[sage-support] Re: Error in Building Sage (particularly ecm-6.4)

[Matthias Goerner]

I get a similar error, this time the instruction is

Error: no such instruction: `shrx %eax,108(%rsp),%r9d'

and I am compiling on

gcc version 4.4.7 20120313 (Red Hat 4.4.7-16) (GCC)

with SAGE_INSTALL_GCC=yes.

It seems to me this is due to sage using its own version of "gcc" but the 
system's version of "as" which does not understand some of the assembly 
instructions of a newer compiler.


I keep running into this problem on old Linux'es and Mac's. Should sage 
also offer to provide its own "as"?


On Monday, January 12, 2015 at 10:41:05 PM UTC-8, Shadab Zafar wrote:
>
> I am trying to build Sage from the current master branch but it errors in 
> installing ecm.
>
> The ending part of the log is:
>
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I./x86_64 
> -I/home/dufferzafar/dev/sage/local/include 
> -I/home/dufferzafar/dev/sage/local/include -march=native -g -O3 -fPIC -MT 
> libecm_la-pp1.lo -MD -MP -MF .deps/libecm_la-pp1.Tpo -c pp1.c -o 
> libecm_la-pp1.o
> mv -f .deps/libecm_la-pp1.Tpo .deps/libecm_la-pp1.Plo
> /bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  
> -I./x86_64 -I/home/dufferzafar/dev/sage/local/include 
> -I/home/dufferzafar/dev/sage/local/include  -march=native -g -O3  -fPIC -MT 
> libecm_la-getprime.lo -MD -MP -MF .deps/libecm_la-getprime.Tpo -c -o 
> libecm_la-getprime.lo `test -f 'getprime.c' || echo './'`getprime.c
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I./x86_64 
> -I/home/dufferzafar/dev/sage/local/include 
> -I/home/dufferzafar/dev/sage/local/include -march=native -g -O3 -fPIC -MT 
> libecm_la-getprime.lo -MD -MP -MF .deps/libecm_la-getprime.Tpo -c 
> getprime.c -o libecm_la-getprime.o
> /tmp/ccp6Wox5.s: Assembler messages:
> /tmp/ccp6Wox5.s:137: Error: no such instruction: `vfmadd312sd 
> offset(%rip),%xmm0,%xmm3'
> /tmp/ccp6Wox5.s:713: Error: no such instruction: `vfmadd312sd 
> .LC12(%rip),%xmm0,%xmm2'
> make[5]: *** [libecm_la-getprime.lo] Error 1
> make[5]: Leaving directory 
> `/home/dufferzafar/dev/sage/local/var/tmp/sage/build/ecm-6.4.4/src'
> make[4]: *** [all-recursive] Error 1
> make[4]: Leaving directory 
> `/home/dufferzafar/dev/sage/local/var/tmp/sage/build/ecm-6.4.4/src'
> make[3]: *** [all] Error 2
> make[3]: Leaving directory 
> `/home/dufferzafar/dev/sage/local/var/tmp/sage/build/ecm-6.4.4/src'
> Error building GMP-ECM.
>
>
> I have also attached the complete log file.
>
> System Info:
>
> Linux version 3.5.0-57-generic (buildd@tipua) (gcc version 4.6.3 
> (Ubuntu/Linaro 4.6.3-1ubuntu5) ) #84~precise1-Ubuntu SMP
>

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Found local metadata for ecm-6.4.4
Using cached file /projects/snapreg/sage-6.9/upstream/ecm-6.4.4.tar.bz2
ecm-6.4.4

Setting up build directory for ecm-6.4.4
Finished set up

Host system:
Linux math31184.math.gatech.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 
12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux

C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/projects/snapreg/sage-6.9/local/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../src/configure --prefix=/projects/snapreg/sage-6.9/local 
--with-local-prefix=/projects/snapreg/sage-6.9/local 
--with-gmp=/projects/snapreg/sage-6.9/local 
--with-mpfr=/projects/snapreg/sage-6.9/local 
--with-mpc=/projects/snapreg/sage-6.9/local --with-system-zlib 
--disable-multilib --disable-nls --enable-languages=c,c++,fortran 
--disable-libitm  
Thread model: posix
gcc version 4.9.2 (GCC) 

patching file x86_64/mulredc10.asm
patching file x86_64/mulredc11.asm
patching file x86_64/mulredc12.asm
patching file x86_64/mulredc13.asm
patching file x86_64/mulredc14.asm
patching file x86_64/mulredc15.asm
patching file x86_64/mulredc16.asm
patching file x86_64/mulredc17.asm
patching file x86_64/mulredc18.asm
patching file x86_64/mulredc19.asm
patching file x86_64/mulredc1_10.asm
patching file x86_64/mulredc1_11.asm
patching file x86_64/mulredc1_12.asm
patching file x86_64/mulredc1_13.asm
patching file x86_64/mulredc1_14.asm
patching file x86_64/mulredc1_15.asm
patching file x86_64/mulredc1_16.asm
patching file x86_64/mulredc1_17.asm
patching file x86_64/mulredc1_18.asm
patching file x86_64/mulredc1_19.asm
patching file x86_64/mulredc1_2.asm
patching file x86_64/mulredc1_20.asm
patching file x86_64/mulredc1_3.asm
patching file x86_64/mulredc1_4.asm
patching file 

[sage-support] Re: Issue Displaying 3D Images in SageCell

[Andrey Novoseltsev]

On Monday, 8 February 2016 20:09:49 UTC-7, kcrisman wrote:
>
>
>
>
> I have created html code for a website that has an embedded SageCell 
>> within it. The code plots a 3D image of two lines obtained from the RK4 
>> solution of two differential equations. In SMC, using show(line1+line2) 
>> outputs a 3D image that can be rotated using the mouse. However, in the 
>> embedded SageCell, it outputs the 3D image but it is no longer movable. 
>> From my extensive google searching, I am guessing it is due to some issue 
>> with jmol in the SageCell. Is there a way around this to make the 3D image 
>> movable like it is in SMC? Changing the viewer to tachyon produces the same 
>> problem.
>>
>>
> Hmm, that's interesting.  Probably it just isn't becoming auto-live like 
> it's supposed to when embedded.  E.g. try 
> http://sagecell.sagemath.org/?z=eJwrLshILUrV0AQADokC2Q===sage and 
> that should (after a slight pause) start being rotatable.  What happens 
> when you click on the image you get in the Sage cell - does it become live 
> after a bit? 
>

It may depend on the browser as well, I suspect I only made JSmol work in 
Firefox. It should not be terribly hard to do it for other browsers, but 
other things got higher priority on my little time and nobody else works on 
SageMathCell. Pull requests welcome, as they say ;-)

As a workaround, one can try to use "threejs(your_plot_here)" and hope for 
the best - the quality is not as good as in JSmol and in certain cases I 
saw plots completely disappear for no clear reason. 

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[sage-support] Re: Sage 7.1.beta2 app half-broken

[Ivan Andrus]

I’m sorry I haven’t been keeping up with Sage development as much as I would 
like.  

The file src/mac-app/start-sage.sh could probably use a bit of love from 
someone.  I’m planning to get to it, hopefully soon, but it’s just a shell 
script largely unrelated to the rest of Sage.app, so changing it shouldn’t 
require any specific knowledge of the app.

Anyway, on line 27 I try to find the SAGE_ROOT variable, and I add a trailing 
slash.  Based on the errors this looks wrong.  In fact the entire idea of 
setting SAGE_ROOT seems misguided now.  I think I added it for two reasons.  
First, so that the path could contain spaces, and second to avoid changing sage 
location repeatedly after the app moved. 

But, especially if someone creates an installer, we can probably just assert 
that there are no spaces in the path, in which case a lot of the script could 
be simplified.

-Ivan

> On Feb 8, 2016, at 1:08 PM, Dima Pasechnik  wrote:
> 
> First, I get a different error when I try opening Sage.app:
> “SageMath-7.1.beta2.app” can’t be opened because it is from an unidentified 
> developer.
> (OK, this is expected)
> If I override this by holding Control while opening it, I still get an error; 
> the browser pops up with message
> The Sage server is currently starting. Please wait...
> 
> but then I get a pop-up with an error.
> 
> The log says:
> 
> Setting environment variables
> /Users/dima/tmp/SageMath-7.1.beta2.app/Contents/Resources/start-sage.sh: line 
> 43: spkg/bin/sage-env: No such file or directory
> Warning: overwriting SAGE_ROOT environment variable:
> Old SAGE_ROOT=/Users/dima/tmp/SageMath-7.1.beta2.app/Contents/Resources/sage/
> New SAGE_ROOT=/Users/dima/tmp/SageMath-7.1.beta2.app/Contents/Resources/sage
> Checking install location
> 
> ERROR:  The Sage installation tree has moved
> 
> from 
> /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma
>   to /Users/dima/tmp/SageMath-7.1.beta2.app/Contents/Resources/sage
> 
> This is not supported, and Sage will not work. To install Sage from a
> binary package:
> ... etc...
> 
> Now, if in Sage app I go to Terminal Session menu and start Sage from there, 
> I see the patching script running in terminal and then the Sage terminal 
> session starting (and working)
> 
> Now, if I quit, and then start Sage.app again, everything works as it should.
> 
> I'd say this is not good enough for an average user...
> Probably one should write (create, I imagine there are OSX tools for this) a 
> custom installer
> to do this automatically.
> 
> Dima
> 
> 
> ---
> On Monday, February 8, 2016 at 4:26:48 PM UTC, Szabolcs Horvát wrote:
> I tried the app version.  I copied it to /Applications, then I started 
> it.  I get: 
> 
> ERROR:  The Sage installation tree has moved 
> 
> from 
> /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma
>  
>   to /Applications/SageMath-7.1.beta2.app/Contents/Resources/sage 
> 
> This was the very first time I stared it. 
> 
> On 8 February 2016 at 15:46, Dima Pasechnik  
> wrote: 
> > I did try 7.1beta2 (non-app version) on OSX 10.11, it worked for me. 
> > (note that once you started Sage for the 1st time, it cannot be moved to 
> > another location then). 
> > What exactly does not work for you with 7.1beta2? 
> > 
> > 
> > 
> > On Monday, February 8, 2016 at 2:20:03 PM UTC, Szabolcs Horvát wrote: 
> >> 
> >> I have two questions about Sage 7.0: 
> >> 
> >>  - Will it be available on OS X?  Currently there seems to be downloads 
> >> for 6.10 and 7.1beta2 but not 7.0.  The 7.1beta2 fails on startup. 
> >> 
> >>  - Is there a list of major changes (other than the list of tickets 
> >> closed)?  Does the bump in the major version from 6 to 7 signify big 
> >> changes? 
> > 
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