Re: [sage-support] Re: Sage 9.8.rc1 builds, but reports an empty list of packages failed.

[Dr. David Kirkby]

On Sat, 11 Feb 2023 at 22:11, Dima Pasechnik  wrote:

>
>
> I'm just running
>>
>> make -j ptestlong
>>
>
> yes. Although -j without a parameter is a bit risky...
>

Point taken Dima about using -j without a parameter. That could have been
tricky if doctesting had used thousands of threads.

TLDR: I have sage  9.8 built and passed all tests with the latest R. The
rpy in Sage is compatible with the latest R, and does not need updating
just to work with the current version of R

There are a couple of things bugging me.

* Sage is only doctesting with 8 threads.
* A message "pytest is not installed in the venv, skip checking tests that
rely on it" This is despite I have pytest - admittedly an old version.
* A weird failure of 'make' when pytest was not installed.

*This is what I did. *

1) Deleted anything and everything related to Conda. The fact it had
changed my prompt to have "(base)" in it, and the prompt seemed to take a
long time to appear when a terminal was opened, was not giving me a good
feeling. I felt the system was in charge of me, rather than the other way
around. 

2) Deleting *everything* Conda related meant deleting the recent R. The R I
had was from the Ubuntu repository, which is R version 3.6.3 (2020-02-29) -
i.e. almost 3 years old.

3) Built Sage with the old R 3.6.3

$ ./configure
$ make -j 50 ptestlong

sage built okay, using the old R.

When running the doctests I saw this message

*"Doctesting 4451 files using 8 threads"*

Why does Sage not use 50 threads when running the tests, but only 8? I'd
told make to use 50.

The following was the result of the doctesting. The build failed.

sage -t --long --warn-long 41.7
--random-seed=247878169657737533415589408317275108273
src/sage/tests/cmdline.py
[217 tests, 47.85 s]
--
sage -t --long --warn-long 41.7
--random-seed=247878169657737533415589408317275108273
src/sage/rings/polynomial/polynomial_quotient_ring_element.py * # 6
doctests failed*
--
Total time for all tests: 1898.7 seconds
cpu time: 12100.3 seconds
cumulative wall time: 13160.6 seconds
Features detected for doctesting:
4ti2,cvxopt,dvipng,gfan,graphviz,imagemagick,lrslib,nauty,palp,pandoc,pdf2svg,pdftocairo,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.misc.cython,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx
*pytest is not installed in the venv*, skip checking tests that rely on it
make[2]: *** [Makefile:273: test] Error 1
make[2]: Leaving directory '/home/drkirkby/sage-9.8'
make[1]: *** [Makefile:288: ptest] Error 2
make[1]: Leaving directory '/home/drkirkby/sage-9.8'
make: *** [Makefile:294: ptestlong] Error 2
drkirkby@canary:~/sage-9.8$

I expected to see a list of the tests that failed, but I didn't see any
list, despite polynomial_quotient_ring_element.py indicated 6 failures.

Next I decided to

1) Build the latest R from source, as I did not want a 3-year old version.
That needed quite a bit of work to get all the dependencies R wanted for an
optimal configuration. I'm not surprised that maintaining the R package was
difficult.

2) Install pytest as there was an error message about it not being
installed in the venv, whatever the venv is. (Typo for environment?) That
gave me pytest version 4.6.9. I see the latest is 7.x, so I assume 4.6.9 is
pretty old

3) Rebuild Sage.

$ ./configure
$ make -j 50 ptestlong.

This time, with pytest present, there's an error message it is not, but the
build does not fail. All tests pass. So the rpy in Sage is compatible with
the latest R, and does not need updating just to work with the current
version of R.


sage -t --long --warn-long 61.6
--random-seed=244047359021345785605807767847544173245
src/sage/libs/flint/fmpz_poly_mat.pxd
[0 tests, 0.00 s]
sage -t --long --warn-long 61.6
--random-seed=244047359021345785605807767847544173245
src/sage/schemes/toric/sheaf/__init__.py
[0 tests, 0.00 s]
--
*All tests passed!*
--
Total time for all tests: 1873.0 seconds
cpu time: 12087.9 seconds
cumulative wall time: 13194.0 seconds
Features detected for doctesting:
4ti2,cvxopt,dvipng,gfan,graphviz,imagemagick,lrslib,nauty,palp,pandoc,pdf2svg,pdftocairo,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.misc.cython,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx
pytest is not installed in the venv, skip checking tests that rely on it
make[2]: Leaving directory '/home/drkirkby/sage-9.8

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Re: [sage-support] Re: Sage 9.8.rc1 builds, but reports an empty list of packages failed.

[Dr. David Kirkby]

On Sat, 11 Feb 2023 at 22:22, julian...@gmail.com 
wrote:

> Hi Dave,
>
> On Saturday, February 11, 2023 at 10:33:04 PM UTC+2 David Kirkby wrote:
> (base) drkirkby@canary:~$ command -v R
> /home/drkirkby/miniforge3/bin/R
>
> something went wrong in your conda setup I believe. With the instructions
> in the documentation, R should be installed in the sage-dev environment and
> not in the base environment. Probably that mix caused trouble in the
> process at some point.
>
> julian
>

Thank you. I was not too keen on that condra setup. I didn’t understand
what it was doing. it changed my shell prompt, and increased the time for
the prompt to appear, which I was not expecting.

I have R in /usr/bin too. I dont know the version of that, and I am not
near the computer.

I started to build Sage from the source code, but stopped the process
before it had finished. The computer is in my lab, which is part of the
garage. I didn’t want to leave the computer on all night using power. It
takes 200 W when idle. 

I will restart later on.

Dave

>
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>
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Kirkby Microwave Ltd,
drkir...@kirkbymicrowave.co.uk
https://www.kirkbymicrowave.co.uk/
Telephone 01621-680100./ +44 1621 680100

Registered in England & Wales, company number 08914892.
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Re: [sage-support] Re: Sage 9.8.rc1 builds, but reports an empty list of packages failed.

[Dr. David Kirkby]

On Sat, 11 Feb 2023 at 21:31, Dima Pasechnik  wrote:

> we have 9.8 now :-)
> https://github.com/sagemath/sage/releases
>

Okay, I'm trying again.

It seems an unusual build process.
* There's a configure.ac, but no configure script.
* I typed make, which then builds a configure script, and exits with an
error message, telling one to run configure.
* The configure script suggested I added some packages, which I did.
* I run "make distclean" with the intention of starting fresh. But noticed
"make distclean" did not delete the configure script it had built earlier.
So it seems "make distclean" is not really working in the usual way.

I'm just running

make -j ptestlong

I don't know if that's still the way to run the tests. This is a reasonably
quick machine (52 cores), so I should be able to get though the tests
quickly if they run in parallel

After I'd written everything above, I just see your message about github.
I'll do that if I get any more issues.

Dave

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Re: [sage-support] Re: Sage 9.8.rc1 builds, but reports an empty list of packages failed.

[Dr. David Kirkby]

On Sat, 11 Feb 2023 at 21:06, Dima Pasechnik  wrote:

> On Sat, Feb 11, 2023 at 8:33 PM David Kirkby  wrote:
>
>> /home/drkirkby/miniforge3/bin/R
>
>
> Oh, you build in Conda...
> This might be a bit of a problem - it's not too well-tested for sure.
> Did you see https://doc.sagemath.org/html/en/installation/conda.html ?
>

Yes, someone suggested that I believe, when I had another problem earlier.
I basically followed the instructions there. It that's not tested well,
I'll download

https://www.mirrorservice.org/sites/www.sagemath.org/devel/sage-9.8.rc1.tar.gz

and see what happens. I might as well do the release candidate - I'm not
going to be doing anything serious with this now, so I don't mind the bugs.
If there is a real problem building with the latest R, I guess that should
be fixed before a new release.

I saw a comment from someone on one of the Sage mailing lists about the
version of R being packaged with Sage is old.

Dave

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[sage-support] Re: Sage 9.8.rc1 builds, but reports an empty list of packages failed.

[David Kirkby]

It looks like sagemath_doc_html-none.is failing to build - full log of that 
package only at 

https://www.kirkbymicrowave.co.uk/sagemath_doc_html-none.log

This is the end of the logfile. 

Build finished. The built documents can be found in 
/home/drkirkby/sage/local/share/doc/sage/inventory/en/reference/modfrm
[combinat ] no targets are out of date.
[combinat ] The inventory files are in 
../../local/share/doc/sage/inventory/en/reference/combinat.
Build finished. The built documents can be found in 
/home/drkirkby/sage/local/share/doc/sage/inventory/en/reference/combinat
Error in glue(.Internal(R.home()), "library", "base", "R", "base", sep = 
.Platform$file.sep) : 
  4 arguments passed to .Internal(paste) which requires 3
Error: could not find function "attach"
Error: object '.ArgsEnv' not found
Fatal error: unable to initialize the JIT

make[4]: *** [Makefile:28: doc-inventory--reference-interfaces] Error 2
make[3]: *** [Makefile:45: doc-inventory-reference] Error 2
(base) drkirkby@canary:~/sage$ scp 
/home/drkirkby/sage/logs/pkgs/sagemath_doc_html-none.log 
k...@kirkbymicrowave.co.uk:
sagemath_doc_html-none.log 
100%  162KB   2.5MB/s   
00:00
(base) drkirkby@canary:~/sage$


On Friday, 10 February 2023 at 20:17:38 UTC David Kirkby wrote:

> I got this rather weird error on Ubuntu 20.04. It says the following 
> packages failed to build, but does not say what they were! The hardware is 
> a Dell 7920 with 2 x 26 core CPUs and 384 GB RAM. 
>
> I put config.log here 
> https://www.kirkbymicrowave.co.uk/config.log
>
> and a compressed version of install.log here
> https://www.kirkbymicrowave.co.uk/install.log.bz2
>
>
> make[3]: *** [Makefile:3262: 
> /home/drkirkby/sage/local/var/lib/sage/installed/sagemath_doc_html-none] 
> Error 2
> make[2]: *** [Makefile:2766: all-start] Error 2
> make[2]: Leaving directory '/home/drkirkby/sage/build/make'
>
> real47m17.658s
> user220m4.574s
> sys14m6.540s
>
> install.log.bz2***
> Error building Sage.
>
> The following package(s) may have failed to build (not necessarily
> during this run of 'make all-start'):
>
> It is safe to delete any log files and build directories, but they
> contain information that is helpful for debugging build problems.
> WARNING: If you now run 'make' again, the build directory of the
> same version of the package will, by default, be deleted. Set the
> environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
>
> make[1]: *** [Makefile:40: all-start] Error 1
> make[1]: Leaving directory '/home/drkirkby/sage'
> make: *** [Makefile:13: all] Error 2
>
> *Trying to run the tests, it reports the following, which is not in the 
> log file uploaded. *
>
> real0m55.972s
> user8m4.622s
> sys0m47.623s
> ***
> Error building Sage.
>
> The following package(s) may have failed to build (not necessarily
> during this run of 'make all-start'):
>
> * package: sagemath_doc_html-none
>   last build time: Feb 10 20:12
>   log file:/home/drkirkby/sage/logs/pkgs/sagemath_doc_html-none.log
>
> It is safe to delete any log files and build directories, but they
> contain information that is helpful for debugging build problems.
> WARNING: If you now run 'make' again, the build directory of the
> same version of the package will, by default, be deleted. Set the
> environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
>
> make[1]: *** [Makefile:40: all-start] Error 1
> make[1]: Leaving directory '/home/drkirkby/sage'
> make: *** [Makefile:13: all] Error 2
>
>
>
>

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[sage-support] Sage 9.8.rc1 builds, but reports an empty list of packages failed.

[David Kirkby]

I got this rather weird error on Ubuntu 20.04. It says the following 
packages failed to build, but does not say what they were! The hardware is 
a Dell 7920 with 2 x 26 core CPUs and 384 GB RAM. 

I put config.log here 
https://www.kirkbymicrowave.co.uk/config.log

and a compressed version of install.log here
https://www.kirkbymicrowave.co.uk/install.log.bz2


make[3]: *** [Makefile:3262: 
/home/drkirkby/sage/local/var/lib/sage/installed/sagemath_doc_html-none] 
Error 2
make[2]: *** [Makefile:2766: all-start] Error 2
make[2]: Leaving directory '/home/drkirkby/sage/build/make'

real47m17.658s
user220m4.574s
sys14m6.540s
install.log.bz2***
Error building Sage.

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

It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make[1]: *** [Makefile:40: all-start] Error 1
make[1]: Leaving directory '/home/drkirkby/sage'
make: *** [Makefile:13: all] Error 2

*Trying to run the tests, it reports the following, which is not in the log 
file uploaded. *

real0m55.972s
user8m4.622s
sys0m47.623s
***
Error building Sage.

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

* package: sagemath_doc_html-none
  last build time: Feb 10 20:12
  log file:/home/drkirkby/sage/logs/pkgs/sagemath_doc_html-none.log

It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make[1]: *** [Makefile:40: all-start] Error 1
make[1]: Leaving directory '/home/drkirkby/sage'
make: *** [Makefile:13: all] Error 2



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Re: [sage-support] Sagemath binary is old and fails to install properly on Ubuntu 20.04.5 LTS

[David Kirkby]

On Wednesday, 8 February 2023 at 11:27:23 UTC dim...@gmail.com wrote:
Hi Dave, 

Hi Dima

We aren't maintaining Ubuntu/Debian packages, so this report should 
not have gone here. :-)  
Some years/releases Debian packaging of Sage is in good shape, some 
years it's falling behind, 
but we are trying to be helpful. (Debian is permanently short on 
hands, and also slowed down 
by their rather slow workflow...) 

In which case 

https://doc.sagemath.org/html/en/installation/index.html

should be updated to reflect that. As should 

https://doc.sagemath.org/html/en/installation/binary.html#linux

which says "SageMath used to provide pre-built binaries for several Linux 
flavors. This has been discontinued, as most major Linux distributions have 
up-to-date distribution packages providing SageMath. See Linux package 
managers 
 
for information." 

Dave 

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[sage-support] Sagemath binary is old and fails to install properly on Ubuntu 20.04.5 LTS

[David Kirkby]

Some of you may remember me - I did a fair amount of work porting Sage to 
Solaris SPARC. 

I wanted to try sage, and could not be bothered to build from source, so 
thought I'd just install a binary onto a Dell 7920 tower workstation (2 x 
26-core 2.0 GHz CPUs with 384 GB RAM) running Ubuntu 20.04.5 LTS. 

*1) First sage is not installed, and never has been on this system. *
drkirkby@canary:~/Desktop$ sage

Command 'sage' not found, but can be installed with:

sudo apt install sagemath-common

*2) I try to install Sage - this gives a number of error messages. *
drkirkby@canary:~/Desktop$ sudo apt install sagemath-common
[sudo] password for drkirkby: 
Reading package lists... Done
Building dependency tree   
Reading state information... Done
The following packages were automatically installed and are no longer 
required:
  chromium-codecs-ffmpeg-extra gstreamer1.0-vaapi guile-2.2
  libalgorithm-c3-perl libaqbanking-data libaqbanking44
  libb-hooks-endofscope-perl libb-hooks-op-check-perl libcgi-fast-perl
  libcgi-pm-perl libclass-c3-perl libclass-c3-xs-perl
  libclass-data-inheritable-perl libclass-inspector-perl
  libclass-method-modifiers-perl libclass-singleton-perl
  libclass-xsaccessor-perl libcommon-sense-perl libdata-optlist-perl
  libdate-manip-perl libdatetime-format-strptime-perl 
libdatetime-locale-perl
  libdatetime-perl libdatetime-timezone-perl libdbi1 
libdevel-callchecker-perl
  libdevel-caller-perl libdevel-lexalias-perl libdevel-stacktrace-perl
  libdynaloader-functions-perl libeval-closure-perl libexception-class-perl
  libfcgi-perl libfile-sharedir-perl libfinance-quote-perl libfwupdplugin1
  libgstreamer-plugins-bad1.0-0 libgwengui-gtk3-0 libgwenhywfar-data
  libgwenhywfar79 libhtml-tableextract-perl libjson-parse-perl libjson-perl
  libjson-xs-perl libllvm11 libmodule-implementation-perl
  libmodule-runtime-perl libmro-compat-perl libnamespace-autoclean-perl
  libnamespace-clean-perl libofx7 libosp5 libpackage-stash-perl
  libpackage-stash-xs-perl libpadwalker-perl libparams-classify-perl
  libparams-util-perl libparams-validationcompiler-perl libreadonly-perl
  libref-util-perl libref-util-xs-perl librole-tiny-perl libspecio-perl
  libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
  libsub-install-perl libsub-quote-perl libtext-template-perl
  libtypes-serialiser-perl libva-wayland2 libvariable-magic-perl libxmlb1
  libxstring-perl shim
Use 'sudo apt autoremove' to remove them.
The following NEW packages will be installed
  sagemath-common
0 to upgrade, 1 to newly install, 0 to remove and 39 not to upgrade.
Need to get 16.2 MB of archives.
After this operation, 205 MB of additional disk space will be used.
Get:1 http://gb.archive.ubuntu.com/ubuntu focal/universe amd64 
sagemath-common all 9.0-1ubuntu4 [16.2 MB]
Fetched 16.2 MB in 1s (11.0 MB/s)   
Selecting previously unselected package sagemath-common.
(Reading database ... 382458 files and directories currently installed.)
Preparing to unpack .../sagemath-common_9.0-1ubuntu4_all.deb ...
Unpacking sagemath-common (9.0-1ubuntu4) ...
Setting up sagemath-common (9.0-1ubuntu4) ...
/usr/lib/python3/dist-packages/sage/combinat/root_system/branching_rules.py:1753
: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if len(stypes) is not 2:
/usr/lib/python3/dist-packages/sage/graphs/graph_latex.py:1159: 
SyntaxWarning: '
str' object is not callable; perhaps you missed a comma?
  raise TypeError('%s option must be a dictionary, not %s' (name, value))
/usr/lib/python3/dist-packages/sage/graphs/graph_latex.py:1168: 
SyntaxWarning: '
str' object is not callable; perhaps you missed a comma?
  raise TypeError('%s option must be a dictionary, not %s' (name, value))
/usr/lib/python3/dist-packages/sage/graphs/graph_latex.py:1175: 
SyntaxWarning: '
str' object is not callable; perhaps you missed a comma?
  raise TypeError('%s option must be a dictionary, not %s' (name, value))
/usr/lib/python3/dist-packages/sage/graphs/graph_latex.py:1182: 
SyntaxWarning: '
str' object is not callable; perhaps you missed a comma?
  raise TypeError('%s option must be a dictionary, not %s' (name, value))
/usr/lib/python3/dist-packages/sage/graphs/graph_latex.py:1189: 
SyntaxWarning: '
str' object is not callable; perhaps you missed a comma?
  raise TypeError('%s option must be a dictionary, not %s' (name, value))
/usr/lib/python3/dist-packages/sage/graphs/graph_latex.py:1196: 
SyntaxWarning: '
str' object is not callable; perhaps you missed a comma?
  raise TypeError('%s option must be a dictionary, not %s' (name, value))
/usr/lib/python3/dist-packages/sage/graphs/graph_latex.py:1203: 
SyntaxWarning: '
str' object is not callable; perhaps you missed a comma?
  raise TypeError('%s option must be a dictionary, not %s' (name, value))
Processing triggers for man-db (2.9.1-1) ..


*3) I thought I would upgrade the system and try again. (Yes, I should have 
done that before trying to install, but I have not known failing to do 

Re: [sage-support] Ssh problems

[Dr. David Kirkby (Kirkby Microwave Ltd)]

On 21 February 2017 at 17:48, Simon King  wrote:

>
> Is the problem on my side?
>
> Also I see that (unlike in the past) I could not do
>   ssh simonk...@sage.math.washington.edu
> (on two different laptops). It tells me "Permission denied (publickey)".
>


drkirkby@hawk:~/openssh-7.4p1$ ./ssh kir...@sage.math.washington.edu
Permission denied (publickey).

I get the same, but I have not logged in for some time. But I tried to a
week or two ago and could not ssh in either.

Dave

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Re: [sage-support] Why cannot Sage run as a native application on Windows

[Dr. David Kirkby (Kirkby Microwave Ltd)]

On 16 Jan 2015 14:45, William Stein wst...@gmail.com wrote:

 On Fri, Jan 16, 2015 at 1:59 AM, 张秦川 gofortu...@gmail.com wrote:
  Python can be used on windows. And sage is written in python.
  So why cannot Sage run as a native application on Windows.

 Because people haven't done the work to make it happen.

What you say is correct. I think your answer would have been appropriate if
someone asked about Sage not running on VMS, HP-UX, AIX, tru64, IRIX, DOS
etc.

But I think you should elaborate a bit more since the question was about
Cygwin. The truth is a lot of people have put a lot of effort into this.
Mike Hansen is a name that immediately comes to my mind, as I know he was
working very hard on that, at the same time I was working on the Solaris
port. I think we all believed it would be done soon.  I would not have
been surprised if the Cygwin port was completed before the Solaris port, as
there were more working on that.

But I believe that there have been others since then working on a Cygwin
port.

So while the statement:

Because people haven't done the work to make it happen

Is correct,  I feel it is inappropriate to not to elaborate a bit.

Dave

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Re: [sage-support] Why cannot Sage run as a native application on Windows

[Dr. David Kirkby (Kirkby Microwave Ltd)]

On 23 Jan 2015 21:24, Jeroen Demeyer jdeme...@cage.ugent.be wrote:

 On 2015-01-23 22:19, Dr. David Kirkby (Kirkby Microwave Ltd) wrote:

 But I think you should elaborate a bit more since the question was about
 Cygwin.

 I think the original question was native on Windows, i.e. without Cygwin.
This was clarified in a follow-up post.

Ah,
In which case my comments should be ignored.

Dave.

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Re: [sage-support] is it possible to keep writing y(x) instead of just y in differential equations?

[Dr. David Kirkby]

On 4 August 2014 04:56, Nasser M. Abbasi nma%12000@gtempaccount.com wrote:
 I am a sage newbie so please be easy on me.

Nasser,

Others may not know this, but I know you are an expert in Mathematica,
as I recall your name from the Mathematica forums. I see you now have
38 demonstrations on the Wolfram Research site.

http://demonstrations.wolfram.com/author.html?author=Nasser+M.+Abbasi

I wonder what made you start using Sage?

I hope you get your questions answered.

Dave (a Sage developer).

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Re: [sage-support] Want all real solutions to a Simple trig equation

[Dr. David Kirkby]

I
On 3 May 2014 16:54, Javier Marquez drquij...@gmail.com wrote:

  solve(sin(x)==1/2,x) produces only one solution. Is here a way to have
sage produce all real solutions ? Thx

Is there not an infinite number of solutions? If so, it would be difficult
to get them all

Dave

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Re: [sage-support] sage vs matlab

[David Kirkby]

On 4 March 2013 16:55, Luis Finotti luis.fino...@gmail.com wrote:
 Dear all,

 I will give a couple of informal talks on Sage.  A question that will
 certainly be asked is how Sage compares with MATLAB, probably in regards of
 performance and functionality in modeling and other applied math
 applications.

I think Sage would have a hard job breaking into the MATLAB
strongholds in engineering. It is used to control a lot of instruments
and data collection.

Agilent, who are probably the world's premier test equipment
manufacturer do not generally sell products like MATLAB. However, if
you purchase an eligible instrument Agilent well sell a MATLAB
license.

http://www.home.agilent.com/agilent/editorial.jspx?cc=USlc=engckey=2001996nid=-0.781262id=2001996

Perhaps Sage, linked into all the required open-source sotware could
perhaps do everything MATLAB can. What it wont have what is acceptance
in the industry like MATLAB does.

Dave (a Chartered Engineer, not a mathematician!)

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Re: [sage-support] sage vs matlab

[David Kirkby]

On 4 March 2013 17:51, Dan Aldrich daldr...@earthlink.net wrote:
 I've been using Sage for about 3 years now. One thing that hit me was when I
 got into the 3rd year Electrical Engineering classes, my Matlab usage was
 increasing because professors wanted all homework done in Matlab not Sage.

This is not surprising, given what I said about the use of MATLAB in
engineering in a post of mine. If you are doing electrical
engineering, then undoubtably having MATLAB on your CV is going to be
more useful than having Sage on your CV. I'm not a great fan of
MATLAB, but there is no doubt it is an industry standard tool.

Another bit of software worth knowing for for electronic engineers is
Labview. I would not be surprised if you get introduced to that either
in an EE course.

Octave is an open-source clone of MATLAB, but as much as I am a fan of
open-source, and have spent days (weeks) developing Sage, I would say
forget about Octave and just learn MATLAB. Get that on your CV Then at
a later date if you work for a small company or start up your own and
want to remain legal, you might use Octave instead. But get MATLAB on
your CV and Labview too if you get the chance.

Dave

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Re: [sage-support] Light version of sage for undergraduate students

[David Kirkby]

On 6 February 2013 08:17, Christophe BAL projet...@gmail.com wrote:
 Hello,
 it could be very useful for undergraduate students to have a light version
 of sage so as to not have such a huge program to install.

Is it really that huge, given the size of disks now? If a copy was
held in your university, it should be quick for someone to download it
there.

I can't help feeling that introducing students to lite versions of
software is a bad idea. They don't get to see all the functionality
There is no light version of Mathematica for students - they get the
fully functionality. Same for MATALB.

Last time I checked, Mathematica was a 500 MB download. A trial of
Labview is over 1 GB.

Dave

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Re: [sage-support] Mathematica interface has changed in V9 ?

[David Kirkby]

On 28 December 2012 17:55, Ivan Andrus darthand...@gmail.com wrote:
 On Dec 28, 2012, at 4:47 PM, David Kirkby david.kir...@onetel.net wrote:

 Mathematica were not tested regularly - I don't know if that has
 changed.

 Of course, the Mathematica interface cannot be tested as often as everything 
 else because not everyone has a license.  However,  #13540 would be a good 
 step towards getting it (and other optional tests) tested more.

 -Ivan

It is fairly easy to get a trial license for Mathematica. The last I
knew, it was as simple as

1) Creating an account on the Wolfram Research web site
2) Request a trial.
3) You get sent a download link
4) Download, and run. It connects to the internet to get a trial license key.

and away you go. At one point someone had to approve your trial, but
now they seem to have dispensed with any human interaction, and one
can get the trial immediately.

That was the case last I looked, which was about 6 months ago. Things
might have changed.



Dave

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Re: [sage-support] Mathematica interface has changed in V9 ?

[David Kirkby]

On 31 December 2012 17:09, William Stein wst...@gmail.com wrote:


 On Mon, Dec 31, 2012 at 8:54 AM, David Kirkby david.kir...@onetel.net
 wrote:

 On 28 December 2012 17:55, Ivan Andrus darthand...@gmail.com wrote:
  On Dec 28, 2012, at 4:47 PM, David Kirkby david.kir...@onetel.net
  wrote:

  Mathematica were not tested regularly - I don't know if that has
  changed.
 
  Of course, the Mathematica interface cannot be tested as often as
  everything else because not everyone has a license.  However,  #13540 would
  be a good step towards getting it (and other optional tests) tested more.
 
  -Ivan

 It is fairly easy to get a trial license for Mathematica. The last I
 knew, it was as simple as

 1) Creating an account on the Wolfram Research web site
 2) Request a trial.
 3) You get sent a download link
 4) Download, and run. It connects to the internet to get a trial license
 key.

 and away you go. At one point someone had to approve your trial, but
 now they seem to have dispensed with any human interaction, and one
 can get the trial immediately.

 That was the case last I looked, which was about 6 months ago. Things
 might have changed.


 It goes without saying, but this isn't sustainable.  You get 30 days, and
 then it's over.

It's enough to do a periodic check Sage still works with Mathematica

I know when I tried to use the Sage- Mathematica interface, and found
it was broke, it became apparent it had been broken for many months.
That could be avoided.

Dave

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Re: [sage-support] Mathematica interface has changed in V9 ?

[David Kirkby]

On 28 December 2012 14:53, Emmanuel Charpentier
emanuel.charpent...@gmail.com wrote:
 Note to (potential) users of the sage interface to Mathematica : something
 seems to have changed in Mathematica version 9 interface with the rest of
 the world.

 Setup(s) : Debian wheezy with self-compiled sage v 5.4.1 then v 5.5,
 Mathematica Linux 64 bits V8 then V9.
 (1) sage v 5.4 -- Mathematica V8 : OK
 (2)sage v 5.5 -- Mathematica V9 : doesn't work. Sage reports to be unable
 to start Mathematica. However, Mathematica works both from the command line
 (math) or from the GUI (mathematica).
 (3) sage v 5.5 -- Mathematica V8 : OK again.

 I've also seen (1) and (3) on a smallish 32 bit machine (Again, debian
 wheezy + self-compiled sage (this was slooow..)).

 Shouldn't I open a ticket on this ?

It would be best to open a ticket.

 Hints on further relevant information ?

IMHO, the way Sage calls Mathematica is not optimal. I recall opening
a ticket before, when Sage would not work with my version of
Mathematica. It turns out that the optional interfaces like
Mathematica were not tested regularly - I don't know if that has
changed.

If you look at this post a month or so by me:

https://groups.google.com/forum/?fromgroups=#!searchin/sage-devel/mathematica$20kirkby/sage-devel/tF5QApfHUHE/3FRgjYrg1QsJ

you will see I had intended emailing something to the FSF and Wolfram
Research to try to get a better way of interfacing to Mathematica.
What responses were received from Sage developers, were negative, so I
never bothered emailing Wolfram Research or the FSF.

Technically the best way to produce an interface will be using the
MathLink protocol in Mathematica. The issue is the license condictions
of this. It can be used free for commerical use, but not for
commerical use. This conflicts with the GPL, though I'm not convinced
that could not be circulated if the interface was an optional
component, that did not by default link to the Mathematica libraries.

There is an open-source (GPL) program called 'jmath'

http://robotics.caltech.edu/~radford/jmath/

which links to Mathematica in a way that is technially better. Exactly
what the legal situation of that is, I don't know, and if you read the
authors comments, he had conflicting answers from different sources.
That was why I intended emailing the FSF and Wolfram Research. But as
I say, all comments were negative.

Dave

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Re: [sage-support] Mathematica interface has changed in V9 ?

[David Kirkby]

On 28 December 2012 16:41, Volker Braun vbraun.n...@gmail.com wrote:
 On Friday, December 28, 2012 4:19:11 PM UTC, William wrote:

 I disagree.  The only reason Sage doesn't have an interface to Mathematica
 written using the MathLink protocol is that nobody has got around to
 writting such an interface. I would like to strongly encourage people to
 write one.


 Is there actually a MathLink wire protocol that is documented (and stable
 across Mathematica versions)? All MathLink docs I ever saw just show you how
 to use shared library that Mathematica comes with.

I guess this depends on your definition of protocol. Personally I
would say using Mathlink

http://reference.wolfram.com/mathematica/tutorial/MathLinkAndExternalProgramCommunicationOverview.html

would provide a protocol which is stable across mathematica versions.
I know I used jmath with many versions, and I never knew it to break,
whereas the current way in Sage is fragile.

But, as you say, that does involve linking to a Wolfram Research
library and it also requires using one of their header files. Their
license permits this for non-commerical use, or one can get a
commerical license, for which I assume you have to pay.

Dave

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Re: [sage-support] Mathematica interface has changed in V9 ?

[David Kirkby]

On 28 December 2012 16:47, William Stein wst...@gmail.com wrote:
 also make it an optional sage package).

This is what I was thinking, but I personally thought it worth asking
WRI exactly where we stood if using their protocol.

At the end of the day, anything you do to circumvent using their
shared library, WRI could put a stop to without changing any code -
just their license conditions. When Mathematica 10 comes out, one of
the conditions of that license is that you can't control Mathematica
from external programs without the use of the Mathlink library. At
which point, although the code would work, it would be against the
license to use it.

Hence my feeling it is better to ask WRI, and work with them rather
than against them.

 The other alternative is reverse engineering the protocol for the
 Mathematica REPL.  I can't imagine it is very complicated, since there are a
 few canonical choices for such things.

 William

'jmath' has existed for years as a nice GPL'ed front end for
Mathematica, and as far as I'm aware, WRI have never tried to stop it.
So I don't think they would care if Sage implement something similar.
But I personally would rather ask. You see a draft of a mesage I
intended sending, but also the negative comments about it, so I never
bothered.



Dave

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Re: [sage-support] Mathematica interface has changed in V9 ?

[David Kirkby]

On 29 December 2012 02:39, William Stein wst...@gmail.com wrote:


 On Fri, Dec 28, 2012 at 5:11 PM, David Kirkby david.kir...@onetel.net
 wrote:

 On 28 December 2012 16:47, William Stein wst...@gmail.com wrote:
  also make it an optional sage package).

 This is what I was thinking, but I personally thought it worth asking
 WRI exactly where we stood if using their protocol.

 At the end of the day, anything you do to circumvent using their
 shared library, WRI could put a stop to without changing any code -
 just their license conditions. When Mathematica 10 comes out, one of
 the conditions of that license is that you can't control Mathematica
 from external programs without the use of the Mathlink library. At


 That would not be a problem at all.  The very sentence that you were
 half-quoting from my email started: It will also link in the wolfram
 mathlink library... so the mathlink library is used.

The issue there is it can't be used for commerical use - at leasat
without getting a mathlink license.

 which point, although the code would work, it would be against the
 license to use it.


 I don't even know what to ask them.  Do you want them to change their
 license so that it is GPL-compatible -- that seems ridiculous.

I think it is ridiculous you asking me such a question.

IF Sage could do what jmath does, without breaching the GPL and
without breaching Wolfram Research's license, then that would be good.
I'm not so sure it is possible, but it might be.

I don't see any issue with you creating a program which can link into
the Mathlink library. It is less clear to me what license the person
using the code is then govenend by if they chose to link to the WRI
library.

 jmath does not seem to be an example of reverse engineering the MathLink
 wire protocol.  The jmath website
 (http://robotics.caltech.edu/~radford/jmath/) explains that jmath is simply
 an application that links in the MathLink library.

Agreed. So why do you first mention reverse engineering? I don't see
the point in trying to reverse engineer anything myself.

Dave

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Re: [sage-support] Re: Why don't I get random numbers?

[David Kirkby]

On 21 October 2012 11:30, LFS lfahlb...@gmail.com wrote:
 Hiya Dmitrii
 Thanks so much for your quick reply, but I am still getting the same
 problem.

I don't know if this the best way in Sage, but it is common practice
to seed the random number generator from the number of seconds since
the Epoch (1/1/1970). So every time you seed it, you get a different
sequence.

Another option is to seed it with some bytes from /dev/random or
/dev/urandom. In fact, /dev/urandom gives about as good as you can get
for random numbers, as they are consider cryptographically secure.
However, if there is insufficent entropy in the system, /dev/urandom
will block, and give no data.

One advantage of using a pseudo random number generator is that it is
possible to repeat an experiment, using the same seed, and you will
get the same numbers. That's not possible if you use /dev/random or
/dev/urandom.

Dave

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Re: [sage-support] Re: Why don't I get random numbers?

[David Kirkby]

On 21 October 2012 11:42, LFS lfahlb...@gmail.com wrote:
 Hiya Dimitri, It might actually be working. Not sure, but when I increased
 the number of sets ns, it does looks better. Still alot of repeats, but the
 histogram looks better. Linda

If there is a number of repeats, something is defnitely wrong. It
should either give you pseudo-random numbers if seeded properly, or a
100% preproducible set of numbers if seeded with a fixed seed.

It should not look better, but still not right. Something is wrong in
that case.

Dave

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Re: [sage-support] Re: Why don't I get random numbers?

[David Kirkby]

One simple way to get a qualitative feel for the quality of random
numbers is to take them two at a tim, staring with the first two being
x1, y1. So you gererate:

x1, y1
x2, y2
x3, y3 etc

then plot a graph of x,y for all parts xn, yn

The graph should look like a scatter graph, with no obvious pattern.
There are more quantitive measures to check them. I'll give you a
reference to my PhD these if you want it, as I looked at random number
quality in some detail for Monte Carlo simulations.

Dave

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Re: [sage-support] Re: Why don't I get random numbers?

[David Kirkby]

On 21 October 2012 12:03, LFS lfahlb...@gmail.com wrote:
 Hiya Dave,
 What would the line of code look like to reseed it with the epoch thing each
 time I call it?
 Thanks so much,

 Linda

The truth is I don't know off hand. I've spent a lot of time porting
Sage to Solaris, but have not used it much at all. I'm sure Python has
some code to get the get the seconds since the Epoch. One thing to
watch with this method, is if you call it too often (less than once
per second), you will be seeding it with the same number, and so get
the same sequence. I know someone who came unstuck. It wa ok on a slow
computer, but when he went to a fast computer, the things went all
wrong, as he was seeding it with the same numbers.

I'll try to find an example in the Sage manual. I'm sure it must have
something on this, but personally I don't know how to best do it. I'm
just relying on my experience of using pseudo-random numbers in C code
for Monte Carlo modelling.

dave

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Re: [sage-support] Re: Why don't I get random numbers?

[David Kirkby]

On 21 October 2012 12:03, LFS lfahlb...@gmail.com wrote:
 Hiya Dave,
 What would the line of code look like to reseed it with the epoch thing each
 time I call it?
 Thanks so much,

 Linda


http://www.sagemath.org/doc/reference/sage/misc/randstate.html

says

If set_random_seed() is called with no arguments, then a new seed is
automatically selected. On operating systems that support it, the new
seed comes from os.urandom(); this is intended to be a truly random
(not pseudo-random), cryptographically secure number. (Whether it is
actually cryptographically secure depends on operating system details
that are outside the control of Sage.)


I tend to disagree with what's quoted there. The seed will be truely
random, but the sequence of numbers will not be. They will still be
preudo random.

Sage no doubt has endless ways of generating random numbers, and that
method might only work for one or more of the RNGs, but not all of
them.


Dave


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Re: [sage-support] Re: Why don't I get random numbers?

[David Kirkby]

On 21 October 2012 13:04, LFS lfahlb...@gmail.com wrote:
 yes - i finally saw that and took the call to the GDDinit out of the loop
 and this may be working, but I don't know how to explain this to the
 kiddies.
 Probably should have just stuck with Excel where I understand the
 generators. Too complicated by far.
 Thanks everyone for your help.

But kids are used to Windows,so if you can encourage them to use a
non-Windows system, it would be useful as a side-benefit.

I'm not sure if it ever happened, but I know an 8-year old contacted
William about being a Sage developer.

Dave

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Re: [sage-support] Re: demo server down

[Dr. David Kirkby]

On 28/09/2012 18:56, William Stein wrote:


In the next few months, I'll be launching the service described here,
which you'll have the opportunity to financially support:

http://wstein.org/grants/2012-rrf/rrf.pdf

  -- William


I read that, and two things come to mind.

1) A minor one, but Ghz should be changed to GHz in numerous places.

2) Do you really think you are the best person to do what you propose, or would 
it be better to get a computer scientist to do it? To me at least, this does not 
require any maths, but a good computing background, and so is not the job for a 
mathematician, but a computer scientist.


Dave

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Re: [sage-support] Re: Sage's running too slowly

[David Kirkby]

On 3 September 2012 04:49, Nathann Cohen nathann.co...@gmail.com wrote:
 Honestly I don't think it's very constructive to tell users that they
 should install a different operating system in order to use Sage, and
 that is basically what this dual-booting suggestion amounts to


 I totally agree with that. And I think that it is not very constructive to
 say that Sage supports windows either, when it requires users to install a
 virtual machine.
 It does not, and saying the opposite is bad avertisement.

I've had a few disagreements with Nathann before, but in this case I
agree with him. It's probably true that 99% of Windows software would
work on Linux if you run it under a virtual machine, but it's not true
to say it supports Linux.

I run 3 versions of Windows on my OpenSolaris machine  (Windows XP
64-bit, Windows XP and Windows 7). Does it really mean all the
software I run supports OpenSolaris? I would say NO.

As a matter of interest, does this sub-domain need to exist

http://windows.sagemath.org/


Dave

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Re: [sage-support] Re: Sage's running too slowly

[David Kirkby]

On 3 September 2012 08:49, Volker Braun vbraun.n...@gmail.com wrote:
 On Monday, September 3, 2012 4:49:05 AM UTC+1, Nathann Cohen wrote:

 It supports Windows as much as any Linux software that does not support
 windows -- install a virtual machine and run it inside. And it convices
 people that Sage is hard to install, hard to use, and slower than it
 actually is :-P


 Given the lack of fork() on windows, running Sage in a virtual machine is
 probably faster than running it under Cygwin. Especially if you have a
 modern CPU with hardware virtualization support. Also, Cygwin is 32-bit
 only.

I don't doubt what you say about speed on Cygwin or the fact Cygwin is
only 32-bit. But Nathann still makes valid points.

I produce software which runs on Unix and Linux, but I never claim it
works on Windows, despite the fact I'm 99.999% sure it would compile
on a virtual machine running Linux, Solaris, OpenBSD, FreeBSD, SCO or
any Unix or Unix-like system.

Dave

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Re: [sage-support] Sage's running too slowly

[David Kirkby]

On 31 August 2012 21:20, Guilherme Boaviagem Ribeiro
guilherme.boavia...@gmail.com wrote:
 Hi everyone,

 I have installed Sage (with the file sage-5.0-disk1.vmdk) on my Windows
 64-bits (4 GB RAM, and processor of 2.4 GHz), and it is already running in
 my Virtual Box. But it's way too slow, even for the simplest commands, does
 anyone have any idea of what could be the reason for this? My virtual
 machine is running Sage in Fedora with 512 MB of memory and 16 MB of video
 memory.

512 MB of RAM seems far too low to me. As someone else pointed out,
Sage is not a small program. Personally I'd look at the possibility of
shrinking the Windows partition a bit, and dual-booting with Linux.
Then you will have the full 4 GB for Sage.

I found the best way to shrink the Windows partition under Windows
Vista was to get a trial of a 3rd party parition tool. I forget what
it is, but it could defragment the disk far more than Windows could.
You also need to disable the hybernation mode temporarily, and turn
off the ability to page to disk. If you do both of them, you should be
able to shrink the partition, then install Linux.

That would be my preffered solution with only 4 GB in a laptop.

Dave

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Re: [sage-support] Re: Sage's running too slowly

[David Kirkby]

On 1 September 2012 13:23, Keshav Kini keshav.k...@gmail.com wrote:

 Honestly I don't think it's very constructive to tell users that they
 should install a different operating system in order to use Sage, and
 that is basically what this dual-booting suggestion amounts to -
 dual-booting is unlikely to be a very convenient way for anyone to use
 Sage unless they start using the Sage-capable OS for their other
 programs as well. The ability to multitask is something that everyone
 assumes these days. I doubt many people are willing to reboot their
 computer and do nothing but type code in Sage for a stretch of time,
 then reboot again and do everything other than Sage for a stretch of
 time. This doesn't make sense.

 -Keshav

Dual booting will double the amount of RAM Sage can get. It's probably
not realistic to allocate more than 2 GB to the VM, but dual booting
will double that amount to 4 GB.

I suspect 90% of the time people are using computers is to browse the
web or read email - both of which can be done very easily from Linux,
so its not really a case of only using Sage on Linux.

Dual booting is a bit less convenient than a VM, but it will allow
significantly better performance on a laptop with limited RAM.

Dave

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Re: [sage-support] Re: How could I fit this data?

[David Kirkby]

On 26 August 2012 10:33, Volker Braun vbraun.n...@gmail.com wrote:
 Sounds very much like a non-linear fit will be able to figure out the 8
 unknown parameters. You need a formula (model) for impedance(frequency)
 depending on the parameters.

That is what I thought might be a problem. I have no idea if its even
possible to determine formual. Not even any real sensible guess, other
than the fact the terms which depend on frequency^3 will likely be
less important if measurements are made at low frequencies only. The
basic way to use a vector network analyzer is

1) The 8 scalar parameters of the open and short circuit are
programmed into the firmware of the VNA. Those practically never
change.

2) After switching on the VNA, leaving it to warm up for an hour,
presses a CAL button, choses from a list of calibration kits. The
instructure then tell you to connect the open, short and load.

3) The computer in the VNA then works out the systematic errors in the
VNA and applies a 12 point error correction to all measurments. Those
errors will change with temperature, so if the temperature changes by
more than 1 deg C, one has to do a new calibration. But there is no
way to find out the correction factors the VNA applies.

Note, the 4 parameters of the open and 4 paramters of the short are
not considered to be temperature dependant, but the systematic errors
in the VNA are.

If I change the 8 paramters in the network analyzer which describe the
open and short, then I need go through the calibration routine again.
If I dont do that, and only change the numbers, these will be ignored,
as the network analyzer only uses those 8 numbers when computing the
12 point error correction.

I think if one only makes measurements at one port of the VNA, then
less than 12 error terms will be needed.

The mathematics of how the 12 point error correction is computed from
the measurements the VNA makes of the calibration standards can be
found in the literature. One can't read those paramters from the VNA,
but it might be possible to determine what they are, if one takes note
of the measurements, uses the data for the know calibration constants,
and works out the error correction terms.


 Having complex values is a bit of an extra
 complication since fitting in Sage only works for real numbers. For
 starters, you could look only at abs(impedance). You can emulate complex
 outputs by having two real output values in the model, but Sage allows only
 scalar models. GSL has some useful support here, but its not wrapped in
 Sage.

I suspect I need a complex fit. I very much doubt the absolute
magnitude of the impedance will be very useful. A scaler network
analyzer looks at the abosolute magnitude only, and calibration for
scaler network analyzers is a lot simpler than for vector models.

I could calibrate the VNA with a good calibration kit, then measure
the complex impedance of the open circuit at every frequency. There
will only be 4 unknowns of the open-circuit. But I don't have any idea
how to compute the 4 scaler quantities.

Perhaps this is why good calibration sets cost a lot of money! They
range in price from about $1500 to over $2.



Dave.

 http://www.sagemath.org/doc/reference/sage/numerical/optimize.html#sage.numerical.optimize.find_fit



 On Sunday, August 26, 2012 1:06:17 AM UTC+1, Dr. David Kirkby wrote:

 I'm trying to work out how to solve an engineering problem. I'm hoping
 Sage can help me, but I can't work out the maths of it. I'm hoping
 someone here might be able to.

 A vector network analyzer (VNA) is a bit of electronic test equipment
 which measures complex impedance values as a function of frequency.
 Let's assume at 500 differenct frequencies. The VNA should be
 calibrated prior to making a measurement. It's calibrated using some
 standard devices.

 * A 50 Ohm resistor. Assumed to be perfect.
 * A short circuit, which is not perfect, and so it is characterised by
 4 parameters called Ts, L0, L1 and L2.
 * A open circuit, which is not perfect, and so it is characterised by
 4 parameters called To, C0, C1 and C2.

 These standards are expensive (several thousand $'s).

 Knowing the true values of these 8 paramters, which are pre-programmed
 into the firmware of the VNA, the computer in the VNA can calculate a
 set of correction coefficients which can remove most of its systematic
 errors. The values of these 8 parameters are all known. But how they
 affect the measurements is not known. But the point is, that using
 these high quality standards, on a good VNA, the results are accurate.

 Now comes the tricky bit.

 I have a second VNA, which is differnet from the first. It too uses
 the 50 Ohm resistor, short circuit and open circuit. But it uses a
 different set of open and short circuits. These are cheap or home-made
 ones, for which we don't know the values of the 8 parameters Ts, L0,
 L1, L2, To, C0, C1 and C2.

 So if I program in 8 random values for these paramters into the second
 VNA, and take

Re: [sage-support] Re: How could I fit this data?

[David Kirkby]

On 26 August 2012 10:33, Volker Braun vbraun.n...@gmail.com wrote:
 Sounds very much like a non-linear fit will be able to figure out the 8
 unknown parameters. You need a formula (model) for impedance(frequency)
 depending on the parameters.

Maybe this is not as hard as I thought, and wrote half an hour ago.

There is a very simple model for the impedance of a transmission line
of length l, terminated in some known impedance. So I have a model of
an upen circuit with 4 unknowns. Having calibrated the VNA, I will
know what the measured impedance is at 500 or so frequencies. That's a
fairly simple non-linear fit.

Then I repeat the process for the short circuit to find out the other
4 parameters.

None of this requires access to the correction factors that the VNA
computes during its calibration routine.

Since you Sage does not have such a complex fitting routine, it might
be possible to expose that from GSL as you say, or if Mathematica has
it, I'd be tempted to use that.

I would have only 4 unknown scalar quantities, which are fixed with
frequency, and 500 measurements of the complex impedance taken with
the VNA

Perhaps I was making harder work of this than I needed to - nothing
unusual for me!

Dave

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[sage-support] How could I fit this data?

[David Kirkby]

I'm trying to work out how to solve an engineering problem. I'm hoping
Sage can help me, but I can't work out the maths of it. I'm hoping
someone here might be able to.

A vector network analyzer (VNA) is a bit of electronic test equipment
which measures complex impedance values as a function of frequency.
Let's assume at 500 differenct frequencies. The VNA should be
calibrated prior to making a measurement. It's calibrated using some
standard devices.

* A 50 Ohm resistor. Assumed to be perfect.
* A short circuit, which is not perfect, and so it is characterised by
4 parameters called Ts, L0, L1 and L2.
* A open circuit, which is not perfect, and so it is characterised by
4 parameters called To, C0, C1 and C2.

These standards are expensive (several thousand $'s).

Knowing the true values of these 8 paramters, which are pre-programmed
into the firmware of the VNA, the computer in the VNA can calculate a
set of correction coefficients which can remove most of its systematic
errors. The values of these 8 parameters are all known. But how they
affect the measurements is not known. But the point is, that using
these high quality standards, on a good VNA, the results are accurate.

Now comes the tricky bit.

I have a second VNA, which is differnet from the first. It too uses
the 50 Ohm resistor, short circuit and open circuit. But it uses a
different set of open and short circuits. These are cheap or home-made
ones, for which we don't know the values of the 8 parameters Ts, L0,
L1, L2, To, C0, C1 and C2.

So if I program in 8 random values for these paramters into the second
VNA, and take a mesurement at 500 frequencies, I can be 99.% sure
the resuts will be wrong.

Is there any way, by comparing

* True values, measured on a VNA with good calibration standards
* Incorrect values, measured on a VNA with standards which have
unknown coefficents

I can work out what the value of these 8 coefficients should be?

It is tediuous to change the coefficents in the VNA, so comparting
results at 500 frequencies with lots of different values for the 8
paramters is not practical.

Would programming in 8 differents sets of coefficients be sufficient
to work out the correct values? (That would be 64 coefficents in
total). That would be very tedious to do, but it might be possible. It
*may* be possible to program them by computer, but I am not sure of
that. They might need to be entered manually with keys on the VNA,
which will be tedious.

Can anyone help me with the maths, and give me an idea what functions
in Sage might help.

I'm guessing this is some non-linear fitting problem, but I'm not sure.

Dave

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Re: [sage-support] Sage crashes when starts

[David Kirkby]

On 20 July 2012 18:26, tvn nguyenthanh...@gmail.com wrote:
 I am trying to run Sage 5.1 from a computer at work running Debian and it
 crashes right when starts up  ..


 wooly Fri Jul 20:13:26:00 (210)
 ~/Src/Devel/SAGE/sage-5.1-linux-64bit-ubuntu_12.04_lts-x86_64-Linux
 $ uname -a
 Linux wooly 2.6.32-5-amd64 #1 SMP Sun May 6 05:12:07 UTC 2012 x86_64
 GNU/Linux

 wooly Fri Jul 20:13:26:02 (211)
 ~/Src/Devel/SAGE/sage-5.1-linux-64bit-ubuntu_12.04_lts-x86_64-Linux
 $ ./sage
 --
 | Sage Version 5.1, Release Date: 2012-07-09 |
 | Type notebook() for the browser-based notebook interface.|
 | Type help() for help.|
 --
 'import site' failed; use -v for traceback
 Traceback (most recent call last):

Did you build from source or download a binary?

The usual reccomenedation when people get problems is to build Sage
from source code. That normallly works without problems. You are
unlikely to need to install any other packages, as Sage comes with
most things included - even a compiler! (At leat I think the compiler
is included now - it certainly will be soon if it is not already)


Dave

Dave

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Re: [sage-support] Re: Sage crashes when starts

[David Kirkby]

On 20 July 2012 18:57, Keshav Kini keshav.k...@gmail.com wrote:
 David Kirkby david.kir...@onetel.net writes:
 The usual reccomenedation when people get problems is to build Sage
 from source code. That normallly works without problems. You are
 unlikely to need to install any other packages, as Sage comes with
 most things included - even a compiler! (At leat I think the compiler
 is included now - it certainly will be soon if it is not already)

 GCC is currently included in Sage, though if the system has a native GCC
 which is deemed sufficient for Sage's purposes, Sage doesn't install the
 GCC it ships.

 -Keshav

Thank you.

I have some older Sun hardware here (both x86 and SPARC). It will be
interesting to try Sage on them again, as it used to build and pass
all tests on both. One issue before was the need to install a more up
to date version of gcc. I'll give it a try some time.



Dave

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Re: [sage-support] The future of Mathematica?

[David Kirkby]

On 26 June 2012 12:56, Eric Kangas eric.c.kan...@gmail.com wrote:
 I first started using Mathematica 5.8 before I bought my student edition of
 6.0 as a physics student at CWU.

There was no version 5.8 of Mathematica. To the best of my knowledge,
the latest in the 5 series was 5.2 (probably with a 5.2.1 or similar
with just bug fixes).

 However I don't use it anymore, but still
 have the windows drive that it is on just in case. I spent $90 for access to
 that copy. I tried to start a fresh new copy, and was denied full access
 since it was a different copy.

Contact their support line. I've found them quite helpful - at least
in moving the professional version. Also, when a licensed had expired,
they renewed it for a month or two, expecting the uni to renew the
license.

 Which I think is completely wrong. I was then
 forward to the sites pay page for access to version 8. From what I have seen
 from the pictures, and read the information about version 8. I have noticed
 that version 8 now has full access to wolfram alpha, Wolfram's giant
 database, at an additional cost. Which I think is completely none scientist
 of him for doing that.

What makes you think you have to pay for the integration? I have not
looked much, but

http://reference.wolfram.com/mathematica/guide/WolframAlphaIntegration.html

mentions nothing about payment.

 Access to any form of information should be free for
 anyone.

I disagree. If someone pays staff to collect information, there is no
reason they should not sell itl Just look at all the scientific
journals. Your uni might give you free access to al/most of them,
it's only because they have paid for it.

 Plus I take it that his coding is also proprietary?

Yes. I see somewhere (forget where), that someone had asked Stephen
Wolfram if he would open-source an early version. He said no, since he
did not think it a good idea that someone used an old copy. Of course
his real reason might be (probably is), very different.

 There are a few
 things that I have done on Mathematica that I can't do on sage at this time.
 Which is keeping me from being able to publish my findings on some of my
 projects I have done in College.

Ask here, and perhaps someone knows a way of doing it

 Since I didn't have access to a
 professional version of Mathematica, and I am not a student at this time.

I think that gives you the opportunity to upgrade to the pro version
at a much reduced cost.

 From what I have experience with the way Wolfram has his program setup he is
 only in it for the money, and nothing else anymore.

Was he EVER in it for any other reason? I suspect not.

 Which I think will be
 his downfall eventually as more and more people turn
 to Sage, or any other
 freeware program that is out there. What do any of you others think about
 the future of Mathematica?

I don't see Sage being a big threat to Mathematica, especially as
William has said it is a waste of time trying a true native port to
Windows. I tend to agree with him too. Whilst one has to mess around
with VirtualBox rather than a true native port, I don't see Sage being
a big threat.

Symbolics in Mathematica, which is one of its strong points, are
better than Sages.

The other aspect is that there is no commercial paid support. As such,
it is difficult to justify using in industry. Contrast that with
open-source projects like Apache and Wireshark.

I guess Mathematica must be commercially successful, but looking at
the number of jobs requiring skills in Mathematica, I know it is very
small. What there are seem to be mainly in the finance industry. In
contrast, MATLAB seems far more useful toe learn, as a lot of jobs
want MATLAB skills.



Dave

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Re: [sage-support] Sage-5.0 under solaris 10

[David Kirkby]

On 17 May 2012 16:57, Rob McMahon robmcmaho...@gmail.com wrote:

 Answering my own question: it's this line from
 spkg/build/prereq-1.0/configure{,.ac}

   if test x`file $SAGE_FORTRAN_LIB | grep 32-bit | grep \dynamic lib\ `
 = 'x'

 Having set my path up to get GNU make, it was also picking up a different
 version of `file' which says shared object instead of dynamic lib.
  Moving on ...

 Rob

I guess we could change the call to file to /usr/bin/file. I suspect
the file command will be in /usr/bin on any platform.

But with the gcc package now part of Sage, I think using the Solaris

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Re: [sage-support] Re: Application/Use of Sage in IT company or Industries

[David Kirkby]

On 14 May 2012 05:23, William Stein wst...@gmail.com wrote:

 * Code is depreciated quite regularly,

 deprecated.   depreciated is a completely different word.

Sorry. An unfortunate error, though I could think of worst words with
a similar spelling!

Dave

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Re: [sage-support] Re: Application/Use of Sage in IT company or Industries

[Dr. David Kirkby]

On 05/13/12 06:36 PM, Robert Miller wrote:


I think that Sage can be a very hard sell for sysadmin/ops type people in
industry, because it is a very big install


Sage is similar in size to Mathematica, and probably MATLAB and Maple too. The 
binary installations for all of these packages are 100's of MB.



and the latest versions aren't
available through debian or things like pip or easy_install.


That is more likely to be an issue.


Although we
here all realize that Sage Just Works, when someone in that sort of role
looks at Sage as a project that might need to be installed on their
production servers, they easily bristle.


Production servers and Sage will never mix in the eyes of a competent system 
admin who values his/her job.



For me at least, it is hard to justify using Sage for commercial purposes. There 
are several reasons


* You can't buy a commercial support contract. So any support issues must be on 
a public forum. (Compare this to Apache and Wireshark, which are two open-source 
tools used a lot commercially).


* It's not a native Windows application. (Personally I'm not fan of Windows, but 
not everyone shares my views.)


* Code is depreciated quite regularly, so if I write something today, there's a 
reasonable probability it wont work for someone else in two years time with a 
different version of Sage.


* There's a fairly high probability that on Linux at least, a later version of 
Linux wont run an earlier version of Sage.


* I don't feel the software is tested enough.

* It does not have the pedigree of packages like MATLAB.

Dave

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Re: [sage-support] Application/Use of Sage in IT company or Industries

[David Kirkby]

William,

I think you are being overly negative, although I agree the question
could have been put a little better.

If someone is thinking of using Sage in industry, they are likely to
want to know how much it is used in industry.

I think I'd answer this by pointing out some of the advantages
compared to commerical, sotware.

On 10 May 2012 12:06, William Stein wst...@gmail.com wrote:
 On Thu, May 10, 2012 at 1:22 AM, Priyanka Kapoor
 anjalicool.kapoor...@gmail.com wrote:
 I want to ask that what is the use of sage? Why should we use it?
 Where its being used till date?

 That's kind of impossible to answer.  Imagine if somebody asked you:

   What is the use of mathematics?  Why should we use mathematics?
 Where is mathematics being used until now?

  -- William

 These questions might be simple and i want to know before i go deep in
 sage. Please everyone on this mailing list reply that why you use
 sage?
 Whatever i think about sage is that sage is helpful for teaching maths.




 --
 Priyanka Kapoor

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Re: [sage-support] Will Sage 4.8 run on Scientific Linux 5.4?

[David Kirkby]

On 10 April 2012 19:15, rvaug...@gmail.com rvaug...@gmail.com wrote:
 Sage 4.3.4 runs fine on SL 5.4.

 Sage 4.8 complains:
 (/lib64/libc.so.6: version `GLIBC_2.14' not found ).

 -Richard Vaughn

As Dima suggested, you are using an old version, but the fact you say
it working on a later version, suggested you might have reasons not to
upgrade.

When does the error occur - post a log file, or at least a relevenat
part of one.

Not everyone can upgrade software whenever they like. I know of
companies running 10+ year old operating systems, simply because they
have millions of pounds in development time invested in systems, and
if its working, there is no need to fix it. No IT person is going to
risk an upgrade, which could cost the company millions if it goes
wrong, when a system is currently working well.

In the commerical evenironment, there is not the desire to upgrade as
quickly as universites and indviduals do.

Did you get this problem building from source, or from a binary you
downloaded? A build from source is far more likely to work.

If you Google the error message, there are lots of links about it.

Dave

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Re: [sage-support] Building on Solaris 10 - cvxopt will not build

[Dr. David Kirkby]

On 02/29/12 12:40 AM, deSitter wrote:

Hello,

Two issues, one solved by brute force, the other needs a new cvxopt-1.1.3 
package.

I am using gcc 4.6.2 newly built and tested, and the Sun linker. I have Sun 
Studio 12 installed. I built gcc4 with the gcc 3.4.6 package from Sunfreeware. 
During this process, I needed iconv and that collided with the iconv package in 
Sage. I simply removed the package from the spkg directory and the build 
continued on through ATLAS and to numpy.

During the compilation of base.c from cvxopt-1.1.3, an error was generated 
_Imaginary_I undefined. It appears the issue is with the complex.h header 
file used by gcc. A simple fix is to include complex.h in base.c, but since errors cause 
the spkg to be re-extraced and built new after each error, that's not an option. What is 
needed is a new cvxopt-1.1.3 package that fixes the issue with complex.h.

-drl



Is this SPARC or x86?

Can you give us the output of

$ isainfo  -v

Sage is regularly built on OpenSolaris 06/09 with gcc 4.6.0, as a Sun Ultra 27 
(quad core Xeon 3.33 GHz). This is how gcc was configured.


drkirkby@hawk:~$ gcc -v
Using built-in specs.
COLLECT_GCC=/usr/local/gcc-4.6.0/bin/gcc
COLLECT_LTO_WRAPPER=/usr/local/gcc-4.6.0/libexec/gcc/i386-pc-solaris2.11/4.6.0/lto-wrapper
Target: i386-pc-solaris2.11
Configured with: ../gcc-4.6.0/configure --prefix=/usr/local/gcc-4.6.0 
--with-gmp=/usr/local/gcc-4.6.0 --with-mpfr=/usr/local/gcc-4.6.0 
--with-mpc=/usr/local/gcc-4.6.0 --enable-languages=c,c++,fortran --with-gnu-as 
--with-as=/usr/local/binutils-2.20/bin/as --without-gnu-ld --with-ld=/usr/ccs/bin/ld

Thread model: posix
gcc version 4.6.0 (GCC)

I have personally built Sage on both Solaris 10 x86 and Solaris 10 SPARC. It 
can't be built with the Sun compiler though.


Sage can be built 64-bit on Solaris, but it is not very useful. On 64-bit SPARC 
Sage works, but is very unstable. On x86 64-bit, R needs to be built with the 
Sun compiler, not gcc.

http://trac.sagemath.org/sage_trac/ticket/9040
Sage then segfaults at startup on 64-bit x86.


Dave

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Re: [sage-support] Question about cycles per second in SAGE

[David Kirkby]

On 14 February 2012 03:40, juaninf juan...@gmail.com wrote:

 Hi everybody.

 Exists any command in SAGE to get the spent cpu-cycles per second in
 SAGE?


What do you mean by spent cycles per second? Time must be measured in
seconds, not inverse seconds, so I assume you don't mean time.

I believe you will find that bencharkes that try to measure MFLOPS (million
floating point operatiions per second), is a bit meaningless. In facts,
MFLOPS is also known as Meaningless Indicator of Performance).

http://books.google.co.uk/books?id=R8RLniX5DNQCpg=PA14lpg=PA14dq=MFLOPS++meaninglesssource=blots=iqHzUuFrxxsig=4pVcA_oX7G_RKuGmLpwLsKxwICMhl=ensa=Xei=rkM6T--KJOem0QWR3_meCwved=0CCUQ6AEwAA#v=onepageq=MFLOPS%20%20meaninglessf=false

What are you actually trying to achieve by knowing whatever you want to
know?

Dave

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Re: [sage-support] Help with plotting from Mathematica using SageTeX

[David Kirkby]

On 24 December 2011 18:27, Sony skosw...@gmail.com wrote:
 In section 4.2 of the SageLaTeX manual (page 11) explains how to
 create a LaTeX document with a Mathematica plot using SageLaTeX.  I
 tried the following code but no output is produced.  I get an error
 message Example3 not found.

I don't think the interface to Mathematica is particularly well
designed. I've had several problems with it in the past, and gave up
using it.

I think part of the issue is the WRI keep changing Mathematica, so
what works on one version on one operating system might not work on
another. I personally think if we were to provide an interface to
Mathematica, it should be using Wolfram Reserach's Mathlink protocol.

http://www.wolfram.com/solutions/mathlink/

 I've used that a very small amount in the past myself, but there is
quite a nice text-based front end for Mathematica

http://robotics.caltech.edu/~radford/jmath/

written by someone else, which allows one to recall commands and edit
them. That uses MathLink.

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Re: [sage-support] Help with plotting from Mathematica using SageTeX

[David Kirkby]

On 26 December 2011 19:28, William Stein wst...@gmail.com wrote:
 On Mon, Dec 26, 2011 at 11:03 AM, David Kirkby david.kir...@onetel.net 
 wrote:
 On 24 December 2011 18:27, Sony skosw...@gmail.com wrote:
 In section 4.2 of the SageLaTeX manual (page 11) explains how to
 create a LaTeX document with a Mathematica plot using SageLaTeX.  I
 tried the following code but no output is produced.  I get an error
 message Example3 not found.

 I don't think the interface to Mathematica is particularly well
 designed. I've had several problems with it in the past, and gave up
 using it.

 What problems?  Are there any corresponding open trac tickets or bug
 reports about your problems?

http://trac.sagemath.org/sage_trac/ticket/10968

Note that another ticket

http://trac.sagemath.org/sage_trac/ticket/9032

which was closed (I gave it positive review), was not a complete cure,
but the patch reduced the number of failures from 12 to 2.

I know the MMA interface was broken for some time, as the optional
packages were not being tested.



 I'm not aware of a single aspect of the Sage -- Mathematica
 interface that is version or operating system dependent.    I'm not
 saying there aren't any, just that I'm not aware of any.

  I personally think if we were to provide an interface to
 Mathematica, it should be using Wolfram Reserach's Mathlink protocol.

 http://www.wolfram.com/solutions/mathlink/

 A quick google search found a Python interface to Mathematica via
 mathlink here, which you can probably easily install into any copy of
 Sage:

   http://library.wolfram.com/infocenter/MathSource/585/

 William

Perhaps, but the WRI GUI or jmath text-based front end seems to work
well for me.

Dave

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Re: [sage-support] Help with plotting from Mathematica using SageTeX

[David Kirkby]

On 26 December 2011 19:51, David Kirkby david.kir...@onetel.net wrote:
 On 26 December 2011 19:28, William Stein wst...@gmail.com wrote:

 What problems?  Are there any corresponding open trac tickets or bug
 reports about your problems?

 http://trac.sagemath.org/sage_trac/ticket/10968

 Note that another ticket

 http://trac.sagemath.org/sage_trac/ticket/9032

 which was closed (I gave it positive review), was not a complete cure,
 but the patch reduced the number of failures from 12 to 2.

Correction,
http://trac.sagemath.org/sage_trac/ticket/8495
fixes some MMA issues, but others remain, and are in #10968.

Note, I found the bug I reported in #8495, which was later opened as
#10968, within 1-2 minutes of testing with the most basic of examples
of Mathematica usage. You can't get much simpler than finding a
numerical approximation of Pi.

If I understand it correclty, the test failures noted on #8495, which
took 13 months to fix, were introduced much earlier in #3587, but
nobody had noticed.

I know pexpect has been the source of numerous issues in Sage, so I'm
not about to rely on pexpect when I can use an interface developed for
Mathematica by Wolfram Research, which would undergo far more testing
than the Mathematica inferface we have in Sage, which is an optional
package underging very limited testing.



Dave

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[sage-support] Book on Sage published.

[Dr. David Kirkby]

I got an email from the publisher today confirming the book on Sage has been 
published, although the web site still says to be published in May 2011.


http://www.packtpub.com/sage-beginners-guide/book

Some fraction of sales will go to Sage, though I'm not sure what fraction, or if 
there needs to be a minimum number of books sold first.


Having been a reviewer, I know the book address more numerical problems, 
plotting and has nothing whatsoever to do with number theory, which is clearly 
one of Sage's strongest points. There's a bit on using Maxima for symbolic 
calculations.


We have a long way to go to get the number of books written about Sage as there 
is for MATLAB or Mathematica. I think there are over 500 for Mathematica and 
MATLAB must have many times that.


But I think it's useful to have a book written about Sage that not from William 
or someone else at the uni of Washington. (That said, there are numerous points 
in the book where a developer would know more. This problem is compounded 
somewhat by the fact that some of the documentation on Sage is wrong. The 
install from source section was very bad until recently, and as someone 
mentioned, there's a lot of confusing references to VirtualBox and VMware, with 
one bit of documentation recommending VirtualBox and the other VMware.


Anyway, I should have a copy of the book soon. I've not seen it in full yet, as 
I've only seen drafts.


Dave

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Re: [sage-support] Re: install additional package

[Dr. David Kirkby]

On 05/ 4/11 10:19 PM, John Cremona wrote:

Simon,

I have tried and failed to load the large SW database (and complained
about this to William yesterday).  All the spkg_install scripts is to
move a whole lot of files, but it uses the command mv -r which is
illegal on my machines (ubuntu linux).

Which READMA were you referring to?

John


'mv' does not have any -r option according to POSIX

http://pubs.opengroup.org/onlinepubs/9699919799/utilities/mv.html

NAME

mv - move files

SYNOPSIS

mv [-if] source_file target_file

mv [-if] source_file... target_dir


So anyone writing scripts with a -r option to mv is asking for trouble.


Dave

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Re: [sage-support] Re: Trouble with sage installation on Ubuntu 11.04

[Dr. David Kirkby]

On 04/30/11 09:59 PM, Alex Lara wrote:

The command ./sage -f python (after install libssl-dev) did not work,
but  sage -f python-2.6.4.p10.spkg did work (I think).
I ran make test. The following test failed:

sage -t  -force_lib devel/sage/sage/rings/number_field/
number_field.py

Do you think my build is ok now?

Best regards---Alex


In a word, No. What version of Sage are you trying to build?

Can you show us the output of the test log file (test.log, ptest.log, 
ptestlong.log or whatever it is in your case). We need to see the bit where the 
test fails - not the complete log.


If you have not run the long tests, I suggest you run them too.


$ make testlong
(run each test serially)

or

$ make ptestlong
(if you have a multi-core and/or multi-processor machine, which will run tests 
in parallel to reduce the time needed to run them).


I have a faint recollection of number_field.py might have failed on one of the 
recent alpha releases, but has been fixed. Depending on what you are using, you 
might have hit a problem that's been solved. But I could be mistaken about this 
anyway - I lose track of the test failures, which are quite common in the early 
alpha releases.



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Q: What is the most annoying thing in e-mail?

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Re: [sage-support] Difficulties with Sage installation on ubuntu 10.04 lts

[David Kirkby]

On 27 April 2011 13:46, jean-pierre.peigneux
jean-pierre.peign...@wanadoo.fr wrote:
 Ok I tried without success ,below there is the ouput of the try,could
 you make other suggestions,thanks:

To me it seems your Fortran compiler is not functioning properly.

It would help if you configured your system to show error messages in English.

 sage -f mpir atlas

 cd 
 /home/peigneux/Bureau/Sage/sage-4.6.2-linux-32bit-ubuntu_10.04_lts-i686-Linux-i686-Linux/spkg/build/atlas-3.8.3.p16/ATLAS-build
  ; ./xprobe_comp -v 0 -o atlconf.txt -O 1 -A 20 -Si nof77 0  -Fa ic '-fPIC' 
 -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -C 
 if 
 '/home/peigneux/Bureau/Sage/sage-4.6.2-linux-32bit-ubuntu_10.04_lts-i686-Linux-i686-Linux/local/bin/sage_fortran'
  -Fa if '-fPIC'  -b 32  config1.out
 built-in:0: internal compiler error: Instruction non permise
 Please submit a full bug report,
 with preprocessed source if appropriate.
 See file:///usr/share/doc/gcc-4.4/README.Bugs for instructions.
 make[2]: *** [IRunF77Comp] Erreur 1

That certainly indicates a compiler issue.


 Unable to find usable compiler for F77; abortingMake sure compilers are
 in your path, and specify good compilers to configure

Your initial problem with Sage's prereq script had an issue with
your Fortran compiler. William suggested you basically ignored that
and tried to install ATLAS. But that generates an internal compiler
error.

I believe others have built Sage with Ubuntu 10.10, so I think it's
safe to say there's a problem with your setup, and not with Sage.

Since your C compiler appears to be working, I would suggest your
build GCC with C, C++ and Fortran support. GCC 4.5.2 would be a good
choice - do NOT use gcc 4.6.0.

I don't know about others, but I can't think of anything else.

Have you been building lots of programs as root? That increases the
chances of you messing up your system. I believe your system is messed
up in some way.

Dave


Dave

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Re: [sage-support] Difficulties with Sage installation on ubuntu 10.04 lts

[David Kirkby]

On 27 April 2011 17:20, David Kirkby david.kir...@onetel.net wrote:

 I believe others have built Sage with Ubuntu 10.10, so I think it's
 safe to say there's a problem with your setup, and not with Sage.

Sorry, I mean ?I believe,others have built Sage with Ubuntu 10.04 - I
myself have built it with Ubuntu 10.10.

Dave

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Re: [sage-support] Re: Difficulties with Sage installation on ubuntu 10.04 lts

[Dr. David Kirkby]

On 04/26/11 05:27 PM, jean-pierre.peigneux wrote:

Thank you for fast answer ;I am joining the output of cat /proc/cpuinfo
just below:

processor   : 0
vendor_id   : AuthenticAMD
cpu family  : 6
model   : 8
model name  : AMD Athlon(tm) XP 2000+
stepping: 1
cpu MHz : 1666.732
cache size  : 256 KB
fdiv_bug: no
hlt_bug : no
f00f_bug: no
coma_bug: no
fpu : yes
fpu_exception   : yes
cpuid level : 1
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat
pse36 mmx fxsr sse syscall mmxext 3dnowext 3dnow up
bogomips: .46
clflush size: 32
cache_alignment : 32
address sizes   : 34 bits physical, 32 bits virtual
power management: ts

I tried the compilation of sage from the source but I got troubles with
fortran  just below are the end of the compiling messages:
...
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking whether we are using the GNU Fortran compiler... (cached) yes
checking whether f77 accepts -g... (cached) yes
checking for Fortran flag needed to allow free-form source... none
configure: Your Fortran compiler accepts free-format source code
configure: which older F77 compilers do not. This does not 100%
configure: guarantee your compiler is suitable for building SAGE
configure: but it probably is.
checking if gcc accepts -dumpversion option... yes
checking gcc version... 4.4.3
checking if g++ accepts -dumpversion option... yes
checking g++ version... 4.4.3
/usr/bin/f77: Illegal option: -dumpversion
configure: Although gcc and g++ are both version 4.4.3
configure: the Fortran compiler f77 is some other version.
configure: The output from f77 --version is below.

/usr/bin/f77: Illegal option: --version

configure: Exiting since the Fortran compiler is not the same
configure: error: version as the C and C++ compilers
  ERROR: You do not have all of the prerequisites needed
  to build Sage from source.  See the errors above.
make[1]: *** [installed/prereq-0.7] Erreur 1
make[1]: quittant le répertoire « /home/peigneux/Bureau/sage-4.6.2/spkg
»

real0m7.010s
user0m3.916s
sys 0m2.284s
Error building Sage.
make: *** [build] Erreur 1

I don't know how to get the proper fortran compiler version ,If you have
advices they are welcome.Thanks


Can you post the output of the following commands. (I've shown the output on my 
system, but your will be different).


drkirkby@hawk:~$ command -v gcc
/usr/local/gcc-4.6.0-delayed/bin/gcc

drkirkby@hawk:~$ command -v g++
/usr/local/gcc-4.6.0-delayed/bin/g++

drkirkby@hawk:~$ command -v gfortran
/usr/local/gcc-4.6.0-delayed/bin/gfortran

drkirkby@hawk:~$ /usr/bin/f77
NOTICE: Invoking /usr/bin/f90 -f77 -ftrap=%none
Usage: f90 [ options ] files.  Use 'f90 -flags' for details

drkirkby@hawk:~$ gcc -v
Using built-in specs.
COLLECT_GCC=/usr/local/gcc-4.6.0/bin/gcc
COLLECT_LTO_WRAPPER=/usr/local/gcc-4.6.0/libexec/gcc/i386-pc-solaris2.11/4.6.0/lto-wrapper
Target: i386-pc-solaris2.11
Configured with: ../gcc-4.6.0/configure --prefix=/usr/local/gcc-4.6.0 
--with-gmp=/usr/local/gcc-4.6.0 --with-mpfr=/usr/local/gcc-4.6.0 
--with-mpc=/usr/local/gcc-4.6.0 --enable-languages=c,c++,fortran --with-gnu-as 
--with-as=/usr/local/binutils-2.20/bin/as --without-gnu-ld --with-ld=/usr/ccs/bin/ld

Thread model: posix
gcc version 4.6.0 (GCC)

drkirkby@hawk:~$ gfortran -v
Using built-in specs.
COLLECT_GCC=/usr/local/gcc-4.6.0/bin/gfortran
COLLECT_LTO_WRAPPER=/usr/local/gcc-4.6.0/libexec/gcc/i386-pc-solaris2.11/4.6.0/lto-wrapper
Target: i386-pc-solaris2.11
Configured with: ../gcc-4.6.0/configure --prefix=/usr/local/gcc-4.6.0 
--with-gmp=/usr/local/gcc-4.6.0 --with-mpfr=/usr/local/gcc-4.6.0 
--with-mpc=/usr/local/gcc-4.6.0 --enable-languages=c,c++,fortran --with-gnu-as 
--with-as=/usr/local/binutils-2.20/bin/as --without-gnu-ld --with-ld=/usr/ccs/bin/ld

Thread model: posix
gcc version 4.6.0 (GCC)

It looks to me that you have a strange Fortran compiler.

It could be that you don't actually have 'gfortran' installed, though it's hard 
to know for sure.


--
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A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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Re: [sage-support] Re: Are there people using today any of the three recommended solutions for Windows on the sage site?

[Dr. David Kirkby]

On 04/23/11 04:41 PM, kcrisman wrote:


This is a little OT, but just for reference, the R devels have made it
clear that without an X and display actually present, Cairo is the
only way to go to get this to work.  With your setup, you presumably
have a display in your VM, so your solution makes sense.   See #8868
for a ticket tracking this, though I think Joal knows about it :)

- kcrisman



I've not been following this, but note that there are virtual X displays which 
appear to accept graphics, but in fact throw it to /dev/null. Xvfb is one I know 
of - there may be others.


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Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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Re: [sage-support] Install problem Ubuntu 10.10

[David Kirkby]

On 12 April 2011 17:55, H hskog...@gmail.com wrote:
 Hi-
 I have been trying to install Sage on my laptop running Ubuntu 10.10.
 I downloaded the binary tar files and extracted them. I ran Sage in a
 terminal, after it is done resetting paths there is ImportError
 Traceback (most recent call last) and then it seems to import a bunch
 of stuff. Everything looks standard until the end when I get

 ImportError: libgfortran.so.3: cannot open shared object file: No such
 file or directory

I thought Sage binaries provided the fortran library, so I'm surprosed
you get this problem. But try:

$ sudo apt-get install gfortran


Dave

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Re: [sage-support] An error occurred while installing cddlib-094f.p8

[David Kirkby]

On 9 April 2011 16:27, Olalékan ABOU BAKAR amp...@gmail.com wrote:
 I felt that I have provided enough details..
 Sage version: 4.6.2
 OS: Centos 5 32 bits
 Error encountered: Re: [sage-support] An error occurred while installing
 cddlib-094f.p8
 That was the only error.. And it didn't build..
 I have successfuly installed Sage on Ubuntu and Redhat boxes with no
 problem.
 Is it any clearer now?

When you get an error like:

An error occurred while installing cddlib-094f.p8

you will have tens or hundred of lines above that. They will show what
the error is. The information you have provided does not allow anyone
to help you.

Dave

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[sage-support] Re: building sage on OpenSolaris x86

[Dr. David Kirkby]

On 04/ 6/11 09:33 AM, Apostolos Syropoulos wrote:

Hello,

Well I have tried to compile sage on OpenIndiana and it does not compile. In 
particular, it stops as follows

/bin/sh ./libtool --tag=CC --mode=link gcc -DSQLITE_THREADSAFE=0  
-DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g  -O2-o sqlite3  shell.o 
./libsqlite3.la -lreadline -lcurses
gcc -DSQLITE_THREADSAFE=0 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -o 
.libs/sqlite3 shell.o  ./.libs/libsqlite3.so -lreadline -lcurses  -Wl,--rpath 
-Wl,/home/apostolo/gnu/sage-4.6.2/local/lib
ld: fatal: unrecognized option '--'
ld: fatal: use the -z help option for usage information
collect2: ld returned 1 exit status
make[2]: *** [sqlite3] Error 1
make[2]: Leaving directory 
`/home/apostolo/gnu/sage-4.6.2/spkg/build/sqlite-3.6.22/src'
Error making sqlite

real0m40.314s
user0m35.454s
sys0m4.014s
sage: An error occurred while installing sqlite-3.6.22



The problem is that --rpath option is not recognized; it must be -rpath. 
BTW, I am using




$ autoconf --version


autoconf, libtool and automake are not needed.


$ make --version
GNU Make 3.81


That's fine


$ perl -v

This is perl, v5.8.4 built for i86pc-solaris-64int

Regards,
A.S.


PS Out of curiosity on which version of Solaris x86 you have successfully 
compiled sage?


* Solaris 10 update 5   (Each release of Sage is tested on this)
* OpenSolaris 06/2009   (Each release of Sage is tested on this)
* Solaris 11 Express.   (Sage is not tested much on this. It's on my laptop).

We have built it on Solaris 10 x86 update 5 and OpenSolaris 06/2009. We have not 
tried on OpenIndian. I would have expected it to work on there too.



drkirkby@hawk:~/sage-4.7.alpha2$ cat /etc/release
   OpenSolaris Development snv_134 X86
   Copyright 2010 Sun Microsystems, Inc.  All Rights Reserved.
Use is subject to license terms.
 Assembled 01 March 2010
drkirkby@hawk:~/sage-4.7.alpha2$ ./sage
--
| Sage Version 4.7.alpha2, Release Date: 2011-03-21  |
| Type notebook() for the GUI, and license() for information.|
--
**
**
* Warning: this is a prerelease version, and it may be unstable. *
**
**
sage:

Can you download the sqlite-3.6.22 source code and let us know if you can 
compile that outside of Sage. Or alternatively, if you type


cd spgk/standard
tar xfj sqlite-3.6.22.spkg
cd sqlite-3.6.22/src
./configure
make

that will be exactly the same, as the src directory in any sage package has 
the unmodified source code. (the .spkg files are usually .tar.bz2 files. Just we 
use another name, as the odd few are not compressed).


If Sage makes any patches to it, then the we don't change the src directory, 
so that directory will contain the source code the SQlite group released.


I do note the version in Sage is rather out of date, but it does build on 
Solaris, both SPARC and x86.


Was you as I expected using the GNU version of find before?

--
A: Because it messes up the order in which people normally read text.
Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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[sage-support] Re: building sage on OpenSolaris x86

[David Kirkby]

I'm forwarding this to sage-support.

On 4 April 2011 14:27, Apostolos Syropoulos asyropou...@yahoo.com wrote:


  Hello,

Hell Apostolos

 I am trying to build sage on OpenSolaris and it fails.

What version of OpenSolaris? What build?

 I have installed in my system
 gcc-4.5.2 and I have used the compiler to compile many-many things. I have
 set the environment variables as follows:

 $ export SAGE_FORTRAN=gfortran-4.5.2;
  ; export SAGE_PORT=yes

I would advise you do not set SAGE64=yes, as 64-bit builds on Solaris
or OpenSolaris are not very stable.

 and the configure script complains that

 checking for /usr/lib/libgfortran.so... yes
 configure: The environment variable
 configure: SAGE_FORTRAN_LIB=/usr/lib/libgfortran.so
 configure: is a not a 32-bit dynamic library. SAGE64 was
 configure: not set to yes, so you intend to build 32-bit.
 configure: The environment variables SAGE_FORTRAN_LIB and/or SAGE64
 configure: are not set properly.
 configure: error: Exiting, due to the incorrect configuration of environment 
 var
 iables
  ERROR: You do not have all of the prerequisites needed
  to build Sage from source.  See the errors above.

Odd.

 Note that

 $ ls -l /usr/lib/libgfortran.so
 lrwxrwxrwx 1 root root 20 2010-12-21 20:05 /usr/lib/libgfortran.so - 
 libgfortran.so.3.0.0
 $ ldd /usr/lib/libgfortran.so
     libm.so.2 =     /lib/libm.so.2
     libc.so.1 =     /lib/libc.so.1
     libgcc_s.so.1 =     /usr/lib/libgcc_s.so.1
 $ file /usr/lib/libgfortran.so.3.0.0
 /usr/lib/libgfortran.so.3.0.0: ELF 32-bit LSB shared object, Intel 80386, 
 version 1, dynamically linked, not stripped

 So obviously the configuration script is buggy as it fails to detect that 
 this is indeed the correct
 library. However, I have checked that


Can you give me the output of

$ command -v file

The script checks if a library is 32-bit or 64-bit by greping the
output of file.  Your version of 'file' is giving a very different
output file to what I get:

Could it be that you have the GNU version of file in your PATH
before the Sun one? If so, a simple fix would be to copy the Sun one
to somewhere else and put that somewhere else first in the PATH.

IF that is the problem, I will change the script so it calls
/usr/bin/file, and so not a GNU version.

 $ export SAGE_FORTRAN_LIB=/usr/lib/libgfortran.so.3.0.0

 does not help and I am getting exactly the same message. And of course
 it fails to configure with

 $ export SAGE64=yes

 giving a similar error message. Can you please tell me what is going on?

 Regards,
 A.S.



 --
 Apostolos Syropoulos
 Xanthi, Greece
 http://obelix.ee.duth.gr/~apostolo
 http://asyropoulos.wordpress.com
 http://hypercomputation.blogspot.com/


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[sage-support] Re: building sage on OpenSolaris x86

[David Kirkby]

On 4 April 2011 20:09, Apostolos Syropoulos asyropou...@yahoo.com wrote:

 Can you give me the output of

 $ command -v file


 What command?


drkirkby@hawk:~$ command -v file
/usr/bin/file
drkirkby@hawk:~$

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Re: [sage-support] Abridged summary of sage-support@googlegroups.com - 13 Messages in 6 Topics

[Dr. David Kirkby]

On 03/31/11 05:44 AM, Roy Joshua wrote:

Hi,

I tried the suggestion to use the command
SAGE64=yes
export SAGE64
that was suggested as response to my last  message by David Kirkby.
(My last message was that I could not install sage-4.6.2 to a machine
running Centos 5.5. This is a 64 bit machine with i7 8 core processor.)

However that seems to cause another bug with patch-2.5.9.
I am attaching a screen-shot. Hope someone can suggest a solution.

Roy Joshua


Sorry to here about your troubles Roy.

Your report actually highlighted a bug, as the bzip2 package did not try to 
build 64-bit. It is only trying that on Solaris and OS X which is a bug.


But as soon as you tried to build GNU patch, Sage tried to build that 64-bit, 
and it failed. This is the critical bit.



gcc -v
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man 
--infodir=/usr/share/info --enable-shared --enable-threads=posix 
--enable-checking=release --with-system-zlib --enable-__cxa_atexit 
--disable-libunwind-exceptions --enable-libgcj-multifile 
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk 
--disable-dssi --enable-plugin 
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic 
--host=i386-redhat-linux

Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)

Creating a 64-bit version of GNU patch
checking for gcc... gcc
checking for C compiler default output... configure: error: C compiler cannot 
create executables

See `config.log' for more details.
Error configuring GNU patch

real0m0.129s
user0m0.043s
sys 0m0.095s
sage: An error occurred while installing patch-2.5.9

This is clearly a 64-bit machine, but do you have a 32-bit operating system 
installed? This seems rather an old version of gcc (2008), so I'm wondering if 
you have an old release of the operating system.


I think before spending much time on this, you should decide whether this is 
really the operating system you want to run.


It could also be that somehow the BIOS in the machine is stopping this being 
seen as 64-bit. But for whatever reason, your machine is behaving like a 32-bit 
one.


That in itself should not stop Sage building. Sage builds fine on 32-bit 
operating systems and whilst Solaris is 64-bit, Sage does not work very well 
64-bit on there, so we have to build that 32-bit for now.


So your problem with ATLAS is not the 32-bit isssue, but I do wonder if you 
should consider upgrading, or sorting out your hardware in some way, before 
worrying too much about why ATLAS is not building. It would be pointless 
spending a lot of time over that, if you realise your system is configured 
sub-optimally and you want to put another operating system on it.


Dave

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Re: [sage-support] Abridged summary of sage-support@googlegroups.com - 13 Messages in 6 Topics

[Dr. David Kirkby]

On 03/31/11 05:44 AM, Roy Joshua wrote:

Hi,

I tried the suggestion to use the command
SAGE64=yes
export SAGE64
that was suggested as response to my last  message by David Kirkby.
(My last message was that I could not install sage-4.6.2 to a machine
running Centos 5.5. This is a 64 bit machine with i7 8 core processor.)

However that seems to cause another bug with patch-2.5.9.
I am attaching a screen-shot. Hope someone can suggest a solution.

Roy Joshua


It seems your gcc can't create 64-bit binaries. Could it be the operating system 
you have is a 32-bit one? I know the CPU is not, but the OS has to be 64-bit for 
one to run 64-bit code. (In principle one can cross-compile, and create code for 
a system different to what one is running on, but Sage does not support this.)


gcc -v
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man 
--infodir=/usr/share/info --enable-shared --enable-threads=posix 
--enable-checking=release --with-system-zlib --enable-__cxa_atexit 
--disable-libunwind-exceptions --enable-libgcj-multifile 
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk 
--disable-dssi --enable-plugin 
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic 
--host=i386-redhat-linux

Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)

Creating a 64-bit version of GNU patch
checking for gcc... gcc
checking for C compiler default output... configure: error: C compiler cannot 
create executables

See `config.log' for more details.
Error configuring GNU patch

real0m0.129s
user0m0.043s
sys 0m0.095s
sage: An error occurred while installing patch-2.5.9




On Wed, Mar 30, 2011 at 2:29 PM,sage-support+nore...@googlegroups.comwrote:


   Today's Topic Summary

Group: http://groups.google.com/group/sage-support/topics

- trouble installing sage#12f0806f0436b28f_group_thread_0  [4
Updates]
- sage -upgrade problem...#12f0806f0436b28f_group_thread_1  [2
Updates]
- need eigenvectors of complex matrix to arbitrary 
precision#12f0806f0436b28f_group_thread_2[3 Updates]
- How to run a Magma computation with a 
timeout#12f0806f0436b28f_group_thread_3[1 Update]
- list updating#12f0806f0436b28f_group_thread_4  [1 Update]
- sage install on Darwin#12f0806f0436b28f_group_thread_5  [2 Updates]

   Topic: trouble installing 
sagehttp://groups.google.com/group/sage-support/t/acb655b4762983e7

Roy Joshuarrjos...@gmail.com  Mar 29 09:33PM -0400 
^#12f0806f0436b28f_digest_top

Hi,

I have a Dell 980 optiplex machine with i7 processor (8 core), 16GB
RAM.
I tried to install sage on it with OS: Centos 5.5.

I tried both versions sage-4.6.2 and sage-4.5.2 and both crashed.
more...http://groups.google.com/group/sage-support/msg/bed4b2d2a740bcef


Roy Joshuarrjos...@gmail.com  Mar 29 11:27PM -0400 
^#12f0806f0436b28f_digest_top

Hi,

I have a Dell 980 optiplex machine with i7 processor (8 core), 16GB
RAM.
I tried to install sage on it with OS: Centos 5.5.

I tried both versions sage-4.6.2 and sage-4.5.2 and both crashed.
more...http://groups.google.com/group/sage-support/msg/51b48789d78cde66


achrzeszachrz...@wp.pl  Mar 29 11:18PM -0700 
^#12f0806f0436b28f_digest_top

In instalatiopn guide you can find:
SAGE_ATLAS_LIB - if you have an installation of ATLAS on your system
and you want Sage to use it instead of building and installing its own
version of ATLAS, set 
more...http://groups.google.com/group/sage-support/msg/d7e82e72b81bace5


Dr. David Kirkbydavid.kir...@onetel.net  Mar 30 06:08PM +0100 
^#12f0806f0436b28f_digest_top

On 03/30/11 02:33 AM, Roy Joshua wrote:
  Hi,

  I have a Dell 980 optiplex machine with i7 processor (8 core), 16GB
RAM.
  I tried to install sage on it with OS: Centos 5.5.

more...http://groups.google.com/group/sage-support/msg/f8471f6ec38d6f80

   Topic: sage -upgrade 
problem...http://groups.google.com/group/sage-support/t/a85916f850699295

Thierry Dumonttdum...@math.univ-lyon1.fr  Mar 30 06:41PM +0200 
^#12f0806f0436b28f_digest_top

It seems that there is a problem with content.wuala.com.

sage -upgrade



Automatically selected server content.wuala.com 
more...http://groups.google.com/group/sage-support/msg/bfa7939be1878195


kcrismankcris...@gmail.com  Mar 30 10:05AM -0700 
^#12f0806f0436b28f_digest_top

On Mar 30, 12:41 pm, Thierry Dumonttdum...@math.univ-lyon1.fr
wrote:

  sage -upgrade
  


  I am in 4.6.2

Of course, there is nothing to upgrade to at this time, though that
more...http://groups.google.com/group/sage-support/msg/a6d142cb7aaec340

   Topic: need eigenvectors of complex matrix to arbitrary 
precisionhttp://groups.google.com/group/sage-support/t/b532b0e32b0eb927

Ben123ben.is.loca...@gmail.com

Re: [sage-support] trouble installing sage

[Dr. David Kirkby]

On 03/30/11 02:33 AM, Roy Joshua wrote:

Hi,

I have a Dell 980 optiplex machine with i7 processor (8 core), 16GB RAM.
I tried to install sage on it with OS: Centos 5.5.


That's an impressive machine. Clearly not an old relic.



CLEANM -DATL_UCLEANN -DATL_UCLEANK -O -fomit-frame-pointer -fPIC -m32 -c
ATL_dNCmmNN_a1_b0.c


Is this a 32-bit version of Linux? This is building 32-bit, which is not what 
you want on a new high-spec machine.


You could try setting

SAGE64=yes
export SAGE64

and it might force Sage to build 64-bit, as ATLAS at least is building 32-bit on 
your machine.


--
A: Because it messes up the order in which people normally read text.
Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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Re: [sage-support] Re: Sage takes so many time on start up

[David Kirkby]

On 14 March 2011 19:05, Daniel M. danielmeji...@gmail.com wrote:
 My Hard Disk don't need defragmentation(ive checked either windows and
 linux), and have a little less more than a year since i bough it
 cuold it be a bug?

Sage is known to start up quite slowly on some hardware/software.

I personally find it takes only a few seconds on my Sun Ultra 27. That
machine has a quad core 3.33 GHz CPU, but only has standard 7200 rpm
SATA disks - nothing special like SAS disks, which will give higher
performance at considerly higher cost.

But on my laptop, which has a 640 GB 5400 rpm disk, Sage does take
almost half a minute to start up.

Both systems use the ZFS file system - in fact the laptop a later
version, so its not that.

I think you will find solving the startup time is on the TODO list.

Dave

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Re: [sage-support] SAGE cluster?

[David Kirkby]

On 4 March 2011 11:30, Volker Braun vbraun.n...@gmail.com wrote:
 MPI is more comparable to Mathematica's underlying MathLink C libraries. We
 also have an mpi4py optional spkg that maps the C to a Python API,
 essentially one-to-one. Its not pretty, but if you know MPI then you can
 immediately use it. There is a mini-introduction and a sample program at
 http://www.sagemath.org/doc/numerical_sage/parallel_computation.html
 The @parallel decorator could be extended to optionally use MPI as parallel
 processing backend. Right now @parallel(p_iter) supports 'fork',
 'multiprocessing' (threads) and 'reference' (serial execution). It would
 then pickle the function and its arguments, MPI broadcast them to the
 cluster, execute them as a bag-of-tasks, and finally receive the answer from
 the nodes. The only constraint would be that you can't access global
 variables on the compute nodes, obviously. As far as I understand it from
 the link you posted, this is essentially what Mathematica's ParallelTools
 do.
 But again, that only works for embarrassingly parallel workloads. If you
 need a lot of cluster communication then there is no way around learning
 MPI. For example, MPI allows you to
  * send/receive without blocking (a background thread deals with the cluster
 communication);
  * reductions (e.g. each node has a number and you want to add them up) work
 in O(log(n)) and not O(n)
  * support for fast network hardware (Cray's SeaStar interconnect has more
 bandwidth than AMD's hypertransport between CPU and the local RAM!)
 Volker

I think in cases like this, the documentation in Sage should make it
clear what the package actually does and what needs to be learned to
use it. It's easy to jump to the incorrect conclusion that the package
will permit existing Sage code to work on a cluster relativelly
easily, when in fact that's not the case.

Since I understand the Sage optional packages should be supported by
the Sage community, as Sage is, then its impossible for people to give
any real support if we don't have any documentaiton on them.

BTW, I found that OpenMPI builds on both Solaris 10 (SPARC) and
OpenSolaris (x86) if I use the Sun compilers, but not if I use gcc. I
updated #10866 and #10869 to add this information.

Dave

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Re: [sage-support] SAGE cluster?

[Dr. David Kirkby]

On 03/ 3/11 01:46 AM, A. Jorge Garcia wrote:

http://trac.sagemath.org/sage_trac/ticket/8537


Thanx for this ticket info. It looks like this MPI pkg is now
installable as a special pkg? How do I do that? How do I use openMPI and
mpi4py in SAGE after the install?

TIA,
A. Jorge Garcia
Applied Math and CompSci
http://shadowfaxrant.blogspot.com
http://www.youtube.com/calcpage2009




sage -i openmpi

will download and install the OpenMPI package. I assume the same is true of 
mpi4py.

As to how you use them, I have not got a clue. This does not seem to be 
documented in the Sage manual. I suspect this has had very little use


Google found this

http://www.mail-archive.com/sage-devel@googlegroups.com/msg45946.html

Optional packages, are supposed to be supported by the Sage community and run on 
all platforms on which Sage runs. IMHO, this should probably be made 
experimental, as it does not build on all platforms and does not appear to be 
documented.


--
A: Because it messes up the order in which people normally read text.
Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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Re: [sage-support] SAGE cluster?

[Dr. David Kirkby]

On 03/ 2/11 11:34 PM, calcp...@aol.com wrote:

I have the SAGE binary installed on 25 Ubuntu boxes in my classroom.
I wonder if there's anyway to use this as a cluster to run python code
in parallel?  I recall some work to that end some time ago with dSAGE
and the @parallel decorator.  However, dSAGE has not been part of SAGE
for a while and, as I understand it, @parallel works on multicore PCs
but not clusters, grids or clouds, right?

TIA,
A. Jorge Garcia
Applied Math and CompSci
http://shadowfaxrant.blogspot.com
http://www.youtube.com/calcpage2009


There is an optional MPI package, but I don't know if anyone actually uses it.

The version in Sage was very old (3 years old), but it was updated very recently 
to 1.4.3, which is the latest


You might find on the following ticket

http://trac.sagemath.org/sage_trac/ticket/8537

some names of people who might be using it.

--
A: Because it messes up the order in which people normally read text.
Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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Re: [sage-support] Re: New to sage: significant digits, etc.

[David Kirkby]

On 1 March 2011 17:57, sm123123 singh.madhusu...@gmail.com wrote:
 Sigh.

 When I issue a plot() command using the Matlab interface, I get a
 syntax error.

I think the MATLAB interface might be an optional component. Check the docs

Dave

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Re: [sage-support] 3DPlot error

[Dr. David Kirkby]

On 02/28/11 05:00 AM, Thomas Rike wrote:

I'm not sure if this is the right place to ask a question.


Yes it is.

I just downloaded the Sage-4.6.1-OSX-64bit-10.6 app to my 27 iMac and my 
MacBookPro. On my iMac I cannot use parametric_plot3d. The Java applet does not 
run. I get a black screen that shows a small Error Click for details in the 
upper left corner. Upon clicking I get a small pop up window: The application 
failed to run. There was an error while executing the application. Click 
Details for more information. Clicking Details results in  Java Console 
opening showing:



Java Plug-in 1.6.0_22
Using JRE version 1.6.0_22-b04-307-10M3261 Java HotSpot(TM) 64-Bit Server VM
User home directory = /Users/trike

c:   clear console window
f:   finalize objects on finalization queue
g:   garbage collect
h:   display this help message
l:   dump classloader list
m:   print memory usage
o:   trigger logging
p:   reload proxy configuration
q:   hide console
r:   reload policy configuration
s:   dump system and deployment properties
t:   dump thread list
v:   dump thread stack
x:   clear classloader cache
0-5: set trace level ton

Anyone have any idea what is wrong?


I have seen reports of issues with jmol, which would be used for the 3D plot 
causing problems on some Macs. I think a temporary fix will be to use Firefox as 
a browser, but people are looking at this issue.


I don't use a Mac myself, so have not experienced this.
--
A: Because it messes up the order in which people normally read text.
Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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Re: [sage-support] Re: Accessing R documentation trough notebook broken with 4.6.1?

[Dr. David Kirkby]

On 02/28/11 04:08 PM, kcrisman wrote:



On Feb 28, 3:21 am, Andrzej Giniewiczggi...@gmail.com  wrote:

Hello,

today I noticed that I cannot access R docs trough notebook, while it
still works like usual from command line. This is what is inside
notebook when viewed as text:

sage: r.lm?
html!--notruncate--
Traceback (most recent call last):
   File stdin, line 1, inmodule
   File _sage_input_3.py, line 10, inmodule
 exec compile(u'print _support_.docstring(r.lm, globals(),
system=sage)' + '\n', '', 'single')
   File , line 1, inmodule

   File /opt/sage/devel/sagenb/sagenb/misc/support.py, line 263, in docstring
 return html_markup(s)
   File /opt/sage/devel/sagenb/sagenb/misc/support.py, line 288, in 
html_markup
 return 'div class=docstring' + preamble +'pre' + s +'/pre/div'
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position
116: ordinal not in range(128)
/html

Currently I don't have alpha of newer version, so I wanted to ask if
this is still visible with 4.6.2 versions and/or known issue. I've
looked trough track and found few similar issues related to for
example unicode handling in %latex, but not this particular.


I can confirm this in 4.6.2.rc0.


Same here, with 4.6.2.rc1 on OpenSolaris.

Dave

--
A: Because it messes up the order in which people normally read text.
Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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Re: [sage-support] Re: Configuring sage at the bash prompt

[Dr. David Kirkby]

On 02/10/11 09:27 PM, akm wrote:

On Feb 9, 2:39 pm, Harald Schillyharald.schi...@gmail.com  wrote:

e.g.
$ sage -notebook secure=True
ends up as
notebook(secure=True)
in the ipython interpreter.


Thanks for the quick response!  I was looking for a way of adding the
adminpassword and hostname as options of the notebook command.

I may just edit run_notebook.py to pick up the host's name on the fly
and set the admin password similarly.  My team's goal is to be able to
deploy sage using an automated tool such as Chef, removing the need
for any post-installation configuration.

Cheers



Supplying passwords on the command line is generally considered bad practice, as 
these can be picked up with 'ps'.


That said, Sage is hardly designed with security in mind, so one could argue the 
risk is small in comparison to other more serious security risks. But even so, I 
don't think it would be a good idea to permit this to be passed on the command 
line.


Since the password is stored as an md5 hash (I think), it would not be dangerous 
to pass the hash on the command line. For instance if the password was fred, 
one could pass its hash



drkirkby@hawk:~$ echo fred | digest -a md5
08b622ddf7eb7c8e44cdb3bd6362f966
drkirkby@hawk:~$


with something like

sage --password_hash=08b622ddf7eb7c8e44cdb3bd6362f966

But someone has to implement it, and I doubt anyone would jump at doing that. It 
would be seen as a low priority by most I think. But if you wanted to implement 
it yourself...


--
A: Because it messes up the order in which people normally read text.
Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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Re: [sage-support] Re: error while building Sage

[David Kirkby]

On 5 February 2011 08:17, Mate Kosor mate.ko...@gmail.com wrote:
 I don't know why the checks don't work for package python, but if I
 could make a suggestion maybe it would be better that the check ships
 that package because now the check is nonfunctional.

IMHO that would be a bad idea. It's better to be aware of the issue
than just to cover up the failures.The actual tests that fail differ
from system to system.

It should also be noted that a large number of the packages in Sage
have no spkg-check file, so self-tests are not run, even if the
upstream source code has a test suite. I created a list of them at
some point - see the first column only of

http://trac.sagemath.org/sage_trac/ticket/9281

That list is probably not up to date. I've lost count of the number of
spkg-check files I've created, but still more need to be done.

 Also I think that SAGE_CHECK=no should not trigger the check.

Agreed.

Five months ago John Palmieri wrote a fix for this, but as I remarked
on the ticket (#9960) endless changes (which IMHO should have been on
other tickets) were requested by the reviewer, so the patch is still
not merged. Perhaps one day it will be.

Dave

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Re: [sage-support] bool(arcsin(x) == 2*arctan(x/(1+sqrt(1-x^2)))) returns false !!!

[David Kirkby]

On 13 November 2010 04:36, Robert Bradshaw rober...@math.washington.edu wrote:
 On Fri, Nov 12, 2010 at 3:44 PM, Derrick we.sana...@gmail.com wrote:
 Any clue why bool(arcsin(x) == 2*arctan(x/(1+sqrt(1-x^2 returns
 false where the expressions are mathematically equivalent.

 Because an expression being equal to zero is, in general, and
 undecideable question. If it can't tell, it'd rather error on the side
 of caution (not being equal) than claim they're equal.

It's not clear to me why claiming two things are false when they are
true, is any better/worst they are true when in fact they are false.
They are both 100% wrong.

Surely the better approach is to return 'Unknown' or something else to
indicate something is unknown, rather than claim its false when its
true.

Here's the same sort of thing in Mathematica.

In[3]:= 12 == 2

Out[3]= False

In[4]:= 1 == 1

Out[4]= True

In[5]:= AcrSin[x] == 2 ArcTan[x/(1+Sqrt[1+x^2])]

 x
Out[5]= AcrSin[x] == 2 ArcTan[]
2
  1 + Sqrt[1 + x ]


In[7]:= x^3 == x x^2

Out[7]= True

As you can see, when Mathematica does not know if the expression is
true or false, it returns the expression, not True or False.

Dave

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Re: [sage-support] bool(arcsin(x) == 2*arctan(x/(1+sqrt(1-x^2)))) returns false !!!

[David Kirkby]

On 6 December 2010 19:33, Mike Hansen mhan...@gmail.com wrote:
 Here's the same sort of thing in Mathematica.

 In[3]:= 12 == 2

 Out[3]= False

 In[4]:= 1 == 1

 Out[4]= True

 In[5]:= AcrSin[x] == 2 ArcTan[x/(1+Sqrt[1+x^2])]

                                     x
 Out[5]= AcrSin[x] == 2 ArcTan[]
                                            2
                              1 + Sqrt[1 + x ]


 In[7]:= x^3 == x x^2

 Out[7]= True

 As you can see, when Mathematica does not know if the expression is
 true or false, it returns the expression, not True or False.

 Here's the same thing in Sage:

 sage: 12 == 2
 False
 sage: 1 == 1
 True
 sage: arcsin(x) == 2*arctan(x/(1+sqrt(1-x^2)))
 arcsin(x) == 2*arctan(x/(sqrt(-x^2 + 1) + 1))
 sage: x^3 == x*x^2
 x^3 == x^3

 As you see, Sage does the exact same thing; although, it doesn't even
 try to determine if x^3 is equal x^3.  But, the user is _explicitly_
 asking to return either a True or False value -- that's what bool
 does in Python.

 --Mike

Oh, I missed that - it is similar, but not identical to Mathematica's
TrueQ[]. Again, I personally prefer the MMA behavior.

In[9]:= ?TrueQ
TrueQ[expr] yields True if expr is True, and yields False otherwise.

In[10]:= True[ AcrSin[x] == 2 ArcTan[x/(1+Sqrt[1+x^2])]]

   x
Out[10]= True[AcrSin[x] == 2 ArcTan[]]
  2
1 + Sqrt[1 + x ]


Sage's documentation is reasonably clear, though gives no hint it
could claim something to be false when in fact it's true.

Dave

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Re: [sage-support] bool(arcsin(x) == 2*arctan(x/(1+sqrt(1-x^2)))) returns false !!!

[David Kirkby]

On 6 December 2010 19:43, David Kirkby david.kir...@onetel.net wrote:
 On 6 December 2010 19:33, Mike Hansen mhan...@gmail.com wrote:
 Here's the same sort of thing in Mathematica.

 In[3]:= 12 == 2

 Out[3]= False

 In[4]:= 1 == 1

 Out[4]= True

 In[5]:= AcrSin[x] == 2 ArcTan[x/(1+Sqrt[1+x^2])]

                                     x
 Out[5]= AcrSin[x] == 2 ArcTan[]
                                            2
                              1 + Sqrt[1 + x ]


 In[7]:= x^3 == x x^2

 Out[7]= True

 As you can see, when Mathematica does not know if the expression is
 true or false, it returns the expression, not True or False.

 Here's the same thing in Sage:

 sage: 12 == 2
 False
 sage: 1 == 1
 True
 sage: arcsin(x) == 2*arctan(x/(1+sqrt(1-x^2)))
 arcsin(x) == 2*arctan(x/(sqrt(-x^2 + 1) + 1))
 sage: x^3 == x*x^2
 x^3 == x^3

 As you see, Sage does the exact same thing; although, it doesn't even
 try to determine if x^3 is equal x^3.  But, the user is _explicitly_
 asking to return either a True or False value -- that's what bool
 does in Python.

 --Mike

 Oh, I missed that - it is similar, but not identical to Mathematica's
 TrueQ[]. Again, I personally prefer the MMA behavior.

 In[9]:= ?TrueQ
 TrueQ[expr] yields True if expr is True, and yields False otherwise.

 In[10]:= True[ AcrSin[x] == 2 ArcTan[x/(1+Sqrt[1+x^2])]]

Oops, I put in True not TrueQ

Mathematica then behaves the same as Sage

In[1]:= TrueQ[AcrSin[x] == 2 ArcTan[x/(1+Sqrt[1+x^2])]]



Dave

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Re: [sage-support] Re: Sage Solaris binary distribution and libgfortran

[David Kirkby]

On 30 November 2010 09:12, Jean-Pierre Flori jpfl...@gmail.com wrote:


 On 30 nov, 00:34, David Kirkby david.kir...@onetel.net wrote:
 On 29 November 2010 14:49, Jean-Pierre Flori jpfl...@gmail.com wrote:

  It now fails when building sqlite:

   /usr/local/gcc4/bin/gcc -DPACKAGE_NAME=\sqlite\ -DPACKAGE_TARNAME=

 how are you getting Sage to build with a gcc in /usr/local/gcc4/bin/ ?

 If you are doing what seems a logical thing to do (set the CC
 variable), then I'm afraid to say this does not work reliably. Many
 parts of Sage will ignore CC. You *must* make sure the first gcc in
 your path is = 4.0.1.

 I set GG to /usr/local/gcc4/bin/gcc (and CXX...), but also prepended /
 usr/local/gcc4/bin to PATH and /usr/local/gcc4/lib to LD_LIBRARY_PATH
 because of the warnings in the installation guide.
 I set SAGE_FORTRAN and SAGE_FORTRAN_LIB to correct values and copied
 gtar and gmake to tar and make in a custom directory prepended to PATH

I would suggest you unset CC and CXX. Sage certainly builds without
them. Setting them works in some places, and does not in others, so
there's nothing to be gained by setting them really. I doubt that's
the problem here.

 Can you give me the output of

 1) $ command -v gcc
 2) $ gcc --version

 fl...@infres2: 510 gcc -v
 Using built-in specs.
 COLLECT_GCC=gcc
 COLLECT_LTO_WRAPPER=/usr/local/packages/gcc4_10/libexec/gcc/sparc-sun-
 solaris2.10/4.5.1/lto-wrapper
 Target: sparc-sun-solaris2.10
 Configured with: ../configure --prefix=/usr/local/packages/gcc4_10 --
 with-as=/usr/ccs/bin/as --with-ld=/usr/ccs/bin/ld --enable-
 languages=c,c++,fortran,objc,java
 Thread model: posix
 gcc version 4.5.1 (GCC)
 fl...@infres2: 511 command -v gcc
 /usr/local/gcc4/bin/gcc

That looks mostly OK. However, I note that gcc was configured using

./configure

rather than

/[patch/to/configure

In practice, I don't know if that can screw gcc up, but it is
specifically recommended NOT to do this:

http://gcc.gnu.org/install/configure.html

First, we *highly* recommend that GCC be built into a separate
directory from the sources which does *not* reside within the source
tree.

But your gcc was built in a way that is highly recommended not to do so.

When I run gcc --v, I see:

Configured with: ../gcc-4.5.0/configure

which is the way gcc is supposed to be built.

I can try building Sage with gcc 4.5.1, since we have not used 4.5.1
anywere, but we have used 4.5.0 and it builds fine. I just stated a
build on a Sun Blade 1000 running the very first release of Solaris 10
(March 2005). The build has not completed, but sqlite has built ok.

You might want to build gmp, mpfr, mpc and gcc using the gcc is
/usr/sfw/bin. I believe your system admin has not done this properly,
but I must admit, I doubt that is the cause.


Dave




Dave

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[sage-support] Port change for http://t2nb.math.washington.edu

[David Kirkby]

The Internet Assigned Numbers Authority (IANA) is responsible for
maintaining the official assignments of port numbers for specific uses

http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers
http://www.iana.org/assignments/port-numbers

IThe default port for a Sage server (8000) is officially reserved for
Remote Desktop Management and so Sage should not be using that port.
This causes a practical problem, as company firewalls are likely to be
open on port 8080, but not on 8000, which at least one Sage user has
found.

As such, I've made http://t2nb.math.washington.edu:8080 be available
on the correct port, which is 8080. It's still available on port 8000,
but if anyone is aware of a reference to this server on port 8000, I
suggest they edit it and change it to 8080. I've done this on
Wikipedia myself, but nowhere else.

As noted elsewhere, I think Sage should change the default port from
8000 to 8080.

Dave

 Instead we should use 8080, which is designated as an alternative HTTP server.

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Re: [sage-support] Re: Sage Solaris binary distribution and libgfortran

[David Kirkby]

On 18 November 2010 09:01, Jean-Pierre Flori jpfl...@gmail.com wrote:
 Hi,

 Can you send me the output of

 $ gcc -v
 $ gfortran -v
 $ command -v gcc
 $ cmmand -v gfortran

 on your system.

 Here it is:
 bash-3.00$ gcc -v
 Reading specs from /usr/local/packages/gcc3/bin/../lib/gcc/sparc-sun-
 solaris2.10/3.4.3/specs
 Configured with: /sfw10/builds/build/sfw10-patch/usr/src/cmd/gcc/
 gcc-3.4.3/configure --prefix=/usr/sfw --with-as=/usr/ccs/bin/as --
 without-gnu-as --with-ld=/usr/ccs/bin/ld --without-gnu-ld --enable-
 languages=c,c++ --enable-shared
 Thread model: posix
 gcc version 3.4.3 (csl-sol210-3_4-branch+sol_rpath)


 bash: command: gfortran: not found


Those are totally unsuitable for building Sage

 But there are other gcc binaries in /usr/local/gcc4.
 Here is the content of /usr/local/gcc4/bin:
 c++                              jcf-dump
 cc                               sparc-sun-solaris2.10-c++
 cpp                              sparc-sun-solaris2.10-g++
 g++                              sparc-sun-solaris2.10-gcc
 gcc                              sparc-sun-solaris2.10-gcc-4.2.0
 gccbug                           sparc-sun-solaris2.10-gcc-4.4.2
 gcj                              sparc-sun-solaris2.10-gcj
 gcov                             sparc-sun-solaris2.10-gcjh
 gfortran                         sparc-sun-solaris2.10-gfortran

 with:
 bash-3.00$ ./gcc -v
 Using built-in specs.
 Target: sparc-sun-solaris2.10
 Configured with: ../configure --prefix=/usr/local/packages/gcc4_10 --
 with-as=/usr/ccs/bin/as --with-ld=/usr/ccs/bin/ld --enable-
 languages=c,c++,fortran,objc,java
 Thread model: posix
 gcc version 4.4.2 (GCC)
 bash-3.00$ ./gfortran -v

Those are ok, but unless those are in your PATH first, which ~I don't
think is the case, then they will not be used when Sage is built. Sage
will use the first gcc in your path.

Even if you specify a compiler with the CC environment variable, it
will probably fail, as many of the packages in Sage have 'gcc'
hard-coded and will ignore the CC and CXX environment variables.

 Here are some of the computers I have access to:
 - SunOS 5.10 Generic_139555-08 sun4v sparc SUNW,T5140

That will run Sage very slowly. The CPUs are ill suited for scientific
computing.

 - SunOS 5.10 Generic_137137-09 sun4u sparc SUNW,Sun-Blade-1500

That will be quicker for running Sage, despite the fact it is older.


 PS, when you first run Sage, you will need to have /opt/ccs/bin in
 your path, so Sage can find 'm4', which it needs whenever a build of
 Sage is moved.

 There is no /opt/css folder.

See my correction. It is /usr/ccs/bin/m4

I asume using the GNU version of m4 will work, but it is not somethige
that's ever tested on Soliaris.
 For m4, I guess the system uses:
 bash-3.00$ which m4
 /usr/local/bin/m4

 I'll try your library now.

 JP

Be careful. Note I said that you need to have recent versions of *ALL*
the gcc libraries. A failure to have any libgfortran.so will result in
a failure of Sage to run at all. A failure to have recent versions of
the C and C++ libraries will result in odd behaviour. Some of Sage's
self-tests will fail to run properly.

I suggest you run from the top level

make testlong

and wait and see if there are any failures. You might get a few
timeout failures on those systems.

dave

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Re: [sage-support] Re: Sage Solaris binary distribution and libgfortran

[David Kirkby]

On 18 November 2010 13:07, Jean-Pierre Flori jpfl...@gmail.com wrote:
 You were right, there is something wrong with the libgfortran file
 under SAGE_ROOT/local/lib/ .
 It was a symlink to ./../lib/libgfortran.so, strange.

 Sage is working with the libraries you posted above. Thanks !

I'll need to make sure that file gets deleted. It is needed when
building Sage, but it is a nuisance when distributing binaries.

Dave

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Re: [sage-support] Sage Solaris binary distribution and libgfortran

[David Kirkby]

On 17 November 2010 16:35, Jean-Pierre Flori jpfl...@gmail.com wrote:
 Hi,

 I unpacked Sage 4.5.1 binaries on Solaris, but when I try to launch
 Sage, it complains about missing libgfortran:

 ImportError: ld.so.1: python: fatal: libgfortran.so.3: open failed: No
 such file or directory

 I searched a bit and found something which looks related here:
 http://trac.sagemath.org/sage_trac/ticket/8049
 However it does not seem that the library is shipped with Sage.
 Should I ask the admin to install it on the system ?
 I found nothing in the documentation mentionning it is required.

 Thanks in advance.

Basically Solaris does not ship with a new enough version of gcc - in
fact, the gcc it ships with does not even have Fotran support at all.
So somehow you need to get the libraries that Sage uses, which
includes the Fotran library libgfortran.so.

 But you can get it several ways.

If you have a recent gcc that is built with Fortran support, it will
have a file libgfortran.so. You can copy or link that file to
$AGE_ROOT/local/lib/libgfortran.so, where SAGE_ROOT is the directory
where you installed Sage.

You could also trying add the installation directory of gcc to
LD_LIBRARY_PATH - something like

LD_LIBRARY_PATH=/usr/local/gcc-4.5/lib

One other option, which might be easiest for you, is if we make
available a set of the gcc libraries used to build Sage. I think that
might be a good idea. I can't do that just now, but can do it within
24 hours or so.

I'm just about to go out to the London OpenSolaris User Group (LOSUG),
so don't have time to make any binaries now!!! But I can do it soon.

Let me know how you get on.

The binaries for Solaris are a few months old.  We can make some newer
ones available, but that might take a bit more time. Getting your Sage
working should not take long. You don't need the help of your system
admin, but it might help if we make the libraries available, which we
can do under the terms of the LGPL which covers the libraries built by
GCC.

Dave

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Re: [sage-support] Sage Solaris binary distribution and libgfortran

[David Kirkby]

On 17 November 2010 16:35, Jean-Pierre Flori jpfl...@gmail.com wrote:
 Hi,

 I unpacked Sage 4.5.1 binaries on Solaris, but when I try to launch
 Sage, it complains about missing libgfortran:

 ImportError: ld.so.1: python: fatal: libgfortran.so.3: open failed: No
 such file or directory

 I searched a bit and found something which looks related here:
 http://trac.sagemath.org/sage_trac/ticket/8049
 However it does not seem that the library is shipped with Sage.
 Should I ask the admin to install it on the system ?
 I found nothing in the documentation mentionning it is required.

 Thanks in advance.

Download this file

http://boxen.math.washington.edu/home/kirkby/gcc-4.5.1-Solaris-libraries.tar.bz2

and extract its contents in $SAGE_ROOT/local/lib

where $SAGE_ROOT is the directory where you installed Sage.

If there is a file libgfortran.so there, then I suggest you delete it,
as it will be a link to a non-existent file. Some file might need to
be edited - I put some notes in a README.txt

Let us know how you get on with it.

Dave

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Re: [sage-support] Re: Sage Solaris binary distribution and libgfortran

[David Kirkby]

On 17 November 2010 23:56, Jean-Pierre Flori jpfl...@gmail.com wrote:
 Thanks for taking care of this !

 I was just trying to run tests on Solaris for the next Ecl and Maxima
 spgk's...

 I'll try downlaoding your lib tomorrow, I'm not at work right now and
 am too tired to ssh and etc...

No problem.

 Just one point: we've got a quite recent gcc installed on our Solaris,
 I'd say gcc 4.2 or even 4.4.2 not quite sure (gcc4.something at
 least), and there is a gfortran binary installed with it ,but no
 libgfortran.so...

That does not make any sense. To the best of my knowledge, if gcc is
built with Fortran support, then it will have a library
libgfortran.so. However, where that might be on your file system I
don't know.

Can you send me the output of

$ gcc -v
$ gfortran -v
$ command -v gcc
$ cmmand -v gfortran

on your system.

If you have a recent gcc, then my binary library package should not be
necessary. I think what is probaby happening is that the file
libgfortran.so in the Sage binary is a link to a non-existant file on
your file system. In which case it should be deleted.

BTW, what SPARC system do you have? If you have something like an
M3000 or better, then building the latest Sage from source should not
take too long.

If its a Blade 100/2000/2500 or any of the CoolThreads machines,
than building Sage will take a very long time. The CoolThreads (T1, T2
and T2+ CPUs) are not well suited to running Sage, though they will
run it.

http://t2nb.math.washington.edu:8000/

is running in a zone on a Sun T5240. It is quite slow, as those CPUs
are ill suited for this sort of task.

 So i guess we have a recent enough gcc, but not the gfortran lib for
 dynamic linked binaries or something like that (no idea about Solaris
 package managment).

The only packages I'm aware of for a recent gcc will be from
Blastwave. In which case, I think the library might be in
/opt/csw/gcc4/lib/libgfortran.so

If that is your recent gcc, then I would suggest adding
/opt/csw/gcc4/lib/ to your LD_LIBRARY_PATH

$ LD_LIBRARY_PATH=/opt/csw/gcc4/lib/:$LD_LIBRARY_PATH
$ export LD_LIBRARY_PATH

Be aware. if Sage finds a recent gfortran, but the C or C++ libraries
are old, then Sage will run, but it will not run perfectly. One of the
self-tests will fail. Sage must link to recent versions of all the
libraries, and not old ones.

 Of course I might be wrong. I'll be running more test tomorrow
 afternoon.

 Cheers,

No problem. I will be out part of tommorow, but I'll try to respond as
quickly as possible.

PS, when you first run Sage, you will need to have /opt/ccs/bin in
your path, so Sage can find 'm4', which it needs whenever a build of
Sage is moved.

Dave

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Re: [sage-support] Re: Sage Solaris binary distribution and libgfortran

[David Kirkby]

On 18 November 2010 00:59, David Kirkby david.kir...@onetel.net wrote:
 On 17 November 2010 23:56, Jean-Pierre Flori jpfl...@gmail.com wrote:

 PS, when you first run Sage, you will need to have /opt/ccs/bin in
 your path, so Sage can find 'm4', which it needs whenever a build of
 Sage is moved.

 Dave

Correction. You will need /usr/ccs/bin in your path.

Dave

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Re: Re : [sage-support] [fedora14] installation failed

[Dr. David Kirkby]

On 11/15/10 07:29 PM, Mike Witt wrote:

On 11/15/2010 10:57:39 AM, Colombel Bruno wrote:

Hi,

As sage-4.6 doesn't work, i try to install sage-4.4.4 which was
working on Fedora13 :

Host system
uname -a:
Linux localhost.localdomain 2.6.35.6-48.fc14.x86_64 #1 SMP Fri Oct 22
15:36:08 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux


CC Version
gcc -v
Utilisation des specs internes.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.5.1/lto-wrapper

Target: x86_64-redhat-linux
Configuré avec: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info
--with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap
--enable-shared --enable-threads=posix --enable-checking=release
--with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-gnu-unique-object
--enable-linker-build-id
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada,lto
--enable-plugin --enable-java-awt=gtk --disable-dssi
--with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre
--enable-libgcj-multifile --enable-java-maintainer-mode
--with-ecj-jar=/usr/share/java/eclipse-ecj.jar
--disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic
--with-arch_32=i686 --build=x86_64-redhat-linux
Modčle de thread: posix
gcc version 4.5.1 20100924 (Red Hat 4.5.1-4) (GCC)

expr: error while loading shared libraries: libgmp.so.3: cannot enable
executable stack as shared object requires: Permission denied


friendly


I put SELinux in permissive mode (for many reasons), which will
fix this. But if you have stringent security concerns this might
not work for you. If you don't have the GUI for SELinux management,
do: yum install policycoreutils-gui

-Mike

We should really try to sort the problem out. If something is executing the 
stack, it should really not be doing it.


--
A: Because it messes up the order in which people normally read text.
Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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Re: [sage-support] Re: numerical integration of bessel_J functions

[Dr. David Kirkby]

On 11/ 2/09 08:11 PM, svanshaar wrote:


Thanks Jason!  That works perfectly.


I don't know if any of this uses the GNU Scientific library, but there are 
reports of bug in the Bessel functions on there.


gsl_sf_bessel_lnKnu overflows for large nu

which the developers have acknowledged and have corrected. However, Sage will 
not have that correction until a new release of GSL is made.


The GSL bug ID is #31528

Dave

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Re: [sage-support] Sage and Macaulay 2

[Dr. David Kirkby]

On 11/10/10 04:14 PM, doug5y wrote:

Is it required to download and install Macaulay 2 for sage to use it?


Yes, it is optional. I created a ticket the other day

http://trac.sagemath.org/sage_trac/ticket/10117

to say this should be documented, as its not clear from reading the 
documentation that this is so.



I've built sage already, would I have to rebuild sage if I installed
Macaulay 2 after the build?


It should not be necessary to do so. I think typing

$ sage -i /path/to/Macaulay/package
$ sage -b

should be enough to install the package, and rebuild any parts of the library 
that the package has changed. But I've never used this myself.



TIA,
Doug Nadworny





Dave

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Re: [sage-support] Symbolic Product

[Dr. David Kirkby]

On 11/ 9/10 06:52 PM, Geoff wrote:

Hello

Mathematica has a symbolic product so that means Sage should.  I don't
think Sage does.

I found symbolic sum but not symbolic product in the reference files.
I need to be able to define a function of a variable x which involves
several symbolic products from 1 to n or whatever.  I then want to be
able to do a derivative and a limit of this.  I am trying out Sage
because Mathematica doesn't seem to be able to handle this stuff
exactly.  I can define the function just fine but when I try to take
the limit Mathematica can't seem to handle it.  Even when I give n a
value of 2 and the limit should be extremely easy, Mathematica can not
do it.  So, I thought I would see if Sage could handle such a thing.

Any help would be appreciated, thanks

What Mathematica commands were you executing. It would help if you gave us an 
example of what you have done, and what you are trying to achieve and what you 
are expecting.


Likewise, what have you tried in Sage, though in this case it might be more 
restrictive, as you don't believe Sage has the command you want.


Dave

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[sage-support] Fit data, but force fit to go through a given point (x,y)

[David Kirkby]

Assume I have some data of the distance a car will travel (y) vs the
amount of fuel in a car (x). For small amounts of fuel, one would
expect the distance y to be linearly related to x. But if a lot of
fuel is added, the weight of the fuel would then become significant,
and the distance would not increase linearly. So I might have a set of
data like

Fuel (x, litres) Distance (y, km)
0 0
10 50
20 100
30 149
40 195
etc

I might fit a polynomial using find_fit, of the form.

y = a x^2 + b x + c

But one obvious fact is that if the amount of fuel is 0, then the car
can't go anywhere.

It there anyway to fit a curve to some data, but force the fit to go
through the point (0,0)?

Dave

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Re: [sage-support] openSUSE 11.1 support to be discontinued

[Dr. David Kirkby]

On 10/26/10 05:09 PM, todd rme wrote:

Currently the sage build farm only has openSUSE 11.1 builds available.
  However, openSUSE 11.2 came out almost a year ago and openSUSE 11.3
came out several months ago.  With fixes now being implemented for
Sage 4.6, (see http://trac.sagemath.org/sage_trac/ticket/9530), Sage
will build successfully on openSUSE 11.2 and 11.3 for the first time.

Now it is being announced that support for openSUSE 11.1 is being
discontinued entirely on December 31st (see
http://lists.opensuse.org/opensuse-announce/2010-10/msg8.html).
This means no new updates for openSUSE 11.1 will be provided and all
downloads for openSUSE 11.1 will be removed from openSUSE servers.

This will leave Sage without binaries for any supported version of
openSUSE.  Further, it is a security risk to Sage having a
distribution running on their build farm that does not receive
security updates.  For this reason I think openSUSE 11.2 and/or 11.3
should be added to the build farm prior to the release of sage 4.6.
openSUSE 11.1 can then be removed from the build farm then or wait
when it reaches end-of-life.


It's totally unreasonable to expect to hold up releasing Sage 4.6 just because 
openSUSE has decided to stop supporting 11.1 in December.


Currently Sage has no binaries at all for several Linux distributions including 
Debian, Mandriva, Arch or Slackware. Therefore openSUSE is not unique in this 
situation.



I think it is worthwhile doing this now to provide some buffer in case
of any problems.


Do you have a suitable machine that is kept on 24/7 and which you could allow a 
buildbot access to? If so, you have a better chance of getting that integrated.


It's unfortunate, but installing operating systems is not everyones idea of fun 
(once you have done it 20 times, it gets a bit boring), and there is not a queue 
of people offering to set up buildbots.


I think it would be good to have systems with openSUSE 11.2 and 11.3 (not 
everyone has the latest release installed), but someone has to do the work.


Ultimately, if you want a system supported, the best thing is to make it 
available yourself, or offer to manage a virtual machine.


That's what I did with OpenSolaris - just made the machine available to the 
buildbot.


Dave

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Re: [sage-support] Re: installation under snow leopard

[Dr. David Kirkby]

On 10/23/10 12:51 AM, Michael Welsh wrote:


The root password doesn't work with sudo, you need to login as su (just type 
that) first. However, sudo is much easier.

HTH,
Michael



In general there is no user called su, so one can't log in as su.

su is a command to 'switch user'. By default, it switches to the root account, 
but you can be used to switch to any user whose password you know.


Dave

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Re: [sage-support] status of Macaulay2 ?

[Dr. David Kirkby]

On 10/21/10 01:07 PM, Dumont Thierry wrote:

One of my colleague want Macaulay2.

Macaulay2 does not appear in the list of optional packages.
BUT: sage -i macaulay2 downloads the packages.

It says: need gdbm. Ok, we install it.

then: sage -i macaulay2 fails again: no correct autoconf available.


Questions:
1) what about macaulay2 ?
2) Is Sage depending on the autotools installed on the machine ?

Yours
t.d.




During some automatic testing I found an issue with this, and have raised a 
ticket for it. But I have no idea how to fix it.


http://trac.sagemath.org/sage_trac/ticket/10117

Sage should not be relying on autotools, but in this case I get the impression 
the package is somewhat poorly configured.


Dave

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Re: [sage-support] Can't compute modular degree for elliptic curves in 4.5.2

[Dr. David Kirkby]

On 10/20/10 12:07 AM, Justin C. Walker wrote:


On Oct 17, 2010, at 17:50 , gagan wrote:


sage: E=EllipticCurve('11a1');
sage: E.modular_degree();
/Applications/sage/local/bin/sympow: line 3:  9922 Segmentation
fault  ./sympow $*


I can't reproduce this problem (Mac OS X, 10.6.4, Dual Quad Xeon) using 4.4, 
4.5.2, 4.5.3, or 4.6.a3.

Justin

--
Justin C. Walker, Curmudgeon at Large
Director
Institute for the Enhancement of the Director's income


Same here - I can't reproduce it (OpenSolaris on Xeon processor).

Based on an inspection of the source code for SYMPOW, it is the worst I've seen 
in Sage. In fact, it's the worst code I have ever seen. So I personally would 
not be surprised if there are bugs in it.


That said, both John and William use the code for computing the modular degree 
of elliptic curves.


There is a trac ticket open for implementing the Watkins-Delaunay's algorithm 
for computing modular degrees in Sage


http://trac.sagemath.org/sage_trac/ticket/9758

If there is a bug in the code, good luck finding it, as the code is almost 
obfuscated.


Dave

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Re: [sage-support] Can we lock parts of a worksheet?

[Dr. David Kirkby]

On 10/18/10 07:31 AM, Nikos Apostolakis wrote:

Dear group,

we are creating some worksheets to be used in teaching precalculus, and
we wonder if it's possible to have parts of a worksheet locked, so
that the're not easily (read accidentally) editable.  The fear is that
students may accidentally, double click on the text and inadvertently
delete or corrupt the text while they work through the worksheet.  Also
is it possible to have some cells locked? that is the code should not
be easily editable, but stil able to be evaluated?


I'm not aware of one, but there might be.


I've been told that Mathematica has a similar feature for its worksheets.


Yes, one selects the cell, then on the main menu Cell - Cell Properties - 
Editable It is a very useful feature.



TIA,
Nikos Apostolakis




Dave

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[sage-support] Re: Question on Sage math - loading modules

[Dr. David Kirkby]

On Oct 12, 9:15 pm, Jürgen Will jw...@onlinehome.de wrote:
 Hallo,

 how can I load a module like symmetrica into Sage?
 ? symmetrica works, symmetrica ? works, and help(symmetrica) works.

 Thanks.

You would be far better asking on the sage-support mailing list. Just
join at

http://groups.google.com/group/sage-support?hl=en

then you can either post via google groups or via any mail client to:

sage-support@googlegroups.com

help(symmetrica) has several examples of using this.



Dave

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Re: [sage-support] Re: Question on Sage math - loading modules

[David Kirkby]

I should have stated, this below was posted to sci.math.symbolic

http://groups.google.com/group/sci.math.symbolic/browse_thread/thread/1622538c471acba4/bdd157ee61540ca5?hl=en#bdd157ee61540ca5



On 15 October 2010 22:11, Dr. David Kirkby david.kir...@onetel.net wrote:
 On Oct 12, 9:15 pm, Jürgen Will jw...@onlinehome.de wrote:
 Hallo,

 how can I load a module like symmetrica into Sage?
 ? symmetrica works, symmetrica ? works, and help(symmetrica) works.

 Thanks.

 You would be far better asking on the sage-support mailing list. Just
 join at

 http://groups.google.com/group/sage-support?hl=en

 then you can either post via google groups or via any mail client to:

 sage-support@googlegroups.com

 help(symmetrica) has several examples of using this.



 Dave

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Re: [sage-support] suse 11.2

[Dr. David Kirkby]

On 10/12/10 04:07 PM, Martin Rubey wrote:

Martin Rubeymartin.ru...@math.uni-hannover.de  writes:


I just discovered

http://trac.sagemath.org/sage_trac/ticket/8978

does this imply that the binary on sagemath provided for suse 11.1 will
not work on suse 11.2?


It seems it doesn't!  Below what happens.  Any cure?  Is it known which version 
is the last to work?

Many thanks,

Martin

ru...@rp30:~  sage
--
| Sage Version 4.5.3, Release Date: 2010-09-04   |
| Type notebook() for the GUI, and license() for information.|
--
sh: symbol lookup error: 
/opt/local/sage-4.5.3-linux-64bit-opensuse_11.1_x86_64-x86_64-Linux/local/lib/libreadline.so.6:
 undefined symbol: PC


Readline often causes problems with Suse. If you search the archives you might 
find a solution. You could try renaming the file $SAGE_ROOT/local/libreadline* 
to something else and hope for the best.


If you type

tar xvfj readline-$version in the directory $SAGE_ROOT/spkg/standard, then 
change to the directory readline-$version, take a look at spkg-install and read 
it. You will see it does some odd things on Suse.


Sage ships with lots of libraries and sometimes they cause conflicts with the 
system libraries. Readline and suse is a well known example, but as I'm not a 
Linux user, I don't know the details.


Dave

Dave

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Re: [sage-support] Re: What's easiest way to get Sage running on Windows for non-techie students?

[Dr. David Kirkby]

On 10/10/10 04:19 AM, kcrisman wrote:


Yeah, it's still really annoying to get the VMWare itself, though, and
requires giving out semi-personal information, which is perhaps not
what one would want to get students interested in mathematical
software...

I expect students have to do the same to run their copies of Mathematica.

I doubt I'm the only person who types random collections of letters/numbers for 
name, address, phone numbers etc.


Dave

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Re: [sage-support] Re: Segfault when printing a copy of symbolic object

[Dr. David Kirkby]

On 10/ 8/10 02:25 AM, kcrisman wrote:



On Oct 7, 8:50 pm, Mike Hansenmhan...@gmail.com  wrote:

It doesn't have anything to do with the compiler warning messages --
the problem is much simpler than that.  The implementation of
Element.__copy__ is wrong for Expression objects; namely, it doesn't
set the _gobj attribute.  To fix it, we just add a proper
implementation of copy:

 def __copy__(self):
 return new_Expression_from_GEx(self._parent, self._gobj)


LOL - I should have checked that!  Trac isn't working now - can you or
drkirkby put that on the ticket when it comes back up?

- kcrisman



It works for me, as I remarked at

http://trac.sagemath.org/sage_trac/ticket/10099

However, I don't feel able to review completely myself, as I don't understand 
this. But I can report it works on my OpenSolaris machine.


dave

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Re: [sage-support] Segfault when printing a copy of symbolic object

[Dr. David Kirkby]

On 10/ 6/10 03:18 PM, Jean-Pierre Flori wrote:

Sage segfaults when printing a copy of something symbolics :

sage: copy(x)


As I noted earlier, I see this on my machine (Sun Ultra 27 running OpenSolaris). 
However, it must be relatively new, as I do *NOT* see the segfault at


http://t2nb.math.washington.edu:8000

which is running Sage 4.5.1. That said, that's a big-endian machine, which could 
just be relevant.


Dave

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