Sage binaries doesn't work on a Debian Lenny 64bit server with Intel Xeon Dual core and Xen hypervisor

[Johan Oudinet]

Hi,

I've just download the Debian-64bit-intel-xeon version of sage, then
extract, run ./sage and get an unexpected error:

$ ./sage
----------------------------------------------------------------------
| Sage Version 3.2.3, Release Date: 2009-01-05 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
The SAGE install tree may have moved.
Regenerating Python.pyo and .pyc files that hardcode the install PATH
(please wait at
most a few minutes)...
Do not interrupt this.
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (1087, 0))

---------------------------------------------------------------------------
RuntimeError Traceback (most recent call
last)

<SNIP TRACEBACK MESSAGES>

RuntimeError: Unable to start gap because the command 'gap -b -p -T -o
9999G /users/asspro/oudinet/projects/sage-3.2.3-debian-64bit-
intel_xeon-x86_64-Linux/data//extcode/gap/sage.g' failed.

Error importing ipy_profile_sage - perhaps you should run %upgrade?
WARNING: Loading of ipy_profile_sage failed.

The entire log is available here:
http://www.lri.fr/~oudinet/pub/debiansage.log

Since I have no idea how to solve this problem, I hope someone here
has a solution?

[mabshoff]

On Feb 17, 9:41 am, Johan Oudinet <Johan.Oudi...@gmail.com> wrote:
> Hi,

Hi Johan,

No surprise here since that Sage release was build for the last stable
release. In the future Sage 3.3 binaries should be properly marked
since otherwise people end up getting the wrong binaries.

So far no one has set up the needed build machines for lenny so that
we will have binaries for it, but I expect this to happen in the not
too distant future since most Debian people ought to upgrade to lenny
soon.

For now I recommend building from sources.

Cheers,

Michael

[Johan Oudinet]

On Tue, Feb 17, 2009 at 6:52 PM, mabshoff
<Michael...@mathematik.uni-dortmund.de> wrote:
>
>
>
> On Feb 17, 9:41 am, Johan Oudinet <Johan.Oudi...@gmail.com> wrote:
>> Hi,
>
> Hi Johan,
>
>> I've just download the Debian-64bit-intel-xeon version of sage, then
>> extract, run ./sage and get an unexpected error:
>>

>> Since I have no idea how to solve this problem, I hope someone here
>> has a solution?
>
> No surprise here since that Sage release was build for the last stable
> release. In the future Sage 3.3 binaries should be properly marked
> since otherwise people end up getting the wrong binaries.
>
> So far no one has set up the needed build machines for lenny so that
> we will have binaries for it, but I expect this to happen in the not
> too distant future since most Debian people ought to upgrade to lenny
> soon.
>
> For now I recommend building from sources.
>
> Cheers,
>

Thanks Michael for the quick answer. I'll try to build Sage from sources.

Cheers,

--
Johan

[William Stein]

And for the record I'm *currently* installing 32 and 64-bit Debian images.

William

[Johan Oudinet]

I've tried to build from sources sage-3.3 but I still have an
unexpected error when running sage :-(

The log is available here: http://www.lri.fr/~oudinet/pub/debiansage2.log

I add that when I manually try to execute the command gap with the
same options, I get :
$ gap -r -b -p -T -o 9999G /usr/local/sage-3.3/data//extcode/gap/sage.g
@p1.@!19924+@"2014+@#91395+@$7138+@%24361+@&67542+@!24824+@"7764+@#33736+@$5915+@%21601+@&67542+@!48921+@"9581+@#09404+@$3263+@%5248+@&67542+@!2688+@"6321+@#95313+@$0292+@%0796+@&67542+@!3448+@"5201+@#54952+@$8622+@%2475+@&67542+@!7689+@"949+@#89662+@$9281+@%2454+@&67542+@!3448+@"1101+@#75312+@$7761+@%4233+@&67542+@nGAP4,
Version: 4.4.12 of 17-Dec-2008,
x86_64-unknown-linux-gnu-gcc@J@!0012+@"385+@#0944+@$144+@%6262+@&67542+@ngap>
@i

For the record, I've followed the installation guide found here:
http://www.sagemath.org/doc/inst/node8.html

--
Johan

[mabshoff]

On Feb 26, 5:46 am, Johan Oudinet <johan.oudi...@gmail.com> wrote:
> On Tue, Feb 17, 2009 at 9:34 PM, William Stein <wst...@gmail.com> wrote:

Hi Johan,

<SNIP>

> I've tried to build from sources sage-3.3 but I still have an
> unexpected error when running sage :-(
>
> The log is available here:http://www.lri.fr/~oudinet/pub/debiansage2.log
>
> I add that when I manually try to execute the command gap with the
> same options, I get :
> $ gap -r -b -p -T -o 9999G /usr/local/sage-3.3/data//extcode/gap/sage.g
> @p1.@!19924+@"2014+@#91395+@$7138+@%24361+@&67542+@!24824+@"7764+@#33736+@$ 5915+@%21601+@&67542+@!48921+@"9581+@#09404+@$3263+@%5248+@&67542+@!2688+@" 6321+@#95313+@$0292+@%0796+@&67542+@!3448+@"5201+@#54952+@$8622+@%2475+@&67 542+@!7689+@"949+@#89662+@$9281+@%2454+@&67542+@!3448+@"1101+@#75312+@$7761 +@%4233+@&67542+@nGAP4,
> Version: 4.4.12 of 17-Dec-2008,
> x86_64-unknown-linux-gnu-gcc@J@!0012+@"385+@#0944+@$144+@%6262+@&67542+@nga p>
> @i

Ok, that does not look pretty.

Do you have a gap.rc file on your box by any chance, i.e. do you run
GAP with a custom config file?

> For the record, I've followed the installation guide found here:http://www.sagemath.org/doc/inst/node8.html

Ok.

We have seen this or a seemingly similar problem on a build machine we
have access to, so we are investigating. I have made this a critical
issue against 3.4, i.e.

http://trac.sagemath.org/sage_trac/ticket/5385

Three questions:

* Does "sage -gap" give you a working GAP without all that odd
output?
* What is LOCALE set to?
* Could you compress install.log and post a link to it so that I can
download it and take a look? Maybe something common or odd will pop
up.

Cheers,

Michael

> --
> Johan

Cheers,

Michael

[Johan Oudinet]

On Thu, Feb 26, 2009 at 2:55 PM, mabshoff
<Michael...@mathematik.uni-dortmund.de> wrote:
>
>
>
> On Feb 26, 5:46 am, Johan Oudinet <johan.oudi...@gmail.com> wrote:
>> On Tue, Feb 17, 2009 at 9:34 PM, William Stein <wst...@gmail.com> wrote:
>
> Hi Johan,
>
> <SNIP>
>
>> I've tried to build from sources sage-3.3 but I still have an
>> unexpected error when running sage :-(
>>
>> The log is available here:http://www.lri.fr/~oudinet/pub/debiansage2.log
>>
>> I add that when I manually try to execute the command gap with the
>> same options, I get :
>> $ gap -r -b -p -T -o 9999G /usr/local/sage-3.3/data//extcode/gap/sage.g
>> @p1.@!19924+@"2014+@#91395+@$7138+@%24361+@&67542+@!24824+@"7764+@#33736+@$ 5915+@%21601+@&67542+@!48921+@"9581+@#09404+@$3263+@%5248+@&67542+@!2688+@" 6321+@#95313+@$0292+@%0796+@&67542+@!3448+@"5201+@#54952+@$8622+@%2475+@&67 542+@!7689+@"949+@#89662+@$9281+@%2454+@&67542+@!3448+@"1101+@#75312+@$7761 +@%4233+@&67542+@nGAP4,
>> Version: 4.4.12 of 17-Dec-2008,
>> x86_64-unknown-linux-gnu-gcc@J@!0012+@"385+@#0944+@$144+@%6262+@&67542+@nga p>
>> @i
>
>
> Ok, that does not look pretty.
>
> Do you have a gap.rc file on your box by any chance, i.e. do you run
> GAP with a custom config file?

I don't think so. Actually, I don't know what GAP is (so I never used
it) and both "locate gap.rc" and find ~ -name 'gap.rc' don't find
anything.

>
>> For the record, I've followed the installation guide found here:http://www.sagemath.org/doc/inst/node8.html
>
> Ok.
>
> We have seen this or a seemingly similar problem on a build machine we
> have access to, so we are investigating. I have made this a critical
> issue against 3.4, i.e.
>
>  http://trac.sagemath.org/sage_trac/ticket/5385
>
> Three questions:
>
>  * Does "sage -gap" give you a working GAP without all that odd
> output?

"sage -gap" starts without complain, and I can type ?help for
example... but I don't know what do you mean by a "working GAP"

>  * What is LOCALE set to?

I think it is unset:
$echo $LOCALE

$ test -z $LOCALE; echo $?
0

>  * Could you compress install.log and post a link to it so that I can
> download it and take a look? Maybe something common or odd will pop
> up.

Here it is:
http://www.lri.fr/~oudinet/pub/install.log.bz2

--
Johan

[mabshoff]

Thanks Johan,

I poked around a little more and this is likely a pexpect problem. I
checked Sage 3.2.3 with GAP 4.4.10 and it does

[mabshoff@eno sage-3.2.3-eno]$ gap -r -b -p -T -o 9999G
@p1.@!84034+@"8014+@#33295+@$9038+@%53361+@&67542+@!
45214+@"3154+@#74316+@$7925+@%93601+@&67542+@!22041+@"2612+@#45424+@
$6173+@%2928+@&67542+@!0958+@"0221+@#28503+@$1872+@%0686+@&67542+@!
0267+@"839+@#88612+@$3991+@%9375+@&67542+@!45301+@"199+@#47903+@$4012+@
%7844+@&67542+@!3448+@"488+@#82591+@$2721+@%4723+@&67542+@!
7032+@"594+@#2735+@$385+@%1582+@&67542+@nGAP4, Version: 4.4.10 of 02-
Oct-2007, x86_64-unknown-linux-gnu-gcc@J@ngap> @i

This is in contrast to GAP 4.4.12 on an Itanium:

mabshoff@iras:~/build-3.3/sage-3.3-iras> gap -r -b -p -T -o 9999G
@p1.@!52034+@"6014+@#77295+@$2138+@%63361+@&67542+@!
69724+@"5764+@#23736+@$1915+@%90601+@&67542+@!47921+@"9581+@#92504+@
$8263+@%2248+@&67542+@!5588+@"3421+@#75313+@$1292+@%8696+@&67542+@!
7248+@"3201+@#21852+@$6522+@%4375+@&67542+@!6789+@"359+@#06762+@$8281+@
%1354+@&67542+@!6348+@"1101+@#99312+@$2861+@%2133+@&67542+@nGAP4,
Version: 4.4.12 of 17-Dec-2008, ia64-unknown-linux-gnu-gcc@J@!
8212+@"146+@#3254+@$373+@%1162+@&67542+@ngap> @i

GAP 4.4.12 on the same machine as GAP 4.4.10 above:

[mabshoff@eno sage-3.2.3-eno]$ gap -r -b -p -T -o 9999G
@p1.@!84034+@"8014+@#33295+@$9038+@%53361+@&67542+@!
45214+@"3154+@#74316+@$7925+@%93601+@&67542+@!22041+@"2612+@#45424+@
$6173+@%2928+@&67542+@!0958+@"0221+@#28503+@$1872+@%0686+@&67542+@!
0267+@"839+@#88612+@$3991+@%9375+@&67542+@!45301+@"199+@#47903+@$4012+@
%7844+@&67542+@!3448+@"488+@#82591+@$2721+@%4723+@&67542+@!
7032+@"594+@#2735+@$385+@%1582+@&67542+@nGAP4, Version: 4.4.10 of 02-
Oct-2007, x86_64-unknown-linux-gnu-gcc@J@ngap> @i

I am not sure what all that "@XXXX" junk is, but I will try to figure
it out :)

Cheers,

Michael

[mabshoff]

Some more update: "-p" is at fault here, but that startup option isn't
documented in the GAP help, so I have started looking at the source
code what it is exactly supposed to do.

Either way, if you look at interfaces/gap.py in

def _execute_line(self, line, wait_for_prompt=True,
expect_eof=False):

you will see that the info created by "-p" is used and given the
interface to GAP was written by Steve Linton (who is one of the
current GAP maintainers) I am sure that it is done so for a good
reason.

So, what is the fix then? Likely an adjustment to the pexepct
interface for GAP, but so far I have little lead what to do here.
Other people will hopefully have a shorter learning cure for that
code.

Cheers,

Michael

[Johan Oudinet]

Just to mention I also tried sage-3.4 binary for Debian Lenny and got
exactly the same error (but I have to remove a file that warns about
the absence of sse4_1 flag before).

So, it confirms this GAP bug is still present in sage-3.4.

--
Johan