Installation error
See original GitHub issueHi, while installing the package I get the following error.
Collecting git+https://github.com/cornellius-gp/gpytorch.git
Cloning https://github.com/cornellius-gp/gpytorch.git to /tmp/pip-7qp9fn9f-build
Requirement already satisfied: cffi>=1.4.0 in ./.conda/envs/test_env/lib/python3.5/site-packages (from gpytorch==0.1)
Requirement already satisfied: pycparser in ./.conda/envs/test_env/lib/python3.5/site-packages (from cffi>=1.4.0->gpytorch==0.1)
Installing collected packages: gpytorch
Running setup.py install for gpytorch ... error
Complete output from command /u/18/gadichs1/unix/.conda/envs/test_env/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-7qp9fn9f-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-04cqd2t7-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/gpytorch
copying gpytorch/module.py -> build/lib.linux-x86_64-3.5/gpytorch
copying gpytorch/beta_features.py -> build/lib.linux-x86_64-3.5/gpytorch
copying gpytorch/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch
copying gpytorch/settings.py -> build/lib.linux-x86_64-3.5/gpytorch
creating build/lib.linux-x86_64-3.5/test
copying test/__init__.py -> build/lib.linux-x86_64-3.5/test
creating build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/grid_interpolation_kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/linear_kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/additive_grid_interpolation_kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/multiplicative_grid_interpolation_kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/grid_kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/matern_kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/index_kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/spectral_mixture_kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/rbf_kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
copying gpytorch/kernels/periodic_kernel.py -> build/lib.linux-x86_64-3.5/gpytorch/kernels
creating build/lib.linux-x86_64-3.5/gpytorch/mlls
copying gpytorch/mlls/exact_marginal_log_likelihood.py -> build/lib.linux-x86_64-3.5/gpytorch/mlls
copying gpytorch/mlls/marginal_log_likelihood.py -> build/lib.linux-x86_64-3.5/gpytorch/mlls
copying gpytorch/mlls/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/mlls
copying gpytorch/mlls/variational_marginal_log_likelihood.py -> build/lib.linux-x86_64-3.5/gpytorch/mlls
creating build/lib.linux-x86_64-3.5/gpytorch/models
copying gpytorch/models/abstract_variational_gp.py -> build/lib.linux-x86_64-3.5/gpytorch/models
copying gpytorch/models/additive_grid_inducing_variational_gp.py -> build/lib.linux-x86_64-3.5/gpytorch/models
copying gpytorch/models/exact_gp.py -> build/lib.linux-x86_64-3.5/gpytorch/models
copying gpytorch/models/grid_inducing_variational_gp.py -> build/lib.linux-x86_64-3.5/gpytorch/models
copying gpytorch/models/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/models
copying gpytorch/models/variational_gp.py -> build/lib.linux-x86_64-3.5/gpytorch/models
copying gpytorch/models/gp.py -> build/lib.linux-x86_64-3.5/gpytorch/models
creating build/lib.linux-x86_64-3.5/gpytorch/functions
copying gpytorch/functions/dsmm.py -> build/lib.linux-x86_64-3.5/gpytorch/functions
copying gpytorch/functions/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/functions
copying gpytorch/functions/log_normal_cdf.py -> build/lib.linux-x86_64-3.5/gpytorch/functions
copying gpytorch/functions/normal_cdf.py -> build/lib.linux-x86_64-3.5/gpytorch/functions
copying gpytorch/functions/add_diag.py -> build/lib.linux-x86_64-3.5/gpytorch/functions
creating build/lib.linux-x86_64-3.5/gpytorch/variational
copying gpytorch/variational/variational_strategy.py -> build/lib.linux-x86_64-3.5/gpytorch/variational
copying gpytorch/variational/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/variational
copying gpytorch/variational/mvn_variational_strategy.py -> build/lib.linux-x86_64-3.5/gpytorch/variational
creating build/lib.linux-x86_64-3.5/gpytorch/means
copying gpytorch/means/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/means
copying gpytorch/means/mean.py -> build/lib.linux-x86_64-3.5/gpytorch/means
copying gpytorch/means/constant_mean.py -> build/lib.linux-x86_64-3.5/gpytorch/means
creating build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/constant_mul_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/non_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/interpolated_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/kronecker_product_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/matmul_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/mul_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/toeplitz_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/root_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/sum_batch_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/sum_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/block_diagonal_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/diag_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
copying gpytorch/lazy/psd_sum_lazy_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/lazy
creating build/lib.linux-x86_64-3.5/gpytorch/likelihoods
copying gpytorch/likelihoods/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/likelihoods
copying gpytorch/likelihoods/likelihood.py -> build/lib.linux-x86_64-3.5/gpytorch/likelihoods
copying gpytorch/likelihoods/bernoulli_likelihood.py -> build/lib.linux-x86_64-3.5/gpytorch/likelihoods
copying gpytorch/likelihoods/softmax_likelihood.py -> build/lib.linux-x86_64-3.5/gpytorch/likelihoods
copying gpytorch/likelihoods/gaussian_likelihood.py -> build/lib.linux-x86_64-3.5/gpytorch/likelihoods
creating build/lib.linux-x86_64-3.5/gpytorch/libfft
copying gpytorch/libfft/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/libfft
creating build/lib.linux-x86_64-3.5/gpytorch/random_variables
copying gpytorch/random_variables/bernoulli_random_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/random_variables
copying gpytorch/random_variables/dirichlet_random_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/random_variables
copying gpytorch/random_variables/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/random_variables
copying gpytorch/random_variables/gaussian_random_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/random_variables
copying gpytorch/random_variables/samples_random_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/random_variables
copying gpytorch/random_variables/mixture_random_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/random_variables
copying gpytorch/random_variables/random_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/random_variables
copying gpytorch/random_variables/categorical_random_variable.py -> build/lib.linux-x86_64-3.5/gpytorch/random_variables
creating build/lib.linux-x86_64-3.5/gpytorch/utils
copying gpytorch/utils/toeplitz.py -> build/lib.linux-x86_64-3.5/gpytorch/utils
copying gpytorch/utils/linear_cg.py -> build/lib.linux-x86_64-3.5/gpytorch/utils
copying gpytorch/utils/function_factory.py -> build/lib.linux-x86_64-3.5/gpytorch/utils
copying gpytorch/utils/fft.py -> build/lib.linux-x86_64-3.5/gpytorch/utils
copying gpytorch/utils/interpolation.py -> build/lib.linux-x86_64-3.5/gpytorch/utils
copying gpytorch/utils/__init__.py -> build/lib.linux-x86_64-3.5/gpytorch/utils
copying gpytorch/utils/sparse.py -> build/lib.linux-x86_64-3.5/gpytorch/utils
copying gpytorch/utils/stochastic_lq.py -> build/lib.linux-x86_64-3.5/gpytorch/utils
copying gpytorch/utils/lanczos.py -> build/lib.linux-x86_64-3.5/gpytorch/utils
copying gpytorch/utils/circulant.py -> build/lib.linux-x86_64-3.5/gpytorch/utils
creating build/lib.linux-x86_64-3.5/test/kernels
copying test/kernels/test_rbf_kernel.py -> build/lib.linux-x86_64-3.5/test/kernels
copying test/kernels/test_additive_kernel.py -> build/lib.linux-x86_64-3.5/test/kernels
copying test/kernels/test_linear_kernel.py -> build/lib.linux-x86_64-3.5/test/kernels
copying test/kernels/__init__.py -> build/lib.linux-x86_64-3.5/test/kernels
copying test/kernels/test_periodic_kernel.py -> build/lib.linux-x86_64-3.5/test/kernels
creating build/lib.linux-x86_64-3.5/test/functions
copying test/functions/test_dsmm.py -> build/lib.linux-x86_64-3.5/test/functions
copying test/functions/__init__.py -> build/lib.linux-x86_64-3.5/test/functions
copying test/functions/test_log_normal_cdf_test.py -> build/lib.linux-x86_64-3.5/test/functions
copying test/functions/test_add_diag.py -> build/lib.linux-x86_64-3.5/test/functions
creating build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/test_root_lazy_variable.py -> build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/test_diag_lazy_variable.py -> build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/test_block_diagonal_lazy_variable.py -> build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/test_constant_mul_lazy_variable.py -> build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/test_toeplizt_lazy_variable.py -> build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/__init__.py -> build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/test_interpolated_lazy_variable.py -> build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/test_kronecker_product_lazy_variable.py -> build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/test_sum_lazy_variable.py -> build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/test_matmul_lazy_variable.py -> build/lib.linux-x86_64-3.5/test/lazy
copying test/lazy/test_mul_lazy_variable_test.py -> build/lib.linux-x86_64-3.5/test/lazy
creating build/lib.linux-x86_64-3.5/test/util
copying test/util/test_fft.py -> build/lib.linux-x86_64-3.5/test/util
copying test/util/test_cubic_interpolation.py -> build/lib.linux-x86_64-3.5/test/util
copying test/util/test_linear_cg.py -> build/lib.linux-x86_64-3.5/test/util
copying test/util/test_lanczos.py -> build/lib.linux-x86_64-3.5/test/util
copying test/util/__init__.py -> build/lib.linux-x86_64-3.5/test/util
copying test/util/test_sparse.py -> build/lib.linux-x86_64-3.5/test/util
copying test/util/test_toeplitz.py -> build/lib.linux-x86_64-3.5/test/util
copying test/util/test_function_factory.py -> build/lib.linux-x86_64-3.5/test/util
copying test/util/test_interp.py -> build/lib.linux-x86_64-3.5/test/util
copying test/util/test_tridiag.py -> build/lib.linux-x86_64-3.5/test/util
copying test/util/test_circulant.py -> build/lib.linux-x86_64-3.5/test/util
creating build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_simple_gp_classification.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_kissgp_multiplicative_regression.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_kissgp_variational_regression.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_kissgp_kronecker_product_classification.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_kissgp_kronecker_product_regression.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_kissgp_additive_classification.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_multitask_gp_regression.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_kissgp_additive_regression.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_kissgp_gp_regression.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_kissgp_gp_classification.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/__init__.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_spectral_mixture_gp_regression.py -> build/lib.linux-x86_64-3.5/test/examples
copying test/examples/test_simple_gp_regression.py -> build/lib.linux-x86_64-3.5/test/examples
running build_ext
generating cffi module 'build/temp.linux-x86_64-3.5/gpytorch.libfft._libfft.c'
creating build/temp.linux-x86_64-3.5
building 'gpytorch.libfft._libfft' extension
creating build/temp.linux-x86_64-3.5/build
creating build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/tmp
creating build/temp.linux-x86_64-3.5/tmp/pip-7qp9fn9f-build
creating build/temp.linux-x86_64-3.5/tmp/pip-7qp9fn9f-build/gpytorch
creating build/temp.linux-x86_64-3.5/tmp/pip-7qp9fn9f-build/gpytorch/csrc
gcc -pthread -B /u/18/gadichs1/unix/.conda/envs/test_env/compiler_compat -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_CUDA -I/u/18/gadichs1/unix/.conda/envs/test_env/lib/python3.5/site-packages/torch/utils/ffi/../../lib/include -I/u/18/gadichs1/unix/.conda/envs/test_env/lib/python3.5/site-packages/torch/utils/ffi/../../lib/include/TH -I/u/18/gadichs1/unix/.conda/envs/test_env/lib/python3.5/site-packages/torch/utils/ffi/../../lib/include/THC -I/u/18/gadichs1/unix/.conda/envs/test_env/include/python3.5m -c build/temp.linux-x86_64-3.5/gpytorch.libfft._libfft.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/gpytorch.libfft._libfft.o -std=c99
gcc -pthread -B /u/18/gadichs1/unix/.conda/envs/test_env/compiler_compat -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_CUDA -I/u/18/gadichs1/unix/.conda/envs/test_env/lib/python3.5/site-packages/torch/utils/ffi/../../lib/include -I/u/18/gadichs1/unix/.conda/envs/test_env/lib/python3.5/site-packages/torch/utils/ffi/../../lib/include/TH -I/u/18/gadichs1/unix/.conda/envs/test_env/lib/python3.5/site-packages/torch/utils/ffi/../../lib/include/THC -I/u/18/gadichs1/unix/.conda/envs/test_env/include/python3.5m -c /tmp/pip-7qp9fn9f-build/gpytorch/csrc/fft.c -o build/temp.linux-x86_64-3.5/tmp/pip-7qp9fn9f-build/gpytorch/csrc/fft.o -std=c99
/tmp/pip-7qp9fn9f-build/gpytorch/csrc/fft.c:2:19: fatal error: fftw3.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/u/18/gadichs1/unix/.conda/envs/test_env/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-7qp9fn9f-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-04cqd2t7-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-7qp9fn9f-build/
I’m on Ubuntu 16.04, here is my conda list.
# Name Version Build Channel
ca-certificates 2018.1.18 0 conda-forge
certifi 2018.1.18 py35_0 conda-forge
cffi 1.11.5 py35_0 conda-forge
cudatoolkit 8.0 3
cudnn 7.0.5 cuda8.0_0
fftw 3.3.7 0 conda-forge
freetype 2.8.1 0 conda-forge
intel-openmp 2018.0.0 hc7b2577_8
jpeg 9b 2 conda-forge
libedit 3.1 heed3624_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 7.2.0 hdf63c60_3
libgfortran-ng 7.2.0 hdf63c60_3
libpng 1.6.34 0 conda-forge
libstdcxx-ng 7.2.0 hdf63c60_3
libtiff 4.0.9 0 conda-forge
mkl 2018.0.1 h19d6760_4
ncurses 6.0 h9df7e31_2
numpy 1.14.2 py35hdbf6ddf_0
olefile 0.45.1 py35_0 conda-forge
openssl 1.0.2n 0 conda-forge
pillow 5.0.0 py35_0 conda-forge
pip 9.0.2 <pip>
pip 9.0.1 py35_5
pycparser 2.18 py35_0 conda-forge
python 3.5.5 hc3d631a_1
pytorch 0.3.1 py35_cuda8.0.61_cudnn7.0.5_2 pytorch
readline 7.0 ha6073c6_4
setuptools 39.0.1
setuptools 38.5.1 py35_0
six 1.11.0 py35_1 conda-forge
sqlite 3.22.0 h1bed415_0
tk 8.6.7 hc745277_3
torchvision 0.2.0 <pip>
torchvision 0.2.0 py35_0 conda-forge
wheel 0.30.0 py35hd3883cf_1
xz 5.2.3 h55aa19d_2
zlib 1.2.11 ha838bed_2
The gcc version currently is
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.9) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Any help is really appreciated.
Issue Analytics
- State:
- Created 6 years ago
- Comments:10 (10 by maintainers)
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I can’t reproduce this error. Here’s the steps I’ve taken on MacOS (w/o CUDA):
Then, when I’m working in another directory, in an ipython shell
Since you are on Ubuntu, could you try installing fftw via
apt-get
? I think the package names arelibfftw3-3
andlibfftw3-dev
, but it might find them if you just tryfftw3
.I can look further at what the package name is when I’m actually in front of a computer if none of those work 😃.
@gpleiss I think I’ve run in to this issue, I’m not actually totally convinced that installing fftw from conda works every time.