Processing ./deps_bundle/python/python_packages/pip_packages/scikit_cuda-0.5.3-py2.py3-none-any.whl
Skipping wheel build for pycuda, due to binaries being disabled for it.
Installing collected packages: scikit-cuda, pycuda
Running setup.py install for pycuda ... error
ERROR: Command errored out with exit status 1:
command: /home/amax/software/cryosparcnew/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-esltad_h/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-esltad_h/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-record-ziy4avib/install-record.txt --single-version-externally-managed --compile --install-headers /home/amax/software/cryosparcnew/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/include/python3.7m/pycuda
cwd: /tmp/pip-req-build-esltad_h/
Complete output (102 lines):
*************************************************************
*** I have detected that you have not run configure.py.
*************************************************************
*** Additionally, no global config files were found.
*** I will go ahead with the default configuration.
*** In all likelihood, this will not work out.
***
*** See README_SETUP.txt for more information.
***
*** If the build does fail, just re-run configure.py with the
*** correct arguments, and then retry. Good luck!
*************************************************************
*** HIT Ctrl-C NOW IF THIS IS NOT WHAT YOU WANT
*************************************************************
Continuing in 1 seconds...
/home/amax/software/cryosparcnew/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'test_requires'
warnings.warn(msg)
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/pycuda
copying pycuda/_mymako.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/elementwise.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/tools.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/compiler.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/cumath.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/curandom.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/_cluda.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/autoinit.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/debug.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/scan.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/characterize.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/gpuarray.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/driver.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/__init__.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/reduction.py -> build/lib.linux-x86_64-3.7/pycuda
creating build/lib.linux-x86_64-3.7/pycuda/gl
copying pycuda/gl/autoinit.py -> build/lib.linux-x86_64-3.7/pycuda/gl
copying pycuda/gl/__init__.py -> build/lib.linux-x86_64-3.7/pycuda/gl
creating build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/operator.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/pkt_build.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/cg.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/packeted.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/coordinate.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/inner.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/__init__.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
creating build/lib.linux-x86_64-3.7/pycuda/compyte
copying pycuda/compyte/__init__.py -> build/lib.linux-x86_64-3.7/pycuda/compyte
copying pycuda/compyte/dtypes.py -> build/lib.linux-x86_64-3.7/pycuda/compyte
copying pycuda/compyte/array.py -> build/lib.linux-x86_64-3.7/pycuda/compyte
running egg_info
writing pycuda.egg-info/PKG-INFO
writing dependency_links to pycuda.egg-info/dependency_links.txt
writing requirements to pycuda.egg-info/requires.txt
writing top-level names to pycuda.egg-info/top_level.txt
reading manifest file 'pycuda.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'doc/source/_static/*.css'
warning: no files found matching 'doc/source/_templates/*.html'
warning: no files found matching '*.cpp' under directory 'bpl-subset/bpl_subset/boost'
warning: no files found matching '*.html' under directory 'bpl-subset/bpl_subset/boost'
warning: no files found matching '*.inl' under directory 'bpl-subset/bpl_subset/boost'
warning: no files found matching '*.txt' under directory 'bpl-subset/bpl_subset/boost'
warning: no files found matching '*.h' under directory 'bpl-subset/bpl_subset/libs'
warning: no files found matching '*.ipp' under directory 'bpl-subset/bpl_subset/libs'
warning: no files found matching '*.pl' under directory 'bpl-subset/bpl_subset/libs'
writing manifest file 'pycuda.egg-info/SOURCES.txt'
creating build/lib.linux-x86_64-3.7/pycuda/cuda
copying pycuda/cuda/pycuda-complex-impl.hpp -> build/lib.linux-x86_64-3.7/pycuda/cuda
copying pycuda/cuda/pycuda-complex.hpp -> build/lib.linux-x86_64-3.7/pycuda/cuda
copying pycuda/cuda/pycuda-helpers.hpp -> build/lib.linux-x86_64-3.7/pycuda/cuda
copying pycuda/sparse/pkt_build_cython.pyx -> build/lib.linux-x86_64-3.7/pycuda/sparse
running build_ext
building '_driver' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/src
creating build/temp.linux-x86_64-3.7/src/cpp
creating build/temp.linux-x86_64-3.7/src/wrapper
creating build/temp.linux-x86_64-3.7/bpl-subset
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/python
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/python/src
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/python/src/converter
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/python/src/object
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/smart_ptr
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/smart_ptr/src
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/system
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/system/src
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/thread
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/thread/src
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/thread/src/pthread
gcc -pthread -B /home/amax/software/cryosparcnew/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -fwrapv -Wall -O3 -DNDEBUG -fPIC -DBOOST_ALL_NO_LIB=1 -DBOOST_THREAD_BUILD_DLL=1 -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION=1 -DBOOST_PYTHON_SOURCE=1 -Dboost=pycudaboost -DBOOST_THREAD_DONT_USE_CHRONO=1 -DPYGPU_PACKAGE=pycuda -DPYGPU_PYCUDA=1 -DHAVE_CURAND=1 -Isrc/cpp -Ibpl-subset/bpl_subset -I/usr/local/cuda-11/include -I/home/amax/software/cryosparcnew/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/numpy/core/include -I/home/amax/software/cryosparcnew/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/include/python3.7m -c src/cpp/cuda.cpp -o build/temp.linux-x86_64-3.7/src/cpp/cuda.o
In file included from src/cpp/cuda.cpp:4:0:
src/cpp/cuda.hpp:14:18: fatal error: cuda.h: No such file or directory
#include <cuda.h>
^
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/amax/software/cryosparcnew/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-esltad_h/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-esltad_h/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-record-ziy4avib/install-record.txt --single-version-externally-managed --compile --install-headers /home/amax/software/cryosparcnew/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/include/python3.7m/pycuda Check the logs for full command output.
I am having a very similar issue (see below).
Did you ever happen to find a fix for this?
------------------------------------------------------------------------
Preparing to install all pip packages...
------------------------------------------------------------------------
Processing ./deps_bundle/python/python_packages/pip_packages/pycuda-2020.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/scikit_cuda-0.5.3-py2.py3-none-any.whl
Skipping wheel build for pycuda, due to binaries being disabled for it.
Installing collected packages: scikit-cuda, pycuda
Running setup.py install for pycuda ... error
ERROR: Command errored out with exit status 1:
command: /home/nick/CryoSPARC/installation/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-nwq5dreu/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-nwq5dreu/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-record-0io9t3rj/install-record.txt --single-version-externally-managed --compile --install-headers /home/nick/CryoSPARC/installation/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/include/python3.7m/pycuda
cwd: /tmp/pip-req-build-nwq5dreu/
Complete output (99 lines):
*************************************************************
*** I have detected that you have not run configure.py.
*************************************************************
*** Additionally, no global config files were found.
*** I will go ahead with the default configuration.
*** In all likelihood, this will not work out.
***
*** See README_SETUP.txt for more information.
***
*** If the build does fail, just re-run configure.py with the
*** correct arguments, and then retry. Good luck!
*************************************************************
*** HIT Ctrl-C NOW IF THIS IS NOT WHAT YOU WANT
*************************************************************
Continuing in 1 seconds...
/home/nick/CryoSPARC/installation/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'test_requires'
warnings.warn(msg)
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/pycuda
copying pycuda/_mymako.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/elementwise.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/compiler.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/tools.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/scan.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/debug.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/cumath.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/reduction.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/autoinit.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/gpuarray.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/_cluda.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/curandom.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/driver.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/__init__.py -> build/lib.linux-x86_64-3.7/pycuda
copying pycuda/characterize.py -> build/lib.linux-x86_64-3.7/pycuda
creating build/lib.linux-x86_64-3.7/pycuda/gl
copying pycuda/gl/autoinit.py -> build/lib.linux-x86_64-3.7/pycuda/gl
copying pycuda/gl/__init__.py -> build/lib.linux-x86_64-3.7/pycuda/gl
creating build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/inner.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/cg.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/operator.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/packeted.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/__init__.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/pkt_build.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
copying pycuda/sparse/coordinate.py -> build/lib.linux-x86_64-3.7/pycuda/sparse
creating build/lib.linux-x86_64-3.7/pycuda/compyte
copying pycuda/compyte/dtypes.py -> build/lib.linux-x86_64-3.7/pycuda/compyte
copying pycuda/compyte/array.py -> build/lib.linux-x86_64-3.7/pycuda/compyte
copying pycuda/compyte/__init__.py -> build/lib.linux-x86_64-3.7/pycuda/compyte
running egg_info
writing pycuda.egg-info/PKG-INFO
writing dependency_links to pycuda.egg-info/dependency_links.txt
writing requirements to pycuda.egg-info/requires.txt
writing top-level names to pycuda.egg-info/top_level.txt
reading manifest file 'pycuda.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'doc/source/_static/*.css'
warning: no files found matching 'doc/source/_templates/*.html'
warning: no files found matching '*.cpp' under directory 'bpl-subset/bpl_subset/boost'
warning: no files found matching '*.html' under directory 'bpl-subset/bpl_subset/boost'
warning: no files found matching '*.inl' under directory 'bpl-subset/bpl_subset/boost'
warning: no files found matching '*.txt' under directory 'bpl-subset/bpl_subset/boost'
warning: no files found matching '*.h' under directory 'bpl-subset/bpl_subset/libs'
warning: no files found matching '*.ipp' under directory 'bpl-subset/bpl_subset/libs'
warning: no files found matching '*.pl' under directory 'bpl-subset/bpl_subset/libs'
writing manifest file 'pycuda.egg-info/SOURCES.txt'
creating build/lib.linux-x86_64-3.7/pycuda/cuda
copying pycuda/cuda/pycuda-complex-impl.hpp -> build/lib.linux-x86_64-3.7/pycuda/cuda
copying pycuda/cuda/pycuda-complex.hpp -> build/lib.linux-x86_64-3.7/pycuda/cuda
copying pycuda/cuda/pycuda-helpers.hpp -> build/lib.linux-x86_64-3.7/pycuda/cuda
copying pycuda/sparse/pkt_build_cython.pyx -> build/lib.linux-x86_64-3.7/pycuda/sparse
running build_ext
building '_driver' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/src
creating build/temp.linux-x86_64-3.7/src/cpp
creating build/temp.linux-x86_64-3.7/src/wrapper
creating build/temp.linux-x86_64-3.7/bpl-subset
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/python
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/python/src
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/python/src/object
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/python/src/converter
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/system
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/system/src
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/smart_ptr
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/smart_ptr/src
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/thread
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/thread/src
creating build/temp.linux-x86_64-3.7/bpl-subset/bpl_subset/libs/thread/src/pthread
gcc -pthread -B /home/nick/CryoSPARC/installation/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -fwrapv -Wall -O3 -DNDEBUG -fPIC -DBOOST_ALL_NO_LIB=1 -DBOOST_THREAD_BUILD_DLL=1 -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION=1 -DBOOST_PYTHON_SOURCE=1 -Dboost=pycudaboost -DBOOST_THREAD_DONT_USE_CHRONO=1 -DPYGPU_PACKAGE=pycuda -DPYGPU_PYCUDA=1 -DHAVE_CURAND=1 -Isrc/cpp -Ibpl-subset/bpl_subset -I/usr/local/cuda/include -I/home/nick/CryoSPARC/installation/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/numpy/core/include -I/home/nick/CryoSPARC/installation/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/include/python3.7m -c src/cpp/cuda.cpp -o build/temp.linux-x86_64-3.7/src/cpp/cuda.o
gcc: fatal error: cannot execute ‘cc1plus’: execvp: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/nick/CryoSPARC/installation/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-nwq5dreu/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-nwq5dreu/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-record-0io9t3rj/install-record.txt --single-version-externally-managed --compile --install-headers /home/nick/CryoSPARC/installation/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/include/python3.7m/pycuda Check the logs for full command output.