[sage-devel] Re: Final 3.2.2 sources released
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/ >> >> I'm getting >> >> The following packages will be upgraded: >>doc-3.2.2 examples-3.2.2 extcode-3.2.2 genus2reduction-0.3.p4 >> matplotlib-0.98.3.p4 sage-3.2.2 sage_scripts-3.2.2 sphinx-0.5 >> * WARNING: This is a source-based upgrade, which could take hours, >> fail and render your Sage install useless!! >> Traceback (most recent call last): >>File "/Users/robert/sage/current/local/bin/sage-update", line 209, >> in >> do_update() >>File "/Users/robert/sage/current/local/bin/sage-update", line 177, >> in do_update >> if 'Placeholder spkg file' in open(F).readline(): >> IOError: [Errno 21] Is a directory >> Error getting new packages! >> >> Any ideas? > > I think you have an unpacked spkg in $SAGE_ROOT/spkg/standard - delete > that and it should work. The problem has been fixed in a recent > 3.2.2rc, but if you have an old scripts repo (or somehow multiple > heads there) the fix isn't active yet. If that isn't it I don't know > what is wrong. Yes, in fact I had lots of them. It appears to be working now. - Robert --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computational biology project needs distributed processing
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 to a computer cluster > (256 G5 xserves) that seems adequate to handle my need, but the > cluster manager asked about the ability of Sage to be distributed > across processors. I am writing to possibly get answers for him. The > manager and I reviewed the information about DSage, but questions > remain. Specifically, is Sage (or the modules I am using within Sage: > R, Numpy, SQLalchemy) capable of being "fully distributed", or is the > grid computing (i.e. "coarse distribution"?) the only option. I am not quite sure what you mean by 'fully distributed' but if you expect it to just work (TM) on 256 nodes then I guess you're out of luck. Numpy should make use of ATLAS which can be tuned to use all available cores in a multicore, shared memory setting. SQLalchemy probably depends on the database you're interfacing with. R: no clue. I suspect your best shot is more or less embarrassingly parallel coarse grained stuff. However, without a specific example it is hard to say. Hope that helps, Martin -- name: Martin Albrecht _pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99 _www: http://www.informatik.uni-bremen.de/~malb _jab: martinralbre...@jabber.ccc.de --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 3.2.2.rc1 released
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 sage script in my /usr/bin to point to the
unstable one, which I called "wildsage". One of the sage folders I
deleted was for 3.2.1.rc0. With all that in mind, here is the error I
got in qqbar:
sage -t "devel/sage/sage/rings/qqbar.py"
Exception exceptions.TypeError: TypeError(RuntimeError('Unable to
start maxima',),) in 'sage.structure.parent_old._unregister_pair'
ignored
**
File "/Users/mh/sagestuff/wildsage/devel/sage/sage/rings/qqbar.py",
line 2556:
sage: QQbar(I) == QQbar(I * (2^100+1)/(2^100))
Exception raised:
Traceback (most recent call last):
File "/Users/mh/sagestuff/sage-3.2.1.rc0/local/bin/
ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/Users/mh/sagestuff/sage-3.2.1.rc0/local/bin/
sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/Users/mh/sagestuff/sage-3.2.1.rc0/local/bin/
ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "", line 1, in
QQbar(I) == QQbar(I * (Integer(2)**Integer(100)+Integer(1))/
(Integer(2)**Integer(100)))###line 2556:
sage: QQbar(I) == QQbar(I * (2^100+1)/(2^100))
File "element.pyx", line 1102, in
sage.structure.element.RingElement.__mul__ (sage/structure/element.c:
8632)
File "coerce.pyx", line 663, in
sage.structure.coerce.CoercionModel_cache_maps.bin_op (sage/structure/
coerce.c:5359)
File "coerce.pyx", line 1079, in
sage.structure.coerce.CoercionModel_cache_maps.get_action (sage/
structure/coerce.c:9137)
File "coerce.pyx", line 1192, in
sage.structure.coerce.CoercionModel_cache_maps.discover_action (sage/
structure/coerce.c:10066)
File "parent.pyx", line 1063, in
sage.structure.parent.Parent.get_action (sage/structure/parent.c:9294)
File "parent_old.pyx", line 586, in
sage.structure.parent_old.Parent._get_action_ (sage/structure/
parent_old.c:6506)
File "parent_old.pyx", line 197, in
sage.structure.parent_old.Parent.get_action_c (sage/structure/
parent_old.c:2411)
File "parent_old.pyx", line 209, in
sage.structure.parent_old.Parent.get_action_impl (sage/structure/
parent_old.c:2698)
File "parent_old.pyx", line 268, in
sage.structure.parent_old.Parent.get_action_c_impl (sage/structure/
parent_old.c:3359)
File "parent_old.pyx", line 632, in
sage.structure.parent_old._register_pair (sage/structure/parent_old.c:
7314)
NotImplementedError: Infinite loop in multiplication of
0 (parent Symbolic Ring)
and 1 (parent Integer Ring)!
**
1 items had failures:
1 of 4 in __main__.example_64
***Test Failed*** 1 failures.
It looks like its trying to use the maxima from my deleted 3.2.1.rc0
build for some reason.
My ppc powerbook is still slaving away on tests, its almost done and
so far just has timeout failures on eisenstein and calculus.py.
-M. Hampton
On Dec 17, 12:20 pm, mabshoff wrote:
> Hello folks,
>
> here goes 3.2.2.rc1. We finally merge the Sage Words library and with
> that the last major piece of code is in 3.2.2. We also fixed a bad
> memory leak in coercion due to some debug code that snuck in. So 3.2.2
> should be very solid.
>
> Unfortunately there will be a 3.2.2.rc2 with at least an ATLAS update
> since the new sage.math needs excessive build time to build the
> current atlas.spkg. I attempted to monkey patch the fix in, but it
> doesn't work, so we will do the 3.8.2 upgrade in 3.2.2.rc2. But since
> Mike Hansen will rebase 12MB patches for the ReST transition very
> little new code and especially invasive patches will have to wait for
> 3.3.1 or 3.4 - depending if we need to do a quick bug fix release.
>
> Since the sage.math switchover to new hardware is imminent [it has
> been "tomorrow" for about two days now :)] I am sticking the tarball
> also on to sagemath.org. The sage.math only binary will not work on
> the new sage.math hardware, so I will not copy it over.
>
> Sources and a sage.math only binary is in
>
>http://sage.math.washington.edu/home/mabshoff/release-cycles-3.2.2/
>
> You can upgrade to this release by running
>
> ./sage
> -upgradehttp://sage.math.washington.edu/home/mabshoff/release-cycles-3.2.2/sa...
>
> In case sage.math is down and/or unreachable the sources to upgrade as
> well as the tarball is temporarily at
>
> http://sagemath.org/temp/
>
> Please give this release a good beating and report any issues.
>
> Cheers,
>
> Michael
>
> #4237: William Stein:
[sage-devel] Re: Computational biology project needs distributed processing
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 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 to a computer cluster > (256 G5 xserves) that seems adequate to handle my need, but the > cluster manager asked about the ability of Sage to be distributed > across processors. I am writing to possibly get answers for him. The > manager and I reviewed the information about DSage, but questions > remain. Specifically, is Sage (or the modules I am using within Sage: > R, Numpy, SQLalchemy) capable of being "fully distributed", or is the > grid computing (i.e. "coarse distribution"?) the only option. > > If not, is there an alternative that can be "fully distributed"? --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computational biology project needs distributed processing
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 appreciated. Dan On Dec 19, 8:27 am, mhampton wrote: > 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 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 to a computer cluster > > (256 G5 xserves) that seems adequate to handle my need, but the > > cluster manager asked about the ability of Sage to be distributed > > across processors. I am writing to possibly get answers for him. The > > manager and I reviewed the information about DSage, but questions > > remain. Specifically, is Sage (or the modules I am using within Sage: > > R, Numpy, SQLalchemy) capable of being "fully distributed", or is the > > grid computing (i.e. "coarse distribution"?) the only option. > > > If not, is there an alternative that can be "fully distributed"? --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 3.2.2.rc1 released
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 all of my other
> sage builds. I changed the sage script in my /usr/bin to point to the
> unstable one, which I called "wildsage". One of the sage folders I
> deleted was for 3.2.1.rc0. With all that in mind, here is the error I
> got in qqbar:
>
> sage -t "devel/sage/sage/rings/qqbar.py"
> Exception exceptions.TypeError: TypeError(RuntimeError('Unable to
> start maxima',),) in 'sage.structure.parent_old._unregister_pair'
> ignored
> It looks like its trying to use the maxima from my deleted 3.2.1.rc0
> build for some reason.
Something else looks wrong, i.e the string "3.2.1.rc0" should not
appear in the backtrace at all. There can be numerous issues like a
bungled SAGE_ROOT setting at some point that is now causing trouble.
Does maxima from that install work via "sage -maxima"? Just because
the doctest claims that is doesn't start does not mean that it doesn't
work in general. I would also check the repos for unresolved merges,
multiple heads and so on. Some environment variable can also play a
role here. Since linking the sage script just works I would always
recommend linking it into $PATH somewhere under a different name
instead of setting $SAGE_ROOT manually as recommended in the
documentation since it is too easy to scrw that up. The checking code
if SAGE_ROOT is overwritten also makes it too still possible to shoot
yourself in the foot.
> My ppc powerbook is still slaving away on tests, its almost done and
> so far just has timeout failures on eisenstein and calculus.py.
Ok. I would suggest to rerun the failed tests with -long to see what
happens. If the CPU usage stays near 0 it is a synchronization /
maxima issue, but the timeout will be raised after 30 minutes.
> -M. Hampton
Cheers,
Michael
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[sage-devel] Re: Sage 3.2.2.rc1 released
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 source code still makes references to the
sage-3.2.1.rc0 folder. I assume a complete rebuild would probably fix
that.
-Marshall
On Dec 19, 10:07 am, mabshoff wrote:
> 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 all of my other
> > sage builds. I changed the sage script in my /usr/bin to point to the
> > unstable one, which I called "wildsage". One of the sage folders I
> > deleted was for 3.2.1.rc0. With all that in mind, here is the error I
> > got in qqbar:
>
> > sage -t "devel/sage/sage/rings/qqbar.py"
> > Exception exceptions.TypeError: TypeError(RuntimeError('Unable to
> > start maxima',),) in 'sage.structure.parent_old._unregister_pair'
> > ignored
>
>
>
> > It looks like its trying to use the maxima from my deleted 3.2.1.rc0
> > build for some reason.
>
> Something else looks wrong, i.e the string "3.2.1.rc0" should not
> appear in the backtrace at all. There can be numerous issues like a
> bungled SAGE_ROOT setting at some point that is now causing trouble.
> Does maxima from that install work via "sage -maxima"? Just because
> the doctest claims that is doesn't start does not mean that it doesn't
> work in general. I would also check the repos for unresolved merges,
> multiple heads and so on. Some environment variable can also play a
> role here. Since linking the sage script just works I would always
> recommend linking it into $PATH somewhere under a different name
> instead of setting $SAGE_ROOT manually as recommended in the
> documentation since it is too easy to scrw that up. The checking code
> if SAGE_ROOT is overwritten also makes it too still possible to shoot
> yourself in the foot.
>
> > My ppc powerbook is still slaving away on tests, its almost done and
> > so far just has timeout failures on eisenstein and calculus.py.
>
> Ok. I would suggest to rerun the failed tests with -long to see what
> happens. If the CPU usage stays near 0 it is a synchronization /
> maxima issue, but the timeout will be raised after 30 minutes.
>
> > -M. Hampton
>
> Cheers,
>
> Michael
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[sage-devel] Re: Sage 3.2.2.rc1 released
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 since then. So it is not too weird an > event. There is still one issue we have a ticket for that can introduce issues when running -upgrade: When one moves the tree and then run "sage -upgrade" the rebasing of Sage is not run, so that can cause build issues. > Some of the c source code still makes references to the > sage-3.2.1.rc0 folder. What references? In what c sources? If it is in the Cython generated files it shouldn't matter. > I assume a complete rebuild would probably fix that. > > -Marshall Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Install error on Suse 11.1
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 much in advance! Henrik >>> Last lines of install.log: ... pari-2.3.3.p0/SPKG.txt pari-2.3.3.p0/.hgignore Finished extraction Host system uname -a: Linux linux-wccv 2.6.27.7-8-default #1 SMP 2008-11-25 00:02:37 +0100 x86_64 x86_64 x86_64 GNU/Linux GCC Version gcc -v Using built-in specs. Target: x86_64-suse-linux Configured with: ../configure --prefix=/usr --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 -- enable-languages=c,c++,objc,fortran,obj-c++,java,ada --enable- checking=release --with-gxx-include-dir=/usr/include/c++/4.3 --enable- ssp --disable-libssp --with-bugurl=http://bugs.opensuse.org/ --with- pkgversion='SUSE Linux' --disable-libgcj --disable-libmudflap --with- slibdir=/lib64 --with-system-zlib --enable-__cxa_atexit --enable- libstdcxx-allocator=new --disable-libstdcxx-pch --enable-version- specific-runtime-libs --program-suffix=-4.3 --enable-linux-futex -- without-system-libunwind --with-cpu=generic --build=x86_64-suse-linux Thread model: posix gcc version 4.3.2 [gcc-4_3-branch revision 141291] (SUSE Linux) /bin/sh: symbol lookup error: /home/henrik/Pakete/sage-3.2.1/local/lib/ libreadline.so.5: undefined symbol: PC real0m0.001s user0m0.000s sys 0m0.000s sage: An error occurred while installing pari-2.3.3.p0 Please email sage-devel http://groups.google.com/group/sage-devel --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computational biology project needs distributed processing
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 give is greatly > appreciated. > Do you know if your bottlenect is a SQLalchemy thing or a database issue? (My guess is a database issue). In my limited experience and understanding, it seems that PostgreSQL in general handles complex queries better than MySQL, and handles concurrent load better as well. Have you tried that? Jason --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Install error on Suse 11.1
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 11.1rc1. > Any help appreciated, thank you very much in advance! Henrik Please post a link to install.log - do not attach it to the email. We cannot debug this without the install.log. My guess would be that pari picks up a global readline.h. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: how to set an environment variable in sage code?
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' Great, thanks, this is just what I needed. John --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] FireUnit testing framework for JavaScript
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 input and javascript-events. H --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 3.2.2.rc1 released
> 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@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computational biology project needs distributed processing
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 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 >> appreciated. >> > > Do you know if your bottlenect is a SQLalchemy thing or a database > issue? (My guess is a database issue). In my limited experience and > understanding, it seems that PostgreSQL in general handles complex > queries better than MySQL, and handles concurrent load better as well. > Have you tried that? > > Jason > > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Final 3.2.2 sources released
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/mabshoff/release-cycles-3.2.2/sage-3.2.2/ Upgraded rc1 to "final" on Mac OS X, both 10.5.5 and 10.4.11, without problems. All tests passed on 10.5.5, but on 10.4.11, I see one failure: sage -t "devel/sage/sage/dsage/interface/dsage_interface.py" ** File "/Users/tmp/sage-3.2.2.rc1/devel/sage/sage/dsage/interface/ dsage_interface.py", line 567: sage: j Expected: 625 Got: 62500DSAGE00 ** 1 items had failures: 1 of 8 in __main__.example_16 ***Test Failed*** 1 failures. [DSage] Closed connection to localhost [DSage] Closed connection to localhost [DSage] Closed connection to localhost [DSage] Closed connection to localhost For whitespace errors, see the file /Users/tmp/sage-3.2.2.rc1/ tmp/.doctest_dsage_int erface.py [45.9 s] I reran this test by itself and it succeeded. Go figure. Should I create a trac ticket, or is this issue understood? Justin -- Justin C. Walker, Curmudgeon-At-Large Institute for the Enhancement of the Director's Income When LuteFisk is outlawed, Only outlaws will have LuteFisk --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Final 3.2.2 sources released
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 -t "devel/sage/sage/dsage/interface/dsage_interface.py" > ** > File "/Users/tmp/sage-3.2.2.rc1/devel/sage/sage/dsage/interface/ > dsage_interface.py", > line 567: > sage: j > Expected: > 625 > Got: > 62500DSAGE00 > ** > 1 items had failures: > 1 of 8 in __main__.example_16 > ***Test Failed*** 1 failures. > [DSage] Closed connection to localhost > [DSage] Closed connection to localhost > [DSage] Closed connection to localhost > [DSage] Closed connection to localhost > For whitespace errors, see the file /Users/tmp/sage-3.2.2.rc1/ > tmp/.doctest_dsage_int > erface.py > [45.9 s] > > I reran this test by itself and it succeeded. Go figure. > > Should I create a trac ticket, or is this issue understood? I think Gary is working in that area, so we don't need a ticket for the specific doctest failure at the moment. I hit similar issues on occasion, but for now I would suggest we sit back a little and see which patches come down the pipeline. The above looks like a pexpect issue with a marker, but I am not 100% sure. > Justin Cheers, Michael > -- > Justin C. Walker, Curmudgeon-At-Large > Institute for the Enhancement of the Director's Income > > When LuteFisk is outlawed, > Only outlaws will have LuteFisk > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Final 3.2.2 sources released
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, 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 -t "devel/sage/sage/dsage/interface/dsage_interface.py" >> ** >> File "/Users/tmp/sage-3.2.2.rc1/devel/sage/sage/dsage/interface/ >> dsage_interface.py", >> line 567: >> sage: j >> Expected: >> 625 >> Got: >> 62500DSAGE00 >> ** >> 1 items had failures: >> 1 of 8 in __main__.example_16 >> ***Test Failed*** 1 failures. >> [DSage] Closed connection to localhost >> [DSage] Closed connection to localhost >> [DSage] Closed connection to localhost >> [DSage] Closed connection to localhost >> For whitespace errors, see the file /Users/tmp/sage-3.2.2.rc1/ >> tmp/.doctest_dsage_int >> erface.py >> [45.9 s] >> >> I reran this test by itself and it succeeded. Go figure. >> >> Should I create a trac ticket, or is this issue understood? > > I think Gary is working in that area, so we don't need a ticket for > the specific doctest failure at the moment. I hit similar issues on > occasion, but for now I would suggest we sit back a little and see > which patches come down the pipeline. The above looks like a pexpect > issue with a marker, but I am not 100% sure. > >> Justin > > Cheers, > > Michael > >> -- >> Justin C. Walker, Curmudgeon-At-Large >> Institute for the Enhancement of the Director's Income >> >> When LuteFisk is outlawed, >> Only outlaws will have LuteFisk >> > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Final 3.2.2 sources released
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 $ "MAKE=make -j2" make test on Mac OS X, 10.4.11 (Core 2 Duo). Is that what you mean by "parallel"? Justin -- Justin C. Walker, Curmudgeon-At-Large Institute for the Absorption of Federal Funds Men are from Earth. Women are from Earth. Deal with it. --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Install error on Suse 11.1
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 post the install.log file to? File upload here in this group does not work (for me?). Regards, Henrik P.S. The problem is identical for sage 3.2.1 and 3.2.2. --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Install error on Suse 11.1
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, > including header files in /usr/include/readline). Well, that is probably not the real fix and not a good idea, but we will see. > Where may I post the install.log file to? File upload here in this > group does not work (for me?). Yes, I didn't mean attaching the files to the Google group which requires admin privileges. Any place on the web is fine, but make sure to compress the old install.log when the build failed. As a last resort you can send it to me compressed off list, but that is truly the last resort. > Regards, Henrik > > P.S. The problem is identical for sage 3.2.1 and 3.2.2. Ok, I am downloading OpenSUSE 11.1 as a VMWare image, so hopefully I can fix it locally. That should be much easier to fix that way than by remote diagnostics. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 3.2.2.rc1 released
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? > > -cc --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 3.2.2.rc1 released
> 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 it does, could you do it with -verbose to see what's taking so long? -cc --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Install error on Suse 11.1
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 missing symbol. I am poking around what is wrong here, but there is no obvious fix. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: spkg vote: SageTeX
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 SageTeX as a spkg. > > I have a preliminary version ready to go: > > http://sage.math.washington.edu/home/drake/sagetex-2.0.spkg > > The spkg installs a single Python module, sagetex.py, into > the $SAGE_ROOT/local/lib/python tree. The rest of the files it installs > are documentation and TeX files; all those are installed into > $SAGE_ROOT/local/share/texmf/tex/generic/sagetex. The directory fits > with typical TeX installations, so that anyone who wants to use SageTeX > can do something like > > cp -r $SAGE_ROOT/local/share/texmf/* ~/texmf/ > > and run texhash to make their TeX installation aware of the sagetex.sty > file. > > I think having the sagetex.py module built-in to Sage makes sense, as it > makes it easier to use SageTeX (which in any case doesn't work unless > you have Sage installed) and the Python module is under 5KB. The rest of > the spkg is mostly pre-built documentation. > > So, should we include SageTeX as a spkg? > Based on all the +1's it is now an optional spkg. Now everybody can trivially install it by doing sage -i sagetex-2.0 Can you post to sage-devel in one month about moving this from optional to standard, after more people have used it as an optional package? Regarding the actual spkg, looking inside it looks like this: - wst...@sage:~/sage/spkg/optional/sagetex-2.0$ ls example.pdf extractsagecode.py PKG-INFO README.spkg sagetexpackage.ins sagetexparse.py sagetex.sty spkg-install example.tex makestatic.py READMEsagetexpackage.dtx sagetexpackage.pdf sagetex.py setup.py - It seems like the layout and naming of the files in there is just kind of made up -- it somewhat ignores all the standards we decided on for how spkg's should be laid out.After searching for 5 minutes, *I* can't even find anything in the wiki about how spkg's should be laid out, so I'm not surprised you didn't either. Anyway, the best thing to do is to look at one that is in spkg/standard/ and copy the format: src/-- most of your stuff goes in this directory SPKG.txt -- describes the spkg in wiki format spkg-install -- the install script patches -- for patches against upstream (you won't need this) There should not be a README.spkg (that's SPKG.txt) and README above should be moved to src/README. Many thanks! -- William --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
