Re: [sage-devel] Sage 8.2 build question on EC2 AWS Linux

2018-05-07 Thread jonha...@gmail.com 
It's a t2.micro instance, so it looks like 
 1GB.

On Monday, May 7, 2018 at 3:45:49 AM UTC-4, Jeroen Demeyer wrote:
>
> On 2018-05-07 05:02, jonh...@gmail.com  wrote: 
> > [gfortran-7.2.0] MemoryError 
>
> It seems you are running out of memory. How much memory do you have? 
>
> Alternatively, you could install gfortran before building Sage. 
>

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[sage-devel] Sage 8.2 build question on EC2 AWS Linux

2018-05-06 Thread jonha...@gmail.com 
Hi,

I'm having trouble building the latest Sage (8.2) from the github repo 
 on an AWS EC2 instance.  I've included 
the error message and OS version below from running "make".  Any comments 
are appreciated.

Thanks,
-Jon

==

Sage 8.2 Build Error:
---
...
[xz-5.2.2.p0] Finished installing xz-5.2.2.p0.spkg
sage-logger -p 'sage-spkg gfortran-7.2.0' 
'/home/ec2-user/sage/logs/pkgs/gfortran-7.2.0.log'
[gfortran-7.2.0] Found local metadata for gfortran-7.2.0
[gfortran-7.2.0] Attempting to download package gcc-7.2.0.tar.xz from 
mirrors
[gfortran-7.2.0] 
http://mirrors.mit.edu/sage/spkg/upstream/gcc/gcc-7.2.0.tar.xz
[gfortran-7.2.0] 
[..]
[gfortran-7.2.0] gfortran-7.2.0
[gfortran-7.2.0] 
[gfortran-7.2.0] Setting up build directory for gfortran-7.2.0
[gfortran-7.2.0] Traceback (most recent call last):
[gfortran-7.2.0]   File 
"/home/ec2-user/sage/build/bin/sage-uncompress-spkg", line 23, in 
[gfortran-7.2.0] run()
[gfortran-7.2.0]   File 
"/home/ec2-user/sage/build/bin/../sage_bootstrap/uncompress/cmdline.py", 
line 53, in run
[gfortran-7.2.0] archive = open_archive(filename)
[gfortran-7.2.0]   File 
"/home/ec2-user/sage/build/bin/../sage_bootstrap/uncompress/action.py", 
line 38, in open_archive
[gfortran-7.2.0] return cls(filename)
[gfortran-7.2.0]   File 
"/home/ec2-user/sage/build/bin/../sage_bootstrap/uncompress/tar_file.py", 
line 152, in __new__
[gfortran-7.2.0] return SageBaseTarFile(mode="r", fileobj=BytesIO(data))
[gfortran-7.2.0] MemoryError
[gfortran-7.2.0] 

[gfortran-7.2.0] Error: failed to extract 
/home/ec2-user/sage/upstream/gcc-7.2.0.tar.xz
[gfortran-7.2.0] 

[gfortran-7.2.0] Please email sage-devel 
(http://groups.google.com/group/sage-devel)
[gfortran-7.2.0] explaining the problem and including the log file
[gfortran-7.2.0]   /home/ec2-user/sage/logs/pkgs/gfortran-7.2.0.log
[gfortran-7.2.0] Describe your computer, operating system, etc.
[gfortran-7.2.0] 

make[2]: *** 
[/home/ec2-user/sage/local/var/lib/sage/installed/gfortran-7.2.0] Error 1
make[2]: Leaving directory `/home/ec2-user/sage/build/make'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/ec2-user/sage/build/make'




AWS OS Information:
-
[sage]$ cat /etc/os-release
NAME="Amazon Linux"
VERSION="2 (2017.12)"
ID="amzn"
ID_LIKE="centos rhel fedora"
VERSION_ID="2"
PRETTY_NAME="Amazon Linux 2 (2017.12) LTS Release Candidate"
ANSI_COLOR="0;33"
CPE_NAME="cpe:2.3:o:amazon:amazon_linux:2"
HOME_URL="https://amazonlinux.com/;

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Re: [sage-devel] sage -b fails on SageMathCloud

2016-12-31 Thread jonha...@gmail.com 
Hi William,

Yes, I was trying to get some older code to run.  Removing that line fixes 
the build problem.  So GMP is now available without additional includes? 
 That's great!  

Thanks,
-Jon

On Saturday, December 31, 2016 at 1:09:41 PM UTC-5, William wrote:
>
> The error you get is 
>
>Internal compiler error: '../ext/gmp.pxi' not found 
>
> There is no gmp.pxi in your tree: 
>
> ~/SAGE_INSTALL__2016-12-21/sage-7.4$ find . |grep gmp.pxi 
> ~/SAGE_INSTALL__2016-12-21/sage-7.4$ 
>
> In fact gmp.pxi was removed from sage years ago, evidently: 
>
> https://trac.sagemath.org/ticket/10103 
>
> Maybe you merged in some ancient bitrotted code that assumes that 
> gmp.pxi exists still?  Yep: 
>
> ~/SAGE_INSTALL__2016-12-21/sage-7.4$ git status 
> On branch develop 
> Your branch is up-to-date with 'origin/develop'. 
> Changes not staged for commit: 
>   (use "git add ..." to update what will be committed) 
>   (use "git checkout -- ..." to discard changes in working 
> directory) 
>
> modified:   src/sage/quadratic_forms/all.py 
>
> Untracked files: 
>   (use "git add ..." to include in what will be committed) 
>
> src/sage/quadratic_forms/table_hanke.py 
> src/sage/quadratic_forms/table_hanke.pyx 
> src/sage/quadratic_forms/ternary_table.pyx 
>
> On Sat, Dec 31, 2016 at 9:20 AM, jonh...@gmail.com  <
> jonh...@gmail.com > wrote: 
> > Hi, 
> > 
> > I'm trying to rebuild sage with the 'sage -b' command as described here 
> and 
> > get the error below.  Are there some additional shell variables that 
> need to 
> > be set for this to work?  I'm using sage 7.4 build from source on 
> > SageMathCloud. 
> > 
> > Thanks and Happy New Year! 
> > -Jon 
> > 
> >  
> > 
> > ~/SAGE_INSTALL__2016-12-21/sage-7.4$ ./sage -b 
> > (cd . 
> > \ 
> >  && export SAGE_ROOT=/doesnotexist 
> > \ 
> >SAGE_SRC=/doesnotexist 
> > \ 
> >SAGE_SRC_ROOT=/doesnotexist 
> > \ 
> >SAGE_DOC_SRC=/doesnotexist 
> > \ 
> >SAGE_SCRIPTS_DIR=/doesnotexist 
> > \ 
> >SAGE_BUILD_DIR=/doesnotexist 
> > \ 
> > 
> > 
> SAGE_PKGS=/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/build/pkgs
>  
>
> > \ 
> > 
> > 
> SAGE_CYTHONIZED=/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/src/build/cythonized
>  
>
> > \ 
> >  && python -u setup.py build install) 
> > You are using pip version 8.1.2, however version 9.0.1 is available. 
> > You should consider upgrading via the 'pip install --upgrade pip' 
> command. 
> > make[1]: Entering directory 
> > 
> '/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/src'
>  
>
> > make[1]: Nothing to be done for 'all'. 
> > make[1]: Leaving directory 
> > 
> '/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/src'
>  
>
> > Updating Cython code 
> > Enabling Cython debugging support 
> >  
> > Traceback (most recent call last): 
> >   File "setup.py", line 620, in  
> > run_cythonize() 
> >   File "setup.py", line 612, in run_cythonize 
> > 'profile': profile, 
> >   File 
> > 
> "/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
>  
>
> > ependencies.py", line 799, in cythonize 
> > aliases=aliases) 
> >   File 
> > 
> "/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
>  
>
> > ependencies.py", line 704, in create_extension_list 
> > kwds = deps.distutils_info(file, aliases, base).values 
> >   File 
> > 
> "/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
>  
>
> > ependencies.py", line 586, in distutils_info 
> > return (self.transitive_merge(filename, self.distutils_info0, 
> > DistutilsInfo.merge) 
> >   File 
> > 
> "/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
>  
>
> > ependencies.py", line 596, in transitive_merge 
> > node, extract, merge, seen, {}, self.cimported_files)[0] 
> >   File 
> > 
> "/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
>  
>
> > ependencies.py", line 601, in transitive_merge_helper 
> > deps = extract(node) 
> >   File 
> > 
> "/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
>  
>
> > ependencies.py", line 577, in distutils_info0 
> > externs = self.cimports_and_externs(filename)[1] 
> >   File 
> > 
> "/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Utils.p
>  
>
> > y", line 44, in wrapper 
> >

[sage-devel] sage -b fails on SageMathCloud

2016-12-31 Thread jonha...@gmail.com 
Hi,

I'm trying to rebuild sage with the 'sage -b' command as described here 
 and get 
the error below.  Are there some additional shell variables that need to be 
set for this to work?  I'm using sage 7.4 build from source on 
SageMathCloud. 

Thanks and Happy New Year!
-Jon



~/SAGE_INSTALL__2016-12-21/sage-7.4$ ./sage -b
(cd .   
\
 && export SAGE_ROOT=/doesnotexist  
\
   SAGE_SRC=/doesnotexist   
\
   SAGE_SRC_ROOT=/doesnotexist  
\
   SAGE_DOC_SRC=/doesnotexist   
\
   SAGE_SCRIPTS_DIR=/doesnotexist   
\
   SAGE_BUILD_DIR=/doesnotexist 
\
   
SAGE_PKGS=/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/build/pkgs
\
   
SAGE_CYTHONIZED=/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/src/build/cythonized
\
 && python -u setup.py build install)
You are using pip version 8.1.2, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
make[1]: Entering directory 
'/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/src'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory 
'/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/src'
Updating Cython code
Enabling Cython debugging support

Traceback (most recent call last):
  File "setup.py", line 620, in 
run_cythonize()
  File "setup.py", line 612, in run_cythonize
'profile': profile,
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
ependencies.py", line 799, in cythonize
aliases=aliases)
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
ependencies.py", line 704, in create_extension_list
kwds = deps.distutils_info(file, aliases, base).values
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
ependencies.py", line 586, in distutils_info
return (self.transitive_merge(filename, self.distutils_info0, 
DistutilsInfo.merge)
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
ependencies.py", line 596, in transitive_merge
node, extract, merge, seen, {}, self.cimported_files)[0]
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
ependencies.py", line 601, in transitive_merge_helper
deps = extract(node)
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
ependencies.py", line 577, in distutils_info0
externs = self.cimports_and_externs(filename)[1]
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Utils.p
y", line 44, in wrapper
res = cache[args] = f(self, *args)
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
ependencies.py", line 487, in cimports_and_externs
for include in self.included_files(filename):
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Utils.p
y", line 44, in wrapper
res = cache[args] = f(self, *args)
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Build/D
ependencies.py", line 470, in included_files
include_path = self.context.find_include_file(include, None)
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Compile
r/Main.py", line 274, in find_include_file
error(pos, "'%s' not found" % filename)
  File 
"/projects/792d5859-fa0c-4251-93ec-a9cd4c700e1d/SAGE_INSTALL__2016-12-21/sage-7.4/local/lib/python2.7/site-packages/Cython/Compile
r/Errors.py", line 177, in error
raise InternalError(message)
InternalError: Internal compiler error: '../ext/gmp.pxi' not found

Error building the Sage library

[sage-devel] Re: Make check fails for sage 4.6.2 build

2011-04-01 Thread jonha...@gmail.com 
Dear Dave,

That's weird.  Now the test seems to pass.  I had tried it several
times before I wrote, but now it consistently passes.  I'm now a
little worried about the stability of my system...  Any ideas about
what can cause these problems (and tests I can run to detect them)?

Thanks,

-Jon
 =)

P.S.  /proc/version tells me:
Linux version 2.6.18-164.6.1.el5 (mockbuild@ls20-
bc2-14.build.redhat.com) (gcc version 4.1.2 20080704 (Red Hat
4.1.2-46)) #1 SMP Tue Oct 27 11:28:30 EDT 2009

=

jonhanke@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6.2]: ./sage
-t /sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/
sage/misc/preparser.py
sage -t  /sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/
sage/sage/misc/preparser.py
 [7.2 s]

--
All tests passed!
Total time for all tests: 7.2 seconds




On Apr 1, 2:32 pm, David Kirkby david.kir...@onetel.net wrote:
 On 1 April 2011 18:43, Jonathan Hanke jonha...@gmail.com wrote:





  Hi,
  I was building sage 4.6.2 on a Sun Fire 4450 server (called parsley) running
  Redhat linux, and the there was a preparser failure when running make check.
   Is this something I should be concerned about?  I thought that the new sage
  builds are automatically tested on this architecture, so how can make check
  fail?
  Thanks,
  -Jon
   =)
  
  jonhanke@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6.2]: make check
  ...
  --
  The following tests failed:

          sage -t  -force_lib devel/sage/sage/misc/preparser.py
  Total time for all tests: 6133.0 seconds
  Please see /home/jonhanke/.sage//tmp/test.log for the complete log from this
  test.
  jonhanke@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6.2]: sage -t
   -force_lib devel/sage/sage/misc/preparser.py
  sage -t -force_lib devel/sage/sage/misc/preparser.py
  Non-default server settings detected:
      Incoming Server =http://hg.sagemath.org (default)
      Outgoing Server =
  ssh://jonha...@sage.math.washington.edu/sage-4.1.1/devel
  **
  File
  /sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/ 
  preparser.py,
  line 1386:
      sage: sage.misc.preparser.is_loadable_filename('foo.m')
  Expected:
      True
  Got:
      False
  **
  File
  /sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/ 
  preparser.py,
  line 1403:
      sage: load_attach_path()
  Exception raised:
      Traceback (most recent call last):
        File /usr/local/sage-4.6/local/bin/ncadoctest.py, line 1231, in
  run_one_test
          self.run_one_example(test, example, filename, compileflags)
        File /usr/local/sage-4.6/local/bin/sagedoctest.py, line 38, in
  run_one_example
          OrigDocTestRunner.run_one_example(self, test, example, filename,
  compileflags)
        File /usr/local/sage-4.6/local/bin/ncadoctest.py, line 1172, in
  run_one_example
          compileflags, 1) in test.globs
        File doctest __main__.example_19[2], line 1, in module
          load_attach_path()###line 1403:
      sage: load_attach_path()
      NameError: name 'load_attach_path' is not defined
  **

 We are not regularly testing on Redhat Linux on x86 - see

 http://wiki.sagemath.org/SupportedPlatforms

 for what we test on.

 Can you run the test again

 ./sage -t 
 /sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/p 
 reparser.py

 if the failure is reproducible, then it should be added to the trac
 server as a bug. Please state the exact version of Redhat though.

 Dave

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[sage-devel] Sage/GP - clearing out of range error?

2011-01-09 Thread jonha...@gmail.com 
Hi,

After many calls to GP from Sage I get an out of allowed range
error.  I tried cleaning this up by using the
gp.clear_prompts() method, but it doesn't help.  Is there any way to
avoid this error without restarting GP (or restart GP automatically
when this error occurs)?

Thanks,

-Jon
 =)

sage: Q = QuadraticForm(ZZ, 4,  [281, 636, 468, 352,  363, 528, 396,
197, 288,  115])
sage: Q.basis_of_short_vectors()
---
TypeError Traceback (most recent call
last)
.
.
TypeError: Error executing code in GP:
CODE:
 
sage[65539]=Mat([562,636,468,352;636,726,528,396;468,528,394,288;352,396,288,230]);
PARI/GP ERROR:
  ***   at top-level: read(/Users/jonhank
  *** ^
  ***   in function read: sage[65539]=Mat([562,636
  *** ^
  ***   array index (65539) out of allowed range [1-65537].

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[sage-devel] Remote Sage mercurial push/pull installation question

2011-01-04 Thread jonha...@gmail.com 
Hi,

I'm trying to setup the ability to push/pull from a remote Sage
mercurial repository, but am having trouble with the installation on
the remote machine.  For the moment let's say that I don't have root
access (I do, but only via the make command), and have python 2.4 and
mercurial installed in the ~/local directory.  My ~/.bash_profile
looks like

export PATH=${HOME}/local/bin:${PATH}
export PYTHONPATH=${HOME}/local/lib64/python2.4/site-packages
export PATH=${PATH}:${HOME}/local/mercurial-1.4.1:${HOME}/local/
mercurial-1.4.1/mercurial

and which hg gives

~/local/bin/hg

but when I run a sage.pull() it can't find the mercurial to use:

sage: hg_sage.pull()
cd /Users/jonhanke/Documents/SAGE/sage-4.6/devel/sage  hg
status
cd /Users/jonhanke/Documents/SAGE/sage-4.6/devel/sage  hg
status
cd /Users/jonhanke/Documents/SAGE/sage-4.6/devel/sage  hg pull
-u 
ssh://jonha...@parsley.math.uga.edu//sage-4.6/devel/sage-maximal-lattices/sage-maximal-lattices/
jonha...@parsley.math.uga.edu's password:
remote: abort: couldn't find mercurial libraries in [/usr/local/
bin /usr/lib64/python24.zip /usr/lib64/python2.4 /usr/lib64/python2.4/
plat-linux2 /usr/lib64/python2.4/lib-tk /usr/lib64/python2.4/lib-
dynload /usr/lib64/python2.4/site-packages /usr/lib64/python2.4/site-
packages/Numeric /usr/lib64/python2.4/site-packages/PIL /usr/lib64/
python2.4/site-packages/gst-0.10 /usr/lib64/python2.4/site-packages/
gtk-2.0 /usr/lib/python2.4/site-packages]
remote: (check your install and PYTHONPATH)
abort: no suitable response from remote hg!
If it says use 'hg merge' above, then you should
type hg_sage.merge().

Is there Sage a setup howto somewhere for getting this to work?  Any
comments are appreciated.  Thanks,

-Jon
 =)

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[sage-devel] Re: Failed to build Atlas in Sage 4.5.2 on Xenon processor.

2010-11-04 Thread jonha...@gmail.com 
Hi,

I just built sage-4.6 on this machine (Sun Fire X4450 -- with Xenon
processors), and it passes all doctests except for one (see below),
even though the trac ticket

http://trac.sagemath.org/sage_trac/ticket/9864

was postponed to be fixed in 4.6.1.  Thanks to whomever mostly fixed
this!

-Jon
 =)




jonha...@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6]: sage -t
devel/sage/sage/interfaces/qepcad.py
sage -t  devel/sage/sage/interfaces/qepcad.py
Non-default server settings detected:
Incoming Server = http://hg.sagemath.org  (default)
Outgoing Server = ssh://jonha...@sage.math.washington.edu/sage-4.1.1/devel

Traceback (most recent call last):
  File /home/jonhanke/.sage//tmp/qepcad.py, line 18, in module
from qepcad import *
  File /home/jonhanke/.sage/tmp/qepcad.py, line 543, in module
from expect import Expect, ExpectFunction, AsciiArtString
ImportError: No module named expect

 [1.6 s]

--
The following tests failed:


sage -t  devel/sage/sage/interfaces/qepcad.py
Total time for all tests: 1.6 seconds

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