Marek Kaluba | 9 Apr 23:36 2010
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Re: gap -- sage install

On Tuesday 30 March 2010 00:12:46 François Bissey wrote:
> > Thanks for another fix.... but... it doesn't work either;-)
> > 
> > Now emerge sage runs
> > /usr/libexec/gap/gap -m 32 -l /usr/share/gap -r -b -p -T -o 9999G
> > /opt/sage/data//extcode/gap/sage.g
> > 
> > as it should (sage.g IS in the place), but install waits forever.
> > 
> > running it by hand gives:
> > marek-laptop marek # /usr/libexec/gap/gap -m 32 -l /usr/share/gap -r -b
> > -p -T -o 9999G /opt/sage/data//extcode/gap/sage.g
> >  <at> p1.gap: cannot extend the workspace any more
> > 
> > at the moment I emerged -C gap and I am emerging gap once again
> 
> Hi Marek,
> 
> Once gap has emerged I want you to try the following command:
> /usr/libexec/gap/gap -m 32m -l /usr/share/gap -r -b -p -T -o 3900m
> /opt/sage/data//extcode/gap/sage.g
> 
> It looks like the problem may be that sage is trying to use gap with
> too much memory for your computer. It tries to use the settings
> for a 64bits set up - whether or not you have one, let's see what
> happens with the 32bits set up.
> If you still get the message about extending the workspace, could
> you also try "-m 8m" and may be "-o 1024" or something.
> 
> Francois
(Continue reading)

Christopher Schwan | 11 Apr 09:09 2010
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Fwd: Re: gap -- sage install


----------  Forwarded Message  ----------

Subject: Re: [gentoo-science] gap -- sage install
Date: Friday 09 April 2010, 23:36:44
From: Marek Kaluba <mk224 <at> st.amu.edu.pl>
To: gentoo-science <at> lists.gentoo.org

On Tuesday 30 March 2010 00:12:46 François Bissey wrote:
> > Thanks for another fix.... but... it doesn't work either;-)
> > 
> > Now emerge sage runs
> > /usr/libexec/gap/gap -m 32 -l /usr/share/gap -r -b -p -T -o 9999G
> > /opt/sage/data//extcode/gap/sage.g
> > 
> > as it should (sage.g IS in the place), but install waits forever.
> > 
> > running it by hand gives:
> > marek-laptop marek # /usr/libexec/gap/gap -m 32 -l /usr/share/gap -r -b
> > -p -T -o 9999G /opt/sage/data//extcode/gap/sage.g
> >  <at> p1.gap: cannot extend the workspace any more
> > 
> > at the moment I emerged -C gap and I am emerging gap once again
> 
> Hi Marek,
> 
> Once gap has emerged I want you to try the following command:
> /usr/libexec/gap/gap -m 32m -l /usr/share/gap -r -b -p -T -o 3900m
> /opt/sage/data//extcode/gap/sage.g
> 
(Continue reading)

Christopher Schwan | 11 Apr 09:54 2010
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Re: Fwd: Re: gap -- sage install

Hi Marek,

first of all: Good luck with your Masters :)

I have uploaded a new gap revision which includes a patch that could solve 
your problem. Please make sure you have gap-4.4.12-r1 emerged and check if it 
starts up properly (with and/or without -m 32 ... etc). If it does not work, 
we would like to know the output of "uname -a" and "emerge --info".

Cheers,

Christopher

On Sunday 11 April 2010 09:09:29 Christopher Schwan wrote:
> ----------  Forwarded Message  ----------
> 
> Subject: Re: [gentoo-science] gap -- sage install
> Date: Friday 09 April 2010, 23:36:44
> From: Marek Kaluba <mk224 <at> st.amu.edu.pl>
> To: gentoo-science <at> lists.gentoo.org
> 
> On Tuesday 30 March 2010 00:12:46 François Bissey wrote:
> > > Thanks for another fix.... but... it doesn't work either;-)
> > > 
> > > Now emerge sage runs
> > > /usr/libexec/gap/gap -m 32 -l /usr/share/gap -r -b -p -T -o 9999G
> > > /opt/sage/data//extcode/gap/sage.g
> > > 
> > > as it should (sage.g IS in the place), but install waits forever.
> > > 
(Continue reading)

Steven Trogdon | 12 Apr 17:50 2010
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sage-singular

François,

Singular -- good. I do get -fPIC compile issues here on my amd64:

g++ -shared  -o libsingular.so \
         libsingular-tesths.o iparith.o mpsr_Tok.o claptmpl.o \
         grammar.o scanner.o attrib.o eigenval_ip.o extra.o fehelp.o  
feOpt.o ipassign.o ipconv.o ipid.o iplib.o ipprint.o ipshell.o lists.o  
sdb.o fglm.o interpolation.o silink.o subexpr.o janet.o wrapper.o  
libparse.o sing_win.o gms.o pcv.o maps_ip.o walk.o walk_ip.o cntrlc.o  
misc.o calcSVD.o  slInit_Dynamic.o -lkernel -L../kernel -L../factory  
-L../libfac 

-L/var/tmp/portage/sci-mathematics/sage-singular-3.1.0.4.20100214/work/singular-3-1-0-4-20100214/src/build/opt/sage/local/lib64

-lsingfac -lsingcf -lntl -lreadline -lgmp -lomalloc
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../x86_64-pc-linux-gnu/bin/ld:  
libsingular-tesths.o: relocation R_X86_64_32 against `a local symbol'  
can not be used when making a shared object; recompile with -fPIC

I've tinkered with this in the past and the following allowed building  
to proceed.

         sed -e "s: <at> CFLAGS <at> : <at> CFLAGS <at>  -fPIC:" -e  
"s: <at> CXXFLAGS <at> : <at> CXXFLAGS <at>  -fPIC:" \
                 -i */Makefile.in || die "failed to fix CFLAGS in  
Makefile.in files"
         sed -e "s: <at> CFLAGS <at> : <at> CFLAGS <at>  -fPIC:" -e  
"s: <at> CXXFLAGS <at> : <at> CXXFLAGS <at>  -fPIC:" \
                 -i factory/GNUmakefile.in || die "failed to fix CFLAGS  
(Continue reading)

François Bissey | 12 Apr 21:22 2010
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Re: sage-singular

> François,
> 
> Singular -- good. I do get -fPIC compile issues here on my amd64:
> 
> g++ -shared  -o libsingular.so \
>          libsingular-tesths.o iparith.o mpsr_Tok.o claptmpl.o \
>          grammar.o scanner.o attrib.o eigenval_ip.o extra.o fehelp.o
> feOpt.o ipassign.o ipconv.o ipid.o iplib.o ipprint.o ipshell.o lists.o
> sdb.o fglm.o interpolation.o silink.o subexpr.o janet.o wrapper.o
> libparse.o sing_win.o gms.o pcv.o maps_ip.o walk.o walk_ip.o cntrlc.o
> misc.o calcSVD.o  slInit_Dynamic.o -lkernel -L../kernel -L../factory
> -L../libfac
> -L/var/tmp/portage/sci-mathematics/sage-singular-3.1.0.4.20100214/work/sing
> ular-3-1-0-4-20100214/src/build/opt/sage/local/lib64 -lsingfac -lsingcf
> -lntl -lreadline -lgmp -lomalloc
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../x86_64-pc-linux-gnu/bin/
> ld: libsingular-tesths.o: relocation R_X86_64_32 against `a local symbol'
> can not be used when making a shared object; recompile with -fPIC
> 
> I've tinkered with this in the past and the following allowed building
> to proceed.
> 
>          sed -e "s: <at> CFLAGS <at> : <at> CFLAGS <at>  -fPIC:" -e
> "s: <at> CXXFLAGS <at> : <at> CXXFLAGS <at>  -fPIC:" \
>                  -i */Makefile.in || die "failed to fix CFLAGS in
> Makefile.in files"
>          sed -e "s: <at> CFLAGS <at> : <at> CFLAGS <at>  -fPIC:" -e
> "s: <at> CXXFLAGS <at> : <at> CXXFLAGS <at>  -fPIC:" \
>                  -i factory/GNUmakefile.in || die "failed to fix CFLAGS
> in GNUmakefile.in"
(Continue reading)

Steven Trogdon | 12 Apr 22:22 2010
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Re: sage-singular

On   04/12/10 - 14:22:30, François Bissey wrote:
> > François,
> >
> > Singular -- good. I do get -fPIC compile issues here on my amd64:
> >
> > g++ -shared  -o libsingular.so \
> >          libsingular-tesths.o iparith.o mpsr_Tok.o claptmpl.o \
> >          grammar.o scanner.o attrib.o eigenval_ip.o extra.o fehelp.o
> > feOpt.o ipassign.o ipconv.o ipid.o iplib.o ipprint.o ipshell.o  
> lists.o
> > sdb.o fglm.o interpolation.o silink.o subexpr.o janet.o wrapper.o
> > libparse.o sing_win.o gms.o pcv.o maps_ip.o walk.o walk_ip.o  
> cntrlc.o
> > misc.o calcSVD.o  slInit_Dynamic.o -lkernel -L../kernel -L../factory
> > -L../libfac
> >  
> -L/var/tmp/portage/sci-mathematics/sage-singular-3.1.0.4.20100214/work/sing
> > ular-3-1-0-4-20100214/src/build/opt/sage/local/lib64 -lsingfac  
> -lsingcf
> > -lntl -lreadline -lgmp -lomalloc
> >  
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../x86_64-pc-linux-gnu/bin/
> > ld: libsingular-tesths.o: relocation R_X86_64_32 against `a local  
> symbol'
> > can not be used when making a shared object; recompile with -fPIC
> >
> > I've tinkered with this in the past and the following allowed  
> building
> > to proceed.
> >
(Continue reading)

François Bissey | 12 Apr 22:33 2010
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Re: sage-singular

> François,
> 
> Just for reference, adding the -fPIC does allow building of  
> sage-singular here. But sage will not install -- it can't find  
> libsingular.so. I've gotten a similar error in attempts to remove  
> Singular entirely. Sage appears to be very possessive of Singular.

OK, I will violently abuse flag-o-matic for now, singular as a package
is quite nightmarish.
I was hoping I had found all the bits to change in sage to get a clean compile
before going to bed - apparently I was wrong.
I am on it shortly.

Francois

François Bissey | 12 Apr 23:51 2010
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Re: sage-singular

> But sage will not install -- it can't find  
> libsingular.so. I've gotten a similar error in attempts to remove  
> Singular entirely. Sage appears to be very possessive of Singular.
I think it is a sage-env issue from sage-script which will make things fun.

I will try a fix shortly, testing take a while on this little computer but it 
will be live on the overlay if you want to test.

Francois

Steven Trogdon | 13 Apr 00:59 2010
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Re: sage-singular

On   04/12/10 - 16:51:27, François Bissey wrote:
> I think it is a sage-env issue from sage-script which will make  
> things fun.
> 
> I will try a fix shortly, testing take a while on this little  
> computer but it
> will be live on the overlay if you want to test.
> 
> Francois
> 
The install of Sage still fails. The sage-singular install leaves an  
odd symlink for LIB under
/opt/sage/local. LIB points to the portage work directory. Here this is  
usually

LIB -> lib
lib -> lib64

However, this is not the issue. If I fix the symlinks the install of  
sage still fails. I get

cd /var/tmp/portage/sci-mathematics/sage-4.3.5/image//opt/bin/; ./sage  
-c
Setting permissions of DOT_SAGE directory so only you can read and  
write it.
Traceback (most recent call last):
   File  
"/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/bin/sage-eval",  
line 4, in <module>
     from sage.all import *
(Continue reading)

François Bissey | 13 Apr 03:14 2010
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Re: sage-singular

> On   04/12/10 - 16:51:27, François Bissey wrote:
> > I think it is a sage-env issue from sage-script which will make
> > things fun.
> > 
> > I will try a fix shortly, testing take a while on this little
> > computer but it
> > will be live on the overlay if you want to test.
> > 
> > Francois
> 
> The install of Sage still fails. The sage-singular install leaves an
> odd symlink for LIB under
> /opt/sage/local. LIB points to the portage work directory. Here this is
> usually
> 
> LIB -> lib
> lib -> lib64

Good spotting, I will look into that later. In sage they make it to point to
lib(64) which is funny in that it actually originally point to share/singular.
I will make the link relative rather than absolute a little bit later.

> 
> However, this is not the issue. If I fix the symlinks the install of
> sage still fails. I get
> 
> cd /var/tmp/portage/sci-mathematics/sage-4.3.5/image//opt/bin/; ./sage
> -c
> Setting permissions of DOT_SAGE directory so only you can read and
> write it.
(Continue reading)


Gmane