Re: [sage-devel] multithreading performance issues

2016-10-06 Thread Jonathan Bober
ded blas is for constructors: with >> Intel's mkl blas, you can obtain the maximum possible performances of >> tah machines when you use DGEMM (ie product of matrices), due to the >> high arithmetic intensity of matrix vector products. On my 2x8 core >> s

Re: [sage-devel] multithreading performance issues

2016-10-04 Thread Jonathan Bober
, 14.533391952514648) (9, 130.57, 13.497469902038574) (10, 123.67, 11.505426168441772) [...] (60, 779.12, 12.92886209487915) (61, 875.74, 14.310442924499512) (62, 869.82, 14.241307973861694) (63, 813.99, 13.089143991470337) (64, 728.52, 11.443121910095215) On Tue, Oct 4, 2016 at 9:40 PM, Jonath

Re: [sage-devel] multithreading performance issues

2016-10-04 Thread Jonathan Bober
On Tue, Oct 4, 2016 at 9:03 PM, William Stein wrote: > On Tue, Oct 4, 2016 at 12:58 PM, Jonathan Bober wrote: > > No, in 7.3 Sage isn't multithreading in this example: > > > > jb12407@lmfdb1:~$ sage73 > > sage: %time M = ModularSymbols(5113, 2, -1) > > CPU

Re: [sage-devel] multithreading performance issues

2016-10-04 Thread Jonathan Bober
nly R seems to be linked to libgomp (openmp) on my vanilla install. > Curiosity: do you observe the same behaviour in 7.3? > > François > > > On 5/10/2016, at 07:26, Jonathan Bober wrote: > > > > See the following timings: If I start Sage with OMP_NUM_THREADS=1, a >

[sage-devel] multithreading performance issues

2016-10-04 Thread Jonathan Bober
See the following timings: If I start Sage with OMP_NUM_THREADS=1, a particular computation takes 1.52 cpu seconds and 1.56 wall seconds. The same computation without OMP_NUM_THREADS set takes 12.8 cpu seconds and 1.69 wall seconds. This is particularly devastating when I'm running with @parallel

Re: [sage-devel] Re: openblas segfault?

2016-09-30 Thread Jonathan Bober
September 26, 2016 at 11:23:49 PM UTC+2, Jonathan Bober wrote: >> >> On Mon, Sep 26, 2016 at 10:10 PM, Jean-Pierre Flori >> wrote: >> >>> I suspect that perhaps the copy I have the works is working because I >>>> built it as sage 7.3 at some point with SAG

Re: [sage-devel] linbox 64-bit charpoly

2016-09-27 Thread Jonathan Bober
On Tue, Sep 27, 2016 at 8:34 PM, 'Bill Hart' via sage-devel < sage-devel@googlegroups.com> wrote: > > > On Tuesday, 27 September 2016 20:53:28 UTC+2, Jonathan Bober wrote: >> >> On Tue, Sep 27, 2016 at 7:18 PM, 'Bill Hart' via sage-devel < >

Re: [sage-devel] linbox 64-bit charpoly

2016-09-27 Thread Jonathan Bober
On Tue, Sep 27, 2016 at 8:02 PM, William Stein wrote: > On Tue, Sep 27, 2016 at 11:53 AM, Jonathan Bober > wrote: > > On Tue, Sep 27, 2016 at 7:18 PM, 'Bill Hart' via sage-devel > > wrote: > >> > >> I'm pretty sure the charpoly routine in F

Re: [sage-devel] Re: memory management issue: deleted variables not released

2016-09-27 Thread Jonathan Bober
I just noticed this thread because of your recent reply, and happened to read through. (I haven't regularly read sage-devel for a while.) As to your original email: I think there is a subtle python memory management issue there. If you run sage: BIG=myfunction(somevars) sage: BIG=myfunction(somev

Re: [sage-devel] linbox 64-bit charpoly

2016-09-27 Thread Jonathan Bober
x27;t check the version in Sage) and comments from Clement Pernet, I think that Flint uses an explicit Hadamard bound to determine how many primes to use, while Linbox just waits for the CRT'd polynomial to stabilize for a few primes. I have no idea how much of a difference that makes in this case.

Re: [sage-devel] linbox 64-bit charpoly

2016-09-26 Thread Jonathan Bober
On Tue, Sep 27, 2016 at 4:18 AM, William Stein wrote: > On Mon, Sep 26, 2016 at 6:55 PM, Jonathan Bober wrote: > > On Mon, Sep 26, 2016 at 11:52 PM, William Stein > wrote: > >> > >> On Mon, Sep 26, 2016 at 3:27 PM, Jonathan Bober > wrote: > >> > In

Re: [sage-devel] linbox 64-bit charpoly

2016-09-26 Thread Jonathan Bober
On Mon, Sep 26, 2016 at 11:52 PM, William Stein wrote: > On Mon, Sep 26, 2016 at 3:27 PM, Jonathan Bober wrote: > > In the matrix_integer_dense charpoly() function, there is a note in the > > docstring which says "Linbox charpoly disabled on 64-bit machines, since > it

[sage-devel] linbox 64-bit charpoly

2016-09-26 Thread Jonathan Bober
In the matrix_integer_dense charpoly() function, there is a note in the docstring which says "Linbox charpoly disabled on 64-bit machines, since it hangs in many cases." As far as I can tell, that is not true, in the sense that (1) I have 64-bit machines, and Linbox charpoly is not disabled, (2) c

Re: [sage-devel] Re: openblas segfault?

2016-09-26 Thread Jonathan Bober
On Mon, Sep 26, 2016 at 10:10 PM, Jean-Pierre Flori wrote: > I suspect that perhaps the copy I have the works is working because I >> built it as sage 7.3 at some point with SAGE_ATLAS_LIB set and then rebuilt >> it on the develop branch, which didn't get rid of the atlas symlinks that >> were al

Re: [sage-devel] Re: openblas segfault?

2016-09-26 Thread Jonathan Bober
on, Sep 26, 2016 at 7:11 PM, Jonathan Bober wrote: > I've rebuilt again from scratch, twice. Once after clearing all my > possibly questionable environment variables (except for LD_LIBRARY_PATH, > since that is needed for gcc-6.1.0, as set by module add gcc-6.1.0 for me). > Th

Re: [sage-devel] Re: openblas segfault?

2016-09-26 Thread Jonathan Bober
I've rebuilt again from scratch, twice. Once after clearing all my possibly questionable environment variables (except for LD_LIBRARY_PATH, since that is needed for gcc-6.1.0, as set by module add gcc-6.1.0 for me). The second time I did "CFLAGS=-mno-xop make". I can see that flag took effect by ex

Re: [sage-devel] Re: openblas segfault?

2016-09-26 Thread Jonathan Bober
On Mon, Sep 26, 2016 at 1:50 PM, leif wrote: > Jean-Pierre Flori wrote: > > > > > > On Monday, September 26, 2016 at 11:47:00 AM UTC+2, Jonathan Bober wrote: > > > > On Mon, Sep 26, 2016 at 9:44 AM, Dima Pasechnik > > wrote: > > > > &g

Re: [sage-devel] Re: openblas segfault?

2016-09-26 Thread Jonathan Bober
> > On Monday, September 26, 2016 at 11:47:00 AM UTC+2, Jonathan Bober wrote: >> >> On Mon, Sep 26, 2016 at 9:44 AM, Dima Pasechnik wrote: >> >>> >>> >>> On Monday, September 26, 2016 at 2:22:51 AM UTC, Jonathan Bober wrote: >>>> >>>&g

Re: [sage-devel] Re: openblas segfault?

2016-09-26 Thread Jonathan Bober
On Mon, Sep 26, 2016 at 9:44 AM, Dima Pasechnik wrote: > > > On Monday, September 26, 2016 at 2:22:51 AM UTC, Jonathan Bober wrote: >> >> I recompiled with gcc 6.1.0, and get the same segfault. I did a ./sage -i >> gdb to get a better crash report, which is atta

Re: [sage-devel] Re: openblas segfault?

2016-09-25 Thread Jonathan Bober
On Mon, Sep 26, 2016 at 2:00 AM, Dima Pasechnik wrote: surely one can mess everything up with env. vars :-) > Yes, of course, I should have been more specific. I mean 'standard' environment variables (which users like me might use in wrong or 'hackish' ways). e.g., something like module add gc

Re: [sage-devel] Re: openblas segfault?

2016-09-25 Thread Jonathan Bober
on, Sep 26, 2016 at 2:06 AM, Dima Pasechnik wrote: > > > On Sunday, September 25, 2016 at 10:48:51 PM UTC, Jonathan Bober wrote: >> >> That's a good point. It looks like 5.1.0. I will try rebuilding from >> scratch with SAGE_INSTALL_GCC=yes, since that's easi

Re: [sage-devel] Re: [sagemath-admins] trac not responding

2016-09-25 Thread Jonathan Bober
On Mon, Sep 26, 2016 at 1:54 AM, Dima Pasechnik wrote: > > > On Monday, September 26, 2016 at 12:40:23 AM UTC, Jonathan Bober wrote: >> >> Is git still down, or do is the problem just that I don't know what I am >> doing? >> >> jb12407@lmfdb5:/data/

Re: [sage-devel] Re: [sagemath-admins] trac not responding

2016-09-25 Thread Jonathan Bober
Is git still down, or do is the problem just that I don't know what I am doing? jb12407@lmfdb5:/data/local/sage/sage-7.3$ git trac checkout 21596 Loading ticket #21596... Newly created local branch: t/21596/matrix_charpoly_algorithm__flint___destroys_the_polynomial_ring_generator Traceback (most r

Re: [sage-devel] Re: openblas segfault?

2016-09-25 Thread Jonathan Bober
ent versions, you have to reinstall GMP properly. Error configuring GMP-ECM. Is it possible that some environment variable I've set has messed something up? Also, I ran make distclean instead of really starting from scratch. Is that relevant? On Sun, Sep 25, 2016 at 11:48 PM, Jonathan Bober

Re: [sage-devel] Re: openblas segfault?

2016-09-25 Thread Jonathan Bober
) I will report back in 90 minutes, unless I don't, in which case I'll report back in 10 to 24 hours. On Sun, Sep 25, 2016 at 11:31 PM, Dima Pasechnik wrote: > Most probably gcc version used to build Sage is also quite important... > > > On Sunday, September 25, 2016 at

Re: [sage-devel] Re: openblas segfault?

2016-09-25 Thread Jonathan Bober
jb12407@lmfdb5:~$ uname -r 2.6.32-573.3.1.el6.x86_64 On Sun, Sep 25, 2016 at 11:03 PM, Dima Pasechnik wrote: > > > On Sunday, September 25, 2016 at 9:33:42 PM UTC, Jonathan Bober wrote: >> >> I'm getting a segfault on the current development branch of sage (see >&g

[sage-devel] openblas segfault?

2016-09-25 Thread Jonathan Bober
I'm getting a segfault on the current development branch of sage (see below). Is this a known issue and/or effecting anyone else? This does not happen for me in Sage 7.3, although it does happen if I try to go "back in time" with a 'git checkout 7.3' and then rebuild. So just to be certain I built

Re: [sage-devel] Re: [sage-support] huge virtual memory size when launching 7.3

2016-09-21 Thread Jonathan Bober
On Wed, Sep 21, 2016 at 4:41 PM, Jeroen Demeyer wrote: I tested this with a small stand-alone C program: the flags > PROT_NONE | MAP_PRIVATE | MAP_ANONYMOUS > allow to allocate huge amounts of virtual memory, even with overcommit=2. I also tried this. And I alsoo found that the memory does coun

[sage-devel] Re: [sage-support] huge virtual memory size when launching 7.3

2016-09-21 Thread Jonathan Bober
(I'm not completely sure I'm correct about all of that.) I'm probably going to try to modify a clean copy of PARI to do this, or just write some completely separate test code to check that an mmap call with PROT_NONE will work like we think it will work. On Tue, Sep 20, 2016 at 1

Re: [sage-devel] Re: Trac is slow and now it's affecting patchbot

2012-06-14 Thread Jonathan Bober
I think that the experimental trac server is getting hit by Baidu in bad places, and it isn't behaving well. There should be a robots.txt for trac, which should probably completely disallow the experimental installation, and something probably needs to be fixed with the experimental installation.

Re: [sage-devel] Reference manual broken in sagemath.org

2012-06-14 Thread Jonathan Bober
On Wed, Jun 13, 2012 at 10:38 PM, Minh Nguyen wrote: > Hi Jeroen, > > On Thu, Jun 14, 2012 at 3:24 PM, Jeroen Demeyer > wrote: >>> Thank you very much for the report.  The problem has been fixed now. >> Do you know what happened before, what went wrong? > > It has to do with the memory consumpti

[sage-devel] introspection is slow

2012-05-29 Thread Jonathan Bober
see http://trac.sagemath.org/sage_trac/ticket/13057 This seems to be a bad regression. On reasonable machines it can take 5 seconds to get the docstring of an object by using '?'. Does anyone have any idea what happened? I don't see any changes to sage/misc/sagedoc.py or sage/misc/sageinspect.py i

Re: [sage-devel] Re: Upgrading trac

2012-03-21 Thread Jonathan Bober
Perhaps you just had a flaky connection, and the fact that the same file kept failing was just a coincidence? There are some errors in the trac log like [...] File "/usr/lib/python2.5/cgi.py", line 691, in read_lines self.read_lines_to_outerboundary() File "/usr/lib/python2.5/cgi.py", lin

Re: [sage-devel] Re: Upgrading trac

2012-03-20 Thread Jonathan Bober
Whatever is going on, it has to do with trac, and not the database, it seems. apache runs at 100% for a while before returning a response whenever that page is loaded. I wonder if perhaps the issue is with one of the plugins. On Tue, Mar 20, 2012 at 4:40 PM, Maarten Derickx wrote: > > > Le mercre

Re: [sage-devel] Re: Upgrading trac

2012-03-20 Thread Jonathan Bober
On Tue, Mar 20, 2012 at 3:58 AM, leif wrote: > On 20 Mrz., 10:45, P Purkayastha wrote: >> On Tuesday, March 20, 2012 4:43:41 PM UTC+8, Jeroen Demeyer wrote: >> >> > On 2012-03-20 09:17, David Roe wrote: >> > > What link is broken?  I'm finding the link to >> >> >http://trac.sagemath.org/sage_trac

Re: [sage-devel] Re: Sage requires SSL

2012-03-20 Thread Jonathan Bober
On Tue, Mar 20, 2012 at 10:28 AM, Keshav Kini wrote: > I guess Purple Sage will have to switch to git when Sage does, since > their code bases are deeply connected. lmfdb, which I hadn't heard of > before, looks to be a separate codebase (like sagenb is). Is it > switching to git too? If not, then

Re: [sage-devel] Re: Upgrading trac

2012-03-19 Thread Jonathan Bober
I just made a few more changes to the trac/apache configuration. Apache now serves up (some) trac static files directly, instead of having trac do it. This should give better performance, but I don't know whether or not it will actually be anything noticeable. I also decreased the maximum number o

Re: [sage-devel] Re: Releasing more often?

2012-03-07 Thread Jonathan Bober
ote: > On Tue, Mar 6, 2012 at 12:11 PM, Jonathan Bober wrote: > > I am going to be building a VM on sage.math for other purposes soon, so > I'll > > try to make one for this as well. I suppose we would want something like > > Ubuntu 11.10 32-bit desktop edition? > >

Re: [sage-devel] Re: Releasing more often?

2012-03-06 Thread Jonathan Bober
I am going to be building a VM on sage.math for other purposes soon, so I'll try to make one for this as well. I suppose we would want something like Ubuntu 11.10 32-bit desktop edition? (Unfortunately, virtualbox on the *.math machines is really old, or at least it was last time I checked, so usi

Re: [sage-devel] Re: Group collaboration on a branch of Sage

2012-02-29 Thread Jonathan Bober
On Wed, Feb 29, 2012 at 10:12 AM, William Stein wrote: > > It's difficult for me because they are patch in hg format, but I can't > export a patch out of git in hg format. It's possible to import the > code in from the trac ticket, but then if I make changes I have to > export them as a git diff

[sage-devel] integration bug, segfault

2012-02-21 Thread Jonathan Bober
I didn't actually expect the following to work very well, but I definitely did not expect the output that I did get: sage: def IC9E(K, j, a, b, epsilon): : g(t) = 2*pi*i * (a - i*a + 2*b*K + i*2*b*K)*(1+i)*t - (1+i)^2 * 2*i*b*t^2 : f(t) = t^j * exp(g(t)) : return integral(f

Re: [sage-devel] weird behavior of sage in terminal

2012-02-10 Thread Jonathan Bober
On Fri, Feb 10, 2012 at 10:58 AM, Justin C. Walker wrote: > > On 10 Feb, 2012, at 02:06 AM, Jonathan Bober wrote: > > > By "sage in terminal" I mean "not the notebook." > > > > In recent builds (maybe mostly in the sage-5.0-beta series, but maybe

[sage-devel] weird behavior of sage in terminal

2012-02-10 Thread Jonathan Bober
By "sage in terminal" I mean "not the notebook." In recent builds (maybe mostly in the sage-5.0-beta series, but maybe 4.8, and maybe older -- I know that's not too helpful) I've occasionally noticed weird things working with sage from the command line. Sometimes tab completion has just completely

Re: [sage-devel] use "./configure; make" for Sage?

2012-02-08 Thread Jonathan Bober
On Wed, Feb 8, 2012 at 4:00 PM, William Stein wrote: > > After following this whole thread, I still have absolutely no idea > what this "non-trivial project" even is. What functionality is being > proposed to add to the Sage build system? > > -- William > > > I have been wondering the same thin

Re: [sage-devel] Re: [ARM] The failed numerical tests only show the tests are bad!

2012-02-08 Thread Jonathan Bober
On Tue, Feb 7, 2012 at 7:19 PM, Julien Puydt wrote: > Le Tue, 7 Feb 2012 20:23:08 -0800 (PST), > Jason a écrit : > > One benefit of programs like matlab and mathematica is that not only > > do they bring together many different functions with a common syntax, > > but that they (presumably) have s

Re: [sage-devel] [ARM] The failed numerical tests only show the tests are bad!

2012-02-07 Thread Jonathan Bober
See http://trac.sagemath.org/sage_trac/ticket/12449 I made a patch to change the way that sage evaluates symbolic functions for basic python types, and at the same time changed RDF to just use math.gamma() instead of gsl's gamma function. (Note: math.gamma() should be available in sage-5.0 (pytho

Re: [sage-devel] [ARM] The failed numerical tests only show the tests are bad!

2012-02-06 Thread Jonathan Bober
On Mon, Feb 6, 2012 at 3:05 PM, Dr. David Kirkby wrote: > On 02/ 5/12 10:16 PM, Jonathan Bober wrote: > > Never mind all that: the gsl implementation is not very good at all, >> whereas the libc implementation on my machine seems quite good. Old >> (libc): >> >

Re: [sage-devel] [ARM] The failed numerical tests only show the tests are bad!

2012-02-05 Thread Jonathan Bober
lem, but maybe it will work well there. On Sun, Feb 5, 2012 at 2:16 PM, Jonathan Bober wrote: > See http://trac.sagemath.org/sage_trac/ticket/12449 > > I'm in the middle of [hopefully] fixing this by calling the gsl gamma > function. While I'm at it, I'll also make

Re: [sage-devel] [ARM] The failed numerical tests only show the tests are bad!

2012-02-05 Thread Jonathan Bober
See http://trac.sagemath.org/sage_trac/ticket/12449 I'm in the middle of [hopefully] fixing this by calling the gsl gamma function. While I'm at it, I'll also make the evaluation on basic types much faster, as it shouldn't go though Ginac. (Actually, I've already mostly written a fix. I opened the

Re: [sage-devel] Re: [ARM] The failed numerical tests only show the tests are bad!

2012-02-04 Thread Jonathan Bober
On Sat, Feb 4, 2012 at 2:11 PM, Robert Bradshaw < rober...@math.washington.edu> wrote: > > Note that what is broken[1] here is ARM's libc, if one types > "gamma(6.0)" one gets "120." on all systems. It's a > question about gamma(float(6.0)) which is explicitly requesting the > (presuma

Re: [sage-devel] Re: [ARM] The failed numerical tests only show the tests are bad!

2012-02-04 Thread Jonathan Bober
On Sat, Feb 4, 2012 at 8:13 AM, rjf wrote: > > > > If there is a reasonable > > implementation that can guarantee this behavior with no loss in speed and > > no other significant trade-offs, then library designers should use it, > but > > I don't think that it is such a simple issue. > > I think

Re: [sage-devel] Re: sage-5.0.x and OS X 10.7 Lion

2012-02-03 Thread Jonathan Bober
On Tue, Jan 31, 2012 at 3:52 PM, Dr. David Kirkby wrote: > > But it makes the code unportable. What hope do we have with the Sun/Oracle > compiler if idiots use non-standard C? What hope do we have if we try to > build on Windows at some point in the future using a native compiler? All > these GNU

Re: [sage-devel] [ARM] The failed numerical tests only show the tests are bad!

2012-02-03 Thread Jonathan Bober
On Thu, Feb 2, 2012 at 1:16 PM, Julien Puydt wrote: > > Well, if I don't err, $10^{17}$ has 18 decimal digits, which is more than > the 15,95.. that fit in 53 binary digits. > It is not that simple. 15.95 digits is more like a guideline. At issue is whether the number in question can be exactly r

Re: [sage-devel] Re: [ARM] The failed numerical tests only show the tests are bad!

2012-02-02 Thread Jonathan Bober
On Thu, Feb 2, 2012 at 3:05 PM, rjf wrote: > > I don't know about arithmetic on ARM specifically, but there is > something > wrong with a gamma() function that fails to return an integer (perhaps > in float format) when it is > given an integer argument (perhaps in float format), and the answer i

Re: [sage-devel] [ARM] The failed numerical tests only show the tests are bad!

2012-02-02 Thread Jonathan Bober
On Thu, Feb 2, 2012 at 11:23 AM, Julien Puydt wrote: > > Let us consider : > #include > #include > > int > main () > { > long double x; > x=6.0; > printf ("%.20Lf\n", tgammal(x)); > x=10.0; > printf ("%.20Lf\n", tgammal(x)); > return 0; > } > > On an x86_64 box, I get : > $ ./test > 119.99

Re: [sage-devel] [ARM] The failed numerical tests only show the tests are bad!

2012-02-01 Thread Jonathan Bober
I've just been looking at this trying to figure out what was going on and I was just going to say exactly the same thing. I don't really know anything about the whole glibc vs eglibc thing, but I bet the implementation is the same as glibc-2.14.1/sysdeps/ieee754/dbl-64/e_gamma_r.c: double __ieee7

[sage-devel] Re: no space left under /tmp on sage.math

2012-01-31 Thread Jonathan Bober
"Instantly" makes sense. [Maybe everyone knows this.] If a process creates a file, and that file is deleted (either by the original process or by some other process), that file still exists and can be written to by that process until it is closed, and it takes up space on the file system. (I'm not

Re: [sage-devel] Re: VirtualBox

2012-01-10 Thread Jonathan Bober
On Tue, Jan 10, 2012 at 7:17 AM, William Stein wrote: > > On Jan 10, 2012 12:50 AM, "Dima Pasechnik" wrote: > > > > > > > > On Tuesday, 10 January 2012 03:06:14 UTC+8, William wrote: > >> > >> > coLinux looks promising. What does stop one from putting Sage on it > >> > presently? > >> > > >> > D

Re: [sage-devel] importing mpmath in 'sage -python' imports "everything"?

2011-12-13 Thread Jonathan Bober
;, line 28, in init sage.libs.ntl.ntl_ZZ (sage/libs/ntl/ntl_ZZ.cpp:6238) File "integer_ring.pyx", line 1063, in sage.rings.integer_ring.IntegerRing (sage/rings/integer_ring.c:9618) NameError: ZZ On Tue, Dec 13, 2011 at 2:35 AM, Fredrik Johansson < fredrik.johans...@gmail.com> wrote:

[sage-devel] importing mpmath in 'sage -python' imports "everything"?

2011-12-12 Thread Jonathan Bober
Does anyone happen to know why this happens? I have a feeling it is going to annoy my sometime soon. Look how long it takes to import mpmath: $ time sage -python -c "import mpmath; print mpmath.__version__"0.17 real 0m0.809s user 0m0.708s sys 0m0.076s compared to the time it takes to import the

Re: [sage-devel] Re: Sage 4.7.2 make failure on Thinkpad T-40 with Oneiric Ubuntu - maxima fails to build

2011-12-04 Thread Jonathan Bober
Well, here is Dale's install.log: http://sage.math.washington.edu/home/bober/dale-amon-20111203-install.log I don't know what's going wrong. On Sun, Dec 4, 2011 at 4:34 AM, Dale Amon wrote: > On Sun, Dec 04, 2011 at 03:26:23AM -0800, Jonathan Bober wrote: > > On Sat

Re: [sage-devel] Re: Sage 4.7.2 make failure on Thinkpad T-40 with Oneiric Ubuntu - maxima fails to build

2011-12-04 Thread Jonathan Bober
Yes, I had seen some reference to something like that. I think there is also an option to set the cpuid. Unfortunately, these features do not seem to be very well documented. For example, when I search google for "virtualbox synthcpu" I get your mailing list post on the first page of results, even

Re: [sage-devel] Re: Sage 4.7.2 make failure on Thinkpad T-40 with Oneiric Ubuntu - maxima fails to build

2011-12-04 Thread Jonathan Bober
On Sat, Dec 3, 2011 at 3:56 PM, Jonathan Bober wrote: > Would it be enough to do > > export SAGE_FAT_BINARY="yes" > export SAGE_BINARY_BUILD="yes" > export SAGE_ATLAS_ARCH="base" > > before building? > I don't know if this will wor

Re: [sage-devel] Re: Sage 4.7.2 make failure on Thinkpad T-40 with Oneiric Ubuntu - maxima fails to build

2011-12-03 Thread Jonathan Bober
ht also check the md5 sum of your source download, and make sure that nothing went wrong there.) On Sat, Dec 3, 2011 at 5:04 PM, Dale Amon wrote: > On Sat, Dec 03, 2011 at 04:04:48PM -0800, Jonathan Bober wrote: > > On Sat, Dec 3, 2011 at 3:56 PM, Jonathan Bober > wrote: > > &g

Re: [sage-devel] Re: Sage 4.7.2 make failure on Thinkpad T-40 with Oneiric Ubuntu - maxima fails to build

2011-12-03 Thread Jonathan Bober
On Sat, Dec 3, 2011 at 3:56 PM, Jonathan Bober wrote: > > Are other people really having problems building on Ubuntu 11.10? I've had > no problems building sage 4.8.2 on 64-bit Ubuntu 11.10. Also, I just tried > on 32-bit 11.10 in a virtual machine, and sage built wit

Re: [sage-devel] Re: Sage 4.7.2 make failure on Thinkpad T-40 with Oneiric Ubuntu - maxima fails to build

2011-12-03 Thread Jonathan Bober
It's a shame this has gone unreplied to for so long. (Unless I missed a reply in another thread. I'm may be confused by the various threads, which is why I'm only replying on sage-devel.) Are other people really having problems building on Ubuntu 11.10? I've had no problems building sage 4.8.2 on

Re: [sage-devel] Re: or sage-5.0? (Re: [sage-release] Next release: sage-4.7.3 or sage-4.8?)

2011-11-08 Thread Jonathan Bober
On Tue, Nov 8, 2011 at 3:09 AM, Julien Puydt wrote: > > You'll find here http://clefagreg.dnsalias.org/ a distribution aimed at > them. And in fact, several distributions, to be installed on a usb key and > booted, precisely because the students may not have administrative rights > on the machine

Re: [sage-devel] Re: or sage-5.0? (Re: [sage-release] Next release: sage-4.7.3 or sage-4.8?)

2011-11-07 Thread Jonathan Bober
On Sun, Nov 6, 2011 at 5:59 AM, Julien Puydt wrote: > Le 05/11/2011 21:24, Justin C. Walker a écrit : > > There are so many different versions of each library and system (for >> Linux, in particular) >> that it's a practical impossibility to produce a package like Sage that >> will work on the sy

Re: [sage-devel] @parallel doesn't clean up temp directories?

2011-09-19 Thread Jonathan Bober
I just looked at a few machines where I run sage and found that one of them has this problem. It is also the one where I've used @parallel the most. I see at most one subdirectory per host in my .sage directory on *.math, so there's not much of a problem there. I have use @parallel a fair amount t

Re: [sage-devel] Purpose of readlink and realpath in $SAGE_ROOT/sage

2011-08-24 Thread Jonathan Bober
On Thu, Aug 18, 2011 at 9:02 PM, Jeroen Demeyer wrote: > Hello sage-devel, > > Can somebody explain the rationale for the following lines in > $SAGE_ROOT/sage: > if [ "$SAGE_ROOT" = "." ]; then >SAGE_ROOT=`readlink -n "$0" 2> /dev/null` || \ >SAGE_ROOT=`realpath"$0" 2> /dev/null`

Re: [sage-devel] Re: memory leak

2011-07-25 Thread Jonathan Bober
> > back). > > They affect multi polynomial rings used by elliptic curves. > > > > Finally it might be worth having a look at 5949, but I would say it is > > not related. > > > > On 25 juil, 09:55, Jonathan Bober wrote: > > > > > > > &g

[sage-devel] memory leak

2011-07-25 Thread Jonathan Bober
I just found the following memory leak: def leak(): K. = NumberField(x^2 - x - 1) m = get_memory_usage() for n in xrange(10): E = EllipticCurve(K, [3,4,5,6,7]) if n % 1000 == 0: print get_memory_usage() - m sage: leak() 0.0 0.5 1.0 1.0 1.5 2.0 2.0 2.5 3

[sage-devel] hashing number field ideals

2011-07-18 Thread Jonathan Bober
Hi all. I think there's a problem with the following: sage: K. = NumberField(x^2 - x - 1) sage: I = K.ideal(2 * a - 1) sage: I2 = I.factor()[0][0] # I is a prime ideal, so its only factor is itself: sage: print I, I2, I == I2 Fractional ideal (2*a - 1) Fractional ideal (2*a - 1) True # also, the

[sage-devel] Re: fpLLL memory leak

2010-10-27 Thread Jonathan Bober
I should have been a little less lazy before I posted this, I guess. I found out where the leak is (the fpLLL wrapper) on my first try. I don't know what is causing it, though. This is now at http://trac.sagemath.org/sage_trac/ticket/10179 On Wed, 2010-10-27 at 14:24 -0400, Jonathan

[sage-devel] memory leak

2010-10-27 Thread Jonathan Bober
Dear all, There seems to be a memory leak in some code below, in at least versions 4.5 and 4.5.3. For example, if I call it with sage: L = find_candidates_for_large_value(5000) It prints something like: current memory usage: 836.73046875 current memory usage: 836.73046875 current memory usage:

Re: [sage-devel] Re: Improvement of numerical integration routines

2010-09-22 Thread Jonathan Bober
On Sun, 2010-09-19 at 08:12 -0700, rjf wrote: > Any program that computes a quadrature by evaluating the integral at > selected points cannot provide > a rigorous error bound. I don't know what a rigorous "error estimate" > is, unless it is an > estimate of what might be a rigorous bound. And thu

Re: [sage-devel] Improvement of numerical integration routines

2010-09-22 Thread Jonathan Bober
On Thu, 2010-09-16 at 15:48 -0700, maldun wrote: > Hi all! > > I'm currently found some time to work again on ticket #8321 again, and > have added some numerical integration tests. Hi Maldun, I think that improvement of numerical integration would be excellent. I've been somewhat disappointed wi

Re: [sage-devel] Let's collect data on Sage startup time.

2010-03-03 Thread Jonathan Bober
Running these tests gives some information, but it is probably a little hard to interpret. On a fresh boot, sage will take roughly 18 seconds to start up on my machine. Subsequent runs, however, take roughly 1.8 seconds, typically. This is all dependent on many things that the operating system doe

Re: [sage-devel] Trac #8276: Specialist Elliptic curve / Brandt Modules needed...

2010-02-16 Thread Jonathan Bober
At least some errors probably come from the file sage/algebras/quatalg/quaternion_algebra_cython.pyx and I think they should be easily fixable without any knowledge of what is going on by just changing the code to make a copy of the zero matrix. However, I really wonder whether this fix is neces

[sage-devel] -fPIC in PARI and SELinux

2010-01-19 Thread Jonathan Bober
The Sage README.txt contains the text: "On Linux, if you get this error message: " restore segment prot after reloc: Permission denied " the problem is probably related to SELinux." I got this error on a machine on which I don't have root access, so I couldn't try the suggested workarounds.

[sage-devel] log(x) is really slow when x is a float

2010-01-12 Thread Jonathan Bober
I just posted http://trac.sagemath.org/sage_trac/ticket/7918 but I thought I would also send an email here to catch the attention of whomever made the change that caused this slowdown. Hopefully this will be easy to fix. Somewhere between sage 4.1 and sage 4.3, log(x) got really slow when x is a f

[sage-devel] Re: new virtualbox image!

2009-10-28 Thread Jonathan Bober
This might not be too relevant to OS X, since I am running Ubuntu, but I'll put it here for the record anyway, in case it is useful to someone: At some point when the virtualbox image wasn't working for me I recompiled the kernel module this way. I think that I did it after getting a more informa

[sage-devel] Re: new virtualbox image!

2009-10-27 Thread Jonathan Bober
I've just been trying this on Ubuntu and had the same problem. Increasing the video ram in the virtual machine from 4 to 16 MB fixed it, and now it works. (At least, I'm pretty sure that was the change that fixed it.) On Fri, 2009-10-23 at 14:01 -0700, mhampton wrote: > I haven't tried it on Wind

[sage-devel] Re: [sage-support] problem with GCD in notebook

2009-03-03 Thread Jonathan Bober
I'm not sure why you are getting different results from sagenb.com and from the "shell", but I would guess that you must be using two different versions of Sage. Either way... The problem is that when you divide two integers, the result is always a rational number, whether or not that rational nu

[sage-devel] Re: pari slowness

2008-06-09 Thread Jonathan Bober
On Mon, 2008-06-09 at 10:19 -0700, mabshoff wrote: > > [...] > No clue. Can you actually compare the gp binary from Sage directly > with the timings from your self builid binary to eliminate the problem > that libPari is involved here? If the gp binary in Sage is slower by a > factor of three com

[sage-devel] Re: Graph planarity

2008-05-25 Thread Jonathan Bober
Since no one else has responded, I'll go ahead and say that I don't know anything about this. Maybe this email will be a reminder to someone who does know. (Or maybe any questions have already been taken care of off list?) On Fri, 2008-05-23 at 17:12 -0700, William Stein wrote: > On Fri, May 23,

[sage-devel] Re: sloppy mult and div in quaddouble?

2008-04-28 Thread Jonathan Bober
I'm not sure exactly what the speed differences are, but I think that they are quite significant. When writing the partition counting code, which uses quaddouble, I recall that things ran much slower if "sloppy" multiplication and division were not enabled. (However, I have no hard benchmarks to b

[sage-devel] some sort of plotting problem

2008-01-27 Thread Jonathan Bober
Does anyone know what's going on in the following example? I can't seem to reproduce this with a simple example. Basically, I create a few 'callable symbolic expressions', and then define a lambda function that calls a one of them. Ultimately, I have a function Q = lambda x : RR(bound(15000, 15

[sage-devel] Re: generator inconsistencies in finite fields

2008-01-23 Thread Jonathan Bober
I just realized a source of my confusion. The docstring that I quoted was not actually wrong in the way that I thought is was, but was apparently deceptive (to me). Perhaps some people are already aware of this, but GF(5), GF(25), and GF(5^100) are all different types, and so have different docstr

[sage-devel] Re: generator inconsistencies in finite fields

2008-01-21 Thread Jonathan Bober
Ok, I was wrong. I'm convinced that sage has the correct behavior, which I think is: GF(q).gen() returns an element x of GF(q) such that the smallest subfield of GF(q) containing x is GF(q). In this case, the docstring needs to be corrected, because the statement that "All elements x of self are

[sage-devel] generator inconsistencies in finite fields

2008-01-20 Thread Jonathan Bober
I don't like the behavior illustrated below. Briefly, my problem is that GF(p).gen() gives a generator for the additive group of GF(5), while GF(p^n).gen() gives a generator for for multiplicative group of GF(p^n) (n > 1). I would file this 'complaint' directly as a trac bug report, but the docum

[sage-devel] Re: Approximating Ei using polynomials

2008-01-17 Thread Jonathan Bober
I don't know the answer to this for certain, but (assuming you mean eq. 5.1.53 on page 231 - http://www.math.sfu.ca/~cbm/aands/page_231.htm ) it looks to me like this might just a 5th degree polynomial interpolation (in which case, it's of course not something that you can compute to arbitrary pre

[sage-devel] bug in 2.8.15 (somewhere in sage.calculus?)

2007-12-10 Thread Jonathan Bober
Hi all. I just opened ticket #1457 (see below) http://trac.sagemath.org/sage_trac/ticket/1457 The following is hopefully pretty self explanatory: --- The following took place on an Intel Core Duo (32 bit) running Ubuntu 7.10. Hopefully the cause is obvious for s

[sage-devel] Re: Fun Things to do with a Sage Notebook

2007-10-27 Thread Jonathan Bober
On Sat, 2007-10-27 at 17:03 -0500, William Stein wrote: > I think the public free Sage notebook should be configured so that > the sageXX accounts cannot open sockets to the outside world. Period. > If I knew how to configure this in < 30 minutes, I would have done it already. I think that thi

[sage-devel] Re: problem with showing plots from command line

2007-10-23 Thread Jonathan Bober
abshoff wrote: > > > On Oct 23, 6:04 pm, Jonathan Bober <[EMAIL PROTECTED]> wrote: > > > Could you give us the output from echo 'LD_LIBRARY_PATH' and 'ldd xdg- > > > open' with and without sourcing sage-env. If you add an 'echo > > >

[sage-devel] Re: problem with showing plots from command line

2007-10-23 Thread Jonathan Bober
> Could you give us the output from echo 'LD_LIBRARY_PATH' and 'ldd xdg- > open' with and without sourcing sage-env. If you add an 'echo > LD_LIBRARY_PATH' right before xdg-open is called in P.show() > > >From the name of the symbol I would guess that it is a libz > incompability. There was a pat

[sage-devel] problem with showing plots from command line

2007-10-22 Thread Jonathan Bober
Hi folks. I tried to send the following email a few hours ago (but I put the email address in wrong) and I don't feel like rewriting it all. So I should add to it now that I have upgraded sage (so I am running 2.8.8.1) and the error still occurs. Perhaps I should open a ticket for this, but perh

[sage-devel] Re: number_of_partitions

2007-10-14 Thread Jonathan Bober
On Sun, 2007-10-14 at 15:13 -0700, William Stein wrote: > On 10/14/07, Jonathan Bober <[EMAIL PROTECTED]> wrote: > > > > I'm not sure right now, but I'm thinking about it. > > OK, your new code on x86_64 gets essentially every single > number_of_parti

[sage-devel] Re: number_of_partitions

2007-10-14 Thread Jonathan Bober
use the long double type when you use GCC 4.0 or later to develop or in programs targeted at Mac OS X versions earlier than 10.4. I'll probably be back looking at this in a little while. On Sun, 2007-10-14 at 14:53 -0700, William Stein wrote: > On 10/14/07, Jonathan Bober <[EMAIL PROTEC

[sage-devel] Re: number_of_partitions

2007-10-14 Thread Jonathan Bober
I'm not sure right now, but I'm thinking about it. You could try setting long_double_precision = double_precision wherever it is initialized. (This is around line 140 somewhere.) If you do this it will just skip the part of the computation where it uses long doubles (For

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