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#1 2016-06-28 15:30:45

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

[solved] errors in running sagemath

I have just installed sagemath on Arch, however the first run gave me the following error:

[SageTerminalApp] CRITICAL | Bad config encountered during initialization:
[SageTerminalApp] CRITICAL | The 'config' trait of a SageTerminalApp instance must be a Config or None, but a value of class 'traitlets.config.loader.Config' (i.e. {'InteractiveShellApp': {'extensions': ['sage']}, 'SageTerminalApp': {'force_interact': True}, 'TerminalIPythonApp': {'shell_class': <class 'sage.repl.interpreter.SageTerminalInteractiveShell'>, 'display_banner': False, 'test_shell': False, 'verbose_crash': True}, 'InteractiveShell': {'separate_in': '', 'ast_node_interactivity': 'all', 'colors': 'LightBG', 'confirm_exit': False}, 'PromptManager': {'out_template': '', 'in2_template': '....: ', 'in_template': 'sage: ', 'justify': False}, 'ProfileDir': {}}) was specified.

any idea on how to fix it? Looks like I had some previous settings that needs to be remove but I have no idea how to do so.

Thanks

Last edited by pingpong (2016-06-30 15:08:22)

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#2 2016-06-28 15:47:52

madmike_
Member
Registered: 2016-06-28
Posts: 4

Re: [solved] errors in running sagemath

pingpong wrote:

Looks like I had some previous settings that needs to be remove but I have no idea how to do so.

Yes, that is very likely. Do you have a directory called .sage in your home ?

Either move it to .sage_bkp

cd $HOME && mv .sage .sage_bkp

or just delete it:

cd $HOME && rm -rf .sage

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#3 2016-06-28 15:50:05

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

Re: [solved] errors in running sagemath

Thanks madmike. I did try that but the problem persists.

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#4 2016-06-28 15:58:41

madmike_
Member
Registered: 2016-06-28
Posts: 4

Re: [solved] errors in running sagemath

too bad..

you could try to grep through your home and search for some part of the faulty config, like this:

$ grep -r sage.repl.interpreter.SageTerminalInteractiveShell $HOME

and see if some old files come up

This is just a generic approach, I am not familiar with sage at all.

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#5 2016-06-28 16:28:10

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

Re: [solved] errors in running sagemath

Hum, I'm currently away from the machine and will try that tonight.
I wonder if any sagemath user have experienced that.

I also try compiling sage from source on Arch but getting a lot of troubles lately... I was hoping that sagemath will be my solution.

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#6 2016-06-28 19:19:03

arojas
Developer
From: Spain
Registered: 2011-10-09
Posts: 2,093

Re: [solved] errors in running sagemath

How are you running Sage?

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#7 2016-06-28 22:37:30

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

Re: [solved] errors in running sagemath

@arojas. I'm not sure if I understand the question. Well, I just run sage by typing 'sage' at a command prompt. Could the problem have anything to do with ipython on my system?

I have troubles in compling sage on my Arch laptop. So I gave up and try the ABS PKGBUILD but I ran into the above problem.

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#8 2016-06-28 23:47:48

\hbar
Member
Registered: 2014-03-15
Posts: 165

Re: [solved] errors in running sagemath

So you made the package using the 'sagemath' PKGBUILD and installed the package? Silly question: why didn't you just install the package from the repos? Did you change any configuration flags? Or did you want to compile locally for performance gains?

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#9 2016-06-29 00:01:27

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

Re: [solved] errors in running sagemath

Oh... I surely did try the install from the repos directly but getting the same problem. I was hoping by building the package in my machine will fix that. But it didn't happen.

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#10 2016-06-29 01:30:41

arojas
Developer
From: Spain
Registered: 2011-10-09
Posts: 2,093

Re: [solved] errors in running sagemath

Do you have a version of ipython installed other than the one from the official repos?

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#11 2016-06-29 03:41:47

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

Re: [solved] errors in running sagemath

I don't think so. But how do I find out for sure?
When I type 'ipython', it runs and the version is

IPython 4.2.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

and my python version is 3.5.1, python2 version is 2,7,11 and when I type "sage", it gives

┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 7.2, Release Date: 2016-05-15                     │
│ Type "notebook()" for the browser-based notebook interface.        │
│ Type "help()" for help.                                            │
└────────────────────────────────────────────────────────────────────┘
=========
 IPython
=========

Tools for Interactive Computing in Python
=========================================

    A Python shell with automatic history (input and output), dynamic object
    introspection, easier configuration, command completion, access to the
    system shell and more.  IPython can also be embedded in running programs.

Usage

    ipython [subcommand] [options] [-c cmd | -m mod | file] [--] [arg] ...

    If invoked with no options, it executes the file and exits, passing the
    remaining arguments to the script, just as if you had specified the same
    command with python. You may need t

and a page or so more followed by the error message that I posted orginially.

Hopefully, I can have sage runs again on my system again... sad

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#12 2016-06-29 06:46:16

arojas
Developer
From: Spain
Registered: 2011-10-09
Posts: 2,093

Re: [solved] errors in running sagemath

It's not 'ipython', it's 'ipython2'. What is the output of 'which -a ipython2' and 'pacman -Qkk ipython2' ?

Last edited by arojas (2016-06-29 06:47:22)

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#13 2016-06-29 09:16:37

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

Re: [solved] errors in running sagemath

oh, I didn't even have ipython2 in the system. So I install it and here are the output of the commands that you suggested:

~ > which -a ipython2
/usr/bin/ipython2
/sbin/ipython2
/usr/sbin/ipython2
/sbin/ipython2
/usr/sbin/ipython2

and

~ > pacman -Qkk ipython2
ipython2: 727 total files, 0 altered files

Also, I uninstalled the sagemath which I built and use the one strict from the repos after installing ipython2. Unfortunately the same issue persists.

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#14 2016-06-29 09:33:43

arojas
Developer
From: Spain
Registered: 2011-10-09
Posts: 2,093

Re: [solved] errors in running sagemath

How did you install sagemath? Surely not from the Arch repos, since that one depends on ipython2. Please post the exact command you used

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#15 2016-06-29 09:39:48

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

Re: [solved] errors in running sagemath

Thanks for helping me on this problem.
By the way, when I complied sage from source. Here is the last point of failure.

/home/pong/sage-7.2/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x518b)[0x7fd313f890ab]
/home/pong/sage-7.2/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x518b)[0x7fd313f890ab]
/home/pong/sage-7.2/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x518b)[0x7fd313f890ab]
/home/pong/sage-7.2/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x8bc)[0x7fd313f8aabc]
/home/pong/sage-7.2/local/lib/libpython2.7.so.1.0(+0x837bc)[0x7fd313f047bc]
/home/pong/sage-7.2/local/lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7fd313ed3df3]
/home/pong/sage-7.2/local/lib/libpython2.7.so.1.0(+0x144fa0)[0x7fd313fc5fa0]
/home/pong/sage-7.2/local/lib/libpython2.7.so.1.0(Py_Main+0x5b3)[0x7fd313fc66c3]
/usr/lib/libc.so.6(__libc_start_main+0xf1)[0x7fd3131d8741]
python(_start+0x29)[0x4006f9]
------------------------------------------------------------------------
Attaching gdb to process id 8635.

Saved trace to /home/pong/.sage/crash_logs/crash_K_ouz6.log
------------------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occurred.
This probably occurred because a *compiled* module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.
------------------------------------------------------------------------
/home/pong/sage-7.2/build/bin/sage-logger: line 32:  8635 Segmentation fault
./sage --docbuild --no-pdf-links all
html
make[2]: *** [Makefile:1003: doc-html] Error 139
make[2]: Leaving directory '/home/pong/sage-7.2/build/make'
make[1]: *** [Makefile:826: all] Error 2
make[1]: Leaving directory '/home/pong/sage-7.2/build/make'

real    22m29.216s
user    22m5.557s
sys     0m26.567s
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all'):

The build directory may contain configuration files and other potentially
helpful information. WARNING: if you now run 'make' again, the build
directory will, by default, be deleted. Set the environment variable
SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

make: *** [Makefile:18: all] Error 1

I think it is close to the end of the compling process... I looked at the crash log but it is an empty file... I'm running out of ideas.
I will be happy to have SAGE running on the system again either through compling from source or making sagemath working.

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#16 2016-06-29 09:45:08

arojas
Developer
From: Spain
Registered: 2011-10-09
Posts: 2,093

Re: [solved] errors in running sagemath

you didn't answer my question...

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#17 2016-06-29 09:51:39

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

Re: [solved] errors in running sagemath

There is a time difference, I posted my #15 before reading #14.
I use packer so

packer sagemath

and here is the output

~ > packer sagemath
0 community/pari-sage 2.8.2341.g61b65cc-3 [installed]
      Computer algebra system designed for fast computations in number theory. Development snapshot required by SageMath
1 community/sage-notebook 0.13-2
      Browser-based notebook interface for SageMath
2 community/sagemath 7.2-6 [installed]
      Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab
3 community/sagemath-doc 7.2-2
      HTML documentation and inline help for SageMath
4 community/sagemath-src 7.2-2
      Source files for SageMath
5 community/sagetex 3.0-1
      Allows to embed code, results of computations, and plots from SageMath into LaTeX documents
6 aur/sagemath-git 7.2.beta4.r0.g0aec256-1 (2)
    Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab
7 aur/sage-data-odlyzko_zeta 20061209-1 (0)
    Table of zeros of the Riemann zeta function for SageMath
8 aur/sage-data-cremona_ellcurve 20160211-1 (0)
    John Cremona's large database of elliptic curves for SageMath

Type numbers to install. Separate each number with a space.
Numbers:

Obviously now I have sagemath installed otherwise I will hit '2' and it will install sagemath.

Should I now issue something like "sudo pacman -Rncs sagemath' then start over again?

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#18 2016-06-29 11:16:34

Lone_Wolf
Member
From: Netherlands, Europe
Registered: 2005-10-04
Posts: 11,868

Re: [solved] errors in running sagemath

https://wiki.archlinux.org/index.php/AU … ison_table
Check how many green fields packer has.

Use pacman for everything in repos.

what does "pacman -Qi sagemath" output ?


Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.


(A works at time B)  && (time C > time B ) ≠  (A works at time C)

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#19 2016-06-29 14:51:32

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

Re: [solved] errors in running sagemath

Here is the output

~ > pacman -Qi sagemath
Name            : sagemath
Version         : 7.2-6
Description     : Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab
Architecture    : x86_64
URL             : http://www.sagemath.org
Licenses        : GPL
Groups          : None
Provides        : sage-mathematics
Depends On      : ipython2  cysignals  ppl  palp  brial  singular  cliquer  maxima-ecl  gfan  sympow  tachyon
                  python2-rpy2  nauty  python2-matplotlib  python2-scipy  python2-sympy  python2-networkx
                  python2-pillow  libgap  flintqs  lcalc  lrcalc  arb  eclib  gmp-ecm  zn_poly  gd  python2-cvxopt
                  pynac  linbox  rubiks  pari-galdata  pari-seadata-small  planarity  rankwidth
                  sage-data-combinatorial_designs  sage-data-elliptic_curves  sage-data-graphs  sage-data-polytopes_db
                  sage-data-conway_polynomials
Optional Deps   : cython2: to compile cython code [installed]
                  python2-pkgconfig: to compile cython code [installed]
                  jmol: 3D plots
                  sage-notebook: Browser-based (flask) notebook interface
                  sagemath-doc: Documentation and inline help
                  ipython2-notebook: Jupyter notebook interface
                  mathjax: Jupyter notebook interface
                  coin-or-cbc: COIN backend for numerical computations [installed]
                  coin-or-csdp: for computing Lovász theta-function of graphs
                  buckygen: for generating fullerene graphs
                  plantri: for generating some classes of graphs
                  benzene: for generating fusenes and benzenoids
                  modular_decomposition: modular decomposition of graphs [installed]
                  ffmpeg: to export animations to video [installed]
                  imagemagick: to show animations [installed]
                  coxeter3: Coxeter groups implementation [installed]
                  cryptominisat: SAT solver [installed]
                  gap-data: for computing Galois groups
                  lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes
                  python2-igraph: igraph backend for graph theory
                  jupyter-notebook: Jupyter notebook interface
                  atlas-lapack: improved performance for some linear algebra operations
Required By     : None
Optional For    : None
Conflicts With  : sage-mathematics
Replaces        : sage-mathematics
Installed Size  : 235.60 MiB
Packager        : Antonio Rojas <arojas@archlinux.org>
Build Date      : Tue 21 Jun 2016 02:59:57 PM PDT
Install Date    : Wed 29 Jun 2016 02:23:32 AM PDT
Install Reason  : Explicitly installed
Install Script  : No
Validated By    : Signature

Anything suspicious?

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#20 2016-06-30 06:09:06

pingpong
Member
From: Los Angeles
Registered: 2010-12-30
Posts: 104

Re: [solved] errors in running sagemath

It turns out the problem is about my Python2 installation. I realized that because I can use sagetex to call sage without any problem. The issue goes away after I reinstalled python2.

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#21 2016-06-30 07:30:50

WorMzy
Forum Moderator
From: Scotland
Registered: 2010-06-16
Posts: 11,787
Website

Re: [solved] errors in running sagemath

Please don't use [closed], as this denotes a locked thread. Please use [solved] instead.


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