Hello everyone,
I have installed Openmdao, pyOpt and pyoptsparse on my computer. As my program works with the Scipy optimizer, I tried it with a random optimizer of pyoptsparse (that was 'ALPSO'). It worked and I was happy. But it turns out it seems to be the only one working.
Every time I try to use another one (like 'SLSQP', which is the default optimizer !), i get this message "pyOptSparse Error : There was an error importing the compiled SLSQP module", inside a frame made of '-' and '+'.
Does anybody know what to do ? I am using Ubuntu if it changes something.
Thanks to swryan for the link, i found the answer.
One of the possible answer was to put libgfortran.so.3 in anaconda2/lib, but i already had it.
They were also saying the problem was solved when installing anaconda 4.0+ but i also had the latest version.
What worked for me was to run : conda update libgfortran --force
Doing it without the --force retrogrades the scipy, which seems to disable scipy.optimize.least_squares. If you did that, you can then run conda update scipy --force
Did you get any errors when you ran 'python setup.py install' for pyoptsparse? I looked at the setup.py file for pyoptsparse and there are some instructions in there that you could try:
print("\nTo install, run: python setup.py install --user\n\n"
"To build, run: python setup.py build_ext --inplace\n\n"
"For help on C-compiler options run: python setup.py build --help-compiler\n\n"
"For help on Fortran-compiler options run: python setup.py build --help-fcompiler\n\n"
"To specify a Fortran compiler to use run: python setup.py install --user --fcompiler=<fcompiler name>\n\n"
"For further help run: python setup.py build --help"
)
Related
I've read a lot of posts about this but none of the solutions have worked for me. I'm trying to get a module called nsxramlclient installed, shows successful installation with pip but cannot import from any location outside of the /Users/Nathan/Library/Python/2.7/lib/python/site-packages.
Uninstall does work after some fidgeting with brew using the recommendations found with brew doctor. Here are some vitals:
Running OSX python 2.7.10
PIP 18.1
which -a pip = /usr/local/bin/pip
which -a python = shows 2 directories:
/usr/local/bin/python
/usr/bin/python
python -c 'import sys; print(sys.path)'
['', '/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python27.zip', '/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7', '/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin', '/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac', '/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages', '/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk', '/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old', '/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload']
pip list | grep nsxramlclient
nsxramlclient 2.0.7
It has to be a path issue since I'm able to import it from the directory that the module is located. I just don't know the proper method to repair this since I'm fairly new to Python and I don't want to mess it up worse that it is already.
Looks like I did end up getting it to work finally. What I had to do was to re-install python with brew:
brew re-install python#2
then I needed to re-install the modules I needed with pip. Having OTHER issues now but at least this one is fixed.
hopefully this question fits here, I have tried googling and reading "http://pyqt.sourceforge.net/Docs/PyQt4/installation.html" but unfortunately I'm such a newbie in all things linux that I cannot figure out what applies here...
anyway:
I have a virtual env (in Python 2.7)
I am trying to set up labelImg as instructed in : https://github.com/tzutalin/labelImg, specifically I run (with my virtualenv active):
sudo apt-get install pyqt4-dev-tools
sudo pip install lxml (<- did run this as "pip install lxml")
Then I run into problems with this:
make qt4py2
I got error:
"make: *** No rule to make target 'qt4py2'. Stop."
Now from googling I got the impression that I should be in the same directory as the make file when I run make (is this even true?), but when I try to find where pyqt4 is, I cannot find the folder (it is not in ~/.virtualenvs/virP2/lib/python2.7/site-packages$ (virP2 is the name of the virtualenv)
I have also tried to run (with the virP2 still active)
sudo apt-get install python-qt4
but I got:
"python-qt4 is already the newest version"
and I still cannot find where the directory with qt4 files is. (I also looked into the python2.7 folder outside the virtualenv, but it was not there)
Thanks for any advice!
I am attempting to install PyMC using pip install pymc. I believe this command should install PyMC 2.3.6.
PyMC has a few dependencies, which I have in my PATH. I am running OSX 10.11.2 and my PATH includes Python 2.7.13, NumPy 1.12.0, Matplotlib 2.0.0, gcc, and gfortran.
Python (including pip) was installed using Homebrew. NumPy and Matplotlib were installed using pip. The gfortran compiler was downloaded and installed from the GCC Wiki for the purpose of this installation.
Executing pip install pymc yielded lots of output including the following lines.
Collecting pymc
Using cached pymc-2.3.6.tar.gz
Complete output from command python setup.py egg_info:
running egg_info
running build_src
build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
f2py:> build/src.macosx-10.11-x86_64-2.7/pymc/flibmodule.c
creating build
creating build/src.macosx-10.11-x86_64-2.7
creating build/src.macosx-10.11-x86_64-2.7/pymc
IOError: [Errno 2] No such file or directory: 'skip:ppnd7'. Skipping file "skip:ppnd7".
updatevars:gradlike: attempt to change 'dimension(nx)' to 'dimension(na)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension(nx)' to 'dimension(nb)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension (nmu)' to 'dimension(nmu)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension (na)' to 'dimension(na)'. Ignoring.
rmbadname1: Replacing "index" with "index_bn".
Reading fortran codes...
Reading file 'pymc/flib.f' (format:fix,strict)
Line #34 in pymc/flib.f:" PARAMETER (infinity = 1.7976931348623157d308)"
get_parameters: got "unexpected EOF while parsing (<string>, line 0)" on ''
...
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/2f/cr97n5v93mn04c3qbqd7r3q40000gn/T/pip-build-6Zmgcz/pymc/setup.py", line 124, in <module>
**(config_dict))
File "/usr/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
...
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/2f/cr97n5v93mn04c3qbqd7r3q40000gn/T/pip-build-6Zmgcz/pymc/
As suggested in these two pip installation threads about egg_info errors [1, 2], I ran pip install —upgrade setuptools and pip install ez_setup. Once these items were installed I ran into the same types of errors pasted above.
As noted in other package installation threads, I am willing to use conda to install PyMC if I cannot resolve these issues. However, I'd like to investigate this installation issue first.
Would anyone happen to know what my issue is here? Might there be some steps I can take to successfully install PyMC using pip?
I had the same problem. I don't understand the root cause, but I fixed it by downgrading numpy to version 1.10.1: pip install numpy==1.10.1
I also met this problem while trying to install pymc from pip or source code, but I found a solution that might be useful.
The reason that causes the problem might be the file setup.py, in which the script check the compile env. I didn't read the code very carefully, but in the function build_ext() I think the codes first check whether some compile environments have already been installed into OS. If installed, the script will use them as defaults; if not, use ones in somewhere else (the comment says 'from netlib sources').
I infer the problem is caused by the compile environments that have already been installed in the OS, so I modify the file setup.py to skip this part of codes, and let the script use the netlib source. Then I run sudo python setup.py install. There are some error and warning messages, but the folder 'pymc' emerges in python library, and some simple test codes run successfully.
I am building a python package, and I want to distribute it via rpm using python setup.py bdist_rpm. However, I am including a configuration file, and I want any changes in there to remain if I ever upgrade the RPM on the machine it's installed on. Is there anyway to set a flag in the setup.py script or command that I don't want the RPM to replace the configuration file in case of upgrades? I'm on Python 2.7. Thanks!
python setup.py bdist_rpm --spec-only
This will create dist/*.spec, manually edit it. Especially change:
%install
python setup.py install --single-version-externally-managed -O1 --root=$RPM_BUILD_ROOT --record=INSTALLED_FILES
%files -f INSTALLED_FILES
to:
%install
python setup.py install --single-version-externally-managed -O1 --root=$RPM_BUILD_ROOT
%files
%{python_sitelib}/*
%config(noreplace) %{_sysconfdir}/yourconfig.conf
Note: you may add more lines to %files section, it depends what you put in buildroot. If you miss something rpmbuild from next step will report it as error.
Then you can build the SRPM using
rpmbuild -bs dist/*.spec
More resources can be found here:
https://fedoraproject.org/wiki/Packaging:Python
https://fedoraproject.org/wiki/How_to_create_an_RPM_package
I installed python 2.7.5 which is working fine.
I then install scrapy (which, I think, uses twisted internally). My scrapy spider is also working fine.
I installed twisted:
sudo apt-get install python-twisted
Then, I created a sample program using Echo Server code shown here
Here is the code
from twisted.internet import protocol, reactor
class Echo(protocol.Protocol):
def dataReceived(self, data):
self.transport.write(data)
class EchoFactory(protocol.Factory):
def buildProtocol(self, addr):
return Echo()
reactor.listenTCP(1234, EchoFactory())
reactor.run()
I try to run this code using this command:
$ python twistedTester.py
Traceback (most recent call last):
File "twistedTester.py", line 1, in <module>
from twisted.internet import protocol, reactor
ImportError: No module named twisted.internet
Can anyone help me with how I can debug why my twisted package is not being picked up by Python installation?
If you use pip just try:
pip install twisted
The same works with w3lib and lxml.
On some *nix systems this might give you a permission error. If that happens, try:
sudo -H pip install twisted
I figured out why this error was happening. For some reason, using apt-get to install a python package was not installing it right.
So, I had to download a tar ball and install the package from them.
I downloaded Twisted tar from here.
I did a tar xjf Twisted-13.1.0.tar.bz2 - this created a directory called Twisted-13.1.0
next, cd Twisted-13.1.0
Finally, python setup.py install
This gave me an error. Twisted required another package called zope.interface. So, I downloaded tar ball for zope.interface from here. Then, ran this command tar xzf zope.interface-3.6.1.tar.gz That created a folder called zope.interface-3.6.1. So, cd into zope.interface-3.6.1 and run python setup.py install
Note: Depending on your user's rights, you may want to do these commands in sudo mode. Just add the keyword sudo before every command.
please rename the file twisted.py to something else. whenever you import a function from a file the interpreter will search for the file in the current location and then it searches in the library. so if you have any file in the name of "twisted.py" you should probably rename it.
after renaming it. dont fail to remove the twisted.pyc file before running it again.
It happened to me too. Finally I figure out that there is a file named twisted.py my present working directory. I removed twisted.py and twisted.pyc. Problem resolved.
Looks like Twisted may have removed the twisted.internet module from the current release. Pinning on the version required by scrapy (17.9.0) worked for me:
$ pip install twisted==17.9.0
Checking if it's installed:
$ python -c "import twisted.internet; print(twisted.internet)"
<module 'twisted.internet' from '/Users/username/dev/env/redacted-ewmlD2h2/lib/python3.7/site-packages/twisted/internet/__init__.py'>
I figured out why apt-get install python-twisted was not enough or "installing it right", as you said, user1700184.
I use Debian Wheezy and Python 2.7.
I just had to move the folder named "twisted" from /usr/lib/python2.7/dist-packages/ to /usr/lib/python2.7/
The same has to be done with the package "zope" and any other one that you do install but is not retrieved when you try run your code.
However, why this is even necessary in my case is still a mystery since my sys.path does include both /usr/lib/python2.7/ and /usr/lib/python2.7/dist-packages, so whatever was under dist-packages should have been retrieved by the interpreter.
I think it is worth noting that if you use sudo to launch python you are using your original default system python. This is NOT the python that your PATH points to. For example if you are using Anaconda and you have updated your path such that which python points to path/to/anaconda/bin/python, sudo which python will still point to usr/bin/python.
So obviously sudo python twistedTester.py will not find the twisted module. To get around this you should explicitly pass the path to the anaconda python. Like so:
sudo path/to/anaconda/bin/python twistedTester.py