I was having trouble installing a package (plumed) using pip3.6. Specifically, with the command pip3.6 install --user plumed, I got the following error:
Collecting plumed
Using cached plumed-2.6.1.tar.gz (189 kB)
Building wheels for collected packages: plumed
Building wheel for plumed (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-cnvim96k/plumed/setup.py'"'"'; __file__='"'"'/tmp/pip-install-cnvim96k/plumed/setup.py'"'"';f=getattr(tokenize,
'"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-js3bt49u
cwd: /tmp/pip-install-cnvim96k/plumed/
Complete output (17 lines):
Module name plumed
Version number 2.6.1
using available plumed.cpp file
running bdist_wheel
running build
running build_ext
building 'plumed' extension
creating build
creating build/temp.linux-x86_64-3.6
/home/wei-tse/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/wei-tse/anaconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/wei-tse/anaconda3/include -fPIC -I./include -I/usr/include/python3.6m -c plumed.cpp -o build/temp.linux-x86_64-3.6/plumed.o -D__PLUMED_HAS_DLOPEN -D__PLUMED_WRAPPER_LINK_RUNTIME=1 -D__PLUMED_WRAPPER_CXX=1 -D__PLUMED_WRAPPER_IMPLEMENTATION=1 -D__PLUMED_WRAPPER_EXTERN=0 -D__PLUMED_WRAPPER_CXX_DEFAULT_INVALID=1
In file included from /usr/include/python3.6m/Python.h:8:0,
from plumed.cpp:31:
/usr/include/python3.6m/pyconfig.h:3:12: fatal error: x86_64-linux-gnu/python3.6m/pyconfig.h: No such file or directory
# include <x86_64-linux-gnu/python3.6m/pyconfig.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command '/home/wei-tse/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for plumed
Running setup.py clean for plumed
Failed to build plumed
Installing collected packages: plumed
Running setup.py install for plumed ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-cnvim96k/plumed/setup.py'"'"'; __file__='"'"'/tmp/pip-install-cnvim96k/plumed/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-5tvrlz45/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/wei-tse/.local/include/python3.6m/plumed
cwd: /tmp/pip-install-cnvim96k/plumed/
Complete output (17 lines):
Module name plumed
Version number 2.6.1
using available plumed.cpp file
running install
running build
running build_ext
building 'plumed' extension
creating build
creating build/temp.linux-x86_64-3.6
/home/wei-tse/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/wei-tse/anaconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/wei-tse/anaconda3/include -fPIC
-I./include -I/usr/include/python3.6m -c plumed.cpp -o build/temp.linux-x86_64-3.6/plumed.o -D__PLUMED_HAS_DLOPEN -D__PLUMED_WRAPPER_LINK_RUNTIME=1 -D__PLUMED_WRAPPER_CXX=1 -D__PLUMED_WRAPPER_IMPLEMENTATION=1 -D__PLUMED_WRAPPER_EXTERN=0 -D__PLUMED_WRAPPER_CXX_DEFAULT_INVALID=1
In file included from /usr/include/python3.6m/Python.h:8:0,
from plumed.cpp:31:
/usr/include/python3.6m/pyconfig.h:3:12: fatal error: x86_64-linux-gnu/python3.6m/pyconfig.h: No such file or directory
# include <x86_64-linux-gnu/python3.6m/pyconfig.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command '/home/wei-tse/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-cnvim96k/plumed/setup.py'"'"'; __file__='"'"'/tmp/pip-install-cnvim96k/plumed/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-5tvrlz45/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/wei-tse/.local/include/python3.6m/plumed Check the logs for full command output.
I know that there are already a lot of relevant discussions on the forum, but none of the solutions worked for me. I've tried the following solutions:
sudo apt-get install python-dev libxml2-dev libxslt-devsudo apt-get install python3.6-devexport CPLUS_INCLUDE_PATH="$CPLUS_INCLUDE_PATH:/usr/include/x86_64-linux-gnu/python3.6m/pyconfig.hThe weird thing is that I hadpyconfig.hin/usr/include/x86_64-linux-gnu/python3.6m/but it couldn't be found when I used pip3.6. I was using Ubuntu 18.04, so the systematic pip was associated with Python 3.6.9. I'm wondering if there is any solution that could deal with this problem. Thanks!
