[Getfem-users] problem in getfem installation

[Nima Noury]

Dear all,

We are trying to install getfem-4.2 and matlab interface on our Linux  
machine (CentOS), but unfortunately something goes wrong and while  
running demos, matlab crashes (we are using matlab2011b-64bit). We  
would really appreciate it if anyone helps us to solve the problem.

We have tried two different configurations and in both cases the same  
problems occurred:

./configure --with-pic --enable-matlab

or

./configure --enable-matlab --disable-python --enable-superlu  
--with-pic --enable-qhull --enable-mumps=no  
--with-matlab-toolbox-dir=$MATLAB_ROOT/toolbox/getfem_toolbox

then

make -j8

and afterward check and install steps.
Then we tried running some demo files like demo_laplacian.m and  
demo_crack.m and matlab crashed in lines 53 and 58 respectively (which  
refer to the execution of gf_matlab.mexa64). You can see the contents  
of one of matlab crash reports at the end of this message.
If I run demo_bilaplacian.m, following error happens (no matlab crash)

logic_error exception caught
Error using gf_matlab
Error in ../../src/gmm/gmm_opt.h, line 87 T gmm::lu_inverse(const
gmm::dense_matrix<T>&) [with T = double]:
non invertible matrix

Error in gf_mesh_get (line 266)
    [varargout{1:nargout}]=gf_matlab('mesh_get', varargin{:});

Error in gfMesh/get (line 5)
  [varargout{1:nargout}] = gf_mesh_get(obj, varargin{:});

Error in demo_bilaplacian (line 46)
n = get(m, 'normal of faces', flst);

We are using gcc version 4.4.6.

Many thanks in advance for your help,
Nima

PS- Matlab crash report:
------------------------------------------------------------------------
       Segmentation violation detected at Fri Oct  5 10:39:43 2012
------------------------------------------------------------------------

Configuration:
  Crash Decoding  : Disabled
  Current Visual  : 0x21 (class 4, depth 16)
  Default Encoding: UTF-8
  GNU C Library   : 2.12 stable
  MATLAB Root     : /opt/matlab/matlab2011b
  MATLAB Version  : 7.13.0.564 (R2011b)
  Operating System: Linux 2.6.32-131.21.1.el6.x86_64 #1 SMP Tue Nov  
22 19:48:09 GMT 2011 x86_64
  Processor ID    : x86 Family 6 Model 12 Stepping 2, GenuineIntel
  Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java  
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System   : The X.Org Foundation (10707000), display :6.0

Fault Count: 12



Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 00007f39f5a73010  RBX = 0000000000000001
  RCX = 0000004800000008  RDX = 000125db3d2949b0
  RSP = 00007f3965aee680  RBP = 00007f39f3c2bae8
  RSI = 00007f39f3c2bae8  RDI = 00000a9a15555550

   R8 = 000125db3d293320   R9 = 0000004800000008
  R10 = 000000d800000018  R11 = 000000d800000018
  R12 = 0000001200000001  R13 = 00007f39f3c2bb14
  R14 = 000125db3d293320  R15 = 00007f39f3c2bb14

  RIP = 00007f39f5a73c46  EFL = 0000000000010212

   CS = 0033   FS = 0000   GS = 0000


Stack Trace (from fault):
[  0] 0x00007f3a0d6385de      
/opt/matlab/matlab2011b/bin/glnxa64/libmwfl.so+00210398  
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+000158
[  1] 0x00007f3a0d63a62d      
/opt/matlab/matlab2011b/bin/glnxa64/libmwfl.so+00218669
[  2] 0x00007f3a0d63a8f5      
/opt/matlab/matlab2011b/bin/glnxa64/libmwfl.so+00219381  
_ZN2fl4diag13terminate_logEPKcRKNS0_14thread_contextEb+000165
[  3] 0x00007f3a0c6404f5     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00447733  
_ZN2fl4diag13terminate_logEPKcPK8ucontextb+000085
[  4] 0x00007f3a0c63d5b4     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00435636
[  5] 0x00007f3a0c63e333     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00439091
[  6] 0x00007f3a0c63e4c7     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00439495
[  7] 0x00007f3a0c63f85f     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00444511
[  8] 0x00007f3a0c63fa15     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00444949
[  9] 0x00007f3a0b11a4a0                              
/lib64/libpthread.so.0+00062624
[ 10] 0x00007f39f5a73c46          
/opt/matlab/matlab2011b/bin/glnxa64/mkl.so+18406470


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 00007f39f5a73010  RBX = 0000000000000001
  RCX = 0000004800000008  RDX = 0000d28a927e9f30
  RSP = 00007f3964f9a680  RBP = 00007f39f3c2bae8
  RSI = 00007f39f3c2bae8  RDI = 00000a9a15555550

   R8 = 0000d28a927e88a0   R9 = 0000004800000008
  R10 = 000000d800000018  R11 = 000000d800000018
  R12 = 0000001200000001  R13 = 00007f39f3c2bb14
  R14 = 0000d28a927e88a0  R15 = 00007f39f3c2bb14

  RIP = 00007f39f5a73c46  EFL = 0000000000010212

   CS = 0033   FS = 0000   GS = 0000


Stack Trace (from fault):
[  0] 0x00007f3a0d6385de      
/opt/matlab/matlab2011b/bin/glnxa64/libmwfl.so+00210398  
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+000158
[  1] 0x00007f3a0d63a62d      
/opt/matlab/matlab2011b/bin/glnxa64/libmwfl.so+00218669
[  2] 0x00007f3a0d63a8f5      
/opt/matlab/matlab2011b/bin/glnxa64/libmwfl.so+00219381  
_ZN2fl4diag13terminate_logEPKcRKNS0_14thread_contextEb+000165
[  3] 0x00007f3a0c6404f5     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00447733  
_ZN2fl4diag13terminate_logEPKcPK8ucontextb+000085
[  4] 0x00007f3a0c63d5b4     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00435636
[  5] 0x00007f3a0c63e333     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00439091
[  6] 0x00007f3a0c63e4c7     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00439495
[  7] 0x00007f3a0c63f85f     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00444511
[  8] 0x00007f3a0c63fa15     
/opt/matlab/matlab2011b/bin/glnxa64/libmwmcr.so+00444949
[  9] 0x00007f3a0b11a4a0                              
/lib64/libpthread.so.0+00062624
[ 10] 0x00007f39f5a73c46          
/opt/matlab/matlab2011b/bin/glnxa64/mkl.so+18406470