[sage-devel] Re: JavaScript Graph editor

[bbarker]

Agreed +1,

I'll probably be wanting something just like this in the near future.

On May 3, 2:43 pm, Stephen Hartke  wrote:
> On Thu, Apr 30, 2009 at 2:05 AM, Rado  wrote:
> > Here is the result:
> >http://www.math.uiuc.edu/~rkirov2/processing/grapheditor.html
>
> Rado,
>
> This is really cool!  It would be awesome if this was incorporated into
> Sage.
>
> Best wishes,
> Stephen
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[sage-devel] Re: notebook() hangs in SXCE and OpenSolaris

[bbarker]

Hi Michael,

1 and 2 are both outside of zones (they are in the "global zone"), and
they also hang seemingly indefinitely (I haven't kept them running
long enough to prove me wrong yet, other than the one running in the
zone).
Since it is happening on fairly different systems - SXCE (workstation/
server) vs OpenSolaris 2008.11 (laptop), I'm inclined to think it
isn't anything I've done with configuration ... but its hard to say
for sure.
Later I could try running it in a fresh install of some sort, in
virtual box, if you have a specific version/configuration you'd like
me to test with.

I haven't tried this on an official Solaris 10 release yet, but it
seems strange that the bug would crop back up in newer releases of the
OS.


On May 3, 9:58 pm, mabshoff  wrote:
> On May 3, 6:48 pm, "brandon.bar...@gmail.com"
>
>  wrote:
> > Hello,
>
> Hi,
>
> > I'm very happy about the improved Solaris support.  Until recently I
> > was running sage in a linux zone on my workstation, but unfortunately
> > modern linux version support for branded zones is lagging.  I confess
> > I've also been using sagenb.org a bit (which will be running on a
> > T2000 soon?)
>
> Probably, but the GMP/MPIR performance on the T2000 is pathetic per
> "thread" and in effect only 8 or 16 out of 64 threads can use the
> integer or FP units at a time, so scaling out kind of sucks, too.
>
> >   I've tried to run the notebook in 3 different
> > environments (all by simply calling notebook() from the sage shell).
>
> > 1: Updated OpenSolaris 2008.11 (snv_111a)
>
> > 2: SXCE global zone (snv_109)
>
> > 3: SXCE sparse root zone (same machine as (2))
>
> > On all of these, the startup of the notebook seems to hang for several
> > hours at this point:
>
> If the notebook takes forever to initialize this indicates a problem
> with the source of randomness. I know too little about your setup to
> determine if it is the system not providing enough entropy to the zone
> or what else could be interfering here. libgcrypt (which is used to
> create the the keys) used to have a bug that caused it to use way more
> entropy then required and this caused a very long hang on Solaris 10.
> We have since updated and at least on plain vanilla Solaris 10 (i.e.
> no zone) the notebook start is instant. Any chance this gives you a
> hint what is wrong? Does the problem also happen outside the zone?
>
> Cheers,
>
> Michael
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[sage-devel] Re: notebook() hangs in SXCE and OpenSolaris

[bbarker]

lf, *args, **kwds)
163 """
164 def __call__(self, *args, **kwds):
--> 165 return self.notebook(*args, **kwds)
166
167 notebook = run_notebook.notebook_twisted

/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/local/lib/
python2.5/site-packages/sage/server/notebook/run_notebook.pyc in
notebook_twisted(self, directory, port, address, port_tries, secure,
reset, accounts, require_login, server_pool, ulimit, timeout,
open_viewer, sagetex_path, start_path, fork, quiet)
273 if open_viewer:
274 "Open viewer automatically isn't fully implemented.
You have to manually open your web browser to the above URL."
--> 275 return run(port)
276
277

/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/local/lib/
python2.5/site-packages/sage/server/notebook/run_notebook.pyc in run
(port)
257 e = os.system(cmd)
258 if e == 256:
--> 259 raise socket.error
260 return True
261 # end of inner function run

error:





On May 3, 10:14 pm, bbarker  wrote:
> Hi Michael,
>
> 1 and 2 are both outside of zones (they are in the "global zone"), and
> they also hang seemingly indefinitely (I haven't kept them running
> long enough to prove me wrong yet, other than the one running in the
> zone).
> Since it is happening on fairly different systems - SXCE (workstation/
> server) vs OpenSolaris 2008.11 (laptop), I'm inclined to think it
> isn't anything I've done with configuration ... but its hard to say
> for sure.
> Later I could try running it in a fresh install of some sort, in
> virtual box, if you have a specific version/configuration you'd like
> me to test with.
>
> I haven't tried this on an official Solaris 10 release yet, but it
> seems strange that the bug would crop back up in newer releases of the
> OS.
>
> On May 3, 9:58 pm, mabshoff  wrote:
>
> > On May 3, 6:48 pm, "brandon.bar...@gmail.com"
>
> >  wrote:
> > > Hello,
>
> > Hi,
>
> > > I'm very happy about the improved Solaris support.  Until recently I
> > > was running sage in a linux zone on my workstation, but unfortunately
> > > modern linux version support for branded zones is lagging.  I confess
> > > I've also been using sagenb.org a bit (which will be running on a
> > > T2000 soon?)
>
> > Probably, but the GMP/MPIR performance on the T2000 is pathetic per
> > "thread" and in effect only 8 or 16 out of 64 threads can use the
> > integer or FP units at a time, so scaling out kind of sucks, too.
>
> > >   I've tried to run the notebook in 3 different
> > > environments (all by simply calling notebook() from the sage shell).
>
> > > 1: Updated OpenSolaris 2008.11 (snv_111a)
>
> > > 2: SXCE global zone (snv_109)
>
> > > 3: SXCE sparse root zone (same machine as (2))
>
> > > On all of these, the startup of the notebook seems to hang for several
> > > hours at this point:
>
> > If the notebook takes forever to initialize this indicates a problem
> > with the source of randomness. I know too little about your setup to
> > determine if it is the system not providing enough entropy to the zone
> > or what else could be interfering here. libgcrypt (which is used to
> > create the the keys) used to have a bug that caused it to use way more
> > entropy then required and this caused a very long hang on Solaris 10.
> > We have since updated and at least on plain vanilla Solaris 10 (i.e.
> > no zone) the notebook start is instant. Any chance this gives you a
> > hint what is wrong? Does the problem also happen outside the zone?
>
> > Cheers,
>
> > Michael
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[sage-devel] Re: notebook() hangs in SXCE and OpenSolaris

[bbarker]

I posted the above before reading your reply about running gdb ... so
just to be clear, notebook() crashes before Ctrl-C is pressed (but
only when running in sage -gdb).

On May 3, 10:36 pm, bbarker  wrote:
> Some additional information:
>
> Trying to exit the server during hang by pressing Ctrl-C repeatedly
> will only yield the following (repeatedly):
> ^Cselect() error: Interrupted system call
> ^Cselect() error: Interrupted system call
> ^Cselect() error: Interrupted system call
> ^Cselect() error: Interrupted system call
>
> Doing the same after running sage -dbg, notebook() ... will eventually
> crash and fall back to the sage shell:
>
> ~/sage-3.4.1-beta-i86pc+toolchain-SunOS >./sage -gdb
> --
> | Sage Version 3.4.1, Release Date: 2009-04-21                       |
> | Type notebook() for the GUI, and license() for information.        |
> | WARNING: This is a beta release that does not pass all tests.      |
> | For more info seehttp://wiki.sagemath.org/solaris                |
> --
> /export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/local/bin/
> sage-ipython
> GNU gdb 6.3.50_2004-11-23-cvs
> Copyright 2004 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and
> you are
> welcome to change it and/or distribute copies of it under certain
> conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB.  Type "show warranty" for
> details.
> This GDB was configured as "i386-pc-solaris2.11"...
> warning: Unable to find dynamic linker breakpoint function.
> GDB will be unable to debug shared library initializers
> and track explicitly loaded dynamic code.
> warning: Lowest section in /lib/librt.so.1 is .dynamic at 0074
> Python 2.5.2 (r252:60911, Apr 20 2009, 12:01:15)
> [GCC 4.3.2] on sunos5
> Type "help", "copyright", "credits" or "license" for more information.
> sage: notebook()
> The notebook files are stored in: /export/home/brandon/.sage//
> sage_notebook
> **
> *                                                *
> * Open your web browser tohttp://localhost:8000*
> *                                                *
> **
> Traceback (most recent call last):
>   File "/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/
> local/lib/python2.5/site-packages/twisted/application/app.py", line
> 614, in run
>     runApp(config)
>   File "/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/
> local/lib/python2.5/site-packages/twisted/scripts/twistd.py", line 23,
> in runApp
>     _SomeApplicationRunner(config).run()
>   File "/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/
> local/lib/python2.5/site-packages/twisted/application/app.py", line
> 330, in run
>     self.application = self.createOrGetApplication()
>   File "/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/
> local/lib/python2.5/site-packages/twisted/application/app.py", line
> 416, in createOrGetApplication
>     application = getApplication(self.config, passphrase)
> ---  ---
>   File "/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/
> local/lib/python2.5/site-packages/twisted/application/app.py", line
> 427, in getApplication
>     application = service.loadApplication(filename, style, passphrase)
>   File "/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/
> local/lib/python2.5/site-packages/twisted/application/service.py",
> line 368, in loadApplication
>     application = sob.loadValueFromFile(filename, 'application',
> passphrase)
>   File "/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/
> local/lib/python2.5/site-packages/twisted/persisted/sob.py", line 214,
> in loadValueFromFile
>     exec fileObj in d, d
>   File "sage_notebook/twistedconf.tac", line 19, in 
>     worksheet.init_sage_prestart(twist.notebook.get_server(),
> twist.notebook.get_ulimit())
>   File "/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/
> local/lib/python2.5/site-packages/sage/server/notebook/worksheet.py",
> line 156, in init_sage_prestart
>     _a_sage = initialized_sage(server, ulimit)
>   File "/export/home/brandon/sage-3.4.1-beta-i86pc+toolchain-SunOS/
> local/lib/python2.5/site-packages/sage/server/notebook/worksheet.py",
> line 118, in initialized_sage
>     S._start(block_during_init=False)
>   File "/e

[sage-devel] Re: how to submit upgraded biopython spkg for python-2.6?

[bbarker]

Great, glad to see this!  Thanks for the updated spkg.

On Jul 26, 9:47 pm, Marshall Hampton  wrote:
> Ok, I posted my spkg at:
>
> http://trac.sagemath.org/sage_trac/ticket/6634
>
> It would be great if you (tkeller) got a trac account, since currently
> I don't know any other sage developers who have any real interest in
> this (partial exception of William Stein but clearly he has a lot on
> his plate).
>
> -Marshall
>
> On Jul 26, 12:25 pm, Marshall Hampton  wrote:
>
> > Hi,
>
> > Thanks for pointing that out.  I have made a 1.51b spkg, but decided
> > to wait a week or two for the final 1.51 to come out.  But I didn't
> > realize that the 1.49b install was broken.
>
> > Anyway if you have any interest in helping out, you should get a trac
> > account.  Just email William Stein for one.
>
> > I am excited about their cleanup too, I think with a little more work
> > biopython can be made a standard part of sage, but that will require a
> > developer vote.
>
> > -Marshall Hampton
>
> > On Jul 26, 12:05 pm, tkeller  wrote:
>
> > > Thanks for all the recent work upgrading the base python distribution
> > > to 2.6, I imagine it was quite a task. I noticed that installing the
> > > biopython-1.49b spkg is broken from the upgrade . I have upgraded the
> > > spkg to 1.51b and it installs and works fine on my sage-4.1
> > > installation. Is there a place to upload supplemental spkg's , or
> > > should I get a trac account?
>
> > > A side benefit to upgrading the spkg is that the last few patches
> > > finally removed the mxText dependency, so it is now a clean install
> > > aside from requiring Numpy.
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[sage-devel] Re: Building of Sage 4.1 (ECL) on CentOS 5.3 failure

[bbarker]

Hi William,

I built gcc 4.4.0 myself, and used it:

[r...@sagenb ~]# gcc -v
Using built-in specs.
Target: i686-pc-linux-gnu
Configured with: ../gcc-4.4.0/configure --prefix=/usr/local --with-
bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --with-
gmp=/usr/local --with-mpfr=/usr/local --enable-shared --enable-
threads=posix --enable-checking=release --with-system-zlib --enable-
__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c+
+,fortran,java --with-cpu=opteron CC=gcc43 CXX=g++43
Thread model: posix
gcc version 4.4.0 (GCC)


I had the same problem with the included gcc 4.1.2:

[bran...@sagenb sage-4.1]$ 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 4.1.2-44)




On Jul 25, 12:31 pm, William Stein  wrote:
> On Sat, Jul 25, 2009 at 7:24 AM,
>
> brandon.bar...@gmail.com wrote:
>
> > This error message is a bit unusual to me.  I'm trying to build it in
> > a solaris lx zone (apparently modern distros aren't supported yet -
> > centos 5.3 is as close as it gets that I know of):
>
> Which gcc are you using?
>
>
>
>
>
> > from install.log:
> > cp /home/brandon/sage-4.1/spkg/build/ecl-9.4.1/src/src/../contrib/
> > unicode/ucd.dat .
> > if [ -f CROSS-COMPILER ]; then \
> >                ./CROSS-COMPILER compile; \
> >        else \
> >                ECLDIR=`pwd`/ ./ecl_min compile; \
> >        fi
>
> > Internal or unrecoverable error in:
> > Got signal before environment was installed on our thread.
> > /bin/sh: line 4:  3013 Aborted                 ECLDIR=`pwd`/ ./ecl_min
> > compile
> > make[3]: *** [bin/ecl] Error 134
> > make[3]: Leaving directory `/home/brandon/sage-4.1/spkg/build/
> > ecl-9.4.1/src/build'
> > make[2]: *** [all] Error 2
> > make[2]: Leaving directory `/home/brandon/sage-4.1/spkg/build/
> > ecl-9.4.1/src'
> > Failed to build ECL ... exiting
>
> > real    1m13.251s
> > user    0m0.000s
> > sys     0m0.001s
> > sage: An error occurred while installing ecl-9.4.1
> > Please email sage-develhttp://groups.google.com/group/sage-devel
> > explaining the problem and send the relevant part of
> > of /home/brandon/sage-4.1/install.log.  Describe your computer,
> > operating system, etc.
> > If you want to try to fix the problem, yourself *don't* just cd to
> > /home/brandon/sage-4.1/spkg/build/ecl-9.4.1 and type 'make'.
> > Instead type "/home/brandon/sage-4.1/sage -sh"
> > in order to set all environment variables correctly, then cd to
> > /home/brandon/sage-4.1/spkg/build/ecl-9.4.1
> > (When you are done debugging, you can type "exit" to leave the
> > subshell.)
> > make[1]: *** [installed/ecl-9.4.1] Error 1
> > make[1]: Leaving directory `/home/brandon/sage-4.1/spkg'
>
> > real    42m54.614s
> > user    0m0.001s
> > sys     0m0.002s
> > Error building Sage.
>
> > The system is Centos 5.3 (updated) running in a solaris zone:
> > uname -a
> > Linux sagenb 2.6.18 BrandZ fake linux i686 athlon i386 GNU/Linux
>
> > cat /proc/cpuinfo:
> > ...
> > processor       : 3
> > vendor_id       : AuthenticAMD
> > cpu family      : 15
> > model           : 65
> > model name      : Dual-Core AMD Opteron(tm) Processor 2214
> > stepping        : 3
> > cpu MHz         : 2199.944
> > cache size      : 1024 KB
> > fdiv_bug        : no
> > hlt_bug         : no
> > f00f_bug        : no
> > coma_bug        : no
> > fpu             : yes
> > fpu_exception   : yes
> > cpuid level     : 1
> > flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca 
> > cmov
> > pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext lm 3dnowext
> > 3dnow lahf_lm svm altmovcr8 pni cx16
>
> > [bran...@sagenb sage-4.1]$ cat /proc/meminfo
> >        total:     used:    free:  shared: buffers:  cached:
> > Mem:  96536985609192144896461553664        0        0        0
> > Swap:483078553615720325123258753024
> > MemTotal:   9427440 kB
> > MemFree:     450736 kB
> > MemShared:        0 kB
> > Buffers:          0 kB
> > Cached:           0 kB
> > SwapCached:       0 kB
> > Active:           0 kB
> > Inactive:         0 kB
> > HighTotal:        0 kB
> > HighFree:         0 kB
> > LowTotal:   9427440 kB
> > LowFree:     450736 kB
> > SwapTotal:  4717564 kB
> > SwapFree:   3182376 kB
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
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