scipy broke yt? maybe python?
Hi all, I have the yt-conda installation of yt. I am trying to create an absorption spectrum, so need the command "generate_total_fit". yt told me I needed scipy for this to work. yt does not have scipy. So I typed:
pip install scipy
scipy was installed. However, then my submission script no longer worked at all and I was given the error: /var/spool/torque/mom_priv/jobs/50052.mies.stanford.edu.SC: line 26: 3750 Segmentation fault python HI_absorbers.py When I pip uninstall scipy, my code runs again! The only commands in my script are source /home/stonnes/yt-conda/bin/activate python HI_absorbers.py Can anyone help me out with this? Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
Hi Stephanie, It's very hard to say what's going wrong without more information. Can you get a core dump or run python under gdb to get a stack trace at the place where the segmentation fault happens? Can you run this on your laptop? If so, do you get a segmentation fault there? -Nathan On Fri, Jul 1, 2016 at 2:25 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi all,
I have the yt-conda installation of yt. I am trying to create an absorption spectrum, so need the command "generate_total_fit".
yt told me I needed scipy for this to work. yt does not have scipy. So I typed:
pip install scipy
scipy was installed.
However, then my submission script no longer worked at all and I was given the error:
/var/spool/torque/mom_priv/jobs/50052.mies.stanford.edu.SC: line 26: 3750 Segmentation fault python HI_absorbers.py
When I pip uninstall scipy, my code runs again! The only commands in my script are source /home/stonnes/yt-conda/bin/activate python HI_absorbers.py
Can anyone help me out with this?
Thanks! Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Nathan, I am not sure how to get a core dump or how to make gdb give me useful things. But maybe this will help... By running my code via a command line, I find that import h5py import scipy import yt from yt.analysis_modules.cosmological_observation.api import LightRay all are fine. But, from yt.analysis.modules.absorption_spectrum.api import AbsorptionSpectrum from yt.analysis.modules.absorption_spectrum.api import generate_total_fit both give me a Segmentation fault and kick me out of python I can keep trying to figure out how to have gdb give me something useful, but does this give any clues in the meantime? Thanks, Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com On Fri, Jul 1, 2016 at 12:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Stephanie,
It's very hard to say what's going wrong without more information.
Can you get a core dump or run python under gdb to get a stack trace at the place where the segmentation fault happens?
Can you run this on your laptop? If so, do you get a segmentation fault there?
-Nathan
On Fri, Jul 1, 2016 at 2:25 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi all,
I have the yt-conda installation of yt. I am trying to create an absorption spectrum, so need the command "generate_total_fit".
yt told me I needed scipy for this to work. yt does not have scipy. So I typed:
pip install scipy
scipy was installed.
However, then my submission script no longer worked at all and I was given the error:
/var/spool/torque/mom_priv/jobs/50052.mies.stanford.edu.SC: line 26: 3750 Segmentation fault python HI_absorbers.py
When I pip uninstall scipy, my code runs again! The only commands in my script are source /home/stonnes/yt-conda/bin/activate python HI_absorbers.py
Can anyone help me out with this?
Thanks! Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
On Fri, Jul 1, 2016 at 4:00 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi Nathan,
I am not sure how to get a core dump or how to make gdb give me useful things. But maybe this will help...
By running my code via a command line, I find that import h5py import scipy import yt from yt.analysis_modules.cosmological_observation.api import LightRay
all are fine. But,
from yt.analysis.modules.absorption_spectrum.api import AbsorptionSpectrum from yt.analysis.modules.absorption_spectrum.api import generate_total_fit
And both of these succeed when scipy isn't installed? What happens if you do: import scipy.optimize Also you're using the conda-based python that the latest version of the install script builds, right? Maybe you should try the conda binary builds instead: $ pip uninstall scipy $ conda install scipy
both give me a Segmentation fault and kick me out of python
I can keep trying to figure out how to have gdb give me something useful, but does this give any clues in the meantime?
Thanks, Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
On Fri, Jul 1, 2016 at 12:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Stephanie,
It's very hard to say what's going wrong without more information.
Can you get a core dump or run python under gdb to get a stack trace at the place where the segmentation fault happens?
Can you run this on your laptop? If so, do you get a segmentation fault there?
-Nathan
On Fri, Jul 1, 2016 at 2:25 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi all,
I have the yt-conda installation of yt. I am trying to create an absorption spectrum, so need the command "generate_total_fit".
yt told me I needed scipy for this to work. yt does not have scipy. So I typed:
pip install scipy
scipy was installed.
However, then my submission script no longer worked at all and I was given the error:
/var/spool/torque/mom_priv/jobs/50052.mies.stanford.edu.SC: line 26: 3750 Segmentation fault python HI_absorbers.py
When I pip uninstall scipy, my code runs again! The only commands in my script are source /home/stonnes/yt-conda/bin/activate python HI_absorbers.py
Can anyone help me out with this?
Thanks! Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Nathan, Yahoo! doing the conda install instead of pip has fixed it! For completion, though, here are the answers to the other two questions: Yes, it all runs nicely (until scipy is needed) if I don't have scipy installed. If I start python and type import scipy.optimize I get a Segmentation fault --when I used the pip install version. with conda install, import scipy.optimize seems to work fine. Thanks!!! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com On Fri, Jul 1, 2016 at 2:15 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Fri, Jul 1, 2016 at 4:00 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi Nathan,
I am not sure how to get a core dump or how to make gdb give me useful things. But maybe this will help...
By running my code via a command line, I find that import h5py import scipy import yt from yt.analysis_modules.cosmological_observation.api import LightRay
all are fine. But,
from yt.analysis.modules.absorption_spectrum.api import AbsorptionSpectrum from yt.analysis.modules.absorption_spectrum.api import generate_total_fit
And both of these succeed when scipy isn't installed?
What happens if you do:
import scipy.optimize
Also you're using the conda-based python that the latest version of the install script builds, right? Maybe you should try the conda binary builds instead:
$ pip uninstall scipy $ conda install scipy
both give me a Segmentation fault and kick me out of python
I can keep trying to figure out how to have gdb give me something useful, but does this give any clues in the meantime?
Thanks, Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
On Fri, Jul 1, 2016 at 12:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Stephanie,
It's very hard to say what's going wrong without more information.
Can you get a core dump or run python under gdb to get a stack trace at the place where the segmentation fault happens?
Can you run this on your laptop? If so, do you get a segmentation fault there?
-Nathan
On Fri, Jul 1, 2016 at 2:25 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi all,
I have the yt-conda installation of yt. I am trying to create an absorption spectrum, so need the command "generate_total_fit".
yt told me I needed scipy for this to work. yt does not have scipy. So I typed:
pip install scipy
scipy was installed.
However, then my submission script no longer worked at all and I was given the error:
/var/spool/torque/mom_priv/jobs/50052.mies.stanford.edu.SC: line 26: 3750 Segmentation fault python HI_absorbers.py
When I pip uninstall scipy, my code runs again! The only commands in my script are source /home/stonnes/yt-conda/bin/activate python HI_absorbers.py
Can anyone help me out with this?
Thanks! Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
On Fri, Jul 1, 2016 at 4:37 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi Nathan,
Yahoo! doing the conda install instead of pip has fixed it!
The 4th of July weekend is saved!
For completion, though, here are the answers to the other two questions:
Yes, it all runs nicely (until scipy is needed) if I don't have scipy installed.
If I start python and type
import scipy.optimize
I get a Segmentation fault --when I used the pip install version. with conda install, import scipy.optimize seems to work fine.
This must be a bug in scipy then, triggered by pip installing in whatever environment you have set up on this cluster.
Thanks!!! Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
On Fri, Jul 1, 2016 at 2:15 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Fri, Jul 1, 2016 at 4:00 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi Nathan,
I am not sure how to get a core dump or how to make gdb give me useful things. But maybe this will help...
By running my code via a command line, I find that import h5py import scipy import yt from yt.analysis_modules.cosmological_observation.api import LightRay
all are fine. But,
from yt.analysis.modules.absorption_spectrum.api import AbsorptionSpectrum from yt.analysis.modules.absorption_spectrum.api import generate_total_fit
And both of these succeed when scipy isn't installed?
What happens if you do:
import scipy.optimize
Also you're using the conda-based python that the latest version of the install script builds, right? Maybe you should try the conda binary builds instead:
$ pip uninstall scipy $ conda install scipy
both give me a Segmentation fault and kick me out of python
I can keep trying to figure out how to have gdb give me something useful, but does this give any clues in the meantime?
Thanks, Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
On Fri, Jul 1, 2016 at 12:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Stephanie,
It's very hard to say what's going wrong without more information.
Can you get a core dump or run python under gdb to get a stack trace at the place where the segmentation fault happens?
Can you run this on your laptop? If so, do you get a segmentation fault there?
-Nathan
On Fri, Jul 1, 2016 at 2:25 PM, Stephanie Tonnesen <stonnes@gmail.com> wrote:
Hi all,
I have the yt-conda installation of yt. I am trying to create an absorption spectrum, so need the command "generate_total_fit".
yt told me I needed scipy for this to work. yt does not have scipy. So I typed:
pip install scipy
scipy was installed.
However, then my submission script no longer worked at all and I was given the error:
/var/spool/torque/mom_priv/jobs/50052.mies.stanford.edu.SC: line 26: 3750 Segmentation fault python HI_absorbers.py
When I pip uninstall scipy, my code runs again! The only commands in my script are source /home/stonnes/yt-conda/bin/activate python HI_absorbers.py
Can anyone help me out with this?
Thanks! Stephanie
-- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes@gmail.com
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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participants (2)
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Nathan Goldbaum -
Stephanie Tonnesen