Hi I met a problem when I am trying to install dnabert env.
linnabrown opened this issue · comments
Running setup.py install for apex ... error
ERROR: Command errored out with exit status 1: /nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-4x23nl6p/setup.py'"'"'; file='"'"'/tmp/pip-req-build-4x23nl6p/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' --cpp_ext --cuda_ext install --record /tmp/pip-record-elj3n3dy/install-record.txt --single-version-externally-managed --compile --install-headers /nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/include/python3.6m/apex Check the logs for full command output.
Exception information:
Traceback (most recent call last):
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/req/req_install.py", line 854, in install
req_description=str(self.req),
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/operations/install/legacy.py", line 86, in install
raise LegacyInstallFailure
pip._internal.operations.install.legacy.LegacyInstallFailure
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 224, in _main
status = self.run(options, args)
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/cli/req_command.py", line 180, in wrapper
return func(self, options, args)
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 403, in run
pycompile=options.compile,
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/req/init.py", line 90, in install_given_reqs
pycompile=pycompile,
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/req/req_install.py", line 858, in install
six.reraise(*exc.parent)
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_vendor/six.py", line 703, in reraise
raise value
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/operations/install/legacy.py", line 76, in install
cwd=unpacked_source_directory,
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/utils/subprocess.py", line 275, in runner
spinner=spinner,
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/utils/subprocess.py", line 240, in call_subprocess
raise InstallationError(exc_msg)
pip._internal.exceptions.InstallationError: Command errored out with exit status 1: /nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-4x23nl6p/setup.py'"'"'; file='"'"'/tmp/pip-req-build-4x23nl6p/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' --cpp_ext --cuda_ext install --record /tmp/pip-record-elj3n3dy/install-record.txt --single-version-externally-managed --compile --install-headers /nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/include/python3.6m/apex Check the logs for full command output.
1 location(s) to search for versions of pip:
- https://pypi.org/simple/pip/
Fetching project page and analyzing links: https://pypi.org/simple/pip/
Getting page https://pypi.org/simple/pip/
Found index url https://pypi.org/simple
Starting new HTTPS connection (1): pypi.org:443
https://pypi.org:443 "GET /simple/pip/ HTTP/1.1" 200 15763
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Given no hashes to check 159 links for project 'pip': discarding no candidates
Removed build tracker: '/tmp/pip-req-tracker-yu_hhhai'
There are always many problems when installing this package. I assume these problems result from the mismatch of your local cuda version / NCCL version and cudatoolkit version. A possible solution is to install the python-only version as described on the apex github repo.
Thank you for your response. I figured it out!
Running setup.py install for apex ... error
ERROR: Command errored out with exit status 1: /nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-4x23nl6p/setup.py'"'"'; file='"'"'/tmp/pip-req-build-4x23nl6p/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' --cpp_ext --cuda_ext install --record /tmp/pip-record-elj3n3dy/install-record.txt --single-version-externally-managed --compile --install-headers /nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/include/python3.6m/apex Check the logs for full command output.
Exception information:
Traceback (most recent call last):
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/req/req_install.py", line 854, in install
req_description=str(self.req),
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/operations/install/legacy.py", line 86, in install
raise LegacyInstallFailure
pip._internal.operations.install.legacy.LegacyInstallFailureDuring handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 224, in _main
status = self.run(options, args)
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/cli/req_command.py", line 180, in wrapper
return func(self, options, args)
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 403, in run
pycompile=options.compile,
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/req/init.py", line 90, in install_given_reqs
pycompile=pycompile,
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/req/req_install.py", line 858, in install
six.reraise(*exc.parent)
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_vendor/six.py", line 703, in reraise
raise value
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/operations/install/legacy.py", line 76, in install
cwd=unpacked_source_directory,
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/utils/subprocess.py", line 275, in runner
spinner=spinner,
File "/nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/lib/python3.6/site-packages/pip/_internal/utils/subprocess.py", line 240, in call_subprocess
raise InstallationError(exc_msg)
pip._internal.exceptions.InstallationError: Command errored out with exit status 1: /nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-4x23nl6p/setup.py'"'"'; file='"'"'/tmp/pip-req-build-4x23nl6p/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' --cpp_ext --cuda_ext install --record /tmp/pip-record-elj3n3dy/install-record.txt --single-version-externally-managed --compile --install-headers /nas/longleaf/home/lehuang/tool/anaconda/envs/dnabert/include/python3.6m/apex Check the logs for full command output.
1 location(s) to search for versions of pip:
- https://pypi.org/simple/pip/
Fetching project page and analyzing links: https://pypi.org/simple/pip/
Getting page https://pypi.org/simple/pip/
Found index url https://pypi.org/simple
Starting new HTTPS connection (1): pypi.org:443
https://pypi.org:443 "GET /simple/pip/ HTTP/1.1" 200 15763
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Given no hashes to check 159 links for project 'pip': discarding no candidates
Removed build tracker: '/tmp/pip-req-tracker-yu_hhhai'
I also meet the error when i use cudatoolkit=10.2 not 10.0, so i must use 10.0 version ?
Yes, you must make sure the version of cudatoolkit and your local cuda is the same. Please refer to this issue for more details. NVIDIA/apex#550
Closed.