[sage-devel] Re: SageNB -> Jupyter conversion needs testers

2017-04-11 Thread kcrisman 



it does not work for me, or at least I must be doing something wrong.
> I get to the page listing the notebooks to convert, and then, if I click 
> on a notebook, I get a weird page asking for a password or a token.
>

If you paste in the *entire* token from the Terminal, it should work.  This 
is a known issue (Jeroen, which ticket?) but no one has tracked down 
how/when it happens yet.

And I hear you on the console but of course many users will not be using 
that ...

Can you try opening the app again and seeing whether you get the various 
messages directing you to the conversion page again?  I could only ever get 
it once.

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Re: [sage-combinat-devel] How to cite properly if we use Schur and skew Schur functions?

2017-04-11 Thread Anne Schilling 
You should cite Sage-combinat as described here

https://wiki.sagemath.org/combinat/CiteSageCombinat

and Sage as described here

https://wiki.sagemath.org/Publications_using_SageMath

Once your paper is on the arXiv and/or published, make sure to
list it on the publication site:

http://www.sagemath.org/library-publications-combinat.html

Best wishes,

Anne

On 4/11/17 1:03 AM, Egor Maximenko wrote:
> Dear Sage-Combinat developers, jointly with my colleagues we are using Sage 
> to test some formulas involving Schur and skew Schur functions.
> Principally we use SymmetricFunctions(QQ).s(), 
> SymmetricFunctions(QQ).s.skew_schur(), and algebraic operations in the Schur 
> basis.
> What would be the best way to acknowledge the developers?

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[sage-devel] Re: SageNB -> Jupyter conversion needs testers

2017-04-11 Thread Dima Pasechnik 
anyhow, this process, clicking on these old notebooks, does provide copies 
of converted to ipython sagenb notebooks,
but the whole process is very stressful at the moment, I think. This popup 
with password prompt really should not be there...

On Tuesday, April 11, 2017 at 9:44:03 PM UTC+1, Dima Pasechnik wrote:
>
> it does not work for me, or at least I must be doing something wrong.
> I get to the page listing the notebooks to convert, and then, if I click 
> on a notebook, I get a weird page asking for a password or a token.
>
> Password or token:
>  Log in
>
> Token authentication is enabled. You need to open the notebook server with 
> its first-time login token in the URL, or enable a password in order to 
> gain access. The command:
>
> jupyter notebook list
>
> will show you the URLs of running servers with their tokens, which you can 
> copy and paste into your browser. For example:
>
> Currently running servers:http://localhost:/?token=c8de56fa... :: 
> /Users/you/notebooks
>
> Or you can paste just the token value into the password field on this page.
>
> Cookies are required for authenticated access to notebooks.
>
>
>
> What I see above doesn't look as a valid URL, and then WTF is the token I 
> can paste instead?
>
> I tried c8de56fa, it didn't work. I tried clicking on the URL, it brings 
> me back to the page to choose
>
> the notebooks...
>
>  Arrgh... Give me my console any time...
>
>
>
a 

>
>
>
> On Tuesday, April 11, 2017 at 3:04:42 PM UTC+1, kcrisman wrote:
>>
>> This is now default in the Sage 8.0 beta series, and we strongly welcome 
>> testers!  For a limited time only I have posted a binary of the app bundle 
>> at 
>>
>>
>> http://www.math.gordon.edu/~kcrisman/sage-8.0.beta0-OSX_10.11.6-x86_64.app.dmg
>>
>> This should work on both Mac 10.11 and 10.12.   For bandwidth reasons I 
>> would prefer if those with the ability simply upgrade and build from 
>> scratch, but testing this app is also necessary.
>>
>> PLEASE TRY THIS and report back if you are at all interested in making 
>> sure that Sage 8.0 doesn't come with nasty surprises for long-time sagenb 
>> users.  Preliminary testing makes it seem as if we are okay, but it would 
>> be very helpful to have feedback about better/more informative messages for 
>> end users.
>>
>> Note if you haven't downloaded a new one for a while: because it will 
>> first have to patch some names to make sure all paths are correct, the 
>> first launch will take a LONG time.
>>
>

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Re: [sage-devel] Re: Make OpenBLAS Error

2017-04-11 Thread Steven Trogdon 
>From a bash shell where you build Sage:

export OPENBLAS_CONFIGURE="TARGET=ATOM" MAKE="make -j5 -l3.5"

should set the important variables. This is the MAKE I use for a very, very 
old 4 core machine. The OPENBLAS_CONFIGURE variable is alluded to 
in build/pkgs/openblas/spkg-check but I find it no where else. Somewhere in 
the openblas code there is a listing of supported architectures. I don't 
know how many ATOM processor variations there are? And getting the openblas 
code to work properly is probably an upstream issue.

On Tuesday, April 11, 2017 at 2:23:42 PM UTC-5, Ackbach wrote:
>
> All right! Sage 7.6 compiled correctly, so far as I know. I haven't run 
> the tests, but it opens into a notebook in Firefox, and correctly computes
>
> integrate(e^(-x^2),x,-infinity,infinity)
>
> Is there a way to combine the OPENBLAS_CONFIGURE command with the -j4 
> option for using multiple cores to compile? It did take a VERY long time to 
> compile - I think it was about 8 hours. 
>
> In any case, targeting an ATOM processor seems like a common-enough 
> occurrence that it deserves a mention in the manual, if it's not there 
> already (I haven't looked, and please don't shoot me).
>
> Thanks much!
>
> Cheers.
>
> On Tuesday, April 11, 2017 at 6:50:10 AM UTC-4, Ackbach wrote:
>>
>> 7.5.1 failed to build. Looks like the same error as before. I'll try 
>> Steven's linked suggestion with 7.6, and see if that flies. 
>>
>> Thanks for all your help, by the way! 
>>
>> One suggestion: if the OPENBLAS_CONFIGURE="TARGET=ATOM" make command 
>> builds everything correctly, then maybe the next version of Sage could 
>> automate processor detection and do the right switches on that basis? 
>>
>> Cheers.
>>
>> On Tuesday, April 11, 2017 at 12:45:44 AM UTC-4, Steven Trogdon wrote:
>>>
>>> It is curious that 7.5.1 would build but not 7.6. You might get some 
>>> mileage with
>>>
>>> OPENBLAS_CONFIGURE="TARGET=ATOM" make 
>>>
>>> See this thread:
>>>
>>> https://groups.google.com/forum/#!topic/sage-release/3QJoAgg9bgo
>>>
>>> On Monday, April 10, 2017 at 8:00:51 PM UTC-5, Ackbach wrote:

 I'm afraid I don't have that data. I will say I've never been able to 
 compile Sage 7.6 the first time. I have definitely been able to compile 
 7.5.1 and earlier the first time, though sometimes there are still errors. 
 I can try to compile 7.5.1 on this machine and get back to you how it 
 works.

 On Monday, April 10, 2017 at 4:17:38 PM UTC-4, François wrote:
>
> Did it start happening with openblas 0.2.19 or did it suddenly happen 
> one release build openblas 0.2.19 successfully and the next didn’t? 
> I suspect it is a CPU detection problem, we have seen similar logs 
> before on atom chips. 
>
> François 
>
> > On 11/04/2017, at 07:45, Ackbach  wrote: 
> > 
> > Having issues building the same package. Only I get a different log 
> file. I always prefer building Sage from scratch for performance, but 
> have 
> lately been having trouble doing so, as Sage keeps failing to build. 
> Background: 
> > 
> > OS: Debian 8.7, 64-bit. 
> > Sage Version: 7.6. 
> > HW: Lenovo ThinkPad 11e, 120GB SSD, 8GB RAM, Intel Celeron N2940, 
> with 4 cpu cores (as evidenced by the cat /proc/cpuinfo command). 
> > 
> > I follow the instructions for [installing from source](
> http://doc.sagemath.org/html/en/installation/source.html), and I 
> execute the MAKE='make -j4' make command. The compile gets quite a ways 
> into the compile. It finishes compiling maxima, in fact, and then I get 
> the 
> following error message: 
> > 
> > Error building Sage. 
> > 
> > The following package(s) may have failed to build (not necessarily 
> during this run of 'make all'): 
> > 
> > * package: openblas-0.2.19.p0 
> >   log file: 
> /home/akeister/Downloads/sage-7.6/logs/pkgs/openblas-0.2.19.p0.log 
> >   build directory: 
> /home/akeister/Downloads/sage-7.6/local/var/tmp/sage/build/openblas-0.2.19.p0
>  
>
> > 
> > I have attached the indicated log file, where it says to contact 
> this group. You can see that the issue is different from the OP, but it's 
> still a problem compiling that package. 
> > 
> > Ideas? 
> > 
> > Thanks for your time! 
> > 
> > Cheers, 
> > Adrian 
> > 
> > On Wednesday, October 12, 2016 at 12:43:20 PM UTC-4, Ethan Petersen 
> wrote: 
> > Hello all, 
> > 
> > I'm building sage on a Lenovo Thinkpad W540 with Ubuntu 16.04, and 
> there was an "Error building OpenBLAS"/"Error installing package 
> openblas-0.2.19" with a suggestion to email this google group with the 
> attached log file. If anyone has ideas on solving this issue, please let 
> me 
> know! 
> > 
> > Thanks, 
> > 
> > Ethan 
> > 
> > -- 
> > You received this

[sage-devel] Re: SageNB -> Jupyter conversion needs testers

2017-04-11 Thread dimpase 
it does not work for me, or at least I must be doing something wrong.
I get to the page listing the notebooks to convert, and then, if I click on 
a notebook, I get a weird page asking for a password or a token.

Password or token:
 Log in

Token authentication is enabled. You need to open the notebook server with 
its first-time login token in the URL, or enable a password in order to 
gain access. The command:

jupyter notebook list

will show you the URLs of running servers with their tokens, which you can 
copy and paste into your browser. For example:

Currently running servers:
http://localhost:/?token=c8de56fa... :: /Users/you/notebooks

Or you can paste just the token value into the password field on this page.

Cookies are required for authenticated access to notebooks.



What I see above doesn't look as a valid URL, and then WTF is the token I 
can paste instead?

I tried c8de56fa, it didn't work. I tried clicking on the URL, it brings me 
back to the page to choose

the notebooks...

 Arrgh... Give me my console any time...





On Tuesday, April 11, 2017 at 3:04:42 PM UTC+1, kcrisman wrote:
>
> This is now default in the Sage 8.0 beta series, and we strongly welcome 
> testers!  For a limited time only I have posted a binary of the app bundle 
> at 
>
>
> http://www.math.gordon.edu/~kcrisman/sage-8.0.beta0-OSX_10.11.6-x86_64.app.dmg
>
> This should work on both Mac 10.11 and 10.12.   For bandwidth reasons I 
> would prefer if those with the ability simply upgrade and build from 
> scratch, but testing this app is also necessary.
>
> PLEASE TRY THIS and report back if you are at all interested in making 
> sure that Sage 8.0 doesn't come with nasty surprises for long-time sagenb 
> users.  Preliminary testing makes it seem as if we are okay, but it would 
> be very helpful to have feedback about better/more informative messages for 
> end users.
>
> Note if you haven't downloaded a new one for a while: because it will 
> first have to patch some names to make sure all paths are correct, the 
> first launch will take a LONG time.
>

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[sage-combinat-devel] How to cite properly if we use Schur and skew Schur functions?

2017-04-11 Thread Egor Maximenko 
Dear Sage-Combinat developers, jointly with my colleagues we are using Sage 
to test some formulas involving Schur and skew Schur functions.
Principally we use SymmetricFunctions(QQ).s(), 
SymmetricFunctions(QQ).s.skew_schur(), and algebraic operations in the 
Schur basis.
What would be the best way to acknowledge the developers?

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Re: [sage-devel] Re: Make OpenBLAS Error

2017-04-11 Thread Ackbach 
All right! Sage 7.6 compiled correctly, so far as I know. I haven't run the 
tests, but it opens into a notebook in Firefox, and correctly computes

integrate(e^(-x^2),x,-infinity,infinity)

Is there a way to combine the OPENBLAS_CONFIGURE command with the -j4 
option for using multiple cores to compile? It did take a VERY long time to 
compile - I think it was about 8 hours. 

In any case, targeting an ATOM processor seems like a common-enough 
occurrence that it deserves a mention in the manual, if it's not there 
already (I haven't looked, and please don't shoot me).

Thanks much!

Cheers.

On Tuesday, April 11, 2017 at 6:50:10 AM UTC-4, Ackbach wrote:
>
> 7.5.1 failed to build. Looks like the same error as before. I'll try 
> Steven's linked suggestion with 7.6, and see if that flies. 
>
> Thanks for all your help, by the way! 
>
> One suggestion: if the OPENBLAS_CONFIGURE="TARGET=ATOM" make command 
> builds everything correctly, then maybe the next version of Sage could 
> automate processor detection and do the right switches on that basis? 
>
> Cheers.
>
> On Tuesday, April 11, 2017 at 12:45:44 AM UTC-4, Steven Trogdon wrote:
>>
>> It is curious that 7.5.1 would build but not 7.6. You might get some 
>> mileage with
>>
>> OPENBLAS_CONFIGURE="TARGET=ATOM" make 
>>
>> See this thread:
>>
>> https://groups.google.com/forum/#!topic/sage-release/3QJoAgg9bgo
>>
>> On Monday, April 10, 2017 at 8:00:51 PM UTC-5, Ackbach wrote:
>>>
>>> I'm afraid I don't have that data. I will say I've never been able to 
>>> compile Sage 7.6 the first time. I have definitely been able to compile 
>>> 7.5.1 and earlier the first time, though sometimes there are still errors. 
>>> I can try to compile 7.5.1 on this machine and get back to you how it works.
>>>
>>> On Monday, April 10, 2017 at 4:17:38 PM UTC-4, François wrote:

 Did it start happening with openblas 0.2.19 or did it suddenly happen 
 one release build openblas 0.2.19 successfully and the next didn’t? 
 I suspect it is a CPU detection problem, we have seen similar logs 
 before on atom chips. 

 François 

 > On 11/04/2017, at 07:45, Ackbach  wrote: 
 > 
 > Having issues building the same package. Only I get a different log 
 file. I always prefer building Sage from scratch for performance, but have 
 lately been having trouble doing so, as Sage keeps failing to build. 
 Background: 
 > 
 > OS: Debian 8.7, 64-bit. 
 > Sage Version: 7.6. 
 > HW: Lenovo ThinkPad 11e, 120GB SSD, 8GB RAM, Intel Celeron N2940, 
 with 4 cpu cores (as evidenced by the cat /proc/cpuinfo command). 
 > 
 > I follow the instructions for [installing from source](
 http://doc.sagemath.org/html/en/installation/source.html), and I 
 execute the MAKE='make -j4' make command. The compile gets quite a ways 
 into the compile. It finishes compiling maxima, in fact, and then I get 
 the 
 following error message: 
 > 
 > Error building Sage. 
 > 
 > The following package(s) may have failed to build (not necessarily 
 during this run of 'make all'): 
 > 
 > * package: openblas-0.2.19.p0 
 >   log file: 
 /home/akeister/Downloads/sage-7.6/logs/pkgs/openblas-0.2.19.p0.log 
 >   build directory: 
 /home/akeister/Downloads/sage-7.6/local/var/tmp/sage/build/openblas-0.2.19.p0
  

 > 
 > I have attached the indicated log file, where it says to contact this 
 group. You can see that the issue is different from the OP, but it's still 
 a problem compiling that package. 
 > 
 > Ideas? 
 > 
 > Thanks for your time! 
 > 
 > Cheers, 
 > Adrian 
 > 
 > On Wednesday, October 12, 2016 at 12:43:20 PM UTC-4, Ethan Petersen 
 wrote: 
 > Hello all, 
 > 
 > I'm building sage on a Lenovo Thinkpad W540 with Ubuntu 16.04, and 
 there was an "Error building OpenBLAS"/"Error installing package 
 openblas-0.2.19" with a suggestion to email this google group with the 
 attached log file. If anyone has ideas on solving this issue, please let 
 me 
 know! 
 > 
 > Thanks, 
 > 
 > Ethan 
 > 
 > -- 
 > You received this message because you are subscribed to the Google 
 Groups "sage-devel" group. 
 > To unsubscribe from this group and stop receiving emails from it, 
 send an email to sage-devel+...@googlegroups.com. 
 > To post to this group, send email to sage-...@googlegroups.com. 
 > Visit this group at https://groups.google.com/group/sage-devel. 
 > For more options, visit https://groups.google.com/d/optout. 
 >  



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Re: [sage-devel] OSX Xcode 8.3 breaks openblas

2017-04-11 Thread John H Palmieri 
Right, I have haswell.

  John


On Monday, April 10, 2017 at 3:22:49 PM UTC-7, Volker Braun wrote:
>
> It might be hardware specific; I take it you don't have a sandy bridge CPU?
>
>
>
> On Tuesday, April 11, 2017 at 12:19:26 AM UTC+2, John H Palmieri wrote:
>>
>> I ran Xcode to make sure it would update any component pieces and then 
>> ran a build from scratch. Openblas built just fine for me (same Xcode 
>> version).
>>
>

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[sage-devel] Fwd: [sagemath-admins] CDN's mathjax will go by the end of the month

2017-04-11 Thread Dima Pasechnik 
-- Forwarded message --
From: Harald Schilly 
Date: Tue, Apr 11, 2017 at 4:06 PM
Subject: Re: [sagemath-admins] CDN's mathjax will go by the end of the month
To: sagemath-admins 


I'll patch the documentation that's currently online, but of course,
fixing this properly in the sage documentation would be great :-)

On Tue, Apr 11, 2017 at 2:00 PM, Dima Pasechnik  wrote:
>
> In case you missed it: https://www.mathjax.org/
> says that they are shutting down their CDN.
> They will provide a temporary redirect to cdnjs, which is also their
> recommended substitution.
>
> Anyway this has to be looked at.
>
> --
>
> ---
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[sage-devel] Re: Building linbox-1.4.2 fails

2017-04-11 Thread Sho Takemori 
Thank you for answering. It seems that an Amazon EC2 instance doesn't have 
swap by default. I will add swap (and increase the memory) and try 
 building again.

2017年4月11日火曜日 16時11分57秒 UTC+2 Dima Pasechnik:
>
> you're getting
>
>
> g++: internal compiler error: Killed (program cc1plus)
>
>
> which might indicate that you need more memory (or at least more swap).
>
>
>
> On Tuesday, April 11, 2017 at 2:18:38 PM UTC+1, Sho Takemori wrote:
>>
>> Dear all,
>>
>> I try to build Sage using Amazon EC2 t2.micro.
>> But building linbox fails. The attached file is "linbox-1.4.2.log".
>> Building linbox using the latest head of the repository (
>> https://github.com/linbox-team/linbox) succeeds.
>>
>> I tried to build Sage as follows.
>> $ sudo apt-get install -y build-essential m4 git python-pip gdb
>> $ git clone https://github.com/sagemath/binary-pkg.git
>> $ cd binary-pkg
>> $ make bdist-sage-linux
>>
>> Here is some information of the computer.
>> os: Ubuntu Server 16.04 LTS
>> cpu: Intel(R) Xeon(R) CPU E5-2676 v3 @ 2.40GHz
>> memory: 1GiB
>> disc space: 30GiB
>>
>> When making an instance, I choosed "Ubuntu Server 16.04 LTS (HVM), SSD 
>> Volume Type", "t2.micro"
>> "SSD (gp2)" (general type) and made storage of 30GiB.
>>
>> The following is an error message.
>> Any help would be appropriated.
>>
>> Best regards,
>> Sho Takemori
>> ==
>> make[4]: Leaving directory
>>
>> '/home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g/build/make'
>>
>> real1534m41.475s
>> user1415m20.256s
>> sys 91m36.328s
>> ***
>> Error building Sage.
>>
>> The following package(s) may have failed to build (not necessarily
>> during this run of 'make all'):
>>
>> * package: linbox-1.4.2
>>   log file: 
>> /home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g/logs/pkgs/linbox-1.4.2.log
>>   build directory: 
>> /home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g/local/var/tmp/sage/build/linbox-1.4.2
>>
>> 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.
>>
>> Makefile:16: recipe for target 'all' failed
>> make[3]: *** [all] Error 1
>> make[3]: Leaving directory 
>> '/home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g'
>> ERROR:root:Script failed:
>> ERROR:root:export SAGE_FAT_BINARY=yes
>> export SAGE_PARALLEL_SPKG_BUILD=yes
>> export MAKE='make -j1'
>> make || exit 1
>> git gc --aggressive --prune=now
>>
>> Traceback (most recent call last):
>>   File "/home/ubuntu/binary-pkg/tools/binary-pkg/lib/python3.4/runpy.py", 
>> line 170, in _run_module_as_main
>> "__main__", mod_spec)
>>   File "/home/ubuntu/binary-pkg/tools/binary-pkg/lib/python3.4/runpy.py", 
>> line 85, in _run_code
>> exec(code, run_globals)
>>   File "/home/ubuntu/binary-pkg/binary_pkg/cmdline.py", line 78, in 
>> 
>> launch()
>>   File "/home/ubuntu/binary-pkg/binary_pkg/cmdline.py", line 69, in launch
>> config.build_script.run()
>>   File "/home/ubuntu/binary-pkg/binary_pkg/bash_script.py", line 37, in 
>> run
>> ['bash', self._filename], cwd=self._cwd, env=self.env())
>>   File 
>> "/home/ubuntu/binary-pkg/tools/binary-pkg/lib/python3.4/subprocess.py", 
>> line 561, in check_call
>> raise CalledProcessError(retcode, cmd)
>> subprocess.CalledProcessError: Command '['bash', 
>> '/home/ubuntu/binary-pkg/tmp/SageMath/tmp54_ystid.sh']' returned non-zero 
>> exit status 1
>> Makefile:16: recipe for target 'build-sage' failed
>> make[2]: *** [build-sage] Error 1
>> make[2]: Leaving directory '/home/ubuntu/binary-pkg'
>> Makefile:26: recipe for target 'package-sage' failed
>> make[1]: *** [package-sage] Error 2
>> make[1]: Leaving directory '/home/ubuntu/binary-pkg'
>> sage.mk:4: recipe for target 'bdist-sage-linux' failed
>> make: *** [bdist-sage-linux] Error 2
>> ==
>>
>>

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[sage-devel] Re: Building linbox-1.4.2 fails

2017-04-11 Thread Dima Pasechnik 
you're getting


g++: internal compiler error: Killed (program cc1plus)


which might indicate that you need more memory (or at least more swap).



On Tuesday, April 11, 2017 at 2:18:38 PM UTC+1, Sho Takemori wrote:
>
> Dear all,
>
> I try to build Sage using Amazon EC2 t2.micro.
> But building linbox fails. The attached file is "linbox-1.4.2.log".
> Building linbox using the latest head of the repository (
> https://github.com/linbox-team/linbox) succeeds.
>
> I tried to build Sage as follows.
> $ sudo apt-get install -y build-essential m4 git python-pip gdb
> $ git clone https://github.com/sagemath/binary-pkg.git
> $ cd binary-pkg
> $ make bdist-sage-linux
>
> Here is some information of the computer.
> os: Ubuntu Server 16.04 LTS
> cpu: Intel(R) Xeon(R) CPU E5-2676 v3 @ 2.40GHz
> memory: 1GiB
> disc space: 30GiB
>
> When making an instance, I choosed "Ubuntu Server 16.04 LTS (HVM), SSD 
> Volume Type", "t2.micro"
> "SSD (gp2)" (general type) and made storage of 30GiB.
>
> The following is an error message.
> Any help would be appropriated.
>
> Best regards,
> Sho Takemori
> ==
> make[4]: Leaving directory
>
> '/home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g/build/make'
>
> real1534m41.475s
> user1415m20.256s
> sys 91m36.328s
> ***
> Error building Sage.
>
> The following package(s) may have failed to build (not necessarily
> during this run of 'make all'):
>
> * package: linbox-1.4.2
>   log file: 
> /home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g/logs/pkgs/linbox-1.4.2.log
>   build directory: 
> /home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g/local/var/tmp/sage/build/linbox-1.4.2
>
> 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.
>
> Makefile:16: recipe for target 'all' failed
> make[3]: *** [all] Error 1
> make[3]: Leaving directory 
> '/home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g'
> ERROR:root:Script failed:
> ERROR:root:export SAGE_FAT_BINARY=yes
> export SAGE_PARALLEL_SPKG_BUILD=yes
> export MAKE='make -j1'
> make || exit 1
> git gc --aggressive --prune=now
>
> Traceback (most recent call last):
>   File "/home/ubuntu/binary-pkg/tools/binary-pkg/lib/python3.4/runpy.py", 
> line 170, in _run_module_as_main
> "__main__", mod_spec)
>   File "/home/ubuntu/binary-pkg/tools/binary-pkg/lib/python3.4/runpy.py", 
> line 85, in _run_code
> exec(code, run_globals)
>   File "/home/ubuntu/binary-pkg/binary_pkg/cmdline.py", line 78, in 
> 
> launch()
>   File "/home/ubuntu/binary-pkg/binary_pkg/cmdline.py", line 69, in launch
> config.build_script.run()
>   File "/home/ubuntu/binary-pkg/binary_pkg/bash_script.py", line 37, in run
> ['bash', self._filename], cwd=self._cwd, env=self.env())
>   File 
> "/home/ubuntu/binary-pkg/tools/binary-pkg/lib/python3.4/subprocess.py", 
> line 561, in check_call
> raise CalledProcessError(retcode, cmd)
> subprocess.CalledProcessError: Command '['bash', 
> '/home/ubuntu/binary-pkg/tmp/SageMath/tmp54_ystid.sh']' returned non-zero 
> exit status 1
> Makefile:16: recipe for target 'build-sage' failed
> make[2]: *** [build-sage] Error 1
> make[2]: Leaving directory '/home/ubuntu/binary-pkg'
> Makefile:26: recipe for target 'package-sage' failed
> make[1]: *** [package-sage] Error 2
> make[1]: Leaving directory '/home/ubuntu/binary-pkg'
> sage.mk:4: recipe for target 'bdist-sage-linux' failed
> make: *** [bdist-sage-linux] Error 2
> ==
>
>

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[sage-devel] Re: SageNB -> Jupyter conversion needs testers

2017-04-11 Thread kcrisman 
This is now default in the Sage 8.0 beta series, and we strongly welcome 
testers!  For a limited time only I have posted a binary of the app bundle 
at 

http://www.math.gordon.edu/~kcrisman/sage-8.0.beta0-OSX_10.11.6-x86_64.app.dmg

This should work on both Mac 10.11 and 10.12.   For bandwidth reasons I 
would prefer if those with the ability simply upgrade and build from 
scratch, but testing this app is also necessary.

PLEASE TRY THIS and report back if you are at all interested in making sure 
that Sage 8.0 doesn't come with nasty surprises for long-time sagenb users. 
 Preliminary testing makes it seem as if we are okay, but it would be very 
helpful to have feedback about better/more informative messages for end 
users.

Note if you haven't downloaded a new one for a while: because it will first 
have to patch some names to make sure all paths are correct, the first 
launch will take a LONG time.

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Re: [sage-devel] sage.misc.package considered harmful

2017-04-11 Thread Isuru Fernando 
> I welcome the work on the Conda port because it will allow just
that in the medium term. You could replace the whole sage packaging
with Conda and a few scripts to set things up. Once you do that
sage.misc.package should die (and please do not replace it by calls
to Conda).

FYI, I have a branch here, https://github.com/isuruf/sage/commits/conda2
that installs dependencies using conda if it exists and otherwise uses
spkg-install. What it does is it'll install the dependencies using conda if
it finds a file named conda-pkg-name in `build/pkgs//`. This is a
hack, and it'll take a lot of work to replace the sage package manager with
conda.

On Wed, Apr 5, 2017 at 5:00 AM, Francois Bissey <
francois.bis...@canterbury.ac.nz> wrote:

>
> > On 5/04/2017, at 11:25, Nils Bruin  wrote:
> >
> > On Tuesday, April 4, 2017 at 4:01:50 PM UTC-7, François wrote:
> >
> > With the current system you could install and then remove
> > some essential files manually and the doctesting framework
> > would still try to use it. It is installed according to the
> > packaging system after all. runtime testing would have a better
> > chance to avoid broken packages.
> >
> > Hm, I don't see that as an advantage. A broken package shouldn't be just
> avoided, it should be reported, so that it can be repaired or uninstalled.
> Just silently avoiding broken functionality makes it harder to diagnose.
> >
>
> Ha, I was thinking of a different kind of broken. I was thinking
> of user mistake, you are thinking of systemic problems.
>
> I guess the doctesting framework could output a list of software
> not tested because it thinks it is absent or not working.
> A discrepancy could be spotted but that is not as direct, I agree.
>
> François
>
> --
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>

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[sage-devel] Building linbox-1.4.2 fails

2017-04-11 Thread Sho Takemori 
Dear all,

I try to build Sage using Amazon EC2 t2.micro.
But building linbox fails. The attached file is "linbox-1.4.2.log".
Building linbox using the latest head of the repository 
(https://github.com/linbox-team/linbox) succeeds.

I tried to build Sage as follows.
$ sudo apt-get install -y build-essential m4 git python-pip gdb
$ git clone https://github.com/sagemath/binary-pkg.git
$ cd binary-pkg
$ make bdist-sage-linux

Here is some information of the computer.
os: Ubuntu Server 16.04 LTS
cpu: Intel(R) Xeon(R) CPU E5-2676 v3 @ 2.40GHz
memory: 1GiB
disc space: 30GiB

When making an instance, I choosed "Ubuntu Server 16.04 LTS (HVM), SSD 
Volume Type", "t2.micro"
"SSD (gp2)" (general type) and made storage of 30GiB.

The following is an error message.
Any help would be appropriated.

Best regards,
Sho Takemori
==
make[4]: Leaving directory
'/home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g/build/make'

real1534m41.475s
user1415m20.256s
sys 91m36.328s
***
Error building Sage.

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

* package: linbox-1.4.2
  log file: 
/home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g/logs/pkgs/linbox-1.4.2.log
  build directory: 
/home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g/local/var/tmp/sage/build/linbox-1.4.2

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.

Makefile:16: recipe for target 'all' failed
make[3]: *** [all] Error 1
make[3]: Leaving directory 
'/home/ubuntu/binary-pkg/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj24ng0bmdur5g21g'
ERROR:root:Script failed:
ERROR:root:export SAGE_FAT_BINARY=yes
export SAGE_PARALLEL_SPKG_BUILD=yes
export MAKE='make -j1'
make || exit 1
git gc --aggressive --prune=now

Traceback (most recent call last):
  File "/home/ubuntu/binary-pkg/tools/binary-pkg/lib/python3.4/runpy.py", 
line 170, in _run_module_as_main
"__main__", mod_spec)
  File "/home/ubuntu/binary-pkg/tools/binary-pkg/lib/python3.4/runpy.py", 
line 85, in _run_code
exec(code, run_globals)
  File "/home/ubuntu/binary-pkg/binary_pkg/cmdline.py", line 78, in 
launch()
  File "/home/ubuntu/binary-pkg/binary_pkg/cmdline.py", line 69, in launch
config.build_script.run()
  File "/home/ubuntu/binary-pkg/binary_pkg/bash_script.py", line 37, in run
['bash', self._filename], cwd=self._cwd, env=self.env())
  File 
"/home/ubuntu/binary-pkg/tools/binary-pkg/lib/python3.4/subprocess.py", 
line 561, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bash', 
'/home/ubuntu/binary-pkg/tmp/SageMath/tmp54_ystid.sh']' returned non-zero 
exit status 1
Makefile:16: recipe for target 'build-sage' failed
make[2]: *** [build-sage] Error 1
make[2]: Leaving directory '/home/ubuntu/binary-pkg'
Makefile:26: recipe for target 'package-sage' failed
make[1]: *** [package-sage] Error 2
make[1]: Leaving directory '/home/ubuntu/binary-pkg'
sage.mk:4: recipe for target 'bdist-sage-linux' failed
make: *** [bdist-sage-linux] Error 2
==

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Found local metadata for linbox-1.4.2
Attempting to download package linbox-1.4.2.tar.gz from mirrors
http://mirrors-usa.go-parts.com/sage/sagemath/spkg/upstream/linbox/linbox-1.4.2.tar.gz
[..]
linbox-1.4.2

Setting up build directory for linbox-1.4.2
Finished extraction
Applying patches from ../patches...
Applying ../patches/ticket-22318.patch
patching file benchmarks/data/Makefile.in
patching file benchmarks/Makefile.in
patching file benchmarks/matrix/Makefile.in
patching file configure
patching file configure.ac
patching file doc/Makefile.in
patching file examples/Makefile.in
patching file interfaces/driver/Makefile.am
patching file interfaces/driver/Makefile.in
patching file interfaces/kaapi/Makefile.in
patching file interfaces/Makefile.in
patching file interfaces/maple/Makefile.am
patching file interfaces/maple/Makefile.in
patching file

Re: [sage-devel] Re: Make OpenBLAS Error

2017-04-11 Thread Ackbach 
7.5.1 failed to build. Looks like the same error as before. I'll try 
Steven's linked suggestion with 7.6, and see if that flies. 

Thanks for all your help, by the way! 

One suggestion: if the OPENBLAS_CONFIGURE="TARGET=ATOM" make command builds 
everything correctly, then maybe the next version of Sage could automate 
processor detection and do the right switches on that basis? 

Cheers.

On Tuesday, April 11, 2017 at 12:45:44 AM UTC-4, Steven Trogdon wrote:
>
> It is curious that 7.5.1 would build but not 7.6. You might get some 
> mileage with
>
> OPENBLAS_CONFIGURE="TARGET=ATOM" make 
>
> See this thread:
>
> https://groups.google.com/forum/#!topic/sage-release/3QJoAgg9bgo
>
> On Monday, April 10, 2017 at 8:00:51 PM UTC-5, Ackbach wrote:
>>
>> I'm afraid I don't have that data. I will say I've never been able to 
>> compile Sage 7.6 the first time. I have definitely been able to compile 
>> 7.5.1 and earlier the first time, though sometimes there are still errors. 
>> I can try to compile 7.5.1 on this machine and get back to you how it works.
>>
>> On Monday, April 10, 2017 at 4:17:38 PM UTC-4, François wrote:
>>>
>>> Did it start happening with openblas 0.2.19 or did it suddenly happen 
>>> one release build openblas 0.2.19 successfully and the next didn’t? 
>>> I suspect it is a CPU detection problem, we have seen similar logs 
>>> before on atom chips. 
>>>
>>> François 
>>>
>>> > On 11/04/2017, at 07:45, Ackbach  wrote: 
>>> > 
>>> > Having issues building the same package. Only I get a different log 
>>> file. I always prefer building Sage from scratch for performance, but have 
>>> lately been having trouble doing so, as Sage keeps failing to build. 
>>> Background: 
>>> > 
>>> > OS: Debian 8.7, 64-bit. 
>>> > Sage Version: 7.6. 
>>> > HW: Lenovo ThinkPad 11e, 120GB SSD, 8GB RAM, Intel Celeron N2940, with 
>>> 4 cpu cores (as evidenced by the cat /proc/cpuinfo command). 
>>> > 
>>> > I follow the instructions for [installing from source](
>>> http://doc.sagemath.org/html/en/installation/source.html), and I 
>>> execute the MAKE='make -j4' make command. The compile gets quite a ways 
>>> into the compile. It finishes compiling maxima, in fact, and then I get the 
>>> following error message: 
>>> > 
>>> > Error building Sage. 
>>> > 
>>> > The following package(s) may have failed to build (not necessarily 
>>> during this run of 'make all'): 
>>> > 
>>> > * package: openblas-0.2.19.p0 
>>> >   log file: 
>>> /home/akeister/Downloads/sage-7.6/logs/pkgs/openblas-0.2.19.p0.log 
>>> >   build directory: 
>>> /home/akeister/Downloads/sage-7.6/local/var/tmp/sage/build/openblas-0.2.19.p0
>>>  
>>>
>>> > 
>>> > I have attached the indicated log file, where it says to contact this 
>>> group. You can see that the issue is different from the OP, but it's still 
>>> a problem compiling that package. 
>>> > 
>>> > Ideas? 
>>> > 
>>> > Thanks for your time! 
>>> > 
>>> > Cheers, 
>>> > Adrian 
>>> > 
>>> > On Wednesday, October 12, 2016 at 12:43:20 PM UTC-4, Ethan Petersen 
>>> wrote: 
>>> > Hello all, 
>>> > 
>>> > I'm building sage on a Lenovo Thinkpad W540 with Ubuntu 16.04, and 
>>> there was an "Error building OpenBLAS"/"Error installing package 
>>> openblas-0.2.19" with a suggestion to email this google group with the 
>>> attached log file. If anyone has ideas on solving this issue, please let me 
>>> know! 
>>> > 
>>> > Thanks, 
>>> > 
>>> > Ethan 
>>> > 
>>> > -- 
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>>> Groups "sage-devel" group. 
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>>> an email to sage-devel+...@googlegroups.com. 
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>>> > For more options, visit https://groups.google.com/d/optout. 
>>> >  
>>>
>>>

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