Error messages

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The same code runs in series, I also tried with 2 and 4 cpus and it failed with the same error message (although at t=1 for 4 nodes and before writing any output for 2 nodes. It seemed to be consistent when it failed. The same code runs in series, I also tried with 2 and 4 cpus and it failed with the same error message (although at t=1 for 4 nodes and before writing any output for 2 nodes. It seemed to be consistent when it failed.
 +
 +
 +---
 +Gerris Debugging
 +When running gerris debugging after the fact (i.e. as Stephane suggested doing the following)
 +% ulimit -c unlimited
 +% <rerun, crash should display "(core dumped)">
 +% ls core*
 +% gdb gerris3D core
 +gdb> where
 + I get:
 +#0 0x00007fd8198c228e in match_periodic_bc ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#1 0x00007fd8198902a9 in cell_traverse_boundary_leafs ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#2 0x00007fd8198902a9 in cell_traverse_boundary_leafs ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#3 0x00007fd8198902a9 in cell_traverse_boundary_leafs ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#4 0x00007fd8198902a9 in cell_traverse_boundary_leafs ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#5 0x00007fd8198902a9 in cell_traverse_boundary_leafs ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#6 0x00007fd8198902a9 in cell_traverse_boundary_leafs ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#7 0x00007fd8198c5faf in match_box_bc () from /usr/lib64/libgfs3D-1.3.so.2
 +#8 0x00007fd8198c8db3 in domain_foreach () from /usr/lib64/libgfs3D-1.3.so.2
 +#9 0x00007fd8198cde21 in gfs_domain_tag_droplets ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#10 0x00007fd8198ce0ae in gfs_domain_remove_droplets ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#11 0x00007fd8198d6b59 in gfs_remove_droplets_event ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#12 0x00007fd8198d2825 in gfs_event_do () from /usr/lib64/libgfs3D-1.3.so.2
 +#13 0x00007fd81965fcb7 in slist_container_foreach ()
 + from /usr/lib64/libgts-0.7.so.5
 +#14 0x00007fd8198da97f in simulation_run () from /usr/lib64/libgfs3D-1.3.so.2
 +#15 0x00007fd8198dc2a8 in gfs_simulation_run ()
 + from /usr/lib64/libgfs3D-1.3.so.2
 +#16 0x0000000000402d3f in main ()

Revision as of 08:41, 21 November 2011

Emily's Favourite Error Messages


This page is a place for storing error messages so I can compare and contrast.


Nicholson Canyon viscous3D parallel runs

I get the same message on both turbine and the new modelling computer and it occurs at the same position:

Modelling computer: 

   step:       1 t:      0.50000000 dt:  5.000000e-01 cpu:     31.87250000 real:     34.53414900
   MAC projection        before     after       rate
   niter:    7
   residual.bias:   -7.007e-03 -5.369e-05
   residual.first:   7.016e-03  5.373e-05      2
   residual.second:  1.461e-02  7.277e-05    2.1
   residual.infty:   3.525e-02  7.272e-04    1.7
   Approximate projection
   niter:    3
   residual.bias:   -1.151e-04 -5.477e-05
   residual.first:   1.547e-04  5.481e-05    1.4
   residual.second:  5.344e-04  7.187e-05      2
   residual.infty:   2.145e-02  7.902e-04      3
   [NIWA-36410:06625] *** Process received signal ***
   [NIWA-36410:06625] Signal: Segmentation fault (11)
   [NIWA-36410:06625] Signal code: Address not mapped (1)
   [NIWA-36410:06625] Failing at address: 0x8
   [NIWA-36410:06625] [ 0] /lib64/libpthread.so.0(+0xf2d0) [0x7ffb7880b2d0]
   [NIWA-36410:06625] [ 1] /usr/lib64/libgfs3D-1.3.so.2(+0x4728e) [0x7ffb794a628e]
   [NIWA-36410:06625] [ 2] /usr/lib64/libgfs3D-1.3.so.2(+0x152a9) [0x7ffb794742a9]
   [NIWA-36410:06625] *** End of error message ***
   mpirun noticed that job rank 0 with PID 6619 on node NIWA-36410 exited on signal 15 (Terminated).
   7 additional processes aborted (not shown)

Turbine: 

   step:       1 t:      0.50000000 dt:  5.000000e-01 cpu:     54.26500000 real:     57.84363200
   MAC projection        before     after       rate
   niter:    7
   residual.bias:   -7.007e-03 -5.369e-05
   residual.first:   7.016e-03  5.373e-05      2
   residual.second:  1.461e-02  7.277e-05    2.1
   residual.infty:   3.525e-02  7.272e-04    1.7
   Approximate projection
   niter:    3
   residual.bias:   -1.151e-04 -5.477e-05
   residual.first:   1.546e-04  5.481e-05    1.4
   residual.second:  5.338e-04  7.187e-05      2
   residual.infty:   2.141e-02  7.902e-04      3
   [rotor03:20387] *** Process received signal ***
   [rotor03:20387] Signal: Segmentation fault (11) 
   [rotor03:20387] Signal code: Address not mapped (1) 
   [rotor03:20387] Failing at address: 0x8 
   [rotor03:20387] [ 0] /lib64/libpthread.so.0 [0x7f64b72c0c00]
   [rotor03:20387] [ 1] /usr/lib64/libgfs3D-1.3.so.2 [0x7f64b8c0944f]
   [rotor03:20387] [ 2] /usr/lib64/libgfs3D-1.3.so.2 [0x7f64b8bdc609]
   [rotor03:20387] *** End of error message ***
   mpirun noticed that job rank 0 with PID 20381 on node rotor03 exited on signal 15 (Terminated).
   7 additional processes aborted (not shown)

The same code runs in series, I also tried with 2 and 4 cpus and it failed with the same error message (although at t=1 for 4 nodes and before writing any output for 2 nodes. It seemed to be consistent when it failed.


--- Gerris Debugging When running gerris debugging after the fact (i.e. as Stephane suggested doing the following) % ulimit -c unlimited % <rerun, crash should display "(core dumped)"> % ls core* % gdb gerris3D core gdb> where 

I get:
  1. 0 0x00007fd8198c228e in match_periodic_bc () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 1 0x00007fd8198902a9 in cell_traverse_boundary_leafs () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 2 0x00007fd8198902a9 in cell_traverse_boundary_leafs () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 3 0x00007fd8198902a9 in cell_traverse_boundary_leafs () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 4 0x00007fd8198902a9 in cell_traverse_boundary_leafs () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 5 0x00007fd8198902a9 in cell_traverse_boundary_leafs () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 6 0x00007fd8198902a9 in cell_traverse_boundary_leafs () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 7 0x00007fd8198c5faf in match_box_bc () from /usr/lib64/libgfs3D-1.3.so.2
  2. 8 0x00007fd8198c8db3 in domain_foreach () from /usr/lib64/libgfs3D-1.3.so.2
  3. 9 0x00007fd8198cde21 in gfs_domain_tag_droplets () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 10 0x00007fd8198ce0ae in gfs_domain_remove_droplets () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 11 0x00007fd8198d6b59 in gfs_remove_droplets_event () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 12 0x00007fd8198d2825 in gfs_event_do () from /usr/lib64/libgfs3D-1.3.so.2
  2. 13 0x00007fd81965fcb7 in slist_container_foreach () 
  from /usr/lib64/libgts-0.7.so.5
  1. 14 0x00007fd8198da97f in simulation_run () from /usr/lib64/libgfs3D-1.3.so.2
  2. 15 0x00007fd8198dc2a8 in gfs_simulation_run () 
  from /usr/lib64/libgfs3D-1.3.so.2
  1. 16 0x0000000000402d3f in main ()
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