error occurs when running 3d examples
qin...@doane.edu
Hi all,
I have followed your instructions to install the deformetrica successfully, and some 2d examples could be run successfully. However, when I run examples on 3d data, I got the following errors:
(deformetrica) [LiQing@localhost brains]$ deformetrica estimate model.xml data_set.xml -p optimization_parameters.xml
Logger has been set to: WARNING
/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/in_out/xml_parameters.py:574: UserWarning: Unknown entry while parsing the optimization_parameters xml: use-cuda
warnings.warn(msg)
Compiling libKeOpstorch3f2a025ff1 in /home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1:
formula: Sum_Reduction(Exp(-G*SqDist(X,Y)) * P,0)
aliases: G = Pm(0,1); X = Vi(1,3); Y = Vj(2,3); P = Vj(3,3);
dtype : float32
... nvcc fatal : Unsupported gpu architecture 'compute_30'
CMake Error at keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o.Release.cmake:220 (message):
Error generating
/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/./keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o
gmake[3]: *** [CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/build.make:85: CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o] Error 1
gmake[2]: *** [CMakeFiles/Makefile2:210: CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/all] Error 2
gmake[1]: *** [CMakeFiles/Makefile2:272: CMakeFiles/libKeOpstorch3f2a025ff1.dir/rule] Error 2
gmake: *** [Makefile:203: libKeOpstorch3f2a025ff1] Error 2
--------------------- MAKE DEBUG -----------------
Command '['cmake', '--build', '.', '--target', 'libKeOpstorch3f2a025ff1', '--', 'VERBOSE=1']' returned non-zero exit status 2.
/home/LiQing/bin/cmake -S/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/pykeops -B/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1 --check-build-system CMakeFiles/Makefile.cmake 0
/opt/rh/devtoolset-8/root/usr/bin/gmake -f CMakeFiles/Makefile2 libKeOpstorch3f2a025ff1
gmake[1]: Entering directory '/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1'
/home/LiQing/bin/cmake -S/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/pykeops -B/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1 --check-build-system CMakeFiles/Makefile.cmake 0
/home/LiQing/bin/cmake -E cmake_progress_start /home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles 4
/opt/rh/devtoolset-8/root/usr/bin/gmake -f CMakeFiles/Makefile2 CMakeFiles/libKeOpstorch3f2a025ff1.dir/all
gmake[2]: Entering directory '/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1'
/opt/rh/devtoolset-8/root/usr/bin/gmake -f CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/build.make CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/depend
gmake[3]: Entering directory '/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1'
[ 25%] Building NVCC (Device) object CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o
cd /home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core && /home/LiQing/bin/cmake -E make_directory /home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/.
cd /home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core && /home/LiQing/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Release -D generated_file:STRING=/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/./keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o -D generated_cubin_file:STRING=/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/./keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o.cubin.txt -P /home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o.Release.cmake
-- Removing /home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/./keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o
/home/LiQing/bin/cmake -E rm -f /home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/./keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o
-- Generating dependency file: /home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o.NVCC-depend
/usr/local/cuda-11.0/bin/nvcc -M -D__CUDACC__ /home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/pykeops/keops/core/link_autodiff.cu -o /home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1/CMakeFiles/keopslibKeOpstorch3f2a025ff1.dir/keops/core/keopslibKeOpstorch3f2a025ff1_generated_link_autodiff.cu.o.NVCC-depend -m64 -DkeopslibKeOpstorch3f2a025ff1_EXPORTS -D_FORCE_INLINES -DCUDA_BLOCK_SIZE=192 -DUSE_CUDA=1 -D__TYPE__=float -DC_CONTIGUOUS=1 -D__TYPEACC__=float -DSUM_SCHEME=1 -D_GLIBCXX_USE_CXX11_ABI=0 -DUSE_DOUBLE=0 -DUSE_HALF=0 -DMODULE_NAME=libKeOpstorch3f2a025ff1 -DKERNEL_GEOM_TYPE=0 -DKERNEL_SIG_TYPE=0 -DKERNEL_SPHERE_TYPE=0 -DMODULE_NAME_FSHAPE_SCP=fshape_scp_gaussiangaussiangaussian_unoriented_float -Xcompiler ,\"-DUSE_OPENMP\",\"-fopenmp\",\"-Wall\",\"-Wno-unknown-pragmas\",\"-fmax-errors=2\",\"-fPIC\",\"-O3\",\"-DNDEBUG\",\"-O3\" -gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=sm_35 -gencode arch=compute_50,code=sm_50 -gencode arch=compute_52,code=sm_52 -gencode arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61 -gencode arch=compute_70,code=sm_70 -gencode arch=compute_75,code=sm_75 -gencode arch=compute_70,code=compute_70 -gencode arch=compute_75,code=compute_75 --use_fast_math --compiler-options=-fPIC -ccbin /opt/rh/devtoolset-8/root/usr/bin/c++ --pre-include=libKeOpstorch3f2a025ff1.h -DNVCC -I/usr/local/cuda-11.0/include -I/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/pykeops -I/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/pykeops/keops -I/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1 -I/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/torch/include -I/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/torch/include/torch/csrc/api/include
gmake[3]: Leaving directory '/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1'
gmake[2]: Leaving directory '/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1'
gmake[1]: Leaving directory '/home/LiQing/.cache/pykeops-1.4.1-cpython-38/build-libKeOpstorch3f2a025ff1'
--------------------- ----------- -----------------
Done.
Traceback (most recent call last):
File "/home/LiQing/anaconda3/envs/deformetrica/bin/deformetrica", line 8, in <module>
sys.exit(main())
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/__main__.py", line 113, in main
deformetrica.estimate_deterministic_atlas(
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/api/deformetrica.py", line 186, in estimate_deterministic_atlas
self.__launch_estimator(estimator, write_output)
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/api/deformetrica.py", line 506, in __launch_estimator
estimator.update()
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/core/estimators/scipy_optimize.py", line 101, in update
result = minimize(self._cost_and_derivative, self.x0.astype('float64'),
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/scipy/optimize/_minimize.py", line 617, in minimize
return _minimize_lbfgsb(fun, x0, args, jac, bounds,
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/scipy/optimize/lbfgsb.py", line 306, in _minimize_lbfgsb
sf = _prepare_scalar_function(fun, x0, jac=jac, args=args, epsilon=eps,
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/scipy/optimize/optimize.py", line 261, in _prepare_scalar_function
sf = ScalarFunction(fun, x0, args, grad, hess,
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/scipy/optimize/_differentiable_functions.py", line 76, in __init__
self._update_fun()
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/scipy/optimize/_differentiable_functions.py", line 166, in _update_fun
self._update_fun_impl()
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/scipy/optimize/_differentiable_functions.py", line 73, in update_fun
self.f = fun_wrapped(self.x)
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/scipy/optimize/_differentiable_functions.py", line 70, in fun_wrapped
return fun(x, *args)
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/scipy/optimize/optimize.py", line 74, in __call__
self._compute_if_needed(x, *args)
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/scipy/optimize/optimize.py", line 68, in _compute_if_needed
fg = self.fun(x, *args)
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/core/estimators/scipy_optimize.py", line 213, in _cost_and_derivative
attachment, regularity, gradient = self.statistical_model.compute_log_likelihood(
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/core/models/deterministic_atlas.py", line 333, in compute_log_likelihood
return self._compute_attachment_and_regularity(dataset, template_data, template_points, control_points,
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/core/models/deterministic_atlas.py", line 421, in _compute_attachment_and_regularity
new_attachment, new_regularity = DeterministicAtlas._deform_and_compute_attachment_and_regularity(
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/core/models/deterministic_atlas.py", line 351, in _deform_and_compute_attachment_and_regularity
exponential.update()
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/core/model_tools/deformations/exponential.py", line 173, in update
self.shoot()
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/core/model_tools/deformations/exponential.py", line 210, in shoot
new_cp, new_mom = self._euler_step(self.shoot_kernel, self.control_points_t[i], self.momenta_t[i], dt)
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/core/model_tools/deformations/exponential.py", line 483, in _euler_step
return cp + h * kernel.convolve(cp, cp, mom), \
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/deformetrica/support/kernels/keops_kernel.py", line 82, in convolve
res = self.gaussian_convolve[d - 2](gamma, x.contiguous(), y.contiguous(), p.contiguous(), device_id=device_id)
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/pykeops/torch/generic/generic_red.py", line 395, in __call__
out = GenredAutograd.apply(self.formula, self.aliases, backend, self.dtype,
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/pykeops/torch/generic/generic_red.py", line 22, in forward
myconv = LoadKeOps(formula, aliases, dtype, 'torch', optional_flags).import_module()
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/site-packages/pykeops/common/keops_io.py", line 70, in import_module
return importlib.import_module(self.dll_name)
File "/home/LiQing/anaconda3/envs/deformetrica/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 973, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'libKeOpstorch3f2a025ff1'
Is it due to my device configuration? Any help will be appreciated!
Qing
Fleur Gaudfernau
* (Load the right CUDA module) module load cuda/10
* (Create a virtualenv) python -m venv keops-env
* (Activate virtualenv) source keops-env/bin/activate
* (Update pip in the virtualenv, be sure to be in the active virtualenv) python -m pip install -U pip
* (Install pykeops) python -m pip install pykeops
Then you can call deformetrica.