LMFDB, sage binaries, and sage -b question

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aly.d...@gmail.com

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Mar 24, 2016, 12:50:57 PM3/24/16
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Hi all,

On the LMFDB github getting started page,  they have the following directions for Sage setup for use in LMFDB:

sage -i gap_packages sage -i database_gap sage -i pip sage -b

After running these commands, the people who have macs running El Capitan who were running Sage after downloading binaries, are having trouble with Sage.  In particular, after running sage -b, when they try to run Sage again, it tries to start and then crashes.  Does someone know what's going on?  It seems we don't need the sage -b anyway?

Thanks,

Aly

kcrisman

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Mar 24, 2016, 2:35:31 PM3/24/16
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Maybe "make" instead?

kcrisman

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Mar 24, 2016, 2:36:56 PM3/24/16
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Oh, belay that info... you can't build with binaries on Mac - there is a ticket somewhere about enhancing the installation guide to point this out but I can't find it now.

John Cremona

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Mar 24, 2016, 4:21:02 PM3/24/16
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On 24 Mar 2016 18:36, "kcrisman" <kcri...@gmail.com> wrote:
>
> Oh, belay that info... you can't build with binaries on Mac - there is a ticket somewhere about enhancing the installation guide to point this out but I can't find it now.
>

I assume that it is possible to install optional packages and python extras on a mac binary install though
?

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Dima Pasechnik

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Mar 24, 2016, 6:22:45 PM3/24/16
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On Thursday, March 24, 2016 at 8:21:02 PM UTC, John Cremona wrote:


On 24 Mar 2016 18:36, "kcrisman" <kcri...@gmail.com> wrote:
>
> Oh, belay that info... you can't build with binaries on Mac - there is a ticket somewhere about enhancing the installation guide to point this out but I can't find it now.
>

I assume that it is possible to install optional packages and python extras on a mac binary install though


I think it is possible, I'm checking this now (indeed, one needs to run make, and this involves re-cythonising 430 files 
at least once...)

Dima Pasechnik

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Mar 24, 2016, 7:45:18 PM3/24/16
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indeed, the current OSX binary install gets broken if I try to install an optional package.
in more detail, I installed a binary package, ran ./sage once, then
did sage -i gap_packages followed by make.
At the end of make's run I got


cd ../.. && sage-logger './sage --docbuild --no-pdf-links all html ' logs/dochtml.log

/Users/dima/tmp/SageMath/local/bin/python: dlopen(/Users/dima/tmp/SageMath/local/lib/python2.7/site-packages/sage/rings/complex_double.so, 2): Symbol not found: _gsl_complex_abs

  Referenced from: /Users/dima/tmp/SageMath/local/lib/python2.7/site-packages/sage/rings/complex_double.so

  Expected in: flat namespace

 in /Users/dima/tmp/SageMath/local/lib/python2.7/site-packages/sage/rings/complex_double.so; 'sage_setup.docbuild' is a package and cannot be directly executed

make[2]: *** [doc-html] Error 1

make[1]: *** [all] Error 2


Needless to say, Sage does not start, I get 


Oops, Sage crashed. We do our best to make it stable, but...


The crash report is attached.

The import error is the same as above.

Sage_crash_report.txt

John Cremona

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Mar 25, 2016, 5:23:18 AM3/25/16
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Is there a trac ticket for this? Many LMFDB developers use macs
(though not me) and some of those are still on 6.10, while LMFDB
itself now uses 7.0. So that would be very helpful.

John

Dima Pasechnik

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Mar 25, 2016, 6:25:58 AM3/25/16
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