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Re: [Bug 424159] [NEW] Reaction demo fails when GMP is enabled

To: dolfin-dev@xxxxxxxxxx
From: logg <logg@xxxxxxxxx>
Date: Fri, 04 Sep 2009 07:37:36 -0000
Delivered-to: dolfin-dev@xxxxxxxxxx
Reply-to: Bug 424159 <424159@xxxxxxxxxxxxxxxxxx>
Sender: bounces@xxxxxxxxxxxxx
I'm about to merge a big changegroup for ODE solver library from
Benjamin Kehlet. I suspect this to take care of the problem.

--
Anders


On Fri, Sep 04, 2009 at 06:33:38AM -0000, Johannes Ring wrote:
> Public bug reported:
>
> [ Testing Launchpad's email interface [0]. ]
>
> Hi,
>
> There is a problem with demo/ode/reaction/cpp when GMP is enabled. I
> have the latest from HG of all FEniCS packages and this is the output I
> get when I run the demo:
>
> $ ./demo
> Reaction ODE demo needs to be fixed.
> Using 128 bits per digit, eps = 4.701977e-39
> Creating ODE of size 3191.
> Solving ODE over the time interval [0.0, 0.01]
>   Solving primal problem
>     *** Warning: PythonFile: Precision lost. Values will be saved with double precision
>     Initializing continuous Galerkin method cG(1).
>     Using multi-adaptive fixed-point solver.
>     Using discrete tolerance tol = 1e-06....
>     Computing transpose (inverse) of dependency pattern.
>     Time-stepping over the time interval [0, 0.01]
>       *** Warning: Time slab system did not converge.
>       Direct fixed-point iteration does not converge.
>       Trying diagonally damped fixed-point iteration.
>       Rejecting time slab K = 1.000e-05, trying again.
>       Rejecting time slab K = 8.205e-06, trying again.
>       Rejecting time slab K = 6.317e-06, trying again.
>       Rejecting time slab K = 4.628e-06, trying again.
> demo: dolfin/ode/MultiAdaptiveTimeSlab.cpp:939: void dolfin::MultiAdaptiveTimeSlab::cg_feval(dolfin::real*, dolfin::uint, dolfin::uint, dolfin::uint, dolfin::real, dolfin::real, dolfin::real): Assertion `e1 != -1' failed.
> [simula-x61:25117] *** Process received signal ***
> [simula-x61:25117] Signal: Aborted (6)
> [simula-x61:25117] Signal code:  (-6)
> [simula-x61:25117] [ 0] [0xb7f8b440]
> [simula-x61:25117] [ 1] /lib/tls/i686/cmov/libc.so.6(abort+0x101) [0xb5b82a01]
> [simula-x61:25117] [ 2] /lib/tls/i686/cmov/libc.so.6(__assert_fail+0xee) [0xb5b7a10e]
> [simula-x61:25117] [ 3] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin21MultiAdaptiveTimeSlab8cg_fevalEP10__gmp_exprIA1_12__mpf_structS3_EjjjS4_S4_S4_+0x133a) [0xb7e9216a]
> [simula-x61:25117] [ 4] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin29MultiAdaptiveFixedPointSolver9iterationE10__gmp_exprIA1_12__mpf_structS3_EjS4_S4_+0xded) [0xb7eb3b8d]
> [simula-x61:25117] [ 5] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin14TimeSlabSolver5solveEj+0x17b) [0xb7e896bb]
> [simula-x61:25117] [ 6] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin14TimeSlabSolver5solveEv+0x42) [0xb7e89eb2]
> [simula-x61:25117] [ 7] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin21MultiAdaptiveTimeSlab5solveEv+0x117) [0xb7e8f057]
> [simula-x61:25117] [ 8] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin11TimeStepper4stepERNS_11ODESolutionE10__gmp_exprIA1_12__mpf_structS5_ES6_+0x204) [0xb7ea70c4]
> [simula-x61:25117] [ 9] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin11TimeStepper4stepERNS_11ODESolutionE+0x84) [0xb7ea75c4]
> [simula-x61:25117] [10] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin11TimeStepper5solveERNS_11ODESolutionE10__gmp_exprIA1_12__mpf_structS5_ES6_+0x149) [0xb7ea80d9]
> [simula-x61:25117] [11] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin11TimeStepper5solveERNS_11ODESolutionE+0x66) [0xb7ea8426]
> [simula-x61:25117] [12] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin9ODESolver12solve_primalERNS_11ODESolutionE+0x72) [0xb7ea54e2]
> [simula-x61:25117] [13] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin9ODESolver5solveERNS_11ODESolutionE+0x95) [0xb7ea5635]
> [simula-x61:25117] [14] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin9ODESolver5solveEv+0x4b) [0xb7ea5a1b]
> [simula-x61:25117] [15] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin3ODE5solveEv+0x3e) [0xb7e9a51e]
> [simula-x61:25117] [16] ./demo(main+0x454) [0x805a314]
> [simula-x61:25117] [17] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0) [0xb5b6c450]
> [simula-x61:25117] [18] ./demo(_ZN6dolfin3ODE2JTEPK10__gmp_exprIA1_12__mpf_structS3_EPS4_S6_S4_+0x101) [0x8059d71]
> [simula-x61:25117] *** End of error message ***
> Aborted
>
>
> Using gdb I get this:
>
> Program received signal SIGABRT, Aborted.
> [Switching to Thread 0xb57c36c0 (LWP 25525)]
> 0xb7f57410 in __kernel_vsyscall ()
> (gdb) where
> #0  0xb7f57410 in __kernel_vsyscall ()
> #1  0xb5b4d085 in raise () from /lib/tls/i686/cmov/libc.so.6
> #2  0xb5b4ea01 in abort () from /lib/tls/i686/cmov/libc.so.6
> #3  0xb5b4610e in __assert_fail () from /lib/tls/i686/cmov/libc.so.6
> #4  0xb7e5e16a in dolfin::MultiAdaptiveTimeSlab::cg_feval (this=0x8385ef8, f=0x841f344, s0=0, e0=3188, i0=3188,
>     a0=@0xbf84d074, b0=@0xbf84d064, k0=@0xbf84d054) at dolfin/ode/MultiAdaptiveTimeSlab.cpp:939
> #5  0xb7e7fb8d in dolfin::MultiAdaptiveFixedPointSolver::iteration (this=0x841f368, tol=@0xbf84d22c, iter=0,
>     d0=@0xbf84d21c, d1=@0xbf84d20c) at dolfin/ode/MultiAdaptiveFixedPointSolver.cpp:151
> #6  0xb7e556bb in dolfin::TimeSlabSolver::solve (this=0x841f368, attempt=0) at dolfin/ode/TimeSlabSolver.cpp:71
> #7  0xb7e55eb2 in dolfin::TimeSlabSolver::solve (this=0x841f368) at dolfin/ode/TimeSlabSolver.cpp:51
> #8  0xb7e5b057 in dolfin::MultiAdaptiveTimeSlab::solve (this=0x8385ef8) at dolfin/ode/MultiAdaptiveTimeSlab.cpp:118
> #9  0xb7e730c4 in dolfin::TimeStepper::step (this=0xbf84d5cc, u=@0xbf84d6d0, t0=@0xbf84d44c, t1=@0xbf84d45c)
>     at dolfin/ode/TimeStepper.cpp:96
> #10 0xb7e735c4 in dolfin::TimeStepper::step (this=0xbf84d5cc, u=@0xbf84d6d0) at dolfin/ode/TimeStepper.cpp:78
> #11 0xb7e740d9 in dolfin::TimeStepper::solve (this=0xbf84d5cc, u=@0xbf84d6d0, t0=@0xbf84d57c, t1=@0xbf84d58c)
>     at dolfin/ode/TimeStepper.cpp:67
> #12 0xb7e74426 in dolfin::TimeStepper::solve (this=0xbf84d5cc, u=@0xbf84d6d0) at dolfin/ode/TimeStepper.cpp:54
> #13 0xb7e714e2 in dolfin::ODESolver::solve_primal (this=0xbf84d868, u=@0xbf84d6d0) at dolfin/ode/ODESolver.cpp:64
> #14 0xb7e71635 in dolfin::ODESolver::solve (this=0xbf84d868, u=@0xbf84d6d0) at dolfin/ode/ODESolver.cpp:44
> #15 0xb7e71a1b in dolfin::ODESolver::solve (this=0xbf84d868) at dolfin/ode/ODESolver.cpp:33
> #16 0xb7e6651e in dolfin::ODE::solve (this=0xbf84d8a8) at dolfin/ode/ODE.cpp:230
> #17 0x0805a314 in main () at main.cpp:106
> (gdb)
>
>
> If I reduce the size of the variable N from 5000 to 3190, the demo runs fine.
>
> diff -r 717eaa11d058 demo/ode/reaction/cpp/main.cpp
> --- a/demo/ode/reaction/cpp/main.cpp	Thu Sep 03 11:10:26 2009 +0200
> +++ b/demo/ode/reaction/cpp/main.cpp	Thu Sep 03 14:34:57 2009 +0200
> @@ -89,7 +89,7 @@
>    const real epsilon = 0.01;
>    const real gamma = 1000.0;
>    const real L = 1.0;
> -  const unsigned int N = 5000;
> +  const unsigned int N = 3190;
>
>    // Create ODE
>    Reaction ode(N, T, L, epsilon, gamma);
>
> It only seems to affect 32 bits systems since both hardy-i386 [1] and
> mac-osx [2] buildbot slaves has this problem while the demo runs fine on
> jaunty-amd64 and linux64-exp.
>
> The demo also runs fine when GMP is disabled.
>
> [0] https://help.launchpad.net/Bugs/EmailInterface
> [1] http://fenics.org:8080/builders/dolfin-hardy-i386/builds/770/steps/dolfin%20check/logs/demo.log
> [2] http://fenics.org:8080/builders/dolfin-mac-osx/builds/719/steps/dolfin%20check/logs/demo.log
>
>  affects dolfin
>
> ** Affects: dolfin
>      Importance: Undecided
>          Status: New
>

-- 
Reaction demo fails when GMP is enabled
https://bugs.launchpad.net/bugs/424159
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Status in DOLFIN: New

Bug description:
[ Testing Launchpad's email interface [0]. ]

Hi,

There is a problem with demo/ode/reaction/cpp when GMP is enabled. I have the latest from HG of all FEniCS packages and this is the output I get when I run the demo:

$ ./demo 
Reaction ODE demo needs to be fixed.
Using 128 bits per digit, eps = 4.701977e-39
Creating ODE of size 3191.
Solving ODE over the time interval [0.0, 0.01]
  Solving primal problem
    *** Warning: PythonFile: Precision lost. Values will be saved with double precision
    Initializing continuous Galerkin method cG(1).
    Using multi-adaptive fixed-point solver.
    Using discrete tolerance tol = 1e-06....
    Computing transpose (inverse) of dependency pattern.
    Time-stepping over the time interval [0, 0.01]
      *** Warning: Time slab system did not converge.
      Direct fixed-point iteration does not converge.
      Trying diagonally damped fixed-point iteration.
      Rejecting time slab K = 1.000e-05, trying again.
      Rejecting time slab K = 8.205e-06, trying again.
      Rejecting time slab K = 6.317e-06, trying again.
      Rejecting time slab K = 4.628e-06, trying again.
demo: dolfin/ode/MultiAdaptiveTimeSlab.cpp:939: void dolfin::MultiAdaptiveTimeSlab::cg_feval(dolfin::real*, dolfin::uint, dolfin::uint, dolfin::uint, dolfin::real, dolfin::real, dolfin::real): Assertion `e1 != -1' failed.
[simula-x61:25117] *** Process received signal ***
[simula-x61:25117] Signal: Aborted (6)
[simula-x61:25117] Signal code:  (-6)
[simula-x61:25117] [ 0] [0xb7f8b440]
[simula-x61:25117] [ 1] /lib/tls/i686/cmov/libc.so.6(abort+0x101) [0xb5b82a01]
[simula-x61:25117] [ 2] /lib/tls/i686/cmov/libc.so.6(__assert_fail+0xee) [0xb5b7a10e]
[simula-x61:25117] [ 3] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin21MultiAdaptiveTimeSlab8cg_fevalEP10__gmp_exprIA1_12__mpf_structS3_EjjjS4_S4_S4_+0x133a) [0xb7e9216a]
[simula-x61:25117] [ 4] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin29MultiAdaptiveFixedPointSolver9iterationE10__gmp_exprIA1_12__mpf_structS3_EjS4_S4_+0xded) [0xb7eb3b8d]
[simula-x61:25117] [ 5] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin14TimeSlabSolver5solveEj+0x17b) [0xb7e896bb]
[simula-x61:25117] [ 6] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin14TimeSlabSolver5solveEv+0x42) [0xb7e89eb2]
[simula-x61:25117] [ 7] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin21MultiAdaptiveTimeSlab5solveEv+0x117) [0xb7e8f057]
[simula-x61:25117] [ 8] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin11TimeStepper4stepERNS_11ODESolutionE10__gmp_exprIA1_12__mpf_structS5_ES6_+0x204) [0xb7ea70c4]
[simula-x61:25117] [ 9] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin11TimeStepper4stepERNS_11ODESolutionE+0x84) [0xb7ea75c4]
[simula-x61:25117] [10] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin11TimeStepper5solveERNS_11ODESolutionE10__gmp_exprIA1_12__mpf_structS5_ES6_+0x149) [0xb7ea80d9]
[simula-x61:25117] [11] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin11TimeStepper5solveERNS_11ODESolutionE+0x66) [0xb7ea8426]
[simula-x61:25117] [12] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin9ODESolver12solve_primalERNS_11ODESolutionE+0x72) [0xb7ea54e2]
[simula-x61:25117] [13] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin9ODESolver5solveERNS_11ODESolutionE+0x95) [0xb7ea5635]
[simula-x61:25117] [14] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin9ODESolver5solveEv+0x4b) [0xb7ea5a1b]
[simula-x61:25117] [15] /home/johannr/src/hg/dolfin/local/lib/libdolfin.so.0(_ZN6dolfin3ODE5solveEv+0x3e) [0xb7e9a51e]
[simula-x61:25117] [16] ./demo(main+0x454) [0x805a314]
[simula-x61:25117] [17] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0) [0xb5b6c450]
[simula-x61:25117] [18] ./demo(_ZN6dolfin3ODE2JTEPK10__gmp_exprIA1_12__mpf_structS3_EPS4_S6_S4_+0x101) [0x8059d71]
[simula-x61:25117] *** End of error message ***
Aborted


Using gdb I get this:

Program received signal SIGABRT, Aborted.
[Switching to Thread 0xb57c36c0 (LWP 25525)]
0xb7f57410 in __kernel_vsyscall ()
(gdb) where
#0  0xb7f57410 in __kernel_vsyscall ()
#1  0xb5b4d085 in raise () from /lib/tls/i686/cmov/libc.so.6
#2  0xb5b4ea01 in abort () from /lib/tls/i686/cmov/libc.so.6
#3  0xb5b4610e in __assert_fail () from /lib/tls/i686/cmov/libc.so.6
#4  0xb7e5e16a in dolfin::MultiAdaptiveTimeSlab::cg_feval (this=0x8385ef8, f=0x841f344, s0=0, e0=3188, i0=3188, 
    a0=@0xbf84d074, b0=@0xbf84d064, k0=@0xbf84d054) at dolfin/ode/MultiAdaptiveTimeSlab.cpp:939
#5  0xb7e7fb8d in dolfin::MultiAdaptiveFixedPointSolver::iteration (this=0x841f368, tol=@0xbf84d22c, iter=0, 
    d0=@0xbf84d21c, d1=@0xbf84d20c) at dolfin/ode/MultiAdaptiveFixedPointSolver.cpp:151
#6  0xb7e556bb in dolfin::TimeSlabSolver::solve (this=0x841f368, attempt=0) at dolfin/ode/TimeSlabSolver.cpp:71
#7  0xb7e55eb2 in dolfin::TimeSlabSolver::solve (this=0x841f368) at dolfin/ode/TimeSlabSolver.cpp:51
#8  0xb7e5b057 in dolfin::MultiAdaptiveTimeSlab::solve (this=0x8385ef8) at dolfin/ode/MultiAdaptiveTimeSlab.cpp:118
#9  0xb7e730c4 in dolfin::TimeStepper::step (this=0xbf84d5cc, u=@0xbf84d6d0, t0=@0xbf84d44c, t1=@0xbf84d45c)
    at dolfin/ode/TimeStepper.cpp:96
#10 0xb7e735c4 in dolfin::TimeStepper::step (this=0xbf84d5cc, u=@0xbf84d6d0) at dolfin/ode/TimeStepper.cpp:78
#11 0xb7e740d9 in dolfin::TimeStepper::solve (this=0xbf84d5cc, u=@0xbf84d6d0, t0=@0xbf84d57c, t1=@0xbf84d58c)
    at dolfin/ode/TimeStepper.cpp:67
#12 0xb7e74426 in dolfin::TimeStepper::solve (this=0xbf84d5cc, u=@0xbf84d6d0) at dolfin/ode/TimeStepper.cpp:54
#13 0xb7e714e2 in dolfin::ODESolver::solve_primal (this=0xbf84d868, u=@0xbf84d6d0) at dolfin/ode/ODESolver.cpp:64
#14 0xb7e71635 in dolfin::ODESolver::solve (this=0xbf84d868, u=@0xbf84d6d0) at dolfin/ode/ODESolver.cpp:44
#15 0xb7e71a1b in dolfin::ODESolver::solve (this=0xbf84d868) at dolfin/ode/ODESolver.cpp:33
#16 0xb7e6651e in dolfin::ODE::solve (this=0xbf84d8a8) at dolfin/ode/ODE.cpp:230
#17 0x0805a314 in main () at main.cpp:106
(gdb) 


If I reduce the size of the variable N from 5000 to 3190, the demo runs fine.

diff -r 717eaa11d058 demo/ode/reaction/cpp/main.cpp
--- a/demo/ode/reaction/cpp/main.cpp	Thu Sep 03 11:10:26 2009 +0200
+++ b/demo/ode/reaction/cpp/main.cpp	Thu Sep 03 14:34:57 2009 +0200
@@ -89,7 +89,7 @@
   const real epsilon = 0.01;
   const real gamma = 1000.0;
   const real L = 1.0;
-  const unsigned int N = 5000;
+  const unsigned int N = 3190;
 
   // Create ODE
   Reaction ode(N, T, L, epsilon, gamma);

It only seems to affect 32 bits systems since both hardy-i386 [1] and mac-osx [2] buildbot slaves has this problem while the demo runs fine on jaunty-amd64 and linux64-exp. 

The demo also runs fine when GMP is disabled.

[0] https://help.launchpad.net/Bugs/EmailInterface
[1] http://fenics.org:8080/builders/dolfin-hardy-i386/builds/770/steps/dolfin%20check/logs/demo.log
[2] http://fenics.org:8080/builders/dolfin-mac-osx/builds/719/steps/dolfin%20check/logs/demo.log

 affects dolfin
References

[Bug 424159] [NEW] Reaction demo fails when GMP is enabled
From: Johannes Ring, 2009-09-04