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Buildbot failure summary

To: DOLFIN Mailing List <dolfin@xxxxxxxxxxxxxxxxxxx>
From: Johannes Ring <johannr@xxxxxxxxx>
Date: Fri, 28 Sep 2012 13:55:15 +0200
The buildbot page for DOLFIN-trunk
(http://fenicsproject.org:8010/waterfall?project=dolfin&category=dolfin.trunk)
shows that most of the buildslaves (ignoring the quick builders) are
red, that is, they are failing one or more of the tests. Only two of
the nine buildslaves are currently green. These are running Debian sid
and Ubuntu quantal (development branch). Below follows a summary of
the failures on each of the buildslaves.

* lucid-amd64
Buildslave info: http://fenicsproject.org:8010/buildslaves/lucid-amd64
Last build: http://fenicsproject.org:8010/builders/dolfin-trunk-full-lucid-amd64/builds/101
Unit tests failed: la (test, Matrix, Vector), fem (Assembler), book (chapter_1)
  stdio: http://fenicsproject.org:8010/builders/dolfin-trunk-full-lucid-amd64/builds/101/steps/make%20run_unittests/logs/stdio
Comments: All of the unit tests fails with error messages which looks like this:

======================================================================
ERROR: test_matrix_data (__main__.EpetraTester)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./test.py", line 285, in test_matrix_data
    A = as_backend_type(A)
  File "/home/buildbot/fenicsbbot/trunk/dolfin-full/lib/python2.6/site-packages/dolfin/cpp/la.py",
line 5133, in as_backend_type
    subclass = get_tensor_type(tensor)
  File "/home/buildbot/fenicsbbot/trunk/dolfin-full/lib/python2.6/site-packages/dolfin/cpp/la.py",
line 5119, in get_tensor_type
    "dolfin/swig/la/post.i")
  File "/home/buildbot/fenicsbbot/trunk/dolfin-full/lib/python2.6/site-packages/dolfin/cpp/common.py",
line 2041, in dolfin_error
    return _common.dolfin_error(*args)
RuntimeError:

*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at
***
***     https://answers.launchpad.net/dolfin
***
*** Remember to include the error message listed below and, if possible,
*** include a *minimal* running example to reproduce the error.
***
*** -------------------------------------------------------------------------
*** Error:   Unable to Most probably you are trying to do something
with a uBLAS Matrix. Tensor type: 'Matrix'.
*** Reason:  dolfin/swig/la/post.i.
*** Where:   This error was encountered inside Compatability check of
tensor failed..
*** Process: 0
*** -------------------------------------------------------------------------

Regression tests failed: demo/undocumented/mesh-generation/cpp
  stdio: http://fenicsproject.org:8010/builders/dolfin-trunk-full-lucid-amd64/builds/101/steps/make%20run_regressiontests/logs/stdio
  demo.log: http://fenicsproject.org:8010/builders/dolfin-trunk-full-lucid-amd64/builds/101/steps/make%20run_regressiontests/logs/demo.log
Comments: Running the mesh-generation demo results in a segmentation fault.


* oneiric-amd64
Buildslave info: http://fenicsproject.org:8010/buildslaves/oneiric-amd64
Last build: http://fenicsproject.org:8010/builders/dolfin-trunk-full-oneiric-amd64/builds/53
Regression tests failed: demo/pde/stokes-iterative/python
  stdio: http://fenicsproject.org:8010/builders/dolfin-trunk-full-oneiric-amd64/builds/53/steps/make%20run_regressiontests/logs/stdio
  demo.log: http://fenicsproject.org:8010/builders/dolfin-trunk-full-oneiric-amd64/builds/53/steps/make%20run_regressiontests/logs/demo.log
Comments: This failure has already been reported in bug #1052801
(https://bugs.launchpad.net/dolfin/+bug/1052801).


* osx-10.6
Buildslave info: http://fenicsproject.org:8010/buildslaves/osx-10.6
Last build: http://fenicsproject.org:8010/builders/dolfin-trunk-full-osx-10.6/builds/74
Comments: Same error as on oneiric-amd64.


* osx-10.7
Buildslave info: http://fenicsproject.org:8010/buildslaves/osx-10.7
Last build: http://fenicsproject.org:8010/builders/dolfin-trunk-full-osx-10.7/builds/107
Unit tests failed: quadrature (BaryCenter), la (KrylovSolver)
  stdio: http://fenicsproject.org:8010/builders/dolfin-trunk-full-osx-10.7/builds/107/steps/make%20run_unittests/logs/stdio
Comments: The quadrature failure has been there for a very long time,
reported as bug #918178
(https://bugs.launchpad.net/dolfin/+bug/918178). The KrylovSolver test
fails when run in parallel with the following error:

One or more unit tests failed for la (KrylovSolver, Python):
Process 0: Number of global vertices: 1089
Process 0: Number of global cells: 2048
Small graph
Process 0: Partitioned mesh, edge cut is 61.
Process 1: Partitioned mesh, edge cut is 61.
Process 2: Partitioned mesh, edge cut is 61.

Testing DOLFIN la/KrylovSolver interface
----------------------------------------

Testing DOLFIN la/KrylovSolver interface
----------------------------------------

Testing DOLFIN la/KrylovSolver interface
----------------------------------------
FIXME: Preconditioner 'ilu' does not work in parallel, skipping
FIXME: Preconditioner 'icc' does not work in parallel, skipping
FIXME: Preconditioner 'ilu' does not work in parallel, skipping
FIXME: Preconditioner 'icc' does not work in parallel, skipping
FIXME: Preconditioner 'ilu' does not work in parallel, skipping
FIXME: Preconditioner 'icc' does not work in parallel, skipping
FIXME: Preconditioner 'jacobi' does not work in parallel, skipping
FIXME: Preconditioner 'jacobi' does not work in parallel, skipping
FIXME: Preconditioner 'jacobi' does not work in parallel, skipping
FIXME: Preconditioner 'hypre_amg' does not work in parallel, skipping
FIXME: Preconditioner 'hypre_amg' does not work in parallel, skipping
FIXME: Preconditioner 'hypre_amg' does not work in parallel, skipping
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Unknown type. Check for miss-spelling or missing
external package needed for type
 seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/installation.html#external!
[0]PETSC ERROR: Unable to find requested KSP type chebyshev!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11
09:28:45 CST 2012
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Unknown Name on a darwin11. named opeth.local by
buildbot Fri Sep 28 04:30:14 2012
[0]PETSC ERROR: Libraries linked from /Users/buildbot/local/lib
[0]PETSC ERROR: Configure run at Tue Aug 21 11:37:44 2012
[0]PETSC ERROR: Configure options COPTFLAGS=-O2 --with-debugging=0
--with-shared-libraries=1 --with-clanguage=cxx --with-parmetis=1
--with-parmetis-dir=/Users/buildbot/local --download-umfpack=1
--download-hypre=1 --download-mumps=1 --download-scalapack=1
--download-blacs=1 --download-ptscotch=1 --download-scotch=1
--with-ml=1 --with-ml-lib=/Users/buildbot/local/lib/libml.so
--with-ml-include=/Users/buildbot/local/include/trilinos
--prefix=/Users/buildbot/local
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: KSPSetType() line 652 in
/Users/buildbot/local/src/petsc-3.2-p6/src/ksp/ksp/interface/itcreate.c
[0]PETSC ERROR: KSPSetFromOptions() line 292 in
/Users/buildbot/local/src/petsc-3.2-p6/src/ksp/ksp/interface/itcl.c
[0]PETSC ERROR: PCSetUp_MG() line 575 in
/Users/buildbot/local/src/petsc-3.2-p6/src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: PCSetUp_ML() line 789 in
/Users/buildbot/local/src/petsc-3.2-p6/src/ksp/pc/impls/ml/ml.c
[0]PETSC ERROR: PCSetUp() line 819 in
/Users/buildbot/local/src/petsc-3.2-p6/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: KSPSetUp() line 260 in
/Users/buildbot/local/src/petsc-3.2-p6/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: KSPSolve() line 379 in
/Users/buildbot/local/src/petsc-3.2-p6/src/ksp/ksp/interface/itfunc.c
[opeth:18527] *** Process received signal ***
[opeth:18527] Signal: Abort trap: 6 (6)
[opeth:18527] Signal code:  (0)
[opeth:18528] *** Process received signal ***
[opeth:18528] Signal: Abort trap: 6 (6)
[opeth:18528] Signal code:  (0)
[opeth:18527] [ 0] 2   libsystem_c.dylib
0x00007fff915abcfa _sigtramp + 26
[opeth:18527] [ 1] 3   ???
0x0000000000000050 0x0 + 80
[opeth:18527] [ 2] 4   libpetsc.dylib
0x000000010548b777
_Z26PetscTraceBackErrorHandlerP19ompi_communicator_tiPKcS2_S2_i14PetscErrorTypeS2_Pv
+ 679
[opeth:18527] [ 3] 5   libpetsc.dylib
0x0000000105488592
_Z10PetscErrorP19ompi_communicator_tiPKcS2_S2_i14PetscErrorTypeS2_z +
338
[opeth:18527] [ 4] 6   libpetsc.dylib
0x00000001058f33e2 _Z10KSPSetTypeP6_p_KSPPKc + 674
[opeth:18527] [ 5] 7   libpetsc.dylib
0x00000001058e945b _Z17KSPSetFromOptionsP6_p_KSP + 3867
[opeth:18527] [ 6] 8   libpetsc.dylib
0x00000001058a467d _Z10PCSetUp_MGP5_p_PC + 3677
[opeth:18527] [ 7] 9   libpetsc.dylib
0x00000001058ffe5a _Z10PCSetUp_MLP5_p_PC + 7354
[opeth:18527] [ 8] 10  libpetsc.dylib
0x00000001058ad5c1 _Z7PCSetUpP5_p_PC + 817
[opeth:18527] [ 9] 11  libpetsc.dylib
0x00000001058eb55c _Z8KSPSetUpP6_p_KSP + 2828
[opeth:18527] [10] 12  libpetsc.dylib
0x00000001058ebe1c _Z8KSPSolveP6_p_KSPP6_p_VecS2_ + 1676
[opeth:18527] [11] 13  libdolfin.1.0.dylib
0x00000001038248f0
_ZN6dolfin17PETScKrylovSolver5solveERNS_11PETScVectorERKS1_ + 1894
[opeth:18527] [12] 14  libdolfin.1.0.dylib
0x0000000103825076
_ZN6dolfin17PETScKrylovSolver5solveERKNS_15PETScBaseMatrixERNS_11PETScVectorERKS4_
+ 186
[opeth:18527] [13] 15  _la.so
0x000000010bc5b7f9 _wrap_PETScKrylovSolver_solve + 5625
[opeth:18527] [14] 16  Python
0x00000001022652a5 PyEval_EvalFrameEx + 18709
[opeth:18527] [15] 17  Python
0x00000001022683e3 fast_function + 179
[opeth:18527] [16] 18  Python
0x000000010226509d PyEval_EvalFrameEx + 18189
[opeth:18527] [17] 19  Python
0x00000001022682a7 PyEval_EvalCodeEx + 2103
[opeth:18527] [18] 20  Python
0x00000001021f558b function_call + 347
[opeth:18527] [19] 21  Python
0x00000001021ccbe1 PyObject_Call + 97
[opeth:18527] [20] 22  Python
0x000000010226595a PyEval_EvalFrameEx + 20426
[opeth:18527] [21] 23  Python
0x00000001022682a7 PyEval_EvalCodeEx + 2103
[opeth:18527] [22] 24  Python
0x00000001021f558b function_call + 347
[opeth:18527] [23] 25  Python
0x00000001021ccbe1 PyObject_Call + 97
[opeth:18527] [24] 26  Python
0x00000001021dea17 instancemethod_call + 503
[opeth:18527] [25] 27  Python
0x00000001021ccbe1 PyObject_Call + 97
[opeth:18527] [26] 28  Python
0x0000000102227e0e slot_tp_call + 94
[opeth:18527] [27] 29  Python
0x00000001021ccbe1 PyObject_Call + 97
[opeth:18527] [28] 30  Python
0x00000001022652b5 PyEval_EvalFrameEx + 18725
[opeth:18527] [29] 31  Python
0x00000001022682a7 PyEval_EvalCodeEx + 2103
[opeth:18527] *** End of error message ***
[opeth:18528] [ 0] 2   libsystem_c.dylib
0x00007fff915abcfa _sigtramp + 26
[opeth:18528] [ 1] 3   ???
0x0000000000000050 0x0 + 80
[opeth:18528] [ 2] 4   libpetsc.dylib
0x00000001052ec777
_Z26PetscTraceBackErrorHandlerP19ompi_communicator_tiPKcS2_S2_i14PetscErrorTypeS2_Pv
+ 679
[opeth:18528] [ 3] 5   libpetsc.dylib
0x00000001052e9592
_Z10PetscErrorP19ompi_communicator_tiPKcS2_S2_i14PetscErrorTypeS2_z +
338
[opeth:18528] [ 4] 6   libpetsc.dylib
0x00000001057543e2 _Z10KSPSetTypeP6_p_KSPPKc + 674
[opeth:18528] [ 5] 7   libpetsc.dylib
0x000000010574a45b _Z17KSPSetFromOptionsP6_p_KSP + 3867
[opeth:18528] [ 6] 8   libpetsc.dylib
0x000000010570567d _Z10PCSetUp_MGP5_p_PC + 3677
[opeth:18528] [ 7] 9   libpetsc.dylib
0x0000000105760e5a _Z10PCSetUp_MLP5_p_PC + 7354
[opeth:18528] [ 8] 10  libpetsc.dylib
0x000000010570e5c1 _Z7PCSetUpP5_p_PC + 817
[opeth:18528] [ 9] 11  libpetsc.dylib
0x000000010574c55c _Z8KSPSetUpP6_p_KSP + 2828
[opeth:18528] [10] 12  libpetsc.dylib
0x000000010574ce1c _Z8KSPSolveP6_p_KSPP6_p_VecS2_ + 1676
[opeth:18528] [11] 13  libdolfin.1.0.dylib
0x00000001036858f0
_ZN6dolfin17PETScKrylovSolver5solveERNS_11PETScVectorERKS1_ + 1894
[opeth:18528] [12] 14  libdolfin.1.0.dylib
0x0000000103686076
_ZN6dolfin17PETScKrylovSolver5solveERKNS_15PETScBaseMatrixERNS_11PETScVectorERKS4_
+ 186
[opeth:18528] [13] 15  _la.so
0x000000010babc7f9 _wrap_PETScKrylovSolver_solve + 5625
[opeth:18528] [14] 16  Python
0x00000001020c92a5 PyEval_EvalFrameEx + 18709
[opeth:18528] [15] 17  Python
0x00000001020cc3e3 fast_function + 179
[opeth:18528] [16] 18  Python
0x00000001020c909d PyEval_EvalFrameEx + 18189
[opeth:18528] [17] 19  Python
0x00000001020cc2a7 PyEval_EvalCodeEx + 2103
[opeth:18528] [18] 20  Python
0x000000010205958b function_call + 347
[opeth:18528] [19] 21  Python
0x0000000102030be1 PyObject_Call + 97
[opeth:18528] [20] 22  Python
0x00000001020c995a PyEval_EvalFrameEx + 20426
[opeth:18528] [21] 23  Python
0x00000001020cc2a7 PyEval_EvalCodeEx + 2103
[opeth:18528] [22] 24  Python
0x000000010205958b function_call + 347
[opeth:18528] [23] 25  Python
0x0000000102030be1 PyObject_Call + 97
[opeth:18528] [24] 26  Python
0x0000000102042a17 instancemethod_call + 503
[opeth:18528] [25] 27  Python
0x0000000102030be1 PyObject_Call + 97
[opeth:18528] [26] 28  Python
0x000000010208be0e slot_tp_call + 94
[opeth:18528] [27] 29  Python
0x0000000102030be1 PyObject_Call + 97
[opeth:18528] [28] 30  Python
0x00000001020c92b5 PyEval_EvalFrameEx + 18725
[opeth:18528] [29] 31  Python
0x00000001020cc2a7 PyEval_EvalCodeEx + 2103
[opeth:18528] *** End of error message ***
--------------------------------------------------------------------------
WARNING: A process refused to die!

Host: opeth.local
PID:  18527

This process may still be running and/or consuming resources.

System test failed:
  stdio: http://fenicsproject.org:8010/builders/dolfin-trunk-full-osx-10.7/builds/107/steps/make%20run_systemtests/logs/stdio
Comments: It seem that SciPy is needed for the test:

======================================================================
ERROR: test_diff_then_integrate (__main__.IntegrateDerivatives)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "assembly_derivatives.py", line 152, in test_diff_then_integrate
    F_diff = F((x1,)) - F((x0,))
  File "/Users/buildbot/fenicsbbot/trunk/lib/python2.7/site-packages/ufl/exproperators.py",
line 369, in _call
    return _eval(self, arg, mapping)
  File "/Users/buildbot/fenicsbbot/trunk/lib/python2.7/site-packages/ufl/exproperators.py",
line 361, in _eval
    return f.evaluate(coord, mapping, component, index_values)
  File "/Users/buildbot/fenicsbbot/trunk/lib/python2.7/site-packages/ufl/mathfunctions.py",
line 259, in evaluate
    error("You must have scipy installed to evaluate bessel functions
in python.")
  File "/Users/buildbot/fenicsbbot/trunk/lib/python2.7/site-packages/ufl/log.py",
line 148, in error
    raise self._exception_type(self._format_raw(*message))
UFLException: You must have scipy installed to evaluate bessel
functions in python.


* precise-amd64
Buildslave info: http://fenicsproject.org:8010/buildslaves/precise-amd64
Last build: http://fenicsproject.org:8010/builders/dolfin-trunk-full-precise-amd64/builds/58
Comments: Same error as on oneiric-amd64.


* precies-i386
Buildslave info: http://fenicsproject.org:8010/buildslaves/precise-i386
Last build: http://fenicsproject.org:8010/builders/dolfin-trunk-full-precise-i386/builds/44
Unit tests failed: la (Matrix, KrylovSolver) plus possibly others
  stdio: http://fenicsproject.org:8010/builders/dolfin-trunk-full-precise-i386/builds/44/steps/make%20run_unittests/logs/stdio
Comments: The tests sometimes hangs and the buildslave time out. This
is probably the same problem as in bug #1036992
(https://bugs.launchpad.net/dolfin/+bug/1036992). I have tried both
PETSc 3.2 and the latest 3.3. The error message when running the
KrylovSolver.py test looks like this:

[2]PETSC ERROR: --------------------- Error Message
------------------------------------
[2]PETSC ERROR: Error in external library!
[2]PETSC ERROR: Error in HYPRE_IJMatrixCreate()!
[2]PETSC ERROR:
------------------------------------------------------------------------
[2]PETSC ERROR: Petsc Release Version 3.3.0, Patch 3, Wed Aug 29
11:26:24 CDT 2012
[2]PETSC ERROR: See docs/changes/index.html for recent updates.
[2]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[2]PETSC ERROR: See docs/index.html for manual pages.
[2]PETSC ERROR:
------------------------------------------------------------------------
[2]PETSC ERROR: Unknown Name on a linux-gnu named prceise32-bbot by
buildbot Fri Sep 28 13:16:17 2012
[2]PETSC ERROR: Libraries linked from /home/buildbot/local/lib
[2]PETSC ERROR: Configure run at Wed Sep 26 14:49:09 2012
[2]PETSC ERROR: Configure options COPTFLAGS=-O2 --with-debugging=0
--with-shared-libraries=1 --with-clanguage=cxx --with-c-support=1
--download-umfpack=1 --download-hypre=1 --download-mumps=1
--download-scalapack=1 --download-blacs=1 --download-ptscotch=1
--download-scotch=1 --download-metis=1 --download-parmetis=1
--with-ml=1 --with-ml-lib=/home/buildbot/local/lib/libml.so
--with-ml-include=/home/buildbot/local/include/trilinos
--prefix=/home/buildbot/local
[2]PETSC ERROR:
------------------------------------------------------------------------
[2]PETSC ERROR: MatHYPRE_IJMatrixCreate() line 71 in
/home/buildbot/local/src/petsc-3.3-p3/src/dm/impls/da/hypre/mhyp.c
[2]PETSC ERROR: PCSetUp_HYPRE() line 100 in
/home/buildbot/local/src/petsc-3.3-p3/src/ksp/pc/impls/hypre/hypre.c
[2]PETSC ERROR: PCSetUp() line 832 in
/home/buildbot/local/src/petsc-3.3-p3/src/ksp/pc/interface/precon.c
[2]PETSC ERROR: KSPSetUp() line 278 in
/home/buildbot/local/src/petsc-3.3-p3/src/ksp/ksp/interface/itfunc.c
[2]PETSC ERROR: KSPSolve() line 402 in
/home/buildbot/local/src/petsc-3.3-p3/src/ksp/ksp/interface/itfunc.c
^Cmpirun: killing job...

Regression tests failed: demo/undocumented/entityintersection/python
(plus others)
  stdio: http://fenicsproject.org:8010/builders/dolfin-trunk-full-precise-i386/builds/44/steps/make%20run_regressiontests/logs/stdio
  demo.log: Not available due to timeout
Comments: Some of the demos hangs and make the buildslave time out.
Not sure which demo, but it is probably the same problem as with the
unit tests. The entityintersection demo fails with the following error
message:

*** Failed
*** Warning: The UnitSphere class is broken and should not be used for
computations. It generates meshes of very bad quality (very thin
tetrahedra).
Total number of cells in Cube: 108
Total number of cells in Sphere: 162
Intersecting pairwise cells of a cube and sphere mesh
Cube cell index | Sphere cell index
------------------------------
Traceback (most recent call last):
  File "demo_entityintersection.py", line 48, in <module>
    if do_intersect(c1,c2):
  File "/home/buildbot/fenicsbbot/trunk/dolfin-full/lib/python2.7/site-packages/dolfin/cpp/mesh.py",
line 348, in do_intersect
    return _mesh.PrimitiveIntersector_do_intersect(*args)
StandardError: CGAL ERROR: precondition violation!
Expr: k.coplanar_orientation_3_object() (*p,*q,*r) == POSITIVE
File: /usr/include/CGAL/Triangle_3_Triangle_3_do_intersect.h
Line: 89


* squeeze-amd64
Buildslave info: http://fenicsproject.org:8010/buildslaves/squeeze-amd64
Last build: http://fenicsproject.org:8010/builders/dolfin-trunk-full-squeeze-amd64/builds/62
Comments: Same unit test errors as on lucid-amd64. These are the only
buildslaves with Python 2.6. Maybe that is the reason?


Johannes
Follow ups

Re: Buildbot failure summary
From: Anders Logg, 2012-09-28