[sage-devel] Re: spkg vote: SageTeX

2008-12-19 Thread William Stein
On Thu, Dec 18, 2008 at 3:52 AM, Dan Drake wrote: > Hello all, > > The SageTeX package needs two basic pieces to work: a pure Python > module, and a pure LaTeX style file. Since a Sage installation is > necessary for either of those pieces to be useful, it seems like it > would be wise to include

[sage-devel] Re: Install error on Suse 11.1

2008-12-19 Thread mabshoff
Hi, no need to send me any logs since I can reproduce this now. The problem is that bash as well as sh on OpenSUSE are dynamically linked against readline, so one we source local/bin/sage-env from an spkg during build and we do have a compiled and installed libreadline.so things blow up with a mi

[sage-devel] Re: Sage 3.2.2.rc1 released

2008-12-19 Thread Craig Citro
> eisenstein_submodule, sorry I wasn't more specific. > Hmm, interesting. Do you have the log? I'm just surprised that anything could cause that file to timeout, especially without causing anything else to timeout. Could I con you into running that test again, and seeing if it still times out? If

[sage-devel] Re: Sage 3.2.2.rc1 released

2008-12-19 Thread mhampton
eisenstein_submodule, sorry I wasn't more specific. -Marshall On Dec 19, 1:00 pm, "Craig Citro" wrote: > > My ppc powerbook is still slaving away on tests, its almost done and > > so far just has timeout failures on eisenstein and calculus.py. > > What file was the eisenstein timeout on? > > -c

[sage-devel] Re: Install error on Suse 11.1

2008-12-19 Thread mabshoff
On Dec 19, 12:56 pm, henrik22 wrote: Hi, > Thank you for the hint. In fact, compilation continues if I > remove the just created readline from sage-3.2.2/local/lib, so that > the pari compilation > is forced to use the version 5.2 already on my computer (/lib64/ > libreadline.so.5.2, > includ

[sage-devel] Re: Install error on Suse 11.1

2008-12-19 Thread henrik22
Thank you for the hint. In fact, compilation continues if I remove the just created readline from sage-3.2.2/local/lib, so that the pari compilation is forced to use the version 5.2 already on my computer (/lib64/ libreadline.so.5.2, including header files in /usr/include/readline). Where may I p

[sage-devel] Re: Final 3.2.2 sources released

2008-12-19 Thread Justin C. Walker
On Dec 19, 2008, at 11:56 , Gary Furnish wrote: > > Was that with a parallel test? I'm aware of the marker issue but > haven't been able to consistently reproduce it. The marker was a > temporary fix to solve even worse race conditions, so its still a step > in the right direction. I ran $ "

[sage-devel] Re: Final 3.2.2 sources released

2008-12-19 Thread Gary Furnish
Was that with a parallel test? I'm aware of the marker issue but haven't been able to consistently reproduce it. The marker was a temporary fix to solve even worse race conditions, so its still a step in the right direction. On Fri, Dec 19, 2008 at 12:51 PM, mabshoff wrote: > > > > On Dec 19,

[sage-devel] Re: Final 3.2.2 sources released

2008-12-19 Thread mabshoff
On Dec 19, 11:45 am, "Justin C. Walker" wrote: > On Dec 18, 2008, at 23:23 , mabshoff wrote: Hi Justin, > Upgraded rc1 to "final" on Mac OS X, both 10.5.5 and 10.4.11, without   > problems. Well, it was two tiny patches :) > All tests passed on 10.5.5, but on 10.4.11, I see one failure: >

[sage-devel] Re: Final 3.2.2 sources released

2008-12-19 Thread Justin C. Walker
On Dec 18, 2008, at 23:23 , mabshoff wrote: > > Hi, > > Sage 3.2.2 is out and the final sources are at > > > http://sage.math.washington.edu/home/mabshoff/release-cycles-3.2.2/sage-3.2.2.tar > > You can also upgrade by running > > ./sage -upgrade > http://sage.math.washington.edu/home/mabshof

[sage-devel] Re: Computational biology project needs distributed processing

2008-12-19 Thread Gary Furnish
Did you test for the sql alchemy bottleneck without using dsage? There were some pretty severe (at times) speed issues fixed with dsage in 3.2.2. On Fri, Dec 19, 2008 at 11:24 AM, Jason Grout wrote: > > Dan wrote: >> Thanks for directing me. >> >> The bottleneck appears to be queries to a MySQL

[sage-devel] Re: Sage 3.2.2.rc1 released

2008-12-19 Thread Craig Citro
> My ppc powerbook is still slaving away on tests, its almost done and > so far just has timeout failures on eisenstein and calculus.py. > What file was the eisenstein timeout on? -cc --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegro

[sage-devel] FireUnit testing framework for JavaScript

2008-12-19 Thread Harald Schilly
I found this blog posting: http://ejohn.org/blog/fireunit/ about http://fireunit.org/ It's a testing framework for javascript, for the firebug extension in firefox. It says it is in a very early stage, but probably interesting for the notebook javascript code - especially because you can simulate

[sage-devel] Re: how to set an environment variable in sage code?

2008-12-19 Thread John H Palmieri
On Dec 18, 10:07 pm, "Craig Citro" wrote: > > How do I set an environment variable in the Sage code? > > From the command line, you can just do: > > sage: import os > > Then os.environ is a dictionary storing your environment variables. In > particular: > > sage: os.environ['SAGE_BANNER'] = 'no'

[sage-devel] Re: Install error on Suse 11.1

2008-12-19 Thread mabshoff
henrik22 wrote: > Hi, Hi Henrik, > on Suse 11.1 with gcc 4.3.2 installation stops early in pari-2.3.3.p0 > with > >/bin/sh: symbol lookup error: /home/henrik/Pakete/sage-3.2.1/local/ > lib/libreadline.so.5: undefined symbol: PC > > I am running on an x64_64 dual core notebook with Suse 11.

[sage-devel] Re: Computational biology project needs distributed processing

2008-12-19 Thread Jason Grout
Dan wrote: > Thanks for directing me. > > The bottleneck appears to be queries to a MySQL database made via > SQLalchemy. I will need to make many complex queries, then do some > simple statistical work on the results. But even the first query is > taking a very long time. Any guidance you can gi

[sage-devel] Install error on Suse 11.1

2008-12-19 Thread henrik22
Hi, on Suse 11.1 with gcc 4.3.2 installation stops early in pari-2.3.3.p0 with /bin/sh: symbol lookup error: /home/henrik/Pakete/sage-3.2.1/local/ lib/libreadline.so.5: undefined symbol: PC I am running on an x64_64 dual core notebook with Suse 11.1rc1. Any help appreciated, thank you very mu

[sage-devel] Re: Sage 3.2.2.rc1 released

2008-12-19 Thread mabshoff
On Dec 19, 8:53 am, mhampton wrote: Hi Marshall, > I reran the test and it passed.  sage -maxima works fine.  I did > realize that I said something incorrect, it looks like the install I > am using was originally from the 3.2.1.rc0 source, and I have upgraded > and renamed it several times si

[sage-devel] Re: Sage 3.2.2.rc1 released

2008-12-19 Thread mhampton
I reran the test and it passed. sage -maxima works fine. I did realize that I said something incorrect, it looks like the install I am using was originally from the 3.2.1.rc0 source, and I have upgraded and renamed it several times since then. So it is not too weird an event. Some of the c sou

[sage-devel] Re: Sage 3.2.2.rc1 released

2008-12-19 Thread mabshoff
On Dec 19, 5:21 am, mhampton wrote: > I had an interesting failure on an intel mac running 10.5.  Let me > describe my setup a bit since I think its relevant: because of the new > upgrade flexibility, I decided to have a "stable" sage and an > "unstable" sage on my machine, and I delete almost

[sage-devel] Re: Computational biology project needs distributed processing

2008-12-19 Thread Dan
Thanks for directing me. The bottleneck appears to be queries to a MySQL database made via SQLalchemy. I will need to make many complex queries, then do some simple statistical work on the results. But even the first query is taking a very long time. Any guidance you can give is greatly appreciat

[sage-devel] Re: Computational biology project needs distributed processing

2008-12-19 Thread mhampton
Can you give a little more detail about what you are doing? Do you have an idea as to what the main bottleneck is in your computation? Cheers, Marshall Hampton On Dec 18, 2:52 pm, Dan wrote: > I have been using Sage for a fairly intense computational biology > project. I have been very please

[sage-devel] Re: Sage 3.2.2.rc1 released

2008-12-19 Thread mhampton
I had an interesting failure on an intel mac running 10.5. Let me describe my setup a bit since I think its relevant: because of the new upgrade flexibility, I decided to have a "stable" sage and an "unstable" sage on my machine, and I delete almost all of my other sage builds. I changed the sag

[sage-devel] Re: Computational biology project needs distributed processing

2008-12-19 Thread Martin Albrecht
On Thursday 18 December 2008, Dan wrote: > I have been using Sage for a fairly intense computational biology > project. I have been very pleased with the software, but when it was > finely time to run my computations I learned that my hardware was > grossly inadequate. I have since gained access

[sage-devel] Re: Final 3.2.2 sources released

2008-12-19 Thread Robert Bradshaw
On Dec 18, 2008, at 11:53 PM, mabshoff wrote: > On Dec 18, 11:50 pm, Robert Bradshaw > wrote: >> On Dec 18, 2008, at 11:23 PM, mabshoff wrote: > > Hi, > >>> You can also upgrade by running >> >>> ./sage -upgradehttp://sage.math.washington.edu/home/mabshoff/ >>> release-cycles-3.2.2/sage-3.2.2/