInUse[], ", Max Memory: ",
       MaxMemoryUsed[]];

      b = -\[Eta]/(I*\[Gamma]*
            C1 - \[Kappa]) + ((\[Eta] + (I*\[Gamma]*C1 - \[Kappa])*
              a)/(I*\[Gamma]*C1 - \[Kappa]))*
         E^(delt*0.0011*(I*\[Gamma]*C1 - \[Kappa]));
      a = b;
      AppendTo[fieldlist3, a];

      Print["fieldlist3 size: ", ByteCount@fieldlist3];
      Print["Memory Used: ", MemoryInUse[], ", Max Memory: ",
       MaxMemoryUsed[]];

      AppendTo[normlist, L*Tr[Abs[wavefn]^2]];

      Print["normlist size: ", ByteCount@normlist];
      Print["Memory Used: ", MemoryInUse[], ", Max Memory: ",
       MaxMemoryUsed[]];

      AppendTo[couplinglist, C1];

      Print["couplinglist size: ", ByteCount@couplinglist];

      Print["Iter no: ", j, " , Memory Used: ", MemoryInUse[],
       ", Max Memory: ", MaxMemoryUsed[]];

      j++;]
     ];

Print["CPU Time: ", cputime];

Print["Exiting Loop - Memory Used: ", MemoryInUse[], ", Max Memory: ",
    MaxMemoryUsed[]];

(* End of the code *)

---------------------

Memory consumption for N0 = 500

Entering Loop - Memory Used: 14028176, Max Memory: 16809016


Memory Used: 14036208, Max Memory: 16809016

solnmatrix size: 2988828

Memory Used: 16224536, Max Memory: 24243360

soln size: 685656272

Memory Used: 702042440, Max Memory: 712914208

wavefn size: 192132

Memory Used: 702138664, Max Memory: 712914208

C1 size: 72

Memory Used: 702119728, Max Memory: 712914208

fieldlist3 size: 104

Memory Used: 702119760, Max Memory: 712914208

normlist size: 48

Memory Used: 702119792, Max Memory: 712914208

couplinglist size: 104

Iter no: 1 , Memory Used: 702119896, Max Memory: 712914208


Memory Used: 702119824, Max Memory: 712914208

solnmatrix size: 2988828

Memory Used: 702117024, Max Memory: 712914208

soln size: 947004752

Memory Used: 963530320, Max Memory: 1660783512

wavefn size: 192132

Memory Used: 963722616, Max Memory: 1660783512

C1 size: 72

Memory Used: 963530480, Max Memory: 1660783512

fieldlist3 size: 184

Memory Used: 963530528, Max Memory: 1660783512

normlist size: 72

Memory Used: 963530536, Max Memory: 1660783512

couplinglist size: 184

Iter no: 2 , Memory Used: 963530616, Max Memory: 1660783512


Memory Used: 963530544, Max Memory: 1660783512

solnmatrix size: 2988828

Memory Used: 963525616, Max Memory: 1660783512

soln size: 1209890576

Memory Used: 1226476640, Max Memory: 2185129408

wavefn size: 192132

Memory Used: 1226669128, Max Memory: 2185129408

C1 size: 72

Memory Used: 1226477184, Max Memory: 2185129408

fieldlist3 size: 264

Memory Used: 1226477424, Max Memory: 2185129408

normlist size: 96

Memory Used: 1226477624, Max Memory: 2185129408

couplinglist size: 264

Iter no: 3 , Memory Used: 1226477896, Max Memory: 2185129408


Memory Used: 1226478016, Max Memory: 2185129408

solnmatrix size: 2988828

Memory Used: 1226473248, Max Memory: 2185129408

soln size: 1413972992

Memory Used: 1430607432, Max Memory: 2652198880

wavefn size: 192132

Memory Used: 1430799888, Max Memory: 2652198880

C1 size: 72

Memory Used: 1430607944, Max Memory: 2652198880

fieldlist3 size: 344

Memory Used: 1430608184, Max Memory: 2652198880

normlist size: 120

Memory Used: 1430608384, Max Memory: 2652198880

couplinglist size: 344

Iter no: 4 , Memory Used: 1430608656, Max Memory: 2652198880


Memory Used: 1430608776, Max Memory: 2652198880

solnmatrix size: 2988828

Memory Used: 1430604008, Max Memory: 2652198880

soln size: 1551949616

Memory Used: 1568617136, Max Memory: 2994333440

wavefn size: 192132

Memory Used: 1568809592, Max Memory: 2994333440

C1 size: 72

Memory Used: 1568617648, Max Memory: 2994333440

fieldlist3 size: 424

Memory Used: 1568617888, Max Memory: 2994333440

normlist size: 144

Memory Used: 1568618088, Max Memory: 2994333440

couplinglist size: 424

Iter no: 5 , Memory Used: 1568618360, Max Memory: 2994333440


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