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, > a...@0xbf84d074, b...@0xbf84d064, k...@0xbf84d054) at > dolfin/ode/MultiAdaptiveTimeSlab.cpp:939 > #5 0xb7e7fb8d in dolfin::MultiAdaptiveFixedPointSolver::iteration > (this=0x841f368, t...@0xbf84d22c, iter=0, > d...@0xbf84d21c, d...@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, t...@0xbf84d44c, t...@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, t...@0xbf84d57c, t...@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 You received this bug notification because you are subscribed to DOLFIN. 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, a...@0xbf84d074, b...@0xbf84d064, k...@0xbf84d054) at dolfin/ode/MultiAdaptiveTimeSlab.cpp:939 #5 0xb7e7fb8d in dolfin::MultiAdaptiveFixedPointSolver::iteration (this=0x841f368, t...@0xbf84d22c, iter=0, d...@0xbf84d21c, d...@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, t...@0xbf84d44c, t...@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, t...@0xbf84d57c, t...@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 _______________________________________________ DOLFIN-dev mailing list [email protected] http://www.fenics.org/mailman/listinfo/dolfin-dev
