>> Program received signal SIGABRT, Aborted.
>> 0x00007fffeb281a75 in *__GI_raise (sig=<value optimized out>)
>> at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
>> in ../nptl/sysdeps/unix/sysv/linux/raise.c
>> ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or
>> directory.
>
> It's just saying that the program was ultimately aborted in a function
> called 'raise' -- which is called when you call abort().
>
> You need to figure out what called abort() (and thereby raise()), for
> example
> by doing a backtrace in the compiler.
Ok, here is what I get for the backtrace. It first catches a throw
exception early in the program (or maybe before it begins? bt has locations
marked as ??), so I backtraced that, let it continue, and backtraced again
when the example crashed at stokes_matrix.reinit(sp) on line 1735. (The two
processes are the same.)
(gdb) catch throw
Catchpoint 1 (throw)
(gdb) run
Starting program:
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32
[Thread debugging using libthread_db enabled]
Catchpoint 1 (exception thrown), 0x00007fffebb35de0 in __cxa_throw ()
from /usr/lib/libstdc++.so.6
(gdb) bt
#0 0x00007fffebb35de0 in __cxa_throw () from /usr/lib/libstdc++.so.6
#1 0x00000000004f7f49 in
boost::copy_exception<boost::exception_detail::bad_alloc_> (e=...)
at
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/contrib/boost/include/boost/exception/detail/exception_ptr.hpp:42
#2 0x00000000004ee2ac in boost::exception_detail::get_bad_alloc<42> ()
at
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/contrib/boost/include/boost/exception/detail/exception_ptr.hpp:80
#3 0x00007ffff69021a1 in __static_initialization_and_destruction_0 (
__initialize_p=1, __priority=65535)
at
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/contrib/boost/include/boost/exception/detail/exception_ptr.hpp:94
#4 0x00007ffff69021d6 in global constructors keyed to multigrid.cc ()
at
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/source/multigrid/multigrid.cc:391
#5 0x00007ffff6a924d6 in __do_global_ctors_aux ()
from
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/lib/libdeal_II.g.so.6.4.pre
#6 0x00007ffff4630c43 in _init ()
from
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/lib/libdeal_II.g.so.6.4.pre
#7 0x00007ffff7fc04c0 in ?? ()
#8 0x00007ffff7debc65 in call_init (main_map=0x7ffff7ffe128,
argc=-137844744,
---Type <return> to continue, or q <return> to quit---
argv=0x7fffffffd748, env=0x7fffffffd758) at dl-init.c:70
#9 _dl_init (main_map=0x7ffff7ffe128, argc=-137844744,
argv=0x7fffffffd748,
env=0x7fffffffd758) at dl-init.c:134
#10 0x00007ffff7dddb2a in _dl_start_user () from
/lib64/ld-linux-x86-64.so.2
#11 0x0000000000000001 in ?? ()
#12 0x00007fffffffdb2f in ?? ()
#13 0x0000000000000000 in ?? ()
(gdb) continue
Continuing.
this is step-32. ref=5
**dof_setup ...
***dof_distribute ... 0.9828 wall, max @0, min=0.9827 @1, avg=0.9827
Number of active cells: 12288 (on 6 levels)
Number of degrees of freedom: 162432 (99840+12672+49920)
***index_sets ... 0.0058 wall, max @1, min=0.0051 @0, avg=0.0055
***make_hanging_nodes_vel ... 0.0262 wall, max @0, min=0.0262 @0,
avg=0.0262
***boundary_values_vel ... 0.2483 wall, max @1, min=0.2391 @0, avg=0.2437
***hanging_nodes_and_bv_temperature ... 0.1670 wall, max @1, min=0.1604
@0, avg=0.1637
***setup_stokes_matrix ... *** glibc detected ***
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32:
free(): invalid pointer: 0x00000000023756c0 ***
======= Backtrace: =========
/lib/libc.so.6(+0x775b6)[0x7fffeb2c55b6]
/lib/libc.so.6(cfree+0x73)[0x7fffeb2cbe83]
/org/centers/ccgo/local/apps/trilinos/10.6.0/lib/libepetra.so(_ZN16Epetra_CrsMatrix15OptimizeStorageEv+0x62b)[0x7fffef171f47]
/org/centers/ccgo/local/apps/trilinos/10.6.0/lib/libepetra.so(_ZN16Epetra_CrsMatrix12FillCompleteERK10Epetra_MapS2_b+0x21f)[0x7fffef1710ed]
/org/centers/ccgo/local/apps/trilinos/10.6.0/lib/libepetra.so(_ZN18Epetra_FECrsMatrix14GlobalAssembleERK10Epetra_MapS2_b+0x29b)[0x7fffef199e89]
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32(_ZN6dealii16TrilinosWrappers12SparseMatrix8compressEv+0x6f)[0x4ea171]
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/lib/libdeal_II.g.so.6.4.pre(_ZN6dealii16TrilinosWrappers12SparseMatrix6reinitERKNS0_15SparsityPatternE+0xe9)[0x7ffff509348d]
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/lib/libdeal_II.g.so.6.4.pre(_ZN6dealii16TrilinosWrappers17BlockSparseMatrix6reinitINS0_20BlockSparsityPatternEEEvRKT_+0xe8)[0x7ffff507166e]
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32(_ZN21BoussinesqFlowProblemILi2EE19setup_stokes_matrixERKSt6vectorIN6dealii8IndexSetESaIS3_EE+0x1a0)[0x507906]
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32(_ZN21BoussinesqFlowProblemILi2EE10setup_dofsEv+0xf73)[0x4fb02b]
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32(_ZN21BoussinesqFlowProblemILi2EE3runEj+0x1b6)[0x4f1ce0]
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32(main+0x142)[0x4dda91]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7fffeb26cc4d]
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32[0x4dd3a9]
======= Memory map: ========
00400000-005c6000 r-xp 00000000 00:20 334708906
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32
007c6000-007cd000 r--p 001c6000 00:20 334708906
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32
007cd000-007cf000 rw-p 001cd000 00:20 334708906
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/examples/step-32/step-32
007cf000-025e8000 rw-p 00000000 00:00 0
[heap]
7fffd8000000-7fffd8021000 rw-p 00000000 00:00 0
7fffd8021000-7fffdc000000 ---p 00000000 00:00 0
7fffdef68000-7fffdfb23000 rw-p 00000000 00:00 0
7fffdfb23000-7fffe3b25000 rw-s 00000000 08:01 2885750
/tmp/openmpi-sessions-jwort...@matterhorn_0/46329/1/shared_mem_pool.matterhorn
7fffe3b25000-7fffe3b32000 r-xp 00000000 08:01 2255506
/usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
7fffe3b32000-7fffe3d31000 ---p 0000d000 08:01 2255506
/usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
7fffe3d31000-7fffe3d32000 r--p 0000c000 08:01 2255506
/usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
7fffe3d32000-7fffe3d33000 rw-p 0000d000 08:01 2255506
/usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
7fffe3d33000-7fffe3d3d000 r-xp 00000000 08:01 2255505
/usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
7fffe3d3d000-7fffe3f3c000 ---p 0000a000 08:01 2255505
/usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
7fffe3f3c000-7fffe3f3d000 r--p 00009000 08:01 2255505
/usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
7fffe3f3d000-7fffe3f3e000 rw-p 0000a000 08:01 2255505
/usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
7fffe3f3e000-7fffe3f56000 r-xp 00000000 08:01 2255479
/usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
7fffe3f56000-7fffe4156000 ---p 00018000 08:01 2255479
/usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
7fffe4156000-7fffe4157000 r--p 00018000 08:01 2255479
/usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
7fffe4157000-7fffe4158000 rw-p 00019000 08:01 2255479
/usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
7fffe4158000-7fffe415b000 r-xp 00000000 08:01 2255478
/usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
7fffe415b000-7fffe435a000 ---p 00003000 08:01 2255478
/usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
7fffe435a000-7fffe435b000 r--p 00002000 08:01 2255478
/usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
7fffe435b000-7fffe435c000 rw-p 00003000 08:01 2255478
/usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
7fffe435c000-7fffe4361000 r-xp 00000000 08:01 2255477
/usr/lib/openmpi/lib/openmpi/mca_coll_sm.so
7fffe4361000-7fffe4560000 ---p 00005000 08:01 2255477
/usr/lib/openmpi/lib/openmpi/mca_coll_sm.so
7fffe4560000-7fffe4561000 r--p 00004000 08:01 2255477
/usr/lib/openmpi/lib/openmpi/mca_coll_sm.so
7fffe4561000-7fffe4562000 rw-p 00005000 08:01 2255477
/usr/lib/openmpi/lib/openmpi/mca_coll_sm.so
7fffe4562000-7fffe4564000 r-xp 00000000 08:01 2255476
/usr/lib/openmpi/lib/openmpi/mca_coll_self.so
7fffe4564000-7fffe4763000 ---p 00002000 08:01 2255476
/usr/lib/openmpi/lib/openmpi/mca_coll_self.so
7fffe4763000-7fffe4764000 r--p 00001000 08:01 2255476
/usr/lib/openmpi/lib/openmpi/mca_coll_self.so
7fffe4764000-7fffe4765000 rw-p 00002000 08:01 2255476
/usr/lib/openmpi/lib/openmpi/mca_coll_self.so
7fffe4765000-7fffe4768000 r-xp 00000000 08:01 2255475
/usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
7fffe4768000-7fffe4967000 ---p 00003000 08:01 2255475
/usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
7fffe4967000-7fffe4968000 r--p 00002000 08:01 2255475
/usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
7fffe4968000-7fffe4969000 rw-p 00003000 08:01 2255475
/usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
7fffe4969000-7fffe496d000 r-xp 00000000 08:01 2255474
/usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
7fffe496d000-7fffe4b6c000 ---p 00004000 08:01 2255474
/usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
7fffe4b6c000-7fffe4b6d000 r--p 00003000 08:01 2255474
/usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
7fffe4b6d000-7fffe4b6e000 rw-p 00004000 08:01 2255474
/usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
7fffe4b6e000-7fffe4b76000 r-xp 00000000 08:01 2255473
/usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
7fffe4b76000-7fffe4d75000 ---p 00008000 08:01 2255473
/usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
7fffe4d75000-7fffe4d76000 r--p 00007000 08:01 2255473
/usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
Program received signal SIGABRT, Aborted.
0x00007fffeb281a75 in *__GI_raise (sig=<value optimized out>)
at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
64 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or
directory.
in ../nptl/sysdeps/unix/sysv/linux/raise.c
(gdb) bt
#0 0x00007fffeb281a75 in *__GI_raise (sig=<value optimized out>)
at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1 0x00007fffeb2855c0 in *__GI_abort () at abort.c:92
#2 0x00007fffeb2bb4fb in __libc_message (do_abort=<value optimized out>,
fmt=<value optimized out>) at
../sysdeps/unix/sysv/linux/libc_fatal.c:189
#3 0x00007fffeb2c55b6 in malloc_printerr (action=3,
str=0x7fffeb395ad3 "free(): invalid pointer", ptr=<value optimized
out>)
at malloc.c:6266
#4 0x00007fffeb2cbe83 in *__GI___libc_free (mem=<value optimized out>)
at malloc.c:3738
#5 0x00007fffef171f47 in Epetra_CrsMatrix::OptimizeStorage
(this=0x13cebc0)
at
/org/centers/ccgo/local/apps/trilinos/trilinos-10.6.0-Source/packages/epetra/src/Epetra_CrsMatrix.cpp:1109
#6 0x00007fffef1710ed in Epetra_CrsMatrix::FillComplete (this=0x13cebc0,
domain_map=..., range_map=..., OptimizeDataStorage=true)
at
/org/centers/ccgo/local/apps/trilinos/trilinos-10.6.0-Source/packages/epetra/src/Epetra_CrsMatrix.cpp:950
#7 0x00007fffef199e89 in Epetra_FECrsMatrix::GlobalAssemble
(this=0x13cebc0,
domain_map=..., range_map=..., callFillComplete=true)
at
/org/centers/ccgo/local/apps/trilinos/trilinos-10.6.0-Source/packages/epetra/src/Epetra_FECrsMatrix.cpp:596
#8 0x00000000004ea171 in dealii::TrilinosWrappers::SparseMatrix::compress
(
this=0x1b635b0)
---Type <return> to continue, or q <return> to quit---
at
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/include/deal.II/lac/trilinos_sparse_matrix.h:2557
#9 0x00007ffff509348d in dealii::TrilinosWrappers::SparseMatrix::reinit (
this=0x1b635b0, sparsity_pattern=...)
at
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/source/lac/trilinos_sparse_matrix.cc:504
#10 0x00007ffff507166e in
dealii::TrilinosWrappers::BlockSparseMatrix::reinit<dealii::TrilinosWrappers::BlockSparsityPattern>
(this=0x7fffffffc430,
block_sparsity_pattern=...)
at
/org/centers/ccgo/local/apps/deal.II/deal.II_w_trilinos/source/lac/trilinos_block_sparse_matrix.cc:179
#11 0x0000000000507906 in BoussinesqFlowProblem<2>::setup_stokes_matrix (
this=0x7fffffff9c50, stokes_partitioning=...) at step-32.cc:1735
#12 0x00000000004fb02b in BoussinesqFlowProblem<2>::setup_dofs (
this=0x7fffffff9c50) at step-32.cc:2004
#13 0x00000000004f1ce0 in BoussinesqFlowProblem<2>::run
(this=0x7fffffff9c50,
ref=5) at step-32.cc:3594
#14 0x00000000004dda91 in main (argc=1, argv=0x7fffffffd748) at
step-32.cc:3686
Jennifer
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