Error running simple stencil example from README

[sinayoko]

Hi, I've installed stencil_code with pip and tried to run the simple Stencil example from the README file by running:

 python simple.py

I get the following error:

 No handlers could be found for logger "ctree.omp"
 Traceback (most recent call last):
   File "simple.py", line 28, in <module>
     out_grid = kernel(in_grid)
   File "/Users/sinayoks/apps/anaconda/lib/python2.7/site-packages/stencil_code/stencil_kernel.py", line 394, in __call__
     return self.specializer(*args, **kwargs)
   File "/Users/sinayoks/apps/anaconda/lib/python2.7/site-packages/ctree/jit.py", line 154, in __call__
     csf = self.finalize(*transform_result)
   File "/Users/sinayoks/apps/anaconda/lib/python2.7/site-packages/stencil_code/stencil_kernel.py", line 356, in finalize
     kernel.codegen()).build()
   File "/Users/sinayoks/apps/anaconda/lib/python2.7/site-packages/pycl.py", line 2199, in build
     clBuildProgram(self, *args, **kw)
   File "/Users/sinayoks/apps/anaconda/lib/python2.7/site-packages/pycl.py", line 2417, in clBuildProgram
     raise BuildProgramFailureError(log)
 pycl.BuildProgramFailureError: <program source>:11:13: warning: unused variable 'r_0'
         int r_0 = tid;
             ^
 <program source>:16:71: error: too many arguments provided to function-like macro invocation
     out_grid[global_index] += block[local_array_macro(local_id0 + -1, None + 1)];
                                                                       ^
 <program source>:16:37: error: use of undeclared identifier 'local_array_macro'
     out_grid[global_index] += block[local_array_macro(local_id0 + -1, None + 1)];
                                     ^
 <program source>:17:70: error: too many arguments provided to function-like macro invocation
     out_grid[global_index] += block[local_array_macro(local_id0 + 0, None + 1)];
                                                                      ^
 <program source>:17:37: error: use of undeclared identifier 'local_array_macro'
     out_grid[global_index] += block[local_array_macro(local_id0 + 0, None + 1)];
                                     ^
 <program source>:18:70: error: too many arguments provided to function-like macro invocation
     out_grid[global_index] += block[local_array_macro(local_id0 + 1, None + 1)];
                                                                      ^
 <program source>:18:37: error: use of undeclared identifier 'local_array_macro'
     out_grid[global_index] += block[local_array_macro(local_id0 + 1, None + 1)];
                                     ^
 <program source>:19:71: error: too many arguments provided to function-like macro invocation
     out_grid[global_index] += block[local_array_macro(local_id0 + -1, None + 0)];
                                                                       ^
 <program source>:19:37: error: use of undeclared identifier 'local_array_macro'
     out_grid[global_index] += block[local_array_macro(local_id0 + -1, None + 0)];
                                     ^
 <program source>:20:70: error: too many arguments provided to function-like macro invocation
     out_grid[global_index] += block[local_array_macro(local_id0 + 0, None + 0)];
                                                                      ^
 <program source>:20:37: error: use of undeclared identifier 'local_array_macro'
     out_grid[global_index] += block[local_array_macro(local_id0 + 0, None + 0)];
                                     ^
 <program source>:21:70: error: too many arguments provided to function-like macro invocation
     out_grid[global_index] += block[local_array_macro(local_id0 + 1, None + 0)];
                                                                      ^
 <program source>:21:37: error: use of undeclared identifier 'local_array_macro'
     out_grid[global_index] += block[local_array_macro(local_id0 + 1, None + 0)];
                                     ^
 <program source>:22:71: error: too many arguments provided to function-like macro invocation
     out_grid[global_index] += block[local_array_macro(local_id0 + -1, None + -1)];
                                                                       ^
 <program source>:22:37: error: use of undeclared identifier 'local_array_macro'
     out_grid[global_index] += block[local_array_macro(local_id0 + -1, None + -1)];
                                     ^
 <program source>:23:71: error: too many arguments provided to function-like macro invocation
     out_grid[global_index] += block[local_array_macro(local_id0 + -1, None + 0)];
                                                                       ^
 <program source>:23:37: error: use of undeclared identifier 'local_array_macro'
     out_grid[global_index] += block[local_array_macro(local_id0 + -1, None + 0)];
                                     ^
 <program source>:24:71: error: too many arguments provided to function-like macro invocation
     out_grid[global_index] += block[local_array_macro(local_id0 + -1, None + 1)];
                                                                       ^
 <program source>:24:37: error: use of undeclared identifier 'local_array_macro'
     out_grid[global_index] += block[local_array_macro(local_id0 + -1, None + 1)];
                                ^

Am I doing this wrong?

[dorthyluu]

Hi,

Were you trying this on the master branch?

[sinayoko]

Hi Dorthy,

Many thanks for getting back to me. I believe I raised this issue after following the instructions in the README file (install with pip install --pre), so I wasn't using the master branch.

In the email I sent Leonard I mentioned something else I tried today. I forked the ucb/stencil_code repo and connected it to Travis then modified the .travis.yml file slightly to remove the deployment part at the end. The Travis build report is available at https://travis-ci.org/ucb-sejits/ctree/jobs/51127888 and it shows 9 failed tests and 7 errors out of 45 tests.

It was the first time I used Travis though so I may have done something wrong.

Sam

[sinayoko]

I've managed to run the code using the ordered_halo_enumeration branch and by following the build commands in https://travis-ci.org/ucb-sejits/stencil_code/jobs/64479703. Most of the tests pass (after using gcc-4.8 and adding -framework OpenCL to ~/.ctree.cfg). Note that I'm using OS X 10.9.

I'm including some of the output of nosetests --verbose for reference:

zero boundary handling should just leave zero's in grid halo ... ok
test_copied_for_c (test.test_boundary_handling.TestBoundaryHandling) ... ok
test_copied_for_ocl (test.test_boundary_handling.TestBoundaryHandling) ... ld: library not found for -lOpenCL
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ERROR
test_copied_for_ocl_1d (test.test_boundary_handling.TestBoundaryHandling) ... ld: library not found for -lOpenCL
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ERROR
test_copied_for_ocl_3d (test.test_boundary_handling.TestBoundaryHandling) ... ld: library not found for -lOpenCL
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ERROR
test_copied_for_python (test.test_boundary_handling.TestBoundaryHandling) ... ok
test_python_clamping (test.test_boundary_handling.TestBoundaryHandling) ... ok
test_compute_local_group_size (test.test_boundary_kernel.TestBoundaryKernel) ... ok
test_exception_for_bad_halo_grid_values (test.test_boundary_kernel.TestBoundaryKernel) ... ok
test_gen_index_in_bounds_conditional (test.test_boundary_kernel.TestBoundaryKernel) ... ok
test_virtual_global_size (test.test_boundary_kernel.TestBoundaryKernel) ... ok
test_2d_heat (test.test_c_end_to_end.TestCEndToEnd) ... ok
test_better_bilateral_filter (test.test_c_end_to_end.TestCEndToEnd) ... ok
test_bilateral_filter (test.test_c_end_to_end.TestCEndToEnd) ... SKIP: not working right now, and is corrupting logs
test_convolution (test.test_c_end_to_end.TestCEndToEnd) ... ok
test_diagnostic_kernel (test.test_c_end_to_end.TestCEndToEnd) ... ok
test_jacobi (test.test_c_end_to_end.TestCEndToEnd) ... ok
test_laplacian (test.test_c_end_to_end.TestCEndToEnd) ... ok
test_laplacian27 (test.test_c_end_to_end.TestCEndToEnd) ... ok
test_1_d (test.test_halo_enumerator.TestHaloEnumerator) ... ok
test_constructor (test.test_halo_enumerator.TestHaloEnumerator) ... ok
test_n_d (test.test_halo_enumerator.TestHaloEnumerator) ... ok
test_with_kernel (test.test_halo_enumerator.TestHaloEnumerator) ... ok
test_compute_local_group_size_1d (test.test_local_size_computer.TestLocalSizeComputer) ... ok
test_compute_local_group_size_2d (test.test_local_size_computer.TestLocalSizeComputer) ... ok
test_compute_local_group_size_3d (test.test_local_size_computer.TestLocalSizeComputer) ... ok
test_local_size_computer_bulky (test.test_local_size_computer.TestLocalSizeComputer) ... ok
test_prod (test.test_local_size_computer.TestLocalSizeComputer) ... ok
test_compute_from_indices (test.test_neighborhood.TestNeighborhood) ... ok
test_moore_neighborhood (test.test_neighborhood.TestNeighborhood) ... ok
test_origin (test.test_neighborhood.TestNeighborhood) ... ok
test_von_neuman_neighborhood (test.test_neighborhood.TestNeighborhood) ... ok
test_2d_heat (test.test_ocl_end_to_end.TestOclEndToEnd) ... ld: library not found for -lOpenCL
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ERROR
test_bilateral_filter (test.test_ocl_end_to_end.TestOclEndToEnd) ... ld: library not found for -lOpenCL
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ERROR
test_laplacian (test.test_ocl_end_to_end.TestOclEndToEnd) ... ld: library not found for -lOpenCL
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ERROR
test_laplacian27 (test.test_ocl_end_to_end.TestOclEndToEnd) ... ld: library not found for -lOpenCL
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ERROR
test_1_d (test.test_ordered_halo_enumerator.TestOrderedOrderedHaloEnumerator) ... ok
test_constructor (test.test_ordered_halo_enumerator.TestOrderedOrderedHaloEnumerator) ... ok
test_n_d (test.test_ordered_halo_enumerator.TestOrderedOrderedHaloEnumerator) ... ok
test_neighbor_direction (test.test_ordered_halo_enumerator.TestOrderedOrderedHaloEnumerator) ... ok
test_no_redundancy (test.test_ordered_halo_enumerator.TestOrderedOrderedHaloEnumerator) ... ok
test_point_to_surface_key (test.test_ordered_halo_enumerator.TestOrderedOrderedHaloEnumerator) ... ok
test_with_kernel (test.test_ordered_halo_enumerator.TestOrderedOrderedHaloEnumerator) ... ok
The function_decl helper ... ok
test_interior_points_loop (test.test_stencil_backend.TestStencilBackend) ... ok
test_attribute (test.test_stencil_frontend.TestStencilFrontend) ... ok
project currently supports two special calls ... ok
if for iterates over interior_points or neighbors a semantic node is returned ... ok
function def renames arguments to generated name ... ok
test_python_to_stencil_model (test.test_stencil_frontend.TestStencilFrontend) ... ok
subscripted variables that are parameters to the kernel function ... ok
test_bad_boundary_handling (test.test_stencil_kernel.TestStencilKernel) ... ok
test_bad_neighborhood_id (test.test_stencil_kernel.TestStencilKernel) ... ok
test_default_distance (test.test_stencil_kernel.TestStencilKernel) ... ok
test_no_kernel_exception (test.test_stencil_kernel.TestStencilKernel) ... ok
test_no_neighborhood (test.test_stencil_kernel.TestStencilKernel) ... ok
test_simple_transform (test.test_stencil_omp_transformer.TestUnroll) ... SKIP: not finished
test_leftover_unroll (test.test_stencil_optimizer.TestUnroll) ... SKIP: Optimizer broken by newcl branch
test_simple_unroll (test.test_stencil_optimizer.TestUnroll) ... SKIP: Optimizer broken by newcl branch

[dorthyluu]

Hi Sam,

I managed to reproduce the error that you got in your original post when using the development branch, but not the master branch. The problem seems to stem from a mistake on our part in the sample code:

The neighborhood in simple.py is defined in terms of a two-dimensional space, but the actual data (in_grid) is a one-dimensional array. If you swap the following lines:

kernel = SimpleKernel()
width = 1024
in_grid = numpy.rand(width).astype(numpy.float32) * 1000

to:

kernel = SimpleKernel()
width = 1024
height = 1024
in_grid = numpy.random.rand(height, width).astype(numpy.float32) * 1000

the example should work as expected. Please let us know if this fixes the problem

[sinayoko]

Hi Dorthy,

I'm afraid it's still not working. I tried this in a new conda environment:

$ conda create -n stencil-issue numpy
$ pip install --pre stencil_code
$ conda install llvmpy
$ cat simple2.py
import numpy
from stencil_code.stencil_kernel import Stencil

class SimpleKernel(Stencil):
    neighborhoods = [[
        (-1, 1),  (0, 1),  (1, 1),
        (-1, 0),  (0, 0),  (1, 0),
        (-1, -1), (-1, 0), (-1, 1)
    ]]

    def kernel(self, in_grid, out_grid):
        for x in self.interior_points(out_grid):
            for y in self.neighbors(x, 0):
                out_grid[x] += in_grid[y]


kernel = SimpleKernel()
width = 1024
in_grid = numpy.random.rand(width, width).astype(numpy.float32) * 1000

out_grid = kernel(in_grid)

When running the code I get the following error

$ python simple2.py
No handlers could be found for logger "ctree.omp"
Traceback (most recent call last):
  File "simple2.py", line 21, in <module>
    out_grid = kernel(in_grid)
  File "/Users/sinayoks/anaconda/envs/sejits-issue/lib/python2.7/site-packages/stencil_code/stencil_kernel.py", line 394, in __call__
    return self.specializer(*args, **kwargs)
  File "/Users/sinayoks/anaconda/envs/sejits-issue/lib/python2.7/site-packages/ctree/jit.py", line 154, in __call__
    csf = self.finalize(*transform_result)
  File "/Users/sinayoks/anaconda/envs/sejits-issue/lib/python2.7/site-packages/stencil_code/stencil_kernel.py", line 361, in finalize
    self.output
  File "/Users/sinayoks/anaconda/envs/sejits-issue/lib/python2.7/site-packages/stencil_code/stencil_kernel.py", line 139, in finalize
    self._c_function = self._compile(entry_name, tree, entry_type)
  File "/Users/sinayoks/anaconda/envs/sejits-issue/lib/python2.7/site-packages/ctree/jit.py", line 86, in _compile
    self._module = project_node.codegen(**kwargs)
  File "/Users/sinayoks/anaconda/envs/sejits-issue/lib/python2.7/site-packages/ctree/nodes.py", line 148, in codegen
    submodule = f._compile(f.codegen(), module.compilation_dir)
  File "/Users/sinayoks/anaconda/envs/sejits-issue/lib/python2.7/site-packages/ctree/c/nodes.py", line 75, in _compile
    ll_module = llvm.core.Module.from_bitcode(bc)
  File "/Users/sinayoks/anaconda/envs/sejits-issue/lib/python2.7/site-packages/llvm/core.py", line 419, in from_bitcode
    raise Exception(errbuf.getvalue())
Exception: Invalid bitcode signature

But it works for me when using the development branch so I'm not too concerned.