[gentoo-science] sage-singular

[gentoo-science] sage-singular

[Steven Trogdon]

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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:@CFLAGS@:@CFLAGS@ -fPIC:" -e  
"s:@CXXFLAGS@:@CXXFLAGS@ -fPIC:" \
                 -i */Makefile.in || die "failed to fix CFLAGS in  
Makefile.in files"
         sed -e "s:@CFLAGS@:@CFLAGS@ -fPIC:" -e  
"s:@CXXFLAGS@:@CXXFLAGS@ -fPIC:" \
                 -i factory/GNUmakefile.in || die "failed to fix CFLAGS  
in GNUmakefile.in"
         sed -e "s:{libdir} \${LIBSINGULAR_LIBS}:{libdir} -Wl,-soname  
\${LIBSINGULAR_LIBS}:" \
                 -i Singular/Makefile.in || die "failed to fix LDFLAGS  
in Makefile.in"

but this may not be the best way to fix things. I did notice that Sage  
builds Singular with -fPIC for all architectures.

Steve

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Re: [gentoo-science] sage-singular

[François Bissey]

> 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:@CFLAGS@:@CFLAGS@ -fPIC:" -e
> "s:@CXXFLAGS@:@CXXFLAGS@ -fPIC:" \
>                  -i */Makefile.in || die "failed to fix CFLAGS in
> Makefile.in files"
>          sed -e "s:@CFLAGS@:@CFLAGS@ -fPIC:" -e
> "s:@CXXFLAGS@:@CXXFLAGS@ -fPIC:" \
>                  -i factory/GNUmakefile.in || die "failed to fix CFLAGS
> in GNUmakefile.in"
>          sed -e "s:{libdir} \${LIBSINGULAR_LIBS}:{libdir} -Wl,-soname
> \${LIBSINGULAR_LIBS}:" \
>                  -i Singular/Makefile.in || die "failed to fix LDFLAGS
> in Makefile.in"
> 
> but this may not be the best way to fix things. I did notice that Sage
> builds Singular with -fPIC for all architectures.
> 
Hi Steve,

indeed you would! -fPIC is mandatory on amd64 I think.
I was concerned that we shouldn't build the binaries or the static libraries
with -fPIC. That being said it looks like all those static libraries are 
useless.

Francois

Re: [gentoo-science] sage-singular

[Steven Trogdon]

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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.
> >
> >          sed -e "s:@CFLAGS@:@CFLAGS@ -fPIC:" -e
> > "s:@CXXFLAGS@:@CXXFLAGS@ -fPIC:" \
> >                  -i */Makefile.in || die "failed to fix CFLAGS in
> > Makefile.in files"
> >          sed -e "s:@CFLAGS@:@CFLAGS@ -fPIC:" -e
> > "s:@CXXFLAGS@:@CXXFLAGS@ -fPIC:" \
> >                  -i factory/GNUmakefile.in || die "failed to fix  
> CFLAGS
> > in GNUmakefile.in"
> >          sed -e "s:{libdir} \${LIBSINGULAR_LIBS}:{libdir}  
> -Wl,-soname
> > \${LIBSINGULAR_LIBS}:" \
> >                  -i Singular/Makefile.in || die "failed to fix  
> LDFLAGS
> > in Makefile.in"
> >
> > but this may not be the best way to fix things. I did notice that  
> Sage
> > builds Singular with -fPIC for all architectures.
> >
> Hi Steve,
> 
> indeed you would! -fPIC is mandatory on amd64 I think.
> I was concerned that we shouldn't build the binaries or the static  
> libraries
> with -fPIC. That being said it looks like all those static libraries  
> are
> useless.
> 
> Francois
> 

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.

Steve


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Re: [gentoo-science] sage-singular

[François Bissey]

> 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

Re: [gentoo-science] sage-singular

[François Bissey]

> 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

Re: [gentoo-science] sage-singular

[Steven Trogdon]

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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 *
   File  
"/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/lib64/python/site-packages/sage/all.py",  
line 72, in <module>
     from sage.rings.all      import *
   File  
"/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/lib64/python/site-packages/sage/rings/all.py",  
line 94, in <module>
     from qqbar import (AlgebraicRealField, is_AlgebraicRealField, AA,
   File  
"/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/lib64/python/site-packages/sage/rings/qqbar.py",  
line 1416, in <module>
     QQxy = QQ['x', 'y']
   File "ring.pyx", line 205, in sage.rings.ring.Ring.__getitem__  
(sage/rings/ring.c:2711)
   File  
"/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/lib64/python/site-packages/sage/rings/polynomial/polynomial_ring_constructor.py",  
line 355, in PolynomialRing
     R = _multi_variate(base_ring, names, n, sparse, order)
   File  
"/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/lib64/python/site-packages/sage/rings/polynomial/polynomial_ring_constructor.py",  
line 453, in _multi_variate
     from sage.rings.polynomial.multi_polynomial_libsingular import  
MPolynomialRing_libsingular
ImportError: libsingular.so: cannot open shared object file: No such  
file or directory

Steve


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Re: [gentoo-science] sage-singular

[François Bissey]

> 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.
> 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 *
>    File
> "/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/lib64/pyt
> hon/site-packages/sage/all.py", line 72, in <module>
>      from sage.rings.all      import *
>    File
> "/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/lib64/pyt
> hon/site-packages/sage/rings/all.py", line 94, in <module>
>      from qqbar import (AlgebraicRealField, is_AlgebraicRealField, AA,
>    File
> "/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/lib64/pyt
> hon/site-packages/sage/rings/qqbar.py", line 1416, in <module>
>      QQxy = QQ['x', 'y']
>    File "ring.pyx", line 205, in sage.rings.ring.Ring.__getitem__
> (sage/rings/ring.c:2711)
>    File
> "/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/lib64/pyt
> hon/site-packages/sage/rings/polynomial/polynomial_ring_constructor.py",
> line 355, in PolynomialRing
>      R = _multi_variate(base_ring, names, n, sparse, order)
>    File
> "/var/tmp/portage/sci-mathematics/sage-4.3.5/image/opt/sage/local/lib64/pyt
> hon/site-packages/sage/rings/polynomial/polynomial_ring_constructor.py",
> line 453, in _multi_variate
>      from sage.rings.polynomial.multi_polynomial_libsingular import
> MPolynomialRing_libsingular
> ImportError: libsingular.so: cannot open shared object file: No such
> file or directory
> 
Yes my fault, and I was away for a bit while the test was underway. I set 
LIBRARY_PATH instead of LD_LIBRARY_PATH. Hopefully _that_ will work.

Francois

Re: [gentoo-science] sage-singular

[Steven Trogdon]

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OK, the latest commit builds here once I remove the symlink

	sage_singular -> Singular

to prevent file collisions.

Steve

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Re: [gentoo-science] sage-singular

[François Bissey]

> OK, the latest commit builds here once I remove the symlink
> 
> 	sage_singular -> Singular
> 
> to prevent file collisions.
> 
I have just commited a fix for that!
Probably while you were sending the email.
Glad it works for you!
With LD_LIBRARY_PATH fix sage was throwing a fit 
at the sage -c after install. Not that it couldn't find
libsingular.so, but that some internal was broken :(

testing here, hopefully I will not go crazy....

Francois