[sage-devel] Re: ImportError: This platform lacks a functioning sem_open implementation, ... see issue 3770

[Volker Braun]

Is there something in the Python build log 
(logs/pkgs/python2-2.7.13.p1.log) that would explain the issue with 
semaphores?


On Thursday, May 11, 2017 at 7:50:33 PM UTC+2, Kamil Pliszka wrote:
>
> Hi,
> I have problem when compiling sage7.6:
>
> ...
> [sagelib-7.6] building 'sage.tests.stl_vector' extension
> [sagelib-7.6] building 'sage.tests.cython' extension
> [sagelib-7.6] Executing 454 commands (using 1 thread)
> [sagelib-7.6] 
> 
> [sagelib-7.6] Traceback (most recent call last):
> [sagelib-7.6]   File "setup.py", line 768, in 
> [sagelib-7.6] ext_modules = ext_modules)
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/distutils/core.py", line 151, in 
> setup
> [sagelib-7.6] dist.run_commands()
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/distutils/dist.py", line 953, in 
> run_commands
> [sagelib-7.6] self.run_command(cmd)
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/distutils/dist.py", line 972, in 
> run_command
> [sagelib-7.6] cmd_obj.run()
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/distutils/command/build.py", line 
> 127, in run
> [sagelib-7.6] self.run_command(cmd_name)
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/distutils/cmd.py", line 326, in 
> run_command
> [sagelib-7.6] self.distribution.run_command(command)
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/distutils/dist.py", line 972, in 
> run_command
> [sagelib-7.6] cmd_obj.run()
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/distutils/command/build_ext.py", 
> line 340, in run
> [sagelib-7.6] self.build_extensions()
> [sagelib-7.6]   File "setup.py", line 514, in build_extensions
> [sagelib-7.6] execute_list_of_commands(compile_commands)
> [sagelib-7.6]   File "setup.py", line 316, in execute_list_of_commands
> [sagelib-7.6] execute_list_of_commands_in_parallel(command_list, 
> nthreads)
> [sagelib-7.6]   File "setup.py", line 263, in 
> execute_list_of_commands_in_parallel
> [sagelib-7.6] pool = Pool(nthreads)
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/multiprocessing/__init__.py", 
> line 232, in Pool
> [sagelib-7.6] return Pool(processes, initializer, initargs, 
> maxtasksperchild)
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/multiprocessing/pool.py", line 
> 138, in __init__
> [sagelib-7.6] self._setup_queues()
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/multiprocessing/pool.py", line 
> 233, in _setup_queues
> [sagelib-7.6] from .queues import SimpleQueue
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/multiprocessing/queues.py", line 
> 48, in 
> [sagelib-7.6] from .synchronize import Lock, BoundedSemaphore, 
> Semaphore, Condition
> [sagelib-7.6]   File 
> "/usr/local/src/sage-7.6/local/lib/python/multiprocessing/synchronize.py", 
> line 59, in 
> [sagelib-7.6] " function, see issue 3770.")
> [sagelib-7.6] ImportError: This platform lacks a functioning sem_open 
> implementation, therefore, the required synchronization primitives needed 
> will not function, see issue 3770.
> [sagelib-7.6] 
> 
> [sagelib-7.6] Error building the Sage library
> [sagelib-7.6] 
> 
> [sagelib-7.6] Please email sage-devel (
> http://groups.google.com/group/sage-devel)
> [sagelib-7.6] explaining the problem and including the relevant part of 
> the log file
> [sagelib-7.6]   /usr/local/src/sage-7.6/logs/pkgs/sagelib-7.6.log
> [sagelib-7.6] Describe your computer, operating system, etc.
> [sagelib-7.6] 
> 
> [sagelib-7.6] make[3]: *** [Makefile:34: sage] Error 1
> [sagelib-7.6] make[3]: Leaving directory '/usr/local/src/sage-7.6/src'
> [sagelib-7.6] 
> [sagelib-7.6] real  0m2.641s
> [sagelib-7.6] user  0m2.474s
> [sagelib-7.6] sys   0m0.150s
> make[2]: *** [Makefile:1040: sagelib] Error 2
> make[2]: Leaving directory '/usr/local/src/sage-7.6/build/make'
> make[1]: *** [Makefile:912: all] Error 2
> make[1]: Leaving directory '/usr/local/src/sage-7.6/build/make'
>
> real0m3.087s
> user0m2.863s
> sys 0m0.192s
> ***
> Error building Sage.
>
> The following package(s) may have failed to build (not necessarily
> during this run of 'make all'):
>
> * package: sagelib-7.6
>   log file: /usr/local/src/sage-7.6/logs/pkgs/sagelib-7.6.log
>   build directory: 
> /usr/local/src/sage-7.6/local/var/tmp/sage/build/sagelib-7.6
>
> The build directory may contain configuration files and other potentially
> helpful information. WARNING: if you now run 'make' again, the build
> directory will, by 

[sage-devel] ImportError: This platform lacks a functioning sem_open implementation, ... see issue 3770

[Kamil Pliszka]

Hi,
I have problem when compiling sage7.6:

...
[sagelib-7.6] building 'sage.tests.stl_vector' extension
[sagelib-7.6] building 'sage.tests.cython' extension
[sagelib-7.6] Executing 454 commands (using 1 thread)
[sagelib-7.6] 

[sagelib-7.6] Traceback (most recent call last):
[sagelib-7.6]   File "setup.py", line 768, in 
[sagelib-7.6] ext_modules = ext_modules)
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/distutils/core.py", line 151, in 
setup
[sagelib-7.6] dist.run_commands()
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/distutils/dist.py", line 953, in 
run_commands
[sagelib-7.6] self.run_command(cmd)
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/distutils/dist.py", line 972, in 
run_command
[sagelib-7.6] cmd_obj.run()
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/distutils/command/build.py", line 
127, in run
[sagelib-7.6] self.run_command(cmd_name)
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/distutils/cmd.py", line 326, in 
run_command
[sagelib-7.6] self.distribution.run_command(command)
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/distutils/dist.py", line 972, in 
run_command
[sagelib-7.6] cmd_obj.run()
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/distutils/command/build_ext.py", 
line 340, in run
[sagelib-7.6] self.build_extensions()
[sagelib-7.6]   File "setup.py", line 514, in build_extensions
[sagelib-7.6] execute_list_of_commands(compile_commands)
[sagelib-7.6]   File "setup.py", line 316, in execute_list_of_commands
[sagelib-7.6] execute_list_of_commands_in_parallel(command_list, 
nthreads)
[sagelib-7.6]   File "setup.py", line 263, in 
execute_list_of_commands_in_parallel
[sagelib-7.6] pool = Pool(nthreads)
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/multiprocessing/__init__.py", 
line 232, in Pool
[sagelib-7.6] return Pool(processes, initializer, initargs, 
maxtasksperchild)
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/multiprocessing/pool.py", line 
138, in __init__
[sagelib-7.6] self._setup_queues()
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/multiprocessing/pool.py", line 
233, in _setup_queues
[sagelib-7.6] from .queues import SimpleQueue
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/multiprocessing/queues.py", line 
48, in 
[sagelib-7.6] from .synchronize import Lock, BoundedSemaphore, 
Semaphore, Condition
[sagelib-7.6]   File 
"/usr/local/src/sage-7.6/local/lib/python/multiprocessing/synchronize.py", 
line 59, in 
[sagelib-7.6] " function, see issue 3770.")
[sagelib-7.6] ImportError: This platform lacks a functioning sem_open 
implementation, therefore, the required synchronization primitives needed 
will not function, see issue 3770.
[sagelib-7.6] 

[sagelib-7.6] Error building the Sage library
[sagelib-7.6] 

[sagelib-7.6] Please email sage-devel 
(http://groups.google.com/group/sage-devel)
[sagelib-7.6] explaining the problem and including the relevant part of the 
log file
[sagelib-7.6]   /usr/local/src/sage-7.6/logs/pkgs/sagelib-7.6.log
[sagelib-7.6] Describe your computer, operating system, etc.
[sagelib-7.6] 

[sagelib-7.6] make[3]: *** [Makefile:34: sage] Error 1
[sagelib-7.6] make[3]: Leaving directory '/usr/local/src/sage-7.6/src'
[sagelib-7.6] 
[sagelib-7.6] real  0m2.641s
[sagelib-7.6] user  0m2.474s
[sagelib-7.6] sys   0m0.150s
make[2]: *** [Makefile:1040: sagelib] Error 2
make[2]: Leaving directory '/usr/local/src/sage-7.6/build/make'
make[1]: *** [Makefile:912: all] Error 2
make[1]: Leaving directory '/usr/local/src/sage-7.6/build/make'

real0m3.087s
user0m2.863s
sys 0m0.192s
***
Error building Sage.

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

* package: sagelib-7.6
  log file: /usr/local/src/sage-7.6/logs/pkgs/sagelib-7.6.log
  build directory: 
/usr/local/src/sage-7.6/local/var/tmp/sage/build/sagelib-7.6

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.
-


seems my semaphores works ok
(read https://groups.google.com/forum/#!topic/sage-devel/uPqvQQ9GzNE)

bash-4.4$ mount | grep shm
tmpfs on /run/shm type tmpfs (rw,nosuid,nodev)

bash-4.4$ cat sem.c 
  

[sage-devel] Re: I need advice on my paper and Sage code on "Classifying bent functions by their Cayley graphs"

[Dima Pasechnik]

You might think about publishing this, with code, 
in http://rescience.github.io/

On Wednesday, May 10, 2017 at 1:25:13 PM UTC+1, Paul Leopardi wrote:
>
> Hello all,
>
> I have just completed the first draft of a paper, "Classifying bent 
> functions by their Cayley graphs". 
> 
>  
> The computational results of the paper are fully reproducible via worksheets 
> in a SageMathCloud public folder 
> 
>  
> and Sage code in a GitHub repository 
> .
> When I developed the code I tried to follow the Sage coding conventions 
> , but my 
> primary goal up until now has been to obtain results and finish the paper 
> while keeping the code as clear and readable as I could.
>
>
> The purpose of the code is to calculate the Cayley graph classifications 
> of the extended translation classes of bent functions, and their duals. All 
> of these terms are defined in the paper, but briefly,
>
>- A* bent function* is a Boolean function on an even number of bits 
>that is as far as possible (in Hamming weight distance) from any affine 
>Boolean function; equivalently a Boolean function whose Walsh-Hadamard 
>transform has constant absolute value.
>- The dual of a bent function *f* is obtained from the Walsh-Hadamard 
>transform of *f*, and is also a bent function.
>- The *Cayley graph* of a Boolean function* f*, with *f(0)=0*, is a 
>graph whose vertices are all the bit vectors of a given dimension, with an 
>edge between vectors x and y if and only if *f(x+y)=1*. This Cayley 
>graph is *strongly regular* if *f* is bent.
>- The *extended translation class* of a bent function *f* on boolean 
>vector space* V* is the set of all functions of the form *g(x) = 
>f(x+b) +  + d*, where *b, c* are in *V* and d is 0 or 1.
>- The *Cayley graph classification* of the extended translation class 
>of a bent function* f* is the set of all isomorphism classes of Cayley 
>graphs of the functions *f(x+b) +  + f(b)*.
>
> The output of the code is displayed in the paper, and in the SageMathCloud 
> worksheets, and (with some exceptions) is also saved as objects of class 
> *BentFunctionCayleyGraphClassification* in both the public folder and the 
> GitHub repository.
>
>
> Questions:
>
>1. Is there a process to ask for a code review of this type of code 
>(i.e. code primarily written to support a paper)?
>2. Do you have any suggestions as to how and where I could publish a 
>fully peer reviewed version of such a long (52 page draft) paper with so 
>many examples, tables and figures?
>3. Is there a process to promote this code, or a part of this code to 
>Sage itself? 
>Note: if this requires a complete rewrite then this could take me some 
>time, as it is a one-person project conducted in my spare time as an 
>Honorary Fellow of the University of Melbourne.
>4. Is there any interest in my further developing this code to include 
>a database (e.g. SQL) of Cayley graph classifications?
>
> Thanks!
>
>
> Paul Leopardi  
>
>
> PS. I have presented this work in stages at the University of Queensland 
> ,
>  
> the University of Newcastle 
> ,
>  
> and RMIT University 
> ,
>  
> and will also present it at 2MCGTC in Malta next month 
> .
>

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[sage-devel] Re: [sage-notebook] new sagenb pre-release, please test

[Dima Pasechnik]

On Thursday, May 11, 2017 at 4:19:22 PM UTC+1, Thierry 
(sage-googlesucks@xxx) wrote:
>
> Hi, 
>
> the "sage -sws2rst" command does not display code block properly (see 
> https://trac.sagemath.org/ticket/22512). 
>
> The following pull request should fix it (to be typed from the sagenb/ 
> repository at <1.0.rc0>): 
>
> git pull http://tmpsagenb.metelu.net/sagenb.git master 
>
> (the sha256sum of the commit is 2cb350173d08ac534485918f08bca849e4ac6126) 
>

merged in the master, thanks.

Dima

>
> Ciao, 
> Thierry 
>
>
>
>
> On Wed, May 10, 2017 at 07:12:26AM -0700, Dima Pasechnik wrote: 
> > 
> > 
> > Please test ​https://github.com/sagemath/sagenb/tree/1.0.rc0 (copy of 
> the 
> > current master) before I go ahead with making a new Sage package. It 
> works 
> > for me following the instructions in HASKING (updated, to take care of 
> > changed names and of the need to deal with mathjax). 
> > 
> > Report issues on github, please. 
> > 
> > 
> > Dima 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-notebook" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-noteboo...@googlegroups.com . 
> > Visit this group at https://groups.google.com/group/sage-notebook. 
> > For more options, visit https://groups.google.com/d/optout. 
>
>

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Re: [sage-devel] broken: http://old.files.sagemath.org/src-old/

[Pedro Cruz]

Thank you.
I've got the file I was looking for.
Pedro

quarta-feira, 10 de Maio de 2017 às 15:32:57 UTC+1, Harald Schilly escreveu:
>
> Hi, yes, the url is correct and file is hosted at 
> http://old.files.sagemath.org/src-old/ 
>
> The only problem was the server wasn't running. I don't know why, 
> something bad must have happened on the server. 
>
> @william, yes, those old tarballs are stored on GCS, too.  It's too 
> expensive to use it for hosting, though. 
>
> -- harald 
>
>
> On Wed, May 10, 2017 at 12:45 AM, William Stein  > wrote: 
> > Hi, 
> > 
> > I *have* a USB drive with all these files still.  It's 36GB of tarballs, 
> from 
> > 
> > sage-v0.3-2005-04-21-src.tar to sage-6.5.tar.gz 
> > 
> > I've posted them here so you can grab the one you want: 
> > 
> > 
> https://k8s.sagemath.org/187e8e97-d814-44c7-a8a5-ca9da39e5234/raw/src-old/index.html
>  
> > 
> > Any new thoughts about to host this stuff? 
> > 
> > Harald: what about uploading them to Google Cloud Storage? 
> > 
> > William 
> > 
> > 
> > On Tue, May 9, 2017 at 8:50 AM, kcrisman  > wrote: 
> >> 
> >> 
> >> On Monday, May 8, 2017 at 10:36:55 AM UTC-4, William wrote: 
> >>> 
> >>> On Mon, May 8, 2017 at 7:17 AM, Pedro Cruz  
> wrote: 
> >>> > Hello, 
> >>> > 
> >>> > I'm looking for version 5.2 and the above link is broken in master 
> >>> > www.sagemath.org pages. 
> >>> > 
> >>> > Some emails, in this forum, are also pointing to that link. 
> >>> > 
> >>> > Where can I find SageMtath 5.2 to try to compile it on Ubuntu 16.04? 
> >>> 
> >>> That's disturbing.  I don't know what the answer is. 
> >>> 
> >> 
> >> I believe that in this very forum some people discussed this and 
> although 
> >> some people (well, me) said it wasn't a good idea, the rest said it 
> wasn't 
> >> worth keeping.  If I recall this - see 
> >> 
> https://groups.google.com/forum/#!searchin/sage-devel/old$20tarballs%7Csort:date/sage-devel/WwguaTyKhE0/4YwXautvJLYJ
>  
> >> from a couple years ago, but that is not the discussion I am thinking 
> of. 
> >> 
> >> -- 
> >> 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. 
> > 
> > 
> > 
> > -- 
> > William (http://wstein.org) 
>

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[sage-devel] Re: [sage-notebook] new sagenb pre-release, please test

[Thierry]

Hi,

the "sage -sws2rst" command does not display code block properly (see
https://trac.sagemath.org/ticket/22512).

The following pull request should fix it (to be typed from the sagenb/
repository at <1.0.rc0>):

git pull http://tmpsagenb.metelu.net/sagenb.git master

(the sha256sum of the commit is 2cb350173d08ac534485918f08bca849e4ac6126)

Ciao,
Thierry




On Wed, May 10, 2017 at 07:12:26AM -0700, Dima Pasechnik wrote:
> 
> 
> Please test ​https://github.com/sagemath/sagenb/tree/1.0.rc0 (copy of the 
> current master) before I go ahead with making a new Sage package. It works 
> for me following the instructions in HASKING (updated, to take care of 
> changed names and of the need to deal with mathjax).
> 
> Report issues on github, please.
> 
> 
> Dima
> 
> -- 
> You received this message because you are subscribed to the Google Groups 
> "sage-notebook" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to sage-notebook+unsubscr...@googlegroups.com.
> Visit this group at https://groups.google.com/group/sage-notebook.
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[sage-devel] Re: new sagenb pre-release, please test

[Dima Pasechnik]

On Thursday, May 11, 2017 at 1:32:39 PM UTC+1, Enrique Artal wrote:
>
> Is there any particular change to test?
>

it's hard to say. It's an incremental update, incorporating perhaps 50 or 
so minor changes and tweaks.
The biggest changes are in making the code more Python-3 ready.
 
 

>
> El miércoles, 10 de mayo de 2017, 16:12:26 (UTC+2), Dima Pasechnik 
> escribió:
>>
>> Please test ​https://github.com/sagemath/sagenb/tree/1.0.rc0 (copy of 
>> the current master) before I go ahead with making a new Sage package. It 
>> works for me following the instructions in HASKING (updated, to take care 
>> of changed names and of the need to deal with mathjax).
>>
>> Report issues on github, please.
>>
>>
>> Dima
>>
>

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Re: [sage-devel] I need advice on my paper and Sage code on "Classifying bent functions by their Cayley graphs"

[Johan S . H . Rosenkilde]

Hi Paul,

>1. Is there a process to ask for a code review of this type of code 
>(i.e. code primarily written to support a paper)?

Alas, one of the weaknesses of the current research publication process...

>2. Do you have any suggestions as to how and where I could publish a 
>fully peer reviewed version of such a long (52 page draft) paper with so 
>many examples, tables and figures?

I'm not an expert on bent functions by a long shot, but I think Journal
of Designs, Codes and Cryptography would be appropriate. Otherwise, look
up recent journal papers on bent functions and see where they publish.

52 pages is quite long, though presumably a lot of this is tables and
pictures. You should be prepared that reviewers might ask you to
drastically shorten the exposition, perhaps by including fewer examples
in the main text and the rest in an online repository.

Another model is to have a shortish version - say 20-30 pages single
column - published in a journal, and then put an extended version on
arXiv.

Good luck.

Best,
Johan


Paul Leopardi writes:

> Hello all,
>
> I have just completed the first draft of a paper, "Classifying bent 
> functions by their Cayley graphs". 
> 
>  
> The computational results of the paper are fully reproducible via worksheets 
> in a SageMathCloud public folder 
> 
>  
> and Sage code in a GitHub repository 
> .
> When I developed the code I tried to follow the Sage coding conventions 
> , but my 
> primary goal up until now has been to obtain results and finish the paper 
> while keeping the code as clear and readable as I could.
>
>
> The purpose of the code is to calculate the Cayley graph classifications of 
> the extended translation classes of bent functions, and their duals. All of 
> these terms are defined in the paper, but briefly,
>
>- A* bent function* is a Boolean function on an even number of bits that 
>is as far as possible (in Hamming weight distance) from any affine Boolean 
>function; equivalently a Boolean function whose Walsh-Hadamard transform 
>has constant absolute value.
>- The dual of a bent function *f* is obtained from the Walsh-Hadamard 
>transform of *f*, and is also a bent function.
>- The *Cayley graph* of a Boolean function* f*, with *f(0)=0*, is a 
>graph whose vertices are all the bit vectors of a given dimension, with an 
>edge between vectors x and y if and only if *f(x+y)=1*. This Cayley 
>graph is *strongly regular* if *f* is bent.
>- The *extended translation class* of a bent function *f* on boolean 
>vector space* V* is the set of all functions of the form *g(x) = f(x+b) 
>+  + d*, where *b, c* are in *V* and d is 0 or 1.
>- The *Cayley graph classification* of the extended translation class of 
>a bent function* f* is the set of all isomorphism classes of Cayley 
>graphs of the functions *f(x+b) +  + f(b)*.
>
> The output of the code is displayed in the paper, and in the SageMathCloud 
> worksheets, and (with some exceptions) is also saved as objects of class 
> *BentFunctionCayleyGraphClassification* in both the public folder and the 
> GitHub repository.
>
>
> Questions:
>
>1. Is there a process to ask for a code review of this type of code 
>(i.e. code primarily written to support a paper)?
>2. Do you have any suggestions as to how and where I could publish a 
>fully peer reviewed version of such a long (52 page draft) paper with so 
>many examples, tables and figures?
>3. Is there a process to promote this code, or a part of this code to 
>Sage itself? 
>Note: if this requires a complete rewrite then this could take me some 
>time, as it is a one-person project conducted in my spare time as an 
>Honorary Fellow of the University of Melbourne.
>4. Is there any interest in my further developing this code to include a 
>database (e.g. SQL) of Cayley graph classifications?
>
> Thanks!
>
>
> Paul Leopardi  
>
>
> PS. I have presented this work in stages at the University of Queensland 
> ,
>  
> the University of Newcastle 
> ,
>  
> and RMIT University 
> ,
>  
> and will also present it at 2MCGTC in Malta next month 
> .

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[sage-devel] Re: new sagenb pre-release, please test

[Enrique Artal]

Is there any particular change to test?

El miércoles, 10 de mayo de 2017, 16:12:26 (UTC+2), Dima Pasechnik escribió:
>
> Please test ​https://github.com/sagemath/sagenb/tree/1.0.rc0 (copy of the 
> current master) before I go ahead with making a new Sage package. It works 
> for me following the instructions in HASKING (updated, to take care of 
> changed names and of the need to deal with mathjax).
>
> Report issues on github, please.
>
>
> Dima
>

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Re: [sage-devel] Re: segfault (involving flint, libthread, randstate)

[Jean-Pierre Flori]

Here's the bt for the latter example:

#0  visit_decref (op=0xfdc9906aac2f2efe, data=0x0) at Modules/gcmodule.c:360
#1  0x3fffad7f61e0 in 
__pyx_tp_traverse_4sage_4misc_9randstate_randstate (
o=0x3ffb1a37c5d0, v=@0x3fffb7f62aa8: 0x3fffb7eb91d0 , 
a=0x0)
at 
/home/jpflori/sage.git/src/build/cythonized/sage/misc/randstate.c:5496
#2  0x3fffb7eb95dc in subtract_refs (
containers=0x3fffb7f4db10 ) at Modules/gcmodule.c:385
#3  collect (generation=) at Modules/gcmodule.c:925
#4  0x3fffb7eba490 in gc_collect (self=, 
args=, kws=) at Modules/gcmodule.c:1121
#5  0x3fffb7dc77cc in PyCFunction_Call (func=0x3fffb0081878, 
arg=, kw=) at Objects/methodobject.c:85
#6  0x3fffb7e5d728 in call_function (oparg=, 
pp_stack=0x3fffa228) at Python/ceval.c:4352

On Thursday, May 11, 2017 at 12:09:55 PM UTC+2, vdelecroix wrote:
>
> The bug also shows up with 
> {{{ 
> sage: a = matrix(QQ, 1) 
> sage: a.randomize() 
> sage: del a 
> sage: import gc 
> sage: gc.collect() 
> }}} 
>
> On 11/05/2017 11:55, Dima Pasechnik wrote: 
> > given libpthread being involved, I guess it might have to do with GIL vs 
> > NOGIL stuff... 
> > 
> > 
> > On Thursday, May 11, 2017 at 10:50:39 AM UTC+1, vdelecroix wrote: 
> >> 
> >> Dear all, 
> >> 
> >> While working on [1] I stumbled on a strange segfault. Namely, with the 
> >> branch applied I got 
> >> 
> >> {{{ 
> >> sage: a = matrix(QQ, 1) 
> >> sage: a.randomize() 
> >> sage: quit 
> >> Exiting Sage (CPU time 0m1.48s, Wall time 0m5.80s). 
> >> 
>  
> >> .../cysignals/signals.so 
> >> .../cysignals/signals.so 
> >> .../cysignals/signals.so 
> >> .../libpthread.so.0 
> >> .../libpython2.7.so.1.0 
> >> .../sage/misc/randstate.so 
> >>  
> >> 
>  
> >> Unhandled SIGSEGV: A segmentation fault occurred. 
> >> 
>  
> >> }}} 
> >> 
> >> I indeed modified the randomization method to use flint random 
> >> generators, you can have a look at commits [2] and [3]. But I don't 
> >> understand at all where the error might come from. 
> >> 
> >> Any help would be more than welcome! 
> >> 
> >>   [1] https://trac.sagemath.org/ticket/22970 
> >>   [2] 
> >> 
> >> 
> https://git.sagemath.org/sage.git/commit?id=b52e2c347a28b301485c6cc5bb221873ca5ac636
>  
> >>   [3] 
> >> 
> >> 
> https://git.sagemath.org/sage.git/commit?id=d5ea72b364534c3ce4374c6d78b54852c8333cc3
>  
> >> 
> >> Best, 
> >> Vincent 
> >> 
> > 
>

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Re: [sage-devel] Re: segfault (involving flint, libthread, randstate)

[Vincent Delecroix]

I confused flint_rand_t and gmp_randstate_t. And our randstate does not 
support flint yet... I will postpone the changes to randomize to another 
ticket.


Sorry for the noise.

On 11/05/2017 11:55, Dima Pasechnik wrote:

given libpthread being involved, I guess it might have to do with GIL vs
NOGIL stuff...


On Thursday, May 11, 2017 at 10:50:39 AM UTC+1, vdelecroix wrote:


Dear all,

While working on [1] I stumbled on a strange segfault. Namely, with the
branch applied I got

{{{
sage: a = matrix(QQ, 1)
sage: a.randomize()
sage: quit
Exiting Sage (CPU time 0m1.48s, Wall time 0m5.80s).

.../cysignals/signals.so
.../cysignals/signals.so
.../cysignals/signals.so
.../libpthread.so.0
.../libpython2.7.so.1.0
.../sage/misc/randstate.so


Unhandled SIGSEGV: A segmentation fault occurred.

}}}

I indeed modified the randomization method to use flint random
generators, you can have a look at commits [2] and [3]. But I don't
understand at all where the error might come from.

Any help would be more than welcome!

  [1] https://trac.sagemath.org/ticket/22970
  [2]

https://git.sagemath.org/sage.git/commit?id=b52e2c347a28b301485c6cc5bb221873ca5ac636
  [3]

https://git.sagemath.org/sage.git/commit?id=d5ea72b364534c3ce4374c6d78b54852c8333cc3

Best,
Vincent





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Re: [sage-devel] Re: segfault (involving flint, libthread, randstate)

[Vincent Delecroix]

The bug also shows up with
{{{
sage: a = matrix(QQ, 1)
sage: a.randomize()
sage: del a
sage: import gc
sage: gc.collect()
}}}

On 11/05/2017 11:55, Dima Pasechnik wrote:

given libpthread being involved, I guess it might have to do with GIL vs
NOGIL stuff...


On Thursday, May 11, 2017 at 10:50:39 AM UTC+1, vdelecroix wrote:


Dear all,

While working on [1] I stumbled on a strange segfault. Namely, with the
branch applied I got

{{{
sage: a = matrix(QQ, 1)
sage: a.randomize()
sage: quit
Exiting Sage (CPU time 0m1.48s, Wall time 0m5.80s).

.../cysignals/signals.so
.../cysignals/signals.so
.../cysignals/signals.so
.../libpthread.so.0
.../libpython2.7.so.1.0
.../sage/misc/randstate.so


Unhandled SIGSEGV: A segmentation fault occurred.

}}}

I indeed modified the randomization method to use flint random
generators, you can have a look at commits [2] and [3]. But I don't
understand at all where the error might come from.

Any help would be more than welcome!

  [1] https://trac.sagemath.org/ticket/22970
  [2]

https://git.sagemath.org/sage.git/commit?id=b52e2c347a28b301485c6cc5bb221873ca5ac636
  [3]

https://git.sagemath.org/sage.git/commit?id=d5ea72b364534c3ce4374c6d78b54852c8333cc3

Best,
Vincent





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[sage-devel] Re: segfault (involving flint, libthread, randstate)

[Dima Pasechnik]

given libpthread being involved, I guess it might have to do with GIL vs 
NOGIL stuff...


On Thursday, May 11, 2017 at 10:50:39 AM UTC+1, vdelecroix wrote:
>
> Dear all, 
>
> While working on [1] I stumbled on a strange segfault. Namely, with the 
> branch applied I got 
>
> {{{ 
> sage: a = matrix(QQ, 1) 
> sage: a.randomize() 
> sage: quit 
> Exiting Sage (CPU time 0m1.48s, Wall time 0m5.80s). 
>  
> .../cysignals/signals.so 
> .../cysignals/signals.so 
> .../cysignals/signals.so 
> .../libpthread.so.0 
> .../libpython2.7.so.1.0 
> .../sage/misc/randstate.so 
>  
>  
> Unhandled SIGSEGV: A segmentation fault occurred. 
>  
> }}} 
>
> I indeed modified the randomization method to use flint random 
> generators, you can have a look at commits [2] and [3]. But I don't 
> understand at all where the error might come from. 
>
> Any help would be more than welcome! 
>
>   [1] https://trac.sagemath.org/ticket/22970 
>   [2] 
>
> https://git.sagemath.org/sage.git/commit?id=b52e2c347a28b301485c6cc5bb221873ca5ac636
>  
>   [3] 
>
> https://git.sagemath.org/sage.git/commit?id=d5ea72b364534c3ce4374c6d78b54852c8333cc3
>  
>
> Best, 
> Vincent 
>

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[sage-devel] segfault (involving flint, libthread, randstate)

[Vincent Delecroix]

Dear all,

While working on [1] I stumbled on a strange segfault. Namely, with the 
branch applied I got


{{{
sage: a = matrix(QQ, 1)
sage: a.randomize()
sage: quit
Exiting Sage (CPU time 0m1.48s, Wall time 0m5.80s).

.../cysignals/signals.so
.../cysignals/signals.so
.../cysignals/signals.so
.../libpthread.so.0
.../libpython2.7.so.1.0
.../sage/misc/randstate.so


Unhandled SIGSEGV: A segmentation fault occurred.

}}}

I indeed modified the randomization method to use flint random 
generators, you can have a look at commits [2] and [3]. But I don't 
understand at all where the error might come from.


Any help would be more than welcome!

 [1] https://trac.sagemath.org/ticket/22970
 [2] 
https://git.sagemath.org/sage.git/commit?id=b52e2c347a28b301485c6cc5bb221873ca5ac636
 [3] 
https://git.sagemath.org/sage.git/commit?id=d5ea72b364534c3ce4374c6d78b54852c8333cc3


Best,
Vincent

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Re: [sage-devel] Sage policy question: require docstrings and doctests?

[Kwankyu Lee]

I agree with Erik.
 

> This distinction between docstrings vs. comments has never been the Sage 
> practice: Sage practice and official policy has always been to use 
> docstrings. Part of the point is that Sage has intentionally tried to blur 
> the line between user and developer, so any documentation should be made as 
> widely available, and as easily available, as possible.
>

Perhaps this was a practice and reality when Sage was not mature. But for 
future and for better software, the right direction should be to make the 
line clear.  I (We are) am not a user and a developer at the same time: 
When I am a user, I would see docstrings and help on a terminal or in a web 
browser. When I am a developer, I would read the comments in the file as 
well as the docstrings. When I am a user, I hate to see irrelevant 
implementation or development details.

For original post and that particular example, I would add docstrings for 
all the four functions.

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Re: [sage-devel] sage on raspberry pi 3 fails to build gcc

[Thierry Dumont]

Le 11/05/2017 à 03:44, Brent Thomas a écrit :
> I have been trying to install sage on a raspberry pi 3. I didn't find a
> binary of any recent version, so I'm trying to build it from source.
> I've run into an error with sage building gcc. The relevant part of the
> gcc-5.4.0.log file is below.
> 

I have succeeded building sage from source on th pi3, possibly 8 months ago.
The installation succeeded without any difficulties.
The only problem was that, due to the lack of memory, I could not run
make in parallel; the compilation took more than 24 hours, but it worked.

t.d.

> g++   -g -DIN_GCC-fno-exceptions -fno-rtti
> -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings
> -Wcast-qual -Wno-format -Wmissing-format-attribute -Woverloaded-virtual
> -pedantic -Wno-long-long -Wno-variadi$
> lto/lto-lang.o lto/lto.o lto/lto-object.o attribs.o
> lto/lto-partition.o lto/lto-symtab.o libbackend.a main.o tree-browser.o
> libcommon-target.a libcommon.a ../libcpp/libcpp.a
> ../libdecnumber/libdecnumber.a  -L/home/pi/$
> collect2: error: ld returned 1 exit status
> ../../src/gcc/lto/Make-lang.in:71: recipe for target 'lto1' failed
> make[6]: *** [lto1] Error 1
> make[6]: Leaving directory
> '/home/pi/Downloads/sage-7.6/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/gcc'
> Makefile:4367: recipe for target 'all-stage1-gcc' failed
> make[5]: *** [all-stage1-gcc] Error 2
> make[5]: Leaving directory
> '/home/pi/Downloads/sage-7.6/local/var/tmp/sage/build/gcc-5.4.0/gcc-build'
> Makefile:19008: recipe for target 'stage1-bubble' failed
> make[4]: *** [stage1-bubble] Error 2
> make[4]: Leaving directory
> '/home/pi/Downloads/sage-7.6/local/var/tmp/sage/build/gcc-5.4.0/gcc-build'
> Makefile:899: recipe for target 'all' failed
> make[3]: *** [all] Error 2
> make[3]: Leaving directory
> '/home/pi/Downloads/sage-7.6/local/var/tmp/sage/build/gcc-5.4.0/gcc-build'
> 
> real64m56.236s
> user53m1.490s
> sys 2m58.710s
> 
> Error installing package gcc-5.4.0
> 
> 
> I've tried setting SAGE_INSTALL_GCC to no and using the default compiler
> (gcc 6.1.0) to build sage. Unfortunately, the ppl library fails to build
> when I do this as it can't find an appropriate version of the gmp
> library. (As a side note I can build ppl directly by setting the
> --with-gmp-prefix flag to the appropriate directory, but I don't know
> how to set this flag when building sage.)
> 
> Any advice on building sage on a raspberry pi would be welcome.
> 
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<>

Re: [sage-devel] Extend crypto module

[Johan S . H . Rosenkilde]

Hi Friedrich

I totally agree with 1) and 2): that kind of implementations would be
very appropriate and valuable to have in Sage. Concerning 3), I would
initially think that doc-tests could be sufficient.

I was loosely involved in some discussions on implementing the McEliece
public-key crypto-system #21352
(https://trac.sagemath.org/ticket/21352) which has since stalled since
the author left it. From there I remember that we noticed some
crufty-ness to the code in sage/crypto. For instance, though there is a
base-class Cipher, it doesn't have abstract methods for encrypting and
decrypting; as a result, it seems that different words has been used for
this all over (at least "enciphering", "encode", "encrypt"). The
existing PublicKeyCipher in sage/crypto/cipher.py is also sort of weird:
e.g. it inherits key() from Cipher, but in the only current
implementation - Blum-Goldwasser class - there is instead public_key()
and private_key(). Perhaps some cleanup and redesign is appropriate
here.

I really don't know about 4). If researchers and teachers find that
they can use a modular, high-level implementation of certain protocols,
then why not? But as with the ciphers themselves, the aim shouldn't be a
competitive, highly optimised implementation, I think, but rather
something that eases understanding and experimentation.

Best,
Johan



Friedrich Wiemer writes:

> Today I stumbled across https://trac.sagemath.org/ticket/11565 in where the 
> design of the crypto module is briefly discussed ...
>
> 1) While RSA might be not the best cipher to point out the following, this 
> certainly holds for block ciphers or other crypto primitives. During my 
> research work I often implement some cipher scheme in python from scratch, 
> because I want to tinker with it, maybe exchange some parts of it, etc. 
> Having these things in sage with a highly modularized design would really 
> ease this kind of work.
>
> 2) Having all the heavy mathematic stuff in sage, we can easily provide 
> implementations of, say, AES that are in fact their mathematical 
> descriptions. I think Rusydi H. Makarim already started working on this. In 
> my opinion, this has at least two advantages: First it is a great 
> educational tool for students to see, how this math "works in real" and 
> helps them in getting a better understanding whats actually going on. 
> Second it would allow to have a collection of reference implementations, 
> which (because of the above modularized approach) allow to easily generate 
> also intermediate test vectors. For me, this last point is really a big 
> plus, because often you only get "coarse-grained" testvectors from cipher 
> specifications like input/output of the whole encryption (sometimes also 
> intermediate results after a single round or so) - but I have never seen a 
> specification, which also provides intermediate results after the inner 
> parts of a round function or so. If you want to implement some optimized 
> version, you might be very happy, to have such test possibilities at hand.
>
> 3) So, from the end of point 2: It would also be nice, to have a lot of 
> test vectors for crypto schemes - maybe its already enough to have these in 
> the doctests, at least this would be a nice starting point.
>
> 4) This last point is somewhat of an abstraction above point 2, combined 
> with 1. Going a level up, to the crypto-protocol level, it would be quite 
> easy to implement protocols like TLS when all the basic crypto stuff is 
> readily available. I was told that there is no free TLS implementation in 
> python available, where you are actually able to exchange parts of the 
> protocol (this again might be interesting if you are doing research on such 
> a protocol). Regarding this point, I'm not sure if sage is the right place 
> to have such a protocol level implementation, because its main aim seem to 
> be a mathematical CAS.
>
> What are your opinions regarding this?

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