[Numpy-discussion] NumPy-Discussion Digest, Vol 67, Issue 43

Peter Plantinga pwp2@students.calvin....
Thu Apr 12 19:26:54 CDT 2012


>
> Really you have to have this setup in order to run a fortran executable,
> but the only thing that comes to mind is the LD_LIBRARY_PATH environment
> variable.  LD_LIBRARY_PATH is a colon separated list of paths that is
> searched for dynamic libraries by both regular programs and by Python.


Thanks for the suggestion! I added the library to LD_LIBRARY_PATH and that
fixed it.

On Thu, Apr 12, 2012 at 4:25 PM, <numpy-discussion-request@scipy.org> wrote:

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> Today's Topics:
>
>   1. physics simulation (Peter Plantinga)
>   2. Re: physics simulation (Tim Cera)
>   3. Re: YouTrack testbed (Travis Oliphant)
>   4. Re: YouTrack testbed (william ratcliff)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Apr 2012 15:24:43 -0400
> From: Peter Plantinga <pwp2@students.calvin.edu>
> Subject: [Numpy-discussion] physics simulation
> To: numpy-discussion@scipy.org
> Message-ID:
>        <CAEy-jdL+mYCQGsuoh2fjLTOPqNotXKjA8y4ch2k1jBzJByU2KQ@mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> I'm trying to run a physics simulation on a cluster. The original program
> is written in fortran, and highly parallelizable. Unfortunately, I've had a
> bit of trouble getting f2py to work with the compiler I'm using (absoft
> v.10.1). The cluster is running Linux v. 12.
>
> When I type just "f2py" I get the following error:
>
> > f2py
> Traceback (most recent call last):
>  File "/opt/absoft10.1/bin/f2py", line 20, in <module>
>    from numpy.f2py import main
>  File "/usr/local/lib/python2.6/dist-packages/numpy/__init__.py", line
> 137, in <module>
>    import add_newdocs
>  File "/usr/local/lib/python2.6/dist-packages/numpy/add_newdocs.py", line
> 9, in <module>
>    from numpy.lib import add_newdoc
>  File "/usr/local/lib/python2.6/dist-packages/numpy/lib/__init__.py", line
> 13, in <module>
>    from polynomial import *
>  File "/usr/local/lib/python2.6/dist-packages/numpy/lib/polynomial.py",
> line 17, in <module>
>    from numpy.linalg import eigvals, lstsq
>  File "/usr/local/lib/python2.6/dist-packages/numpy/linalg/__init__.py",
> line 48, in <module>
>    from linalg import *
>  File "/usr/local/lib/python2.6/dist-packages/numpy/linalg/linalg.py",
> line 23, in <module>
>    from numpy.linalg import lapack_lite
> ImportError: libaf90math.so: cannot open shared object file: No such file
> or directory
>
> It looks like f2py cannot find libaf90math.so, located in
> /opt/absoft10.1/shlib. How can I tell f2py where af90math is?
>
> Thanks for the help!
> Peter Plantinga
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> ------------------------------
>
> Message: 2
> Date: Thu, 12 Apr 2012 15:54:50 -0400
> From: Tim Cera <tim@cerazone.net>
> Subject: Re: [Numpy-discussion] physics simulation
> To: Discussion of Numerical Python <numpy-discussion@scipy.org>
> Message-ID:
>        <CAO5s+D8PpuOhea4u-StF_o5ESXeckV71_MTGQ=OwbiGhbL77=w@mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> >
> > It looks like f2py cannot find libaf90math.so, located in
> > /opt/absoft10.1/shlib. How can I tell f2py where af90math is?
>
>
> Really you have to have this setup in order to run a fortran executable,
> but the only thing that comes to mind is the LD_LIBRARY_PATH environment
> variable.  LD_LIBRARY_PATH is a colon separated list of paths that is
> searched for dynamic libraries by both regular programs and by Python.
>
> Use...
>
> env | grep LD_
>
> to show you the existing LD_LIBRARY_PATH.  To change/append depends on your
> shell.
>
> Kindest regards,
> Tim
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> ------------------------------
>
> Message: 3
> Date: Thu, 12 Apr 2012 15:05:12 -0500
> From: Travis Oliphant <travis@continuum.io>
> Subject: Re: [Numpy-discussion] YouTrack testbed
> To: Discussion of Numerical Python <numpy-discussion@scipy.org>
> Message-ID: <3517E0D6-B8CB-4A3A-A37C-F78860F2D0AA@continuum.io>
> Content-Type: text/plain; charset="iso-8859-1"
>
> This looks good.   Maggie and Bryan are now setting up a Redmine instance
> to try out how hard that is to administer.    I have some experience with
> Redmine and have liked what I've seen in the past.  I think the user
> experience that Ralf is providing feedback on is much more important than
> how hard it is to administer.
>
> NumFocus will dedicate resources to administer the system.
>
> -Travis
>
>
>
>
> On Apr 12, 2012, at 11:43 AM, Ralf Gommers wrote:
>
> >
> >
> > On Tue, Apr 10, 2012 at 9:53 PM, David Cournapeau <cournape@gmail.com>
> wrote:
> >
> >
> > On Tue, Apr 10, 2012 at 8:40 PM, Ralf Gommers <
> ralf.gommers@googlemail.com> wrote:
> >
> >
> > On Mon, Apr 9, 2012 at 10:32 PM, Bryan Van de Ven <bryanv@continuum.io>
> wrote:
> > On 4/3/12 4:18 PM, Ralf Gommers wrote:
> > > Here some first impressions.
> > >
> > > The good:
> > > - It's responsive!
> > > - It remembers my preferences (view type, # of issues per page, etc.)
> > > - Editing multiple issues with the command window is easy.
> > > - Search and filter functionality is powerful
> > >
> > > The bad:
> > > - Multiple projects are supported, but issues are then really mixed.
> > > The way this works doesn't look very useful for combined admin of
> > > numpy/scipy trackers.
> > > - I haven't found a way yet to make versions and subsystems appear in
> > > the one-line issue overview.
> > > - Fixed issues are still shown by default. There are several open
> > > issues filed against youtrack about this, with no reasonable answers.
> > > - Plain text attachments (.txt, .diff, .patch) can't be viewed, only
> > > downloaded.
> > > - No direct VCS integration, only via Teamcity (not set up, so can't
> > > evaluate).
> > > - No useful default views as in Trac
> > > (http://projects.scipy.org/scipy/report).
> >
> > Ralf,  regarding some of the issues:
> >
> > Hi Bryan, thanks for looking into this.
> >
> > I think for numpy/scipy trackers, we could simply run separate instances
> > of YouTrack for each.
> >
> > That would work. It does mean that there's no maintenance advantage over
> using Trac here.
> >
> > Also we can certainly create some standard
> > queries. It's a small pain not to have useful defaults, but it's only a
> > one-time pain. :)
> >
> > That should help.
> >
> > Also, what kind of integration are you looking for with github? There
> > does appear to be the ability to issue commands to youtrack through git
> > commits, which does not depend on TeamCity, as best I can tell:
> >
> > http://confluence.jetbrains.net/display/YTD3/GitHub+Integration
> > http://blogs.jetbrains.com/youtrack/tag/github-integration/
> >
> > I'm not sure this is what you were thinking about though.
> >
> > That does help. The other thing that's useful is to reference commits
> (like commit:abcd123 in current Trac) and have them turned into links to
> commits on Github. This is not a showstopper for me though.
> >
> > For the other issues, Maggie or I can try and see what we can find out
> > about implementing them, or working around them, this week.
> >
> > I'd say that from the issues I mentioned, the biggest one is the
> one-line view. So these two:
> >
> >   - I haven't found a way yet to make versions and subsystems appear in
> >     the one-line issue overview.
> >   - Fixed issues are still shown by default. There are several open
> >     issues filed against youtrack about this, with no reasonable answers.
> >
> > Of course, we'd like to evaluate any other viable issue trackers as
> >
> > well. Do you have any suggestions for other systems besides YouTrack?
> >
> > David wrote up some issues (some of which I didn't check) with current
> Trac and looked at Redmine before. He also mentioned Roundup. See
> http://projects.scipy.org/numpy/wiki/ImprovingIssueWorkflow
> >
> > Redmine does look good from a quick browse (better view, does display
> diffs). It would be good to get the opinions of a few more people on this
> topic.
> >
> > Redmine is "trac on RoR", but it solves two significant issues over trac:
> >   - mass edit (e.g. moving things to a new mileston is simple and doable
> from the UI)
> >   - REST API by default, so that we can build simple command line tools
> on top of it (this changed since I made the wiki page)
> >
> > It is a PITA to install, though, at least if you are not familiar with
> ruby, and I heard it is hard to manage as well.
> >
> > Thanks, that's a clear description of pros and cons. It's also easy to
> play with Redmine at demo.redmine.org. That site allows you to set up a
> new project and try the admin interface.
> >
> > My current list of preferences is:
> >
> > 1. Redmine (if admin overhead is not unreasonable)
> > 2. Trac with performance issues solved
> > 3. Github
> > 4. YouTrack
> > 5. Trac with current performance
> >
> > Ralf
> >
> > _______________________________________________
> > NumPy-Discussion mailing list
> > NumPy-Discussion@scipy.org
> > http://mail.scipy.org/mailman/listinfo/numpy-discussion
>
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> ------------------------------
>
> Message: 4
> Date: Thu, 12 Apr 2012 16:29:23 -0400
> From: william ratcliff <william.ratcliff@gmail.com>
> Subject: Re: [Numpy-discussion] YouTrack testbed
> To: Discussion of Numerical Python <numpy-discussion@scipy.org>
> Message-ID:
>        <CAFt3ydsxsDMDR+PYsHYW_Kq6UVMgPewojm5Vpa85maeWA6fXLQ@mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Has anyone tried Rietveld, Gerrit, or Phabricator?
>
>
>
> On Thu, Apr 12, 2012 at 4:05 PM, Travis Oliphant <travis@continuum.io
> >wrote:
>
> > This looks good.   Maggie and Bryan are now setting up a Redmine instance
> > to try out how hard that is to administer.    I have some experience with
> > Redmine and have liked what I've seen in the past.  I think the user
> > experience that Ralf is providing feedback on is much more important than
> > how hard it is to administer.
> >
> > NumFocus will dedicate resources to administer the system.
> >
> > -Travis
> >
> >
> >
> >
> > On Apr 12, 2012, at 11:43 AM, Ralf Gommers wrote:
> >
> >
> >
> > On Tue, Apr 10, 2012 at 9:53 PM, David Cournapeau <cournape@gmail.com
> >wrote:
> >
> >>
> >>
> >> On Tue, Apr 10, 2012 at 8:40 PM, Ralf Gommers <
> >> ralf.gommers@googlemail.com> wrote:
> >>
> >>>
> >>>
> >>> On Mon, Apr 9, 2012 at 10:32 PM, Bryan Van de Ven <bryanv@continuum.io
> >wrote:
> >>>
> >>>> On 4/3/12 4:18 PM, Ralf Gommers wrote:
> >>>> > Here some first impressions.
> >>>> >
> >>>> > The good:
> >>>> > - It's responsive!
> >>>> > - It remembers my preferences (view type, # of issues per page,
> etc.)
> >>>> > - Editing multiple issues with the command window is easy.
> >>>> > - Search and filter functionality is powerful
> >>>> >
> >>>> > The bad:
> >>>> > - Multiple projects are supported, but issues are then really mixed.
> >>>> > The way this works doesn't look very useful for combined admin of
> >>>> > numpy/scipy trackers.
> >>>> > - I haven't found a way yet to make versions and subsystems appear
> in
> >>>> > the one-line issue overview.
> >>>> > - Fixed issues are still shown by default. There are several open
> >>>> > issues filed against youtrack about this, with no reasonable
> answers.
> >>>> > - Plain text attachments (.txt, .diff, .patch) can't be viewed, only
> >>>> > downloaded.
> >>>> > - No direct VCS integration, only via Teamcity (not set up, so can't
> >>>> > evaluate).
> >>>> > - No useful default views as in Trac
> >>>> > (http://projects.scipy.org/scipy/report).
> >>>>
> >>>> Ralf,  regarding some of the issues:
> >>>>
> >>>
> >>> Hi Bryan, thanks for looking into this.
> >>>
> >>>>
> >>>> I think for numpy/scipy trackers, we could simply run separate
> instances
> >>>> of YouTrack for each.
> >>>
> >>>
> >>> That would work. It does mean that there's no maintenance advantage
> over
> >>> using Trac here.
> >>>
> >>> Also we can certainly create some standard
> >>>> queries. It's a small pain not to have useful defaults, but it's only
> a
> >>>> one-time pain. :)
> >>>>
> >>>
> >>> That should help.
> >>>
> >>>
> >>>> Also, what kind of integration are you looking for with github? There
> >>>> does appear to be the ability to issue commands to youtrack through
> git
> >>>> commits, which does not depend on TeamCity, as best I can tell:
> >>>>
> >>>> http://confluence.jetbrains.net/display/YTD3/GitHub+Integration
> >>>> http://blogs.jetbrains.com/youtrack/tag/github-integration/
> >>>>
> >>>> I'm not sure this is what you were thinking about though.
> >>>>
> >>>
> >>> That does help. The other thing that's useful is to reference commits
> >>> (like commit:abcd123 in current Trac) and have them turned into links
> to
> >>> commits on Github. This is not a showstopper for me though.
> >>>
> >>>>
> >>>> For the other issues, Maggie or I can try and see what we can find out
> >>>> about implementing them, or working around them, this week.
> >>>>
> >>>
> >>> I'd say that from the issues I mentioned, the biggest one is the
> >>> one-line view. So these two:
> >>>
> >>>   - I haven't found a way yet to make versions and subsystems appear in
> >>>     the one-line issue overview.
> >>>   - Fixed issues are still shown by default. There are several open
> >>>     issues filed against youtrack about this, with no reasonable
> >>> answers.
> >>>
> >>>
> >>>> Of course, we'd like to evaluate any other viable issue trackers as
> >>>>
> >>>> well. Do you have any suggestions for other systems besides YouTrack?
> >>>>
> >>>
> >>> David wrote up some issues (some of which I didn't check) with current
> >>> Trac and looked at Redmine before. He also mentioned Roundup. See
> >>> http://projects.scipy.org/numpy/wiki/ImprovingIssueWorkflow
> >>>
> >>> Redmine does look good from a quick browse (better view, does display
> >>> diffs). It would be good to get the opinions of a few more people on
> this
> >>> topic.
> >>>
> >>
> >> Redmine is "trac on RoR", but it solves two significant issues over
> trac:
> >>   - mass edit (e.g. moving things to a new mileston is simple and doable
> >> from the UI)
> >>   - REST API by default, so that we can build simple command line tools
> >> on top of it (this changed since I made the wiki page)
> >>
> >> It is a PITA to install, though, at least if you are not familiar with
> >> ruby, and I heard it is hard to manage as well.
> >>
> >
> > Thanks, that's a clear description of pros and cons. It's also easy to
> > play with Redmine at demo.redmine.org. That site allows you to set up a
> > new project and try the admin interface.
> >
> > My current list of preferences is:
> >
> > 1. Redmine (if admin overhead is not unreasonable)
> > 2. Trac with performance issues solved
> > 3. Github
> > 4. YouTrack
> > 5. Trac with current performance
> >
> > Ralf
> >
> >  _______________________________________________
> > NumPy-Discussion mailing list
> > NumPy-Discussion@scipy.org
> > http://mail.scipy.org/mailman/listinfo/numpy-discussion
> >
> >
> >
> > _______________________________________________
> > NumPy-Discussion mailing list
> > NumPy-Discussion@scipy.org
> > http://mail.scipy.org/mailman/listinfo/numpy-discussion
> >
> >
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>
> End of NumPy-Discussion Digest, Vol 67, Issue 43
> ************************************************
>
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