Opened 14 years ago
Closed 14 years ago
#6445 closed defect (fixed)
[with patch, positive review] pari 2.3.3.p0 problem on 't2' but not my home machine (similar setups!!)
| Reported by: | drkirkby | Owned by: | drkirkby |
|---|---|---|---|
| Priority: | major | Milestone: | sage-4.1.1 |
| Component: | porting: Solaris | Keywords: | solaris pari fPIC |
| Cc: | Merged in: | sage-4.1.1.alpha0 | |
| Authors: | David Kirkby | Reviewers: | Minh Van Nguyen |
| Report Upstream: | N/A | Work issues: | |
| Branch: | Commit: | ||
| Dependencies: | Stopgaps: |
Status badges
Description (last modified by )
Well, is is a bit of an odd one.
I built gcc 4.4.0 to use the Sun linker & assembler on my home machine (Sun Blade 2000, Solaris 10 update 6) and it built 61 packages without issue (see list at the bottom).
On 't2', I only get 6 built
dir-0.1 prereq-0.3 bzip2-1.0.5 sage_scripts-4.1.alpha2 conway_polynomials-0.2 mpir-1.2.p4 termcap-1.3.1.p0 readline-5.2.p6
before pari is generating more than 94,000 error messages!
Building and install PARI
make[2]: Entering directory `/tmp/tmp/sage-4.1.alpha2/spkg/build/pari-2.3.3.p0/src'
Making gp in Osolaris-none
make[3]: Entering directory `/tmp/tmp/sage-4.1.alpha2/spkg/build/pari-2.3.3.p0/src/Osolaris-none'
../config/genkernel ../src/kernel/none/asm0.h > parilvl0.h
cat ../src/kernel/gmp/tune.h ../src/kernel/gmp/int.h ../src/kernel/none/level1.h > parilvl1.h
cat parilvl0.h parilvl1.h > pariinl.h
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -I../src/language -I/tmp/tmp/sage-4.1.alpha2/local/include -o gp.o ../src/gp/gp.c
cd ../src/desc && /usr/bin/perl merge_822 ../functions/*/* > def-solaris-none-20099.tmp
mv ../src/desc/def-solaris-none-20099.tmp ../src/desc/pari.desc
cd ../src/desc && /usr/bin/perl gen_proto gp pari.desc > gp_init-solaris-none-20099.tmp
mv ../src/desc/gp_init-solaris-none-20099.tmp ../src/gp/gp_init.h
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -I../src/graph -o gp_init.o ../src/gp/gp_init.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -I../src/language -I/tmp/tmp/sage-4.1.alpha2/local/include -o gp_rl.o ../src/gp/gp_rl.c
cd ../src/desc && /usr/bin/perl gen_proto highlevel pari.desc > highlvl-solaris-none-20099.tmp
mv ../src/desc/highlvl-solaris-none-20099.tmp ../src/gp/highlvl.h
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -DDL_DFLT_NAME=NULL -o highlvl.o ../src/gp/highlvl.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o whatnow.o ../src/gp/whatnow.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -I../src/graph -o plotport.o ../src/graph/plotport.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o plotnull.o ../src/graph/plotnull.c
cat ../src/kernel/gmp/mp.c ../src/kernel/none/cmp.c ../src/kernel/none/gcdll.c ../src/kernel/none/ratlift.c ../src/kernel/none/invmod.c ../src/kernel/gmp/gcd.c ../src/kernel/none/mp_indep.c ../src/kernel/none/add.c > mp.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -I/tmp/tmp/sage-4.1.alpha2/local/include -o mp.o mp.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o mpinl.o ../src/kernel/none/mpinl.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o Flx.o ../src/basemath/Flx.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o Qfb.o ../src/basemath/Qfb.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o RgX.o ../src/basemath/RgX.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o alglin1.o ../src/basemath/alglin1.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o alglin2.o ../src/basemath/alglin2.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o arith1.o ../src/basemath/arith1.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o arith2.o ../src/basemath/arith2.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o base1.o ../src/basemath/base1.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o base2.o ../src/basemath/base2.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o base3.o ../src/basemath/base3.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o base4.o ../src/basemath/base4.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o base5.o ../src/basemath/base5.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o bibli1.o ../src/basemath/bibli1.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o bibli2.o ../src/basemath/bibli2.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o buch1.o ../src/basemath/buch1.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o buch2.o ../src/basemath/buch2.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o buch3.o ../src/basemath/buch3.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o buch4.o ../src/basemath/buch4.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o galconj.o ../src/basemath/galconj.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o gen1.o ../src/basemath/gen1.cgcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o gen2.o ../src/basemath/gen2.cgcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o gen3.o ../src/basemath/gen3.cgcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o ifactor1.o ../src/basemath/ifactor1.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o perm.o ../src/basemath/perm.cgcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o polarit1.o ../src/basemath/polarit1.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o polarit2.o ../src/basemath/polarit2.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o polarit3.o ../src/basemath/polarit3.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o rootpol.o ../src/basemath/rootpol.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o subcyclo.o ../src/basemath/subcyclo.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o subgroup.o ../src/basemath/subgroup.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o trans1.o ../src/basemath/trans1.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o trans2.o ../src/basemath/trans2.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o trans3.o ../src/basemath/trans3.c
cd ../src/desc && /usr/bin/perl gen_member pari.desc > members-solaris-none-20099.tmp
mv ../src/desc/members-solaris-none-20099.tmp ../src/language/members.h
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o anal.o ../src/language/anal.cgcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o compat.o ../src/language/compat.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o default.o ../src/language/default.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o errmsg.o ../src/language/errmsg.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o es.o ../src/language/es.c
cd ../src/desc && /usr/bin/perl gen_proto basic pari.desc > init-solaris-none-20099.tmp
mv ../src/desc/init-solaris-none-20099.tmp ../src/language/init.h
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o init.o ../src/language/init.cgcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o intnum.o ../src/language/intnum.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o members.o ../src/language/members.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o sumiter.o ../src/language/sumiter.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o aprcl.o ../src/modules/aprcl.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o elldata.o ../src/modules/elldata.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o elliptic.o ../src/modules/elliptic.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o galois.o ../src/modules/galois.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o groupid.o ../src/modules/groupid.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o kummer.o ../src/modules/kummer.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o mpqs.o ../src/modules/mpqs.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o nffactor.o ../src/modules/nffactor.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o part.o ../src/modules/part.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o stark.o ../src/modules/stark.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o subfield.o ../src/modules/subfield.c
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. -I../src/headers -o thue.o ../src/modules/thue.c
rm -f libpari-gmp.so.2.3.3
gcc -o libpari-gmp.so.2.3.3 -shared -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -Wl,-G,-h,libpari-gmp.so.2 mp.o mpinl.o Flx.o Qfb.o RgX.o alglin1.o alglin2.o arith1.o arith2.o base1.o base2.o base3.o base4.o base5.o bibli1.o bibli2.o buch1.o buch2.o buch3.o buch4.o galconj.o gen1.o gen2.o gen3.o ifactor1.o perm.o polarit1.o polarit2.o polarit3.o rootpol.o subcyclo.o subgroup.o trans1.o trans2.o trans3.o anal.o compat.o default.o errmsg.o es.o init.o intnum.o members.o sumiter.o aprcl.o elldata.o elliptic.o galois.o groupid.o kummer.o mpqs.o nffactor.o part.o stark.o subfield.o thue.o -lc -lm -L/tmp/tmp/sage-4.1.alpha2/local/lib -lgmp
Text relocation remains referenced
against symbol offset in file
<unknown> 0x76c alglin2.o
<unknown> 0x770 alglin2.o
<unknown> 0x774 alglin2.o
<SNIP out over 94,000 errors>
__gmpn_mul_1 0xdea0 mp.o
__gmpn_mul_1 0xdf24 mp.o
__gmpn_mul_1 0xdfa8 mp.o
__gmpn_mul_1 0xe02c mp.o
__gmpn_mul_1 0xfa84 mp.o
__gmpn_mul_1 0xfb14 mp.o
__gmpn_mul_1 0xfd28 mp.o
__gmpn_mul_1 0xfdac mp.o
__gmpn_mul_1 0xfe2c mp.o
__gmpn_mul_1 0xfea8 mp.o
__gmpn_mul_1 0xff20 mp.o
__gmpn_mul_1 0xff98 mp.o
__gmpn_rshift 0x48f4 mp.o
__gmpn_rshift 0xe710 mp.o
__gmpn_rshift 0xec7c mp.o
__gmpn_gcd 0x9b2c mp.o
__gmpn_gcdext 0xbd90 mp.o
__gmpn_gcdext 0xcef4 mp.o
__gmpn_add_n 0xb888 mp.o
__gmpn_sub_n 0xb3d8 mp.o
__gmpn_mod_1 0x21dc mp.o
__gmpn_mod_1 0x9640 mp.o
__gmpn_mod_1 0xe220 mp.o
ld: fatal: relocations remain against allocatable but non-writable sections
collect2: ld returned 1 exit status
make[3]: *** [libpari-gmp.so.2.3.3] Error 1
make[3]: Leaving directory `/tmp/tmp/sage-4.1.alpha2/spkg/build/pari-2.3.3.p0/src/Osolaris-none'
make[2]: *** [gp] Error 2
make[2]: Leaving directory `/tmp/tmp/sage-4.1.alpha2/spkg/build/pari-2.3.3.p0/src'
Error building GP
Just for the record, on my home machine, which uses a later version of Solaris 10, but identical versions of Sage and gcc, I got this many packages installed before problems.
Anyway, this is an issue which appears to be unique to t2, so will not to be resolved.
dir-0.1 prereq-0.3 bzip2-1.0.5 sage_scripts-4.1.alpha2 conway_polynomials-0.2 mpir-1.2.p4 termcap-1.3.1.p0 readline-5.2.p6 pari-2.3.3.p0 ntl-5.4.2.p8 eclib-20080310.p7 graphs-20070722 elliptic_curves-0.1 extcode-4.1.alpha2 flint-1.3.0.p1 zlib-1.2.3.p4 sqlite-3.5.3.p4 libgpg_error-1.6.p0 libgcrypt-1.4.3.p0 opencdk-0.6.6 gnutls-2.2.1.p1 libpng-1.2.35 python-2.6.2.p0 freetype-2.3.5.p0 gd-2.0.35.p1 gdmodule-0.56.p5 fortran-20071120.p5 lapack-20071123.p0 atlas-3.8.3.p5 gsl-1.10.p1 iml-1.0.1.p11 ipython-0.9.1.p0 givaro-3.2.13rc2 linbox-1.1.6 f2c-20070816.p1 blas-20070724 numpy-1.3.0 matplotlib-0.98.5.3rc0-svn6910.p3 mercurial-1.1.2 mpfr-2.4.1 mpfi-1.3.4-cvs20071125.p7 pexpect-2.0.p3 pycrypto-2.0.1.p3 pynac-0.1.8.p1 cython-0.11.1.p0 sympy-0.6.4 zodb3-3.7.0.p1 networkx-0.99.p1-fake_really-0.36 quaddouble-2.2.p9 python_gnutls-1.1.4.p3 twisted-8.2.0 singular-3-1-0-2-20090618 scons-1.2.0 symmetrica-2.0.p4 libfplll-3.0.12.p0 boost-cropped-1.34.1 polybori-0.5rc.p8 rpy-1.0.1.p2 r-2.6.1.p22 rubiks-20070912.p8 libm4ri-20090617 ecm-6.2.1.p0 zn_poly-0.9.p1 ghmm-20080813.p0 pyprocessing-0.52 docutils-0.5 setuptools-0.6c9 jinja-1.2
Change History (7)
comment:1 Changed 14 years ago by
| Description: | modified (diff) |
|---|---|
| Owner: | changed from tbd to drkirkby |
| Status: | new → assigned |
comment:2 Changed 14 years ago by
| Keywords: | fPIC added |
|---|---|
| Summary: | pari 2.3.3.p0 problem on 't2' but not my home machine (similar setups!!) → [with patch, needs review] pari 2.3.3.p0 problem on 't2' but not my home machine (similar setups!!) |
This has now been resolved, thanks to Marc Glisse's help after I posted the query to comp.unix.solaris. The PARI code was missing the gcc compiler flag -fPIC. Why PARI built on my own Blade 2000 but not on the 16-core T5240 (t2.math.washington.edu) is not clear to me.
Here's a patch, which adds -fPIC to one of the files used to generate the Makefile that PARI uses.
http://sage.math.washington.edu/home/kirkby/Solaris-fixes/pari/
Basically all my patch does is to add this to the top of spkg-install, which adds -fPIC
# As of PARI 2.3.3, the compiler flag -fPIC is not added on Solaris, but it needs to be. It basically adds: if [ `uname` = "SunOS" ]; then sed 's/-fomit-frame-pointer/-fomit-frame-pointer -fPIC/g' src/config/get_cc > src/config/get_cc.$$ mv src/config/get_cc.$$ src/config/get_cc fi
and remove that below
# PARI doesn't set PIC correctly on Solaris, so we do this. if [ `uname` = "SunOS" ]; then CFLAGS=$CFLAGS" -fPIC" export CFLAGS fi
since the latter code was not working, despite it's obvious attempts to add -fPIC
David Kirkby
comment:3 follow-up: 4 Changed 14 years ago by
It was noted by Minh Nguyen that there were a couple of junk files (spkg-install.orig & spkg-install.patch). These have now been removed.
The package can be found at
http://sage.math.washington.edu/home/kirkby/Solaris-fixes/pari/pari-2.3.3.p1.spkg
Could someone add that with hg for me, as I don't yet know how to use it (sorry).
I meaningful comment would be "Adds -fPIC to allow building on Solaris. Removes a previous unsuccessful attempt at adding -fPIC"
Dave
comment:4 Changed 14 years ago by
| Authors: | → David Kirkby |
|---|---|
| Reviewers: | → Minh Van Nguyen |
| Summary: | [with patch, needs review] pari 2.3.3.p0 problem on 't2' but not my home machine (similar setups!!) → [with patch, positive review] pari 2.3.3.p0 problem on 't2' but not my home machine (similar setups!!) |
Replying to drkirkby:
It was noted by Minh Nguyen that there were a couple of junk files (spkg-install.orig & spkg-install.patch). These have now been removed.
The package can be found at
http://sage.math.washington.edu/home/kirkby/Solaris-fixes/pari/pari-2.3.3.p1.spkg
Could someone add that with hg for me, as I don't yet know how to use it (sorry).
I meaningful comment would be "Adds -fPIC to allow building on Solaris. Removes a previous unsuccessful attempt at adding -fPIC"
I've committed the changes in your name. I also did some minor formatting and fixed some typos. The new spkg is up at http://sage.math.washington.edu/home/mvngu/patch/pari-2.3.3.p1.spkg Wow! The new spkg with your changes successfully builds on t2 and sage.math. All tests passed on sage.math. Thanks, David!
comment:5 Changed 14 years ago by
Thank you too. The changes were limited to Solaris, so should have no effect on another platform.
Dave
comment:6 Changed 14 years ago by
Just to let people know, this has been merged in sage-4.1.1-alpha0. I can't close this ticket because I don't have the privilege to do so. Sorry, folks :-(
comment:7 Changed 14 years ago by
| Merged in: | → sage-4.1.1.alpha0 |
|---|---|
| Resolution: | → fixed |
| Status: | assigned → closed |
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I should have stated, this is with sage-4.1.alpha2