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Trouble with Fink Install of GalSim #348

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RMebane opened this issue Jan 24, 2013 · 9 comments
Closed

Trouble with Fink Install of GalSim #348

RMebane opened this issue Jan 24, 2013 · 9 comments
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@RMebane
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RMebane commented Jan 24, 2013

Hello, I'm an undergraduate student working with Professor Mandelbaum, and I'm having some trouble installing GalSim with fink on my Mac with OS X 10.8.

I've worked with an earlier version of GalSim over this past summer, where I had a lot of difficulty getting it to build against boost, however we were eventually able to get it working. When I tried to update the software this past week, I had similar troubles building against boost, so I decided to try a fink installation.

After updating fink, I ran

fink install galsim

This seemed to work fine, but when I open up the python installed by fink in /sw/bin/python2.7 and try to import galsim, I get the following error:

Richards-MacBook-Pro:~ Rick$ /sw/bin/python2.7
Python 2.7.3 (default, Jul 5 2012, 16:14:02)
[GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.61)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import galsim
Segmentation fault: 11

Since this didn't work, I tried simply uninstalling galsim and reinstalling it, but when I ran "fink remove galsim", I got the following error:

WARNING: galsim is not installed, skipping.

For some reason it's saying galsim is not installed, even though I seemed to install in without any problems earlier.

I then tried to do a fresh installation of fink in case there were some settings in my old fink that were messing it up. When I try to install galsim with this, I get the following error:

Can't resolve dependency "xcode (>= 4.5)" for package "gcc47-4.7.2-1000" (no
matching packages/versions found)
Exiting with failure.

It seems like it's saying it needs xcode to be version 4.5 or above, which
is strange, since my version of Xcode is 4.5.2.

Anyway, I now have two installations of fink on my computer with yield different errors when trying to install galsim.

Thanks!
Rick Mebane

@rmjarvis
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I don't know if anyone has tried it on 10.8 yet. I have 10.6 on my laptop, and I think Barney tested it on 10.7.

However, I do have a new Hackintosh running 10.8 that I haven't yet put fink on, so I'll try to fink install galsim there and see what happens.

@rmjarvis
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I wasn't able to reproduce either one of your errors. From a fresh installation of fink, I selected the default response for everything. Then fink install galsim finished successfully, after which

$ /sw/bin/python2.7
Python 2.7.3 (default, Jan 25 2013, 01:05:38) 
[GCC 4.2.1 Compatible Apple Clang 4.1 ((tags/Apple/clang-421.11.66))] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import galsim
>>> gal = galsim.Sersic(3.4, half_light_radius=2.1)
>>> psf = galsim.Kolmogorov(fwhm=1.5)
>>> pix = galsim.Pixel(0.3)
>>> final = galsim.Convolve(gal,psf,pix)
>>> final.draw().write('test.fits')
>>> 

All seems to be well.

The one thing I see that is different with your trace is the Apple Clang version. Maybe try updating that? Maybe there was a bug in the version of Clang that built your python 2.7?

I think that compiler comes with the XCode distribution, so maybe you didn't fully install the new XCode 4.5.2 that was released Jan. 15, and somehow that's causing trouble.

@barnabytprowe
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Hmmmm, that's true I don't think it has been tested on fink 10.8: 10.7
is the highest I have access to... I'll see if there's someone in the
department too.

On 25 Jan 2013, at 04:06, Mike Jarvis wrote:

I don't know if anyone has tried it on 10.8 yet. I have 10.6 on my
laptop, and I think Barney tested it on 10.7.

However, I do have a new Hackintosh running 10.8 that I haven't yet
put fink on, so I'll try to fink install galsim there and see what
happens.


Reply to this email directly or view it on GitHub.

@rmjarvis
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Another thought -- maybe you have Clang 4.1 installed, which was used for the GalSim compilation, but python27 was installed with a previous XCode that had 3.1, and maybe there is some kind of incompatibility between them.

So. For the first one where you were getting the seg fault, you could try fink rebuild python27 to rebuild it with your current compiler. Maybe also python27-shlibs, numpy-py27, pyfits-py27, yaml-py27, and boost1.35.python27-shlibs, just to be sure (since fink rebuild foo doesn't automatically rebuild packages that depend on foo).

I don't know if that will work, but it might be worth a try.

@rmjarvis
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As to your second fink installation where you did everything from scratch, I found this post that points out that XCode as far as fink is concerned is really the XCode command-line tools. To update that, you need to open XCode, go to Preferences, Downloads tab, and update the "Command Line Tools" there.

@RMebane
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RMebane commented Jan 27, 2013

Updating the Xcode Command Line Tools did the trick, thanks!

@RMebane RMebane closed this as completed Jan 27, 2013
@rmjarvis
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Good. Was this on the new fink installation? Did you get the original fink version to work, or it that one just abandoned? (I want to write an item in the FAQ about this, and I want to get the details right.)

@rmjarvis
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I have a FAQ item here. You can check if I represented everything correctly. (I guessed that the success happened with your second fink installation.)

@RMebane
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RMebane commented Jan 27, 2013

Yes, this was on the new fink installation. I wasn't able to get the original one working, although I didn't try all of the suggestions posted previously since I was able to get the new one working.

I read over the FAQ item, and it seems everything is represented right.

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