Sage 4.6 has PARI problems on Cygwin

[mhansen]

While the spkg builds fine (modulo #10240), it introduces the some errors when building the following extension modules in the Sage library:

gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-1.7.5-i686-2.6/sage/libs/pari/gen.o -L/home/mhansen/sage-4.6/local//lib -L/home/mhansen/sage-4.6/local/lib/python2.6/config -lcsage -lpari -lgmp -lstdc++ -lntl -lpython2.6 -o build/lib.cygwin-1.7.5-i686-2.6/sage/libs/pari/gen.dll
Cannot export bid_get_cyc: symbol not found
Cannot export bid_get_gen: symbol not found
Cannot export bnf_get_cyc: symbol not found
Cannot export bnf_get_fu: symbol not found
Cannot export bnf_get_fu_nocheck: symbol not found
Cannot export bnf_get_gen: symbol not found
Cannot export bnf_get_reg: symbol not found
Cannot export cxcompotor: symbol not found
Cannot export cxtofp: symbol not found
Cannot export gtodouble: symbol not found
Cannot export is_bigint: symbol not found
Cannot export is_intreal_t: symbol not found
Cannot export isintzero: symbol not found
Cannot export nf_get_sign: symbol not found
Cannot export nf_get_zk: symbol not found
Cannot export pari_free: symbol not found
Cannot export pr_get_e: symbol not found
Cannot export pr_get_f: symbol not found
Cannot export pr_get_gen: symbol not found
Cannot export pr_get_p: symbol not found
Cannot export zerocol: symbol not found
Cannot export zeromat: symbol not found
Cannot export zerovec: symbol not found
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-1.7.5-i686-2.6/sage/matrix/matrix_integer_dense.o -L/home/mhansen/sage-4.6/local//lib -L/home/mhansen/sage-4.6/local/lib/python2.6/config -lcsage -liml -lgmp -lm -lpari -lgslcblas -lgslcblas -lstdc++ -lntl -lpython2.6 -o build/lib.cygwin-1.7.5-i686-2.6/sage/matrix/matrix_integer_dense.dll
Cannot export zerocol: symbol not found
Cannot export zeromat: symbol not found

gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-1.7.5-i686-2.6/sage/matrix/matrix_rational_dense.o -L/home/mhansen/sage-4.6/local//lib -L/home/mhansen/sage-4.6/local/lib/python2.6/config -lcsage -lgmp -lpari -lstdc++ -lntl -lpython2.6 -o build/lib.cygwin-1.7.5-i686-2.6/sage/matrix/matrix_rational_dense.dll
Cannot export zerocol: symbol not found
Cannot export zeromat: symbol not found

[jdemeyer]

1) Please try the new PARI spkg from #10114: ​http://sage.math.washington.edu/home/jdemeyer/spkg/pari-2.4.3.alpha.p0.spkg (I doubt this will solve the problem, but it's better to try the latest version anyway)

2) Try compiling PARI outside of Sage, i.e. download ​http://sage.math.washington.edu/home/jdemeyer/spkg/pari-2.4.3.alpha.p0.spkg and then:

$ tar xjf pari-2.4.3.alpha.p0.spkg
$ cd pari-2.4.3.alpha.p0/src
$ ./Configure
$ make gp

3) It would be good to see the full log file (spkg/logs/pari*.log).

4) The functions which fail are all inline functions, so it seems that inline functions are not exported somehow (they should be).

[mhansen]

1) This package still has the same issues.

2) Compiling inside Sage works fine. I can use the gp shell just fine. (Same goes for outside of Sage).

3) ​http://sage.math.washington.edu/home/mhansen/pari-2.4.3.alpha.p0.log

4) I tried building with DISABLE_INLINE, and it did not fix the problem.

[jdemeyer]

Mike, I think you misunderstood step 2). I meant "try to compile the PARI/GP package independently of Sage by doing the following steps:"

$ tar xjf pari-2.4.3.alpha.p0.spkg
$ cd pari-2.4.3.alpha.p0/src
$ ./Configure
$ make gp

[jdemeyer]

Sorry, I'm the one who misunderstood :-) The problem is that PARI/GP compiles fine but the Sage library files depending on PARI do not.

[jdemeyer]

Can you compile the PARI spkg with -DINLINE=inline added to CFLAGS and see if that works?

[jdemeyer]

Sorry, ignore the last post. Since the problem is not with PARI itself, but with the sagelib modules, instead do the following: after the PARI spkg is installed, find the file SAGE_ROOT/local/include/pari/paricfg.h.

Try adding #define INLINE inline there and try again (in any case, it would be useful if you would post the contents of that file).

[mhansen]

Adding that did not work. (I had to added in parisys.h after where it is normally defined.)

The headers are at ​http://sage.math.washington.edu/home/mhansen/paricfg.h and ​http://sage.math.washington.edu/home/mhansen/parisys.h

[fbissey]

You know looking at this output, I can only think that there is a link order problem. Could you show us the bit of log when libcsage is linked? It may seem a bit far fetched but I think libcsage is linked in the wrong order.

[mhansen]

You mean

gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-1.7.5-i686-2.6/sage/libs/pari/gen.o -L/home/mhansen/sage-4.6/local//lib -L/home/mhansen/sage-4.6/local/lib/python2.6/config -lcsage -lpari -lgmp -lstdc++ -lntl -lpython2.6 -o build/lib.cygwin-1.7.5-i686-2.6/sage/libs/pari/gen.dll

?

[fbissey]

No earlier, when you link libcsage, on linux it looks like this:

g++ -o libcsage.so -shared src/convert.os src/interrupt
.os src/mpn_pylong.os src/mpz_pylong.os src/mpz_longlong.os src/stdsage.os src/gmp_globals.os src/ZZ_py
long.os src/ntl_wrap.os -L/usr/lib -L/usr/lib/python/config -lntl -lgmp -lpari -lpython2.6

My own thinking is that on platform, or compiler, where ordering is important pari should be before gmp. However thinking again, I don't know why compilation would break where it does for you and not when you build libcsage.

[mhansen]

It was in the "wrong" order for csage, but after changing that, I still get the same error in building gen.dll.

[fbissey]

Do you have any tools similar to readelf to check that these symbols are in the pari dll that you have built?

[mhansen]

I'm pretty sure the fix is to change

cdef extern:

to

cdef extern from "pari/pari.h":

sage/libs/pari/declinl.pxi . I'll try testing this out later tonight.

[mhansen]

Yep, this is the issue. Cython was generating lines such as

__PYX_EXTERN_C DL_EXPORT(GEN) bid_get_cyc(GEN); /*proto*/

which gcc didn't like in Cygwin.

[dimpase]

Replying to mhansen:

works for me on Windows 7 with Cygwin 1.7.9. Positive review!

(please see more Cygwin-related ready for review tickets on ​http://trac.sagemath.org/sage_trac/wiki/CygwinPort)