cryoem@myrdal:~/cryosparc2/cryosparc_worker$ command -v gcc
/usr/bin/gcc
cryoem@myrdal:~/cryosparc2/cryosparc_worker$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.4.0-1ubuntu1~20.04.1' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-Av3uEd/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 9.4.0 (Ubuntu 9.4.0-1ubuntu1~20.04.1)
cryoem@myrdal:~/cryosparc2/cryosparc_worker$ command -v g++
/usr/bin/g++
cryoem@myrdal:~/cryosparc2/cryosparc_worker$ g++ -v
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.4.0-1ubuntu1~20.04.1' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-Av3uEd/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 9.4.0 (Ubuntu 9.4.0-1ubuntu1~20.04.1)
cryoem@myrdal:~/cryosparc2/cryosparc_worker$ type nvcc
nvcc is /usr/bin/nvcc
cryoem@myrdal:~/cryosparc2/cryosparc_worker$ nvcc -V
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2019 NVIDIA Corporation
Built on Sun_Jul_28_19:07:16_PDT_2019
Cuda compilation tools, release 10.1, V10.1.243
``
`cryoem@myrdal:~/cryosparc2/cryosparc_worker$ ./bin/cryosparcw install-3dflex 2>&1 |tee install-3dflex.log
Installing 3D Flex Refine dependencies…
Collecting package metadata (current_repodata.json): …working… done
Solving environment: …working… failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): …working… done
Solving environment: …working… done
Package Plan
environment location: /home/cryoem/cryosparc2/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env
added / updated specs:
- cuda-nvcc=11.7
- cuda-toolkit=11.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2022.10.11 | h06a4308_0 124 KB
certifi-2022.9.24 | py37h06a4308_0 154 KB
…
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 22.11.1
Please update conda by running
$ conda update -n base -c defaults conda
Found existing installation: pycuda 2020.1
Uninstalling pycuda-2020.1:
Successfully uninstalled pycuda-2020.1
Collecting torch
Using cached torch-1.13.0-cp37-cp37m-manylinux1_x86_64.whl (890.2 MB)
Collecting ninja
Using cached ninja-1.11.1-py2.py3-none-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (145 kB)
Collecting nvidia-cuda-runtime-cu11==11.7.99
Using cached nvidia_cuda_runtime_cu11-11.7.99-py3-none-manylinux1_x86_64.whl (849 kB)
Collecting nvidia-cublas-cu11==11.10.3.66
Using cached nvidia_cublas_cu11-11.10.3.66-py3-none-manylinux1_x86_64.whl (317.1 MB)
Collecting nvidia-cuda-nvrtc-cu11==11.7.99
Using cached nvidia_cuda_nvrtc_cu11-11.7.99-2-py3-none-manylinux1_x86_64.whl (21.0 MB)
Requirement already satisfied: typing-extensions in ./deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages (from torch) (3.7.4.3)
Collecting nvidia-cudnn-cu11==8.5.0.96
Using cached nvidia_cudnn_cu11-8.5.0.96-2-py3-none-manylinux1_x86_64.whl (557.1 MB)
Requirement already satisfied: wheel in ./deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch) (0.38.4)
Requirement already satisfied: setuptools in ./deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch) (59.8.0)
Installing collected packages: nvidia-cublas-cu11, nvidia-cudnn-cu11, nvidia-cuda-runtime-cu11, nvidia-cuda-nvrtc-cu11, torch, ninja
Successfully installed ninja-1.11.1 nvidia-cublas-cu11-11.10.3.66 nvidia-cuda-nvrtc-cu11-11.7.99 nvidia-cuda-runtime-cu11-11.7.99 nvidia-cudnn-cu11-8.5.0.96 torch-1.13.0
Processing ./deps_bundle/python/python_packages/pip_packages/pycuda-2020.1.tar.gz
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status ‘done’
Requirement already satisfied: pytools>=2011.2 in ./deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages (from pycuda==2020.1) (2020.4.4)
Requirement already satisfied: decorator>=3.2.0 in ./deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages (from pycuda==2020.1) (4.4.2)
Requirement already satisfied: appdirs>=1.4.0 in ./deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages (from pycuda==2020.1) (1.4.4)
Requirement already satisfied: mako in ./deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages (from pycuda==2020.1) (1.1.6)
Requirement already satisfied: numpy>=1.6.0 in ./deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages (from pytools>=2011.2->pycuda==2020.1) (1.19.5)
Requirement already satisfied: MarkupSafe>=0.9.2 in ./deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages (from mako->pycuda==2020.1) (2.0.1)
Building wheels for collected packages: pycuda
…
from src/wrapper/wrap_cudadrv.cpp:3:
bpl-subset/bpl_subset/boost/function/function_base.hpp: In instantiation of ‘static void pycudaboost::detail::function::functor_manager_common::manage_small(const pycudaboost::detail::function::function_buffer&, pycudaboost::detail::function::function_buffer&, pycudaboost::detail::function::functor_manager_operation_type) [with Functor = pycudaboost::bi::bind_t<bool, pycudaboost::python::detail::translate_exception<pycuda::error, void ()(const pycuda::error&)>, pycudaboost::_bi::list3<pycudaboost::arg<1>, pycudaboost::arg<2>, pycudaboost::_bi::value<void ()(const pycuda::error&)> > >]’:
bpl-subset/bpl_subset/boost/function/function_base.hpp:364:56: required from ‘static void pycudaboost::detail::function::functor_manager::manager(const pycudaboost::detail::function::function_buffer&, pycudaboost::detail::function::function_buffer&, pycudaboost::detail::function::functor_manager_operation_type, mpl::true_) [with Functor = pycudaboost::bi::bind_t<bool, pycudaboost::python::detail::translate_exception<pycuda::error, void ()(const pycuda::error&)>, pycudaboost::_bi::list3<pycudaboost::arg<1>, pycudaboost::arg<2>, pycudaboost::_bi::value<void ()(const pycuda::error&)> > >; mpl::true_ = mpl_::bool_]’
bpl-subset/bpl_subset/boost/function/function_base.hpp:412:18: required from ‘static void pycudaboost::detail::function::functor_manager::manager(const pycudaboost::detail::function::function_buffer&, pycudaboost::detail::function::function_buffer&, pycudaboost::detail::function::functor_manager_operation_type, pycudaboost::detail::function::function_obj_tag) [with Functor = pycudaboost::_bi::bind_t<bool, pycudaboost::python::detail::translate_exception<pycuda::error, void ()(const pycuda::error&)>, pycudaboost::_bi::list3<pycudaboost::arg<1>, pycudaboost::arg<2>, pycudaboost::_bi::value<void ()(const pycuda::error&)> > >]’
bpl-subset/bpl_subset/boost/function/function_base.hpp:440:20: required from ‘static void pycudaboost::detail::function::functor_manager::manage(const pycudaboost::detail::function::function_buffer&, pycudaboost::detail::function::function_buffer&, pycudaboost::detail::function::functor_manager_operation_type) [with Functor = pycudaboost::_bi::bind_t<bool, pycudaboost::python::detail::translate_exception<pycuda::error, void ()(const pycuda::error&)>, pycudaboost::_bi::list3<pycudaboost::arg<1>, pycudaboost::arg<2>, pycudaboost::_bi::value<void ()(const pycuda::error&)> > >]’
bpl-subset/bpl_subset/boost/function/function_template.hpp:934:13: required from ‘void pycudaboost::function2<R, T1, T2>::assign_to(Functor) [with Functor = pycudaboost::_bi::bind_t<bool, pycudaboost::python::detail::translate_exception<pycuda::error, void ()(const pycuda::error&)>, pycudaboost::_bi::list3<pycudaboost::arg<1>, pycudaboost::arg<2>, pycudaboost::_bi::value<void ()(const pycuda::error&)> > >; R = bool; T0 = const pycudaboost::python::detail::exception_handler&; T1 = const pycudaboost::function0&]’
bpl-subset/bpl_subset/boost/function/function_template.hpp:722:7: required from ‘pycudaboost::function2<R, T1, T2>::function2(Functor, typename pycudaboost::enable_if_c<pycudaboost::type_traits::ice_not<pycudaboost::is_integral::value>::value, int>::type) [with Functor = pycudaboost::_bi::bind_t<bool, pycudaboost::python::detail::translate_exception<pycuda::error, void ()(const pycuda::error&)>, pycudaboost::_bi::list3<pycudaboost::arg<1>, pycudaboost::arg<2>, pycudaboost::_bi::value<void ()(const pycuda::error&)> > >; R = bool; T0 = const pycudaboost::python::detail::exception_handler&; T1 = const pycudaboost::function0&; typename pycudaboost::enable_if_c<pycudaboost::type_traits::ice_not<pycudaboost::is_integral::value>::value, int>::type = int]’
bpl-subset/bpl_subset/boost/python/exception_translator.hpp:20:39: required from ‘void pycudaboost::python::register_exception_translator(Translate, pycudaboost::type) [with ExceptionType = pycuda::error; Translate = void ()(const pycuda::error&)]’
src/wrapper/wrap_cudadrv.cpp:691:74: required from here
bpl-subset/bpl_subset/boost/function/function_base.hpp:318:54: warning: placement new constructing an object of type ‘pycudaboost::detail::function::functor_manager_common<pycudaboost::_bi::bind_t<bool, pycudaboost::python::detail::translate_exception<pycuda::error, void ()(const pycuda::error&)>, pycudaboost::_bi::list3<pycudaboost::arg<1>, pycudaboost::arg<2>, pycudaboost::_bi::value<void ()(const pycuda::error&)> > > >::functor_type’ {aka ‘pycudaboost::_bi::bind_t<bool, pycudaboost::python::detail::translate_exception<pycuda::error, void ()(const pycuda::error&)>, pycudaboost::_bi::list3<pycudaboost::arg<1>, pycudaboost::arg<2>, pycudaboost::_bi::value<void ()(const pycuda::error&)> > >’} and size ‘16’ in a region of type ‘char’ and size ‘1’ [-Wplacement-new=]
318 | new (reinterpret_cast<void*>(&out_buffer.data)) functor_type(*in_functor);
| ~~~~~~~~~^~
error: command ‘gcc’ failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/cryoem/cryosparc2/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/python3.7 -u -c ‘import io, os, sys, setuptools, tokenize; sys.argv[0] = ‘"’"’/tmp/pip-req-build-ekqwfvqg/setup.py’"’"’; file=’"’"’/tmp/pip-req-build-ekqwfvqg/setup.py’"’"’;f = getattr(tokenize, ‘"’"‘open’"’"’, open)(file) if os.path.exists(file) else io.StringIO(’"’"‘from setuptools import setup; setup()’"’"’);code = f.read().replace(’"’"’\r\n’"’"’, ‘"’"’\n’"’"’);f.close();exec(compile(code, file, ‘"’"‘exec’"’"’))’ install --record /tmp/pip-record-5nd9kgf0/install-record.txt --single-version-externally-managed --compile --install-headers /home/cryoem/cryosparc2/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/include/python3.7m/pycuda Check the logs for full command output.