[Getfem-users] Compilation issues

[Nasos Iliopoulos]

Hello all,
I am trying to compile getfem and I am having partial success. I have 
seen posts regarding similar issues in the past but I didn't find  
anything that works for me. I hope I can get some help with my specific 
issues.

Here is my configuration:
OS: Ubuntu 13.04 (raring)
MATLAB 2013b (Release number 30 according to wikipedia)
mpich2, muParser, par+seq mumps, metis (through 
libsuitesparse-metis-dev), python, numpy, scipy
gcc v4.8.1

For the moment I will be happy to have getfem running in SMP using 
python (at least with MUMPS) and single-core using MATLAB. I have to 
note that in all compilation cases I have to tweak the configure script 
to reflect the fact that the script cannot detect my version of MATLAB 
(basically I hard-wire MATLAB_RELEASE=30). Additionally I manually move 
the definition of mumps_error_check(MUMPS_STRUCT &id) in  
gmm/gmm_MUMPS_interface.h towards the beginning of the file since gcc 
4.8 wants it declared  before it is instantiated.

In any case here are my attempts:

1. Parallel build
$ ./configure --with-pic --enable-matlab 
MEX=/usr/local/MATLAB/R2013b/bin/mex --enable-par-mumps 
--enable-paralevel=2 --enable-python
$ make -j 8
$ sudo make install

When I run a python example I get:
$ mpirun -n 4 python demo_step_by_step.py
Attempting to use an MPI routine before initializing MPICH
Attempting to use an MPI routine before initializing MPICH
('1 - 3*x - 3*y + 2*x^2 + 9*x*y + 2*y^2 - 6*x^2*y - 6*x*y^2 + 
4*x^2*y^2', '4*x - 4*x^2 - 12*x*y + 12*x^2*y + 8*x*y^2 - 8*x^2*y^2', '-x 
+ 2*x^2 + 3*x*y - 6*x^2*y - 2*x*y^2 + 4*x^2*y^2', '4*y - 12*x*y - 4*y^2 
+ 8*x^2*y + 12*x*y^2 - 8*x^2*y^2', '16*x*y - 16*x^2*y - 16*x*y^2 + 
16*x^2*y^2', '-4*x*y + 8*x^2*y + 4*x*y^2 - 8*x^2*y^2', '-y + 3*x*y + 
2*y^2 - 2*x^2*y - 6*x*y^2 + 4*x^2*y^2', '-4*x*y + 4*x^2*y + 8*x*y^2 - 
8*x^2*y^2', 'x*y - 2*x^2*y - 2*x*y^2 + 4*x^2*y^2')
('1 - 3*x - 3*y + 2*x^2 + 9*x*y + 2*y^2 - 6*x^2*y - 6*x*y^2 + 
4*x^2*y^2', '4*x - 4*x^2 - 12*x*y + 12*x^2*y + 8*x*y^2 - 8*x^2*y^2', '-x 
+ 2*x^2 + 3*x*y - 6*x^2*y - 2*x*y^2 + 4*x^2*y^2', '4*y - 12*x*y - 4*y^2 
+ 8*x^2*y + 12*x*y^2 - 8*x^2*y^2', '16*x*y - 16*x^2*y - 16*x*y^2 + 
16*x^2*y^2', '-4*x*y + 8*x^2*y + 4*x*y^2 - 8*x^2*y^2', '-y + 3*x*y + 
2*y^2 - 2*x^2*y - 6*x*y^2 + 4*x^2*y^2', '-4*x*y + 4*x^2*y + 8*x*y^2 - 
8*x^2*y^2', 'x*y - 2*x^2*y - 2*x*y^2 + 4*x^2*y^2')
Attempting to use an MPI routine before initializing MPICH
Attempting to use an MPI routine before initializing MPICH

I do not get any errors and the u.pos file is not generated

I get a similar output when I run it without mpirun:
$ python demo_step_by_step.py

Additionally when I run the same example through matlab it crashes and 
it only reports:
Attempting to use an MPI routine before initializing MPICH
Inconsistency detected by ld.so: dl-close.c: 765: _dl_close: Assertion 
`map->l_init_called' failed!

2. Non-parallel build:
$ ./configure --with-pic --enable-matlab 
MEX=/usr/local/MATLAB/R2013b/bin/mex --enable-mumps --enable-python
$ make -j 8
$ sudo make install

Running through the python interface gives the expected results (the 
python script runs and I get the proper answer. I tried both with 
demo_step_by_step and with demo_tripod)

Running though:
$ make check
returns:

PASS: ../tests/dynamic_array.pl
PASS: ../tests/dynamic_tas.pl
PASS: ../tests/test_int_set.pl
PASS: ../tests/test_tree_sorted.pl
PASS: ../tests/poly.pl
PASS: ../tests/test_small_vector.pl
PASS: ../tests/test_kdtree.pl
PASS: ../tests/test_rtree.pl
PASS: ../tests/geo_trans_inv.pl
PASS: ../tests/test_norm.pl
PASS: ../tests/test_mesh.pl
PASS: ../tests/test_interpolation.pl
.............
PASS: ../tests/test_mat_elem.pl
PASS: ../tests/test_slice.pl
PASS: ../tests/integration.pl
...
PASS: ../tests/test_assembly.pl
PASS: ../tests/test_interpolated_fem.pl
PASS: ../tests/test_range_basis.pl
.............
PASS: ../tests/laplacian.pl
./laplacian_with_bricks /tmp/laplacian.param_346  2>&1 failed
FAIL: ../tests/laplacian_with_bricks.pl
./elastostatic /tmp/elas.param_309  2>&1 failed
FAIL: ../tests/elastostatic.pl
FAIL: ../tests/stokes.pl
FAIL: ../tests/plate.pl
PASS: ../tests/test_mesh_im_level_set.pl
FAIL: ../tests/crack.pl
FAIL: ../tests/nonlinear_elastostatic.pl
FAIL: ../tests/nonlinear_membrane.pl
FAIL: ../tests/dynamic_friction.pl
PASS: ../tests/plasticity.pl
FAIL: ../tests/plasticity_old_brick.pl
FAIL: ../tests/helmholtz.pl
PASS: ../tests/schwarz_additive.pl
./bilaplacian /tmp/elas.param_827  2>&1 failed
FAIL: ../tests/bilaplacian.pl
./heat_equation /tmp/heat.param_267  2>&1 failed
FAIL: ../tests/heat_equation.pl
./wave_equation /tmp/wave.param_757  2>&1 failed
FAIL: ../tests/wave_equation.pl
FAIL: ../tests/test_large_sliding_contact.pl
PASS: ../tests/cyl_slicer.pl

....
50 effective experiments with no fault, size = 25 base type : St7complexIfE
solver least square cg  : 0 exp. with no fault
solver bicgstab : 0 exp. with no fault
solver gmres    : 250 exp. with no fault, ratio = 0, average nb iter = 14.4
solver qmr  : 0 exp. with no fault
solver cg   : 200 exp. with no fault, ratio = 0, average nb iter = 21.9
no precond  : 100 exp. with no fault, ratio = 0, average nb iter = 29
diag precond    : 100 exp. with no fault, ratio = 0, average nb iter = 29.8
mr precond  : 0 exp. with no fault
ilu precond : 50 exp. with no fault, ratio = 0, average nb iter = 14.6
ilut precond    : 50 exp. with no fault, ratio = 0, average nb iter = 6.14
ilutp precond   : 50 exp. with no fault, ratio = 0, average nb iter = 1.52
ildlt precond   : 50 exp. with no fault, ratio = 0, average nb iter = 1
ildltt precond  : 50 exp. with no fault, ratio = 0, average nb iter = 19.1
PASS: ../tests/make_gmm_test.pl
=====================
14 of 38 tests failed
=====================
make[2]: *** [check-TESTS] Error 1
make[2]: Leaving directory `/home/nasos/tmp/getfem/getfem-4.2/tests'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/home/nasos/tmp/getfem/getfem-4.2/tests'
make: *** [check-recursive] Error 1


In MATLAB I am getting this:

plotting mesh...
Trace 2 in getfem_models.cc, line 1827: Mass term assembly for Dirichlet 
condition
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_model_get (line 183)
    gf_matlab('model_get', varargin{:});

and in the command terminal:
MKL ERROR: Parameter 8 was incorrect on entry to DGEMM .

note: matlab does not crash at this point but it DOES if I run the 
script again.

I tried to debug it  and it seems that lu_inverse is being fed with a 
zero matrix.

I also tried to PRELOAD my local c and std libs but I am getting the 
same error.

So my questions are:

A. Any suggestions/thoughts with respect to my build configuration/system?
B. How can I enable a debug build so I can search it a little bit more?

Thank you!
Nasos Iliopoulos