JustinThanks,What should I do to resolve this?Looking online, it seems that mpi4py keeps pointing to an old (but nonexistent) MPI from my previous ubuntu version (14.04 i believe). I also tried installing from scratch but keep getting this error.Hi all,So I also recently upgraded my Ubuntu to 16.04 but am running into a different error after updated firedrake:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/justin/Software/firedrake/src/firedrake/ firedrake/__init__.py", line 26, in <module>
from pyop2 import op2# noqa
File "/home/justin/Software/firedrake/src/PyOP2/pyop2/__ init__.py", line 9, in <module>
from op2 import * # noqa
File "/home/justin/Software/firedrake/src/PyOP2/pyop2/op2. py", line 38, in <module>
import backends
File "/home/justin/Software/firedrake/src/PyOP2/pyop2/ backends.py", line 42, in <module>
from mpi import collective
File "/home/justin/Software/firedrake/src/PyOP2/pyop2/mpi. py", line 38, in <module>
from mpi4py import MPI # noqa
ImportError: libmpi.so.1: cannot open shared object file: No such file or directoryOn Tue, Jun 28, 2016 at 7:51 AM, Francis Poulin <fpoulin@uwaterloo.ca> wrote:______________________________Hello David,
Sorry for bugging you, clearly not a firedrake problem I agree.
Not sure why but I had a library missing and the following helped me to resolve it by creating a link
http://www.rainlendar.net/cms/index.php?option=com_kunena&It emid=42&func=view&catid=2&id= 21705
Now I am reinstalling firedrake. I imagine things will work better afterwards.
Cheers, Francis
------------------
Francis Poulin
Associate Professor
Department of Applied Mathematics
University of Waterloo
email: fpoulin@uwaterloo.ca
Web: https://uwaterloo.ca/poulin-research-group/
Telephone: +1 519 888 4567 x32637
From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk ] on behalf of David Ham [David.Ham@imperial.ac.uk]
Sent: Tuesday, June 28, 2016 4:45 AM
To: firedrake
Subject: Re: [firedrake] problems updating and running firedrake
Hi Francis,
Please provide the full output, because the following is based on guesswork because I can't see what is going on.
It is true that curl depends on librtmp. If your curl can't find your rtmp, then something is broken on your system. This has nothing to do with Firedrake.
I *think* that the only time you use curl is to download the firedrake-install script. If you really can't unbreak curl on your system then you can obtain this script by any of the usual ways (wget, download it with a web browser etc.)
Regards,
David
On Mon, 27 Jun 2016 at 19:35 Francis Poulin <fpoulin@uwaterloo.ca> wrote:
Hello David,
Thanks for finding that.
I tried a) and that didn't help the update.
I then tried b) and get an curl error, "error while loading shared libraries: librtmp.so.0".
I have done this before but not sure why this is not working now.
Cheers, Francis
------------------
Francis Poulin
Associate Professor
Department of Applied Mathematics
University of Waterloo
email: fpoulin@uwaterloo.ca
Web: https://uwaterloo.ca/poulin-research-group/
Telephone: +1 519 888 4567 x32637
From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk ] on behalf of David Ham [David.Ham@imperial.ac.uk]
Sent: Monday, June 27, 2016 10:48 AM
To: firedrake
Subject: Re: [firedrake] problems updating and running firedrake
Hi Francis,
It looks like you might have hit the issue they describe here:
Basically datetime was apparently rolled into the python binary in a 2.7 point release. I don't know why this was changed but it makes the python binary in your virtualenv incompatible with your system python install.
According to the thread on askubuntu, you have two options.
a) Apparently you can re-initialise the virtualenv by running:
virtualenv .
in your top Firedrake directory. I'm guessing you should do this with the virtualenv deactivated.
or
b) A fresh Firedrake install should work because it will create a fresh virtualenv based on current Python binary.
Regards,
David
On Mon, 27 Jun 2016 at 15:20 Francis Poulin <fpoulin@uwaterloo.ca> wrote:
Hello,
I recently updated my ubuntu from 14.04 to 16.04. I tried running firedrake and it failed.
I also tried updating firedrake and it failed, see below.
Do I need to install it from scratch or should it be possible to update it with a new OS?
Cheers, Francis
Installing pip dependencies for COFFEE
/home/fpoulin/software/firedrake/bin/pip install -r COFFEE/requirements.txt
Traceback (most recent call last):
File "/home/fpoulin/software/firedrake/bin/pip", line 7, in <module>
from pip import main
File "/home/fpoulin/software/firedrake/local/lib/python2.7/site- packages/pip/__init__.py", line 14, in <module>
from pip.utils import get_installed_distributions, get_prog
File "/home/fpoulin/software/firedrake/local/lib/python2.7/site- packages/pip/utils/__init__. py", line 27, in <module>
from pip._vendor import pkg_resources
File "/home/fpoulin/software/firedrake/local/lib/python2.7/site- packages/pip/_vendor/pkg_resou rces/__init__.py", line 36, in <module>
import plistlib
File "/usr/lib/python2.7/plistlib.py", line 62, in <module>
import datetime
ImportError: No module named datetime
Traceback (most recent call last):
File "../bin/firedrake-update", line 974, in <module>
pip_requirements(p)
File "../bin/firedrake-update", line 377, in pip_requirements
run_pip_install(["-r", "%s/requirements.txt" % package])
File "../bin/firedrake-update", line 364, in run_pip_install
check_call(pipinstall + pipargs)
File "../bin/firedrake-update", line 211, in check_call
subprocess.check_call(arguments, env=env)
File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/fpoulin/software/firedrake/bin/pip', 'install', '-r', 'COFFEE/requirements.txt']' returned non-zero exit status 1
------------------
Francis Poulin
Associate Professor
Department of Applied Mathematics
University of Waterloo
email: fpoulin@uwaterloo.ca
Web: https://uwaterloo.ca/poulin-research-group/
Telephone: +1 519 888 4567 x32637
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