Hi R,
I was installing the latest code on my new workstation, when runTests.py exited with error. On running it on debug mode, I got the following output:
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose']
test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x82bba80, cookie: 1786 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x817b0e3, cookie: 136600713 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! mem_realloc_mem(): error exit! conn_resize() failed!sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
Also running ./postproc.py file.vtk is now throwing error with no fix as i browsed various forums ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./postproc.py cylinder.vtk The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadRequest (invalid request code or no such operation)'. (Details: serial 696 error_code 1 request_code 154 minor_code 19) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.)
The earlier sfepy version on which i was working was throwing no such errors.
Regards.
On Sunday, 16 June 2013 06:46:42 UTC+5:30, Ankit Mahato wrote:
Hi R,
I was installing the latest code on my new workstation, when runTests.py exited with error. On running it on debug mode, I got the following output:
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose']
test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x82bba80, cookie: 1786 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x817b0e3, cookie: 136600713 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! mem_realloc_mem(): error exit! conn_resize() failed!sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
On 06/16/2013 03:26 AM, Ankit Mahato wrote:
Also running ./postproc.py file.vtk is now throwing error with no fix as i browsed various forums ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./postproc.py cylinder.vtk The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadRequest (invalid request code or no such operation)'. (Details: serial 696 error_code 1 request_code 154 minor_code 19) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.)
The earlier sfepy version on which i was working was throwing no such errors.
Hmm, almost nothing changed in postproc.py for a long time. The following command works?
$ mayavi2 -d cylinder.vtk -m Surface
What is your mayavi version?
r.
On Monday, 17 June 2013 00:05:54 UTC+5:30, Robert Cimrman wrote:
On 06/16/2013 03:26 AM, Ankit Mahato wrote:
Also running ./postproc.py file.vtk is now throwing error with no fix as i browsed various forums ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./postproc.py cylinder.vtk The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadRequest (invalid request code or no such operation)'. (Details: serial 696 error_code 1 request_code 154 minor_code 19) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.)
The earlier sfepy version on which i was working was throwing no such errors.
Hmm, almost nothing changed in postproc.py for a long time. The following command works?
$ mayavi2 -d cylinder.vtk -m Surface
Nope. This is throwing the same error.
What is your mayavi version?
Mayavi 4.0.0
r.
On 06/17/2013 12:16 AM, Ankit Mahato wrote:
On Monday, 17 June 2013 00:05:54 UTC+5:30, Robert Cimrman wrote:
On 06/16/2013 03:26 AM, Ankit Mahato wrote:
Also running ./postproc.py file.vtk is now throwing error with no fix as i browsed various forums ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./postproc.py cylinder.vtk The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadRequest (invalid request code or no such operation)'. (Details: serial 696 error_code 1 request_code 154 minor_code 19) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.)
The earlier sfepy version on which i was working was throwing no such errors.
Hmm, almost nothing changed in postproc.py for a long time. The following command works?
$ mayavi2 -d cylinder.vtk -m Surface
Nope. This is throwing the same error.
Then it looks like a Mayavi/VTK installation problem - try asking at the enthought mailing list. Paraview works?
What is your mayavi version?
Mayavi 4.0.0
Same here, works ok...
r.
On Monday, 17 June 2013 03:50:29 UTC+5:30, Robert Cimrman wrote:
On 06/17/2013 12:16 AM, Ankit Mahato wrote:
On Monday, 17 June 2013 00:05:54 UTC+5:30, Robert Cimrman wrote:
On 06/16/2013 03:26 AM, Ankit Mahato wrote:
Also running ./postproc.py file.vtk is now throwing error with no fix
as
i
browsed various forums ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./postproc.py cylinder.vtk The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadRequest (invalid request code or no such operation)'. (Details: serial 696 error_code 1 request_code 154 minor_code 19) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.)
The earlier sfepy version on which i was working was throwing no such errors.
Hmm, almost nothing changed in postproc.py for a long time. The following command works?
$ mayavi2 -d cylinder.vtk -m Surface
Nope. This is throwing the same error.
Then it looks like a Mayavi/VTK installation problem - try asking at the enthought mailing list. Paraview works?
okie. will do so. Paraview is not working. Throwing too many badRequests.
What is your mayavi version?
Mayavi 4.0.0
Same here, works ok...
r.
On 06/17/2013 12:38 AM, Ankit Mahato wrote:
On Monday, 17 June 2013 03:50:29 UTC+5:30, Robert Cimrman wrote:
On 06/17/2013 12:16 AM, Ankit Mahato wrote:
On Monday, 17 June 2013 00:05:54 UTC+5:30, Robert Cimrman wrote:
On 06/16/2013 03:26 AM, Ankit Mahato wrote:
Also running ./postproc.py file.vtk is now throwing error with no fix
as
i
browsed various forums ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./postproc.py cylinder.vtk The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadRequest (invalid request code or no such operation)'. (Details: serial 696 error_code 1 request_code 154 minor_code 19) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.)
The earlier sfepy version on which i was working was throwing no such errors.
Hmm, almost nothing changed in postproc.py for a long time. The following command works?
$ mayavi2 -d cylinder.vtk -m Surface
Nope. This is throwing the same error.
Then it looks like a Mayavi/VTK installation problem - try asking at the enthought mailing list. Paraview works?
okie. will do so. Paraview is not working. Throwing too many badRequests.
Then it is not Mayavi-specific... Looks like a VTK installation problem.
What is your mayavi version?
Mayavi 4.0.0
Same here, works ok...
r.
Hi Ankit,
On 06/16/2013 03:16 AM, Ankit Mahato wrote:
Hi R,
I was installing the latest code on my new workstation, when runTests.py exited with error. On running it on debug mode, I got the following output:
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose']
test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x82bba80, cookie: 1786 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x817b0e3, cookie: 136600713 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! mem_realloc_mem(): error exit! conn_resize() failed!sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
Strange - what is your system architecture - 64 bit or 32 bit? I am running it at 64 bit linux boxes without problems.
To debug it, could you try editing site_cfg.py as follows:
compile_flags = '-g' debug_flags = '-DDEBUG_FMF -DDEBUG_MESH'
then 'make clean; make', run the failing test and send the output?
Also try running it in gdb: $ gdb --exec=python (gdb) run runTests.py --debug tests/test_cmesh.py
and when it segfaults, use 'bt' command to print the backtrace, and send the full output.
Thanks! r.
On Monday, 17 June 2013 00:01:33 UTC+5:30, Robert Cimrman wrote:
Hi Ankit,
On 06/16/2013 03:16 AM, Ankit Mahato wrote:
Hi R,
I was installing the latest code on my new workstation, when runTests.py exited with error. On running it on debug mode, I got the following output:
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose']
test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x82bba80, cookie: 1786 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x817b0e3, cookie: 136600713 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! mem_realloc_mem(): error exit! conn_resize() failed!sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
Strange - what is your system architecture - 64 bit or 32 bit? I am running it at 64 bit linux boxes without problems.
32 bit
To debug it, could you try editing site_cfg.py as follows:
compile_flags = '-g' debug_flags = '-DDEBUG_FMF -DDEBUG_MESH'
then 'make clean; make', run the failing test and send the output?
test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s request connectivity 1 -> 0 build 1 request connectivity 2 -> 2 request connectivity 2 -> 0 request connectivity 0 -> 2 request connectivity 2 -> 0
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ python runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose'] transpose 0 -> 2 n_incident: 6 intersect 2 -> 2 (0) n_incident: 2 n_incident: 6 max. n_incident_vertex: 12 sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5d14cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb5d13ff4, cookie: 137058500 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5d14cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb5d09157, cookie: -3112053 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
Also try running it in gdb: $ gdb --exec=python (gdb) run runTests.py --debug tests/test_cmesh.py
and when it segfaults, use 'bt' command to print the backtrace, and send the full output.
test instance prepared (1 test(s)) [New Thread 0xb5f82b40 (LWP 31930)] [New Thread 0xb5781b40 (LWP 31931)] [New Thread 0xb4f80b40 (LWP 31932)] [New Thread 0xb477fb40 (LWP 31933)] ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s request connectivity 1 -> 0 build 1 request connectivity 2 -> 2 request connectivity 2 -> 0 request connectivity 0 -> 2 request connectivity 2 -> 0
(gdb) run runTests.py --debug tests/test_cmesh.py Starting program: /usr/bin/python runTests.py --debug tests/test_cmesh.py [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/i386-linux-gnu/libthread_db.so.1". <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose'] transpose 0 -> 2 n_incident: 6 intersect 2 -> 2 (0) n_incident: 2 n_incident: 6 max. n_incident_vertex: 12 sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb6585cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb6584ff4, cookie: 137058500 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb6585cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb657a157, cookie: -3112053 mem_free_mem(): error exit! mem_free_mem(): error exit!
Program received signal SIGSEGV, Segmentation fault. 0xb657bea8 in get_local_connectivity (refloc=<optimized out>, cell_vertices=<optimized out>, loc=<optimized out>) at sfepy/fem/extmods/mesh.c:733 733 loc->indices[ic] = cell_vertices->indices[refloc->indices[ic]]; (gdb) bt #0 0xb657bea8 in get_local_connectivity (refloc=<optimized out>, cell_vertices=<optimized out>, loc=<optimized out>) at sfepy/fem/extmods/mesh.c:733 #1 mesh_build (mesh=0x92624ac, dim=1) at sfepy/fem/extmods/mesh.c:428 #2 0xb657ba04 in mesh_setup_connectivity (mesh=0x92624ac, d1=1, d2=0) at sfepy/fem/extmods/mesh.c:294 #3 0xb6564c58 in __pyx_pf_5sfepy_3fem_7extmods_5cmesh_5CMesh_5setup_connectivity (__pyx_v_self=0x92624a4, __pyx_args=0x8d1610c, __pyx_kwds=0x0) at sfepy/fem/extmods/cmesh.c:4089 #4 0x081287ef in ?? () Backtrace stopped: previous frame inner to this frame (corrupt stack?)
Thanks! r.
Thanks for reporting that, the problem should be fixed now in the master repo.
r., being thankful for the virtualbox...
On 06/17/2013 12:28 AM, Ankit Mahato wrote:
On Monday, 17 June 2013 00:01:33 UTC+5:30, Robert Cimrman wrote:
Hi Ankit,
On 06/16/2013 03:16 AM, Ankit Mahato wrote:
Hi R,
I was installing the latest code on my new workstation, when runTests.py exited with error. On running it on debug mode, I got the following output:
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose']
test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x82bba80, cookie: 1786 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x817b0e3, cookie: 136600713 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! mem_realloc_mem(): error exit! conn_resize() failed!sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
Strange - what is your system architecture - 64 bit or 32 bit? I am running it at 64 bit linux boxes without problems.
32 bit
To debug it, could you try editing site_cfg.py as follows:
compile_flags = '-g' debug_flags = '-DDEBUG_FMF -DDEBUG_MESH'
then 'make clean; make', run the failing test and send the output?
test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s request connectivity 1 -> 0 build 1 request connectivity 2 -> 2 request connectivity 2 -> 0 request connectivity 0 -> 2 request connectivity 2 -> 0
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ python runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose'] transpose 0 -> 2 n_incident: 6 intersect 2 -> 2 (0) n_incident: 2 n_incident: 6 max. n_incident_vertex: 12 sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5d14cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb5d13ff4, cookie: 137058500 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5d14cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb5d09157, cookie: -3112053 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
Also try running it in gdb: $ gdb --exec=python (gdb) run runTests.py --debug tests/test_cmesh.py
and when it segfaults, use 'bt' command to print the backtrace, and send the full output.
test instance prepared (1 test(s)) [New Thread 0xb5f82b40 (LWP 31930)] [New Thread 0xb5781b40 (LWP 31931)] [New Thread 0xb4f80b40 (LWP 31932)] [New Thread 0xb477fb40 (LWP 31933)] ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s request connectivity 1 -> 0 build 1 request connectivity 2 -> 2 request connectivity 2 -> 0 request connectivity 0 -> 2 request connectivity 2 -> 0
(gdb) run runTests.py --debug tests/test_cmesh.py Starting program: /usr/bin/python runTests.py --debug tests/test_cmesh.py [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/i386-linux-gnu/libthread_db.so.1". <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose'] transpose 0 -> 2 n_incident: 6 intersect 2 -> 2 (0) n_incident: 2 n_incident: 6 max. n_incident_vertex: 12 sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb6585cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb6584ff4, cookie: 137058500 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb6585cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb657a157, cookie: -3112053 mem_free_mem(): error exit! mem_free_mem(): error exit!
Program received signal SIGSEGV, Segmentation fault. 0xb657bea8 in get_local_connectivity (refloc=<optimized out>, cell_vertices=<optimized out>, loc=<optimized out>) at sfepy/fem/extmods/mesh.c:733 733 loc->indices[ic] = cell_vertices->indices[refloc->indices[ic]]; (gdb) bt #0 0xb657bea8 in get_local_connectivity (refloc=<optimized out>, cell_vertices=<optimized out>, loc=<optimized out>) at sfepy/fem/extmods/mesh.c:733 #1 mesh_build (mesh=0x92624ac, dim=1) at sfepy/fem/extmods/mesh.c:428 #2 0xb657ba04 in mesh_setup_connectivity (mesh=0x92624ac, d1=1, d2=0) at sfepy/fem/extmods/mesh.c:294 #3 0xb6564c58 in __pyx_pf_5sfepy_3fem_7extmods_5cmesh_5CMesh_5setup_connectivity (__pyx_v_self=0x92624a4, __pyx_args=0x8d1610c, __pyx_kwds=0x0) at sfepy/fem/extmods/cmesh.c:4089 #4 0x081287ef in ?? () Backtrace stopped: previous frame inner to this frame (corrupt stack?)
Thanks! r.
working :)
Just out of curiosity: What was the bug R?
On Monday, 17 June 2013 16:29:03 UTC+5:30, Robert Cimrman wrote:
Thanks for reporting that, the problem should be fixed now in the master repo.
r., being thankful for the virtualbox...
On 06/17/2013 12:28 AM, Ankit Mahato wrote:
On Monday, 17 June 2013 00:01:33 UTC+5:30, Robert Cimrman wrote:
Hi Ankit,
On 06/16/2013 03:16 AM, Ankit Mahato wrote:
Hi R,
I was installing the latest code on my new workstation, when
runTests.py
exited with error. On running it on debug mode, I got the following output:
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose']
> test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x82bba80, cookie: 1786 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x817b0e3, cookie: 136600713 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! mem_realloc_mem(): error exit! conn_resize() failed!sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
Strange - what is your system architecture - 64 bit or 32 bit? I am running it at 64 bit linux boxes without problems.
32 bit
To debug it, could you try editing site_cfg.py as follows:
compile_flags = '-g' debug_flags = '-DDEBUG_FMF -DDEBUG_MESH'
then 'make clean; make', run the failing test and send the output?
test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s request connectivity 1 -> 0 build 1 request connectivity 2 -> 2 request connectivity 2 -> 0 request connectivity 0 -> 2 request connectivity 2 -> 0
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ python runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose'] transpose 0 -> 2 n_incident: 6 intersect 2 -> 2 (0) n_incident: 2 n_incident: 6 max. n_incident_vertex: 12 sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5d14cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb5d13ff4, cookie: 137058500 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5d14cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb5d09157, cookie: -3112053 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
Also try running it in gdb: $ gdb --exec=python (gdb) run runTests.py --debug tests/test_cmesh.py
and when it segfaults, use 'bt' command to print the backtrace, and send the full output.
test instance prepared (1 test(s)) [New Thread 0xb5f82b40 (LWP 31930)] [New Thread 0xb5781b40 (LWP 31931)] [New Thread 0xb4f80b40 (LWP 31932)] [New Thread 0xb477fb40 (LWP 31933)] ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s request connectivity 1 -> 0 build 1 request connectivity 2 -> 2 request connectivity 2 -> 0 request connectivity 0 -> 2 request connectivity 2 -> 0
(gdb) run runTests.py --debug tests/test_cmesh.py Starting program: /usr/bin/python runTests.py --debug tests/test_cmesh.py [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/i386-linux-gnu/libthread_db.so.1". <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose'] transpose 0 -> 2 n_incident: 6 intersect 2 -> 2 (0) n_incident: 2 n_incident: 6 max. n_incident_vertex: 12 sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb6585cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb6584ff4, cookie: 137058500 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb6585cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb657a157, cookie: -3112053 mem_free_mem(): error exit! mem_free_mem(): error exit!
Program received signal SIGSEGV, Segmentation fault. 0xb657bea8 in get_local_connectivity (refloc=<optimized out>, cell_vertices=<optimized out>, loc=<optimized out>) at sfepy/fem/extmods/mesh.c:733 733 loc->indices[ic] = cell_vertices->indices[refloc->indices[ic]]; (gdb) bt #0 0xb657bea8 in get_local_connectivity (refloc=<optimized out>, cell_vertices=<optimized out>, loc=<optimized out>) at sfepy/fem/extmods/mesh.c:733 #1 mesh_build (mesh=0x92624ac, dim=1) at sfepy/fem/extmods/mesh.c:428 #2 0xb657ba04 in mesh_setup_connectivity (mesh=0x92624ac, d1=1, d2=0) at sfepy/fem/extmods/mesh.c:294 #3 0xb6564c58 in __pyx_pf_5sfepy_3fem_7extmods_5cmesh_5CMesh_5setup_connectivity (__pyx_v_self=0x92624a4, __pyx_args=0x8d1610c, __pyx_kwds=0x0) at sfepy/fem/extmods/cmesh.c:4089 #4 0x081287ef in ?? () Backtrace stopped: previous frame inner to this frame (corrupt stack?)
Thanks! r.
Look at the last commit :) - basically an uninitialized memory, triggering a spurious free() call.
r.
On 06/17/2013 01:28 PM, Ankit Mahato wrote:
working :)
Just out of curiosity: What was the bug R?
On Monday, 17 June 2013 16:29:03 UTC+5:30, Robert Cimrman wrote:
Thanks for reporting that, the problem should be fixed now in the master repo.
r., being thankful for the virtualbox...
On 06/17/2013 12:28 AM, Ankit Mahato wrote:
On Monday, 17 June 2013 00:01:33 UTC+5:30, Robert Cimrman wrote:
Hi Ankit,
On 06/16/2013 03:16 AM, Ankit Mahato wrote:
Hi R,
I was installing the latest code on my new workstation, when
runTests.py
exited with error. On running it on debug mode, I got the following output:
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ ./runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose']
>> test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x82bba80, cookie: 1786 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0x817b0e3, cookie: 136600713 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! mem_realloc_mem(): error exit! conn_resize() failed!sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5ce4cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0x8bf30b0, cookie: 3 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
Strange - what is your system architecture - 64 bit or 32 bit? I am running it at 64 bit linux boxes without problems.
32 bit
To debug it, could you try editing site_cfg.py as follows:
compile_flags = '-g' debug_flags = '-DDEBUG_FMF -DDEBUG_MESH'
then 'make clean; make', run the failing test and send the output?
test instance prepared (1 test(s)) ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s request connectivity 1 -> 0 build 1 request connectivity 2 -> 2 request connectivity 2 -> 0 request connectivity 0 -> 2 request connectivity 2 -> 0
ankit@ankit-HP-Pavilion-dv4-Notebook-PC:~/sfepy$ python runTests.py --debug tests/test_cmesh.py <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose'] transpose 0 -> 2 n_incident: 6 intersect 2 -> 2 (0) n_incident: 2 n_incident: 6 max. n_incident_vertex: 12 sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5d14cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb5d13ff4, cookie: 137058500 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb5d14cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb5d09157, cookie: -3112053 mem_free_mem(): error exit! mem_free_mem(): error exit! Segmentation fault (core dumped)
Also try running it in gdb: $ gdb --exec=python (gdb) run runTests.py --debug tests/test_cmesh.py
and when it segfaults, use 'bt' command to print the backtrace, and send the full output.
test instance prepared (1 test(s)) [New Thread 0xb5f82b40 (LWP 31930)] [New Thread 0xb5781b40 (LWP 31931)] [New Thread 0xb4f80b40 (LWP 31932)] [New Thread 0xb477fb40 (LWP 31933)] ... mesh: 2_3_2.mesh sfepy: reading mesh (/home/ankit/sfepy/meshes/elements/2_3_2.mesh)... sfepy: ...done in 0.00 s request connectivity 1 -> 0 build 1 request connectivity 2 -> 2 request connectivity 2 -> 0 request connectivity 0 -> 2 request connectivity 2 -> 0
(gdb) run runTests.py --debug tests/test_cmesh.py Starting program: /usr/bin/python runTests.py --debug tests/test_cmesh.py [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/i386-linux-gnu/libthread_db.so.1". <<< directory: tests, test files: 1 <<< tests/test_cmesh.py sfepy: left over: ['data_dir', 'nm', '__builtins__', '_filename', '__file__', '__package__', 'expected', '__doc__', '__name__', 'os', 'TestCommon', 'verbose'] transpose 0 -> 2 n_incident: 6 intersect 2 -> 2 (0) n_incident: 2 n_incident: 6 max. n_incident_vertex: 12 sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb6585cc0, cookie: 0 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb6584ff4, cookie: 137058500 mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 210: ptr: 0xb6585cc0, cookie: 0 mem_free_mem(): error exit! mem_free_mem(): error exit! sfepy/fem/extmods, sfepy/fem/extmods/mesh.c, conn_free, 211: ptr: 0xb657a157, cookie: -3112053 mem_free_mem(): error exit! mem_free_mem(): error exit!
Program received signal SIGSEGV, Segmentation fault. 0xb657bea8 in get_local_connectivity (refloc=<optimized out>, cell_vertices=<optimized out>, loc=<optimized out>) at sfepy/fem/extmods/mesh.c:733 733 loc->indices[ic] = cell_vertices->indices[refloc->indices[ic]]; (gdb) bt #0 0xb657bea8 in get_local_connectivity (refloc=<optimized out>, cell_vertices=<optimized out>, loc=<optimized out>) at sfepy/fem/extmods/mesh.c:733 #1 mesh_build (mesh=0x92624ac, dim=1) at sfepy/fem/extmods/mesh.c:428 #2 0xb657ba04 in mesh_setup_connectivity (mesh=0x92624ac, d1=1, d2=0) at sfepy/fem/extmods/mesh.c:294 #3 0xb6564c58 in __pyx_pf_5sfepy_3fem_7extmods_5cmesh_5CMesh_5setup_connectivity (__pyx_v_self=0x92624a4, __pyx_args=0x8d1610c, __pyx_kwds=0x0) at sfepy/fem/extmods/cmesh.c:4089 #4 0x081287ef in ?? () Backtrace stopped: previous frame inner to this frame (corrupt stack?)
Thanks! r.
participants (2)
-
Ankit Mahato -
Robert Cimrman