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: http://askubuntu.com/questions/509283/python-no-module-named-datetime
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_resources/__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
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&Itemid=42&func=vie... 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<mailto: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<mailto:fpoulin@uwaterloo.ca> Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 ________________________________ From: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> [firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>] on behalf of David Ham [David.Ham@imperial.ac.uk<mailto: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: http://askubuntu.com/questions/509283/python-no-module-named-datetime 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<mailto: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_resources/__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<mailto:fpoulin@uwaterloo.ca> Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637
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 directory 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. What should I do to resolve this? Thanks, Justin On 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& Itemid=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: http://askubuntu.com/questions/509283/python-no-module-named-datetime
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_resources/__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
firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Nevermind! Resolved, this was resolved by doing the following: pip uinstall mpi4py rm $(find ~/.cache -name 'mpi4py*'); pip install mpi4py On Fri, Aug 5, 2016 at 3:06 AM, Justin Chang <jychang48@gmail.com> wrote:
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 directory
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.
What should I do to resolve this?
Thanks, Justin
On 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: http://askubuntu.com/questions/509283/python-no-module-named-datetime
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_resources/__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
firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (3)
-
David Ham
-
Francis Poulin
-
Justin Chang