bigint do not work #539

rtzui · 2012-03-07T19:17:24Z

how to reproduce:

$ git pull
$ make clean;make
$ make test
JULIA test/default
* default
* core
* numbers
* strings
* corelib
* hashing
* arrayops
* sparse
* lapack
* fft
* arpack
* random
* amos
* functional
* bigint
/home/user/julia/lib/libgmp_wrapper.so: undefined symbol: __gmpz_get_si
could not load module libgmp_wrapper
in dlopen at /home/user/julia/jl/base.jl:97
in include at src/boot.jl:192
in load at /home/user/julia/jl/util.jl:174
in include at src/boot.jl:192
in load at /home/user/julia/jl/util.jl:174
in runtests at ./runtests.jl:3
in include at src/boot.jl:192
in load at /home/user/julia/jl/util.jl:174
in load at /home/user/julia/jl/util.jl:186
in runtests at ./runtests.jl:3
in include at src/boot.jl:192
in process_options at /home/user/julia/jl/client.jl:167
in _start at /home/user/julia/jl/client.jl:205
at ../jl/bigint.jl:1
in include at src/boot.jl:192
in load at /home/user/julia/jl/util.jl:174
in include at src/boot.jl:192
in load at /home/user/julia/jl/util.jl:174
in runtests at ./runtests.jl:3
in include at src/boot.jl:192
in load at /home/user/julia/jl/util.jl:174
in load at /home/user/julia/jl/util.jl:186
in runtests at ./runtests.jl:3
in include at src/boot.jl:192
in process_options at /home/user/julia/jl/client.jl:167
in _start at /home/user/julia/jl/client.jl:205
at bigint.jl:2
in include at src/boot.jl:192
in load at /home/user/julia/jl/util.jl:174
in runtests at ./runtests.jl:3
in include at src/boot.jl:192
in load at /home/user/julia/jl/util.jl:174
in load at /home/user/julia/jl/util.jl:186
in runtests at ./runtests.jl:3
in include at src/boot.jl:192
in process_options at /home/user/julia/jl/client.jl:167
in _start at /home/user/julia/jl/client.jl:205
at default.jl:14
in load at /home/user/julia/jl/util.jl:197
in runtests at ./runtests.jl:3
in include at src/boot.jl:192
in process_options at /home/user/julia/jl/client.jl:167
in _start at /home/user/julia/jl/client.jl:205
at ./runtests.jl:48
in include at src/boot.jl:192
in process_options at /home/user/julia/jl/client.jl:167
in _start at /home/user/julia/jl/client.jl:205
make[1]: *** [default] Error 1
make: *** [test] Error 2
$ nm /home/user/julia/lib/libgmp_wrapper.so|grep gmpz
U __gmpz_add
U __gmpz_clear
U __gmpz_cmp
U __gmpz_fdiv_q
U __gmpz_fdiv_r
U __gmpz_get_si
U __gmpz_init
U __gmpz_mul
U __gmpz_pow_ui
U __gmpz_set
U __gmpz_set_si
U __gmpz_set_str
U __gmpz_set_ui
U __gmpz_sqrt
U __gmpz_sub
$ uname -a
Linux tux 3.0.0-16-generic #28-Ubuntu SMP Fri Jan 27 17:44:39 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

nolta · 2012-03-07T19:56:20Z

What happens if you try:

$ cd julia/external
$ make distclean-gmp
$ make clean-gmp-wrapper
$ make

and then run the tests?

rtzui · 2012-03-07T20:24:49Z

Nothing changes. Here is to output of nm julia/lib/libgmp_wrapper.so: http://paste.ubuntu.com/873567/

nolta · 2012-03-07T20:37:04Z

And what's the output of ls external/root/lib/*gmp*?

rtzui · 2012-03-07T20:41:14Z

$ ls external/root/lib/gmp
external/root/lib/libgmp.a external/root/lib/libgmp.so.10
external/root/lib/libgmp.la external/root/lib/libgmp.so.10.0.4
external/root/lib/libgmp.so external/root/lib/libgmp_wrapper.so
$ strace make test
http://paste.ubuntu.com/873586/

nolta · 2012-03-07T21:15:29Z

Ok, how about the output of the following:

$ readelf -d lib/libgmp_wrapper.so
$ ldd lib/libgmp_wrapper.so
$ julia --version

Sorry, just kind of spinning my wheels here since i can't reproduce your problem.

rtzui · 2012-03-07T21:21:43Z

$ readelf -d lib/libgmp_wrapper.so

Dynamic section at offset 0x2e40 contains 21 entries:
Tag Type Name/Value
0x0000000000000001 (NEEDED) Shared library: [libc.so.6]
0x000000000000000f (RPATH) Library rpath: [/home/user/julia/external/root/lib]
0x000000000000000c (INIT) 0x13c8
0x000000000000000d (FINI) 0x1a98
0x000000006ffffef5 (GNU_HASH) 0x1f0
0x0000000000000005 (STRTAB) 0xac0
0x0000000000000006 (SYMTAB) 0x358
0x000000000000000a (STRSZ) 1046 (bytes)
0x000000000000000b (SYMENT) 24 (bytes)
0x0000000000000003 (PLTGOT) 0x202fe8
0x0000000000000002 (PLTRELSZ) 960 (bytes)
0x0000000000000014 (PLTREL) RELA
0x0000000000000017 (JMPREL) 0x1008
0x0000000000000007 (RELA) 0xfa8
0x0000000000000008 (RELASZ) 96 (bytes)
0x0000000000000009 (RELAENT) 24 (bytes)
0x000000006ffffffe (VERNEED) 0xf78
0x000000006fffffff (VERNEEDNUM) 1
0x000000006ffffff0 (VERSYM) 0xed6
0x000000006ffffff9 (RELACOUNT) 1
0x0000000000000000 (NULL) 0x0
$ ldd lib/libgmp_wrapper.so
linux-vdso.so.1 => (0x00007fff11bff000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f865c225000)
/lib64/ld-linux-x86-64.so.2 (0x00007f865c7ee000)

$ ./julia --version
julia version 0.0.0-prerelease
Commit 2126420 (2012-03-07 13:58:44)

I guess it's quite up to date. It's a 64 bit system.

I don't think this helps, but here it is: $ md5sum lib/libgmp_wrapper.so
0b633a196ab658cea31beffd7502c0d4

nolta · 2012-03-07T21:32:47Z

Thanks, now we're getting somewhere. I don't know why, but the wrapper isn't being linked against libgmp. Perhaps the -lgmp flag has gone missing? Did you edit external/Makefile? What's the output of:

$ grep GMP_LIB external/Makefile

nolta · 2012-03-07T21:44:53Z

Also, could you git pull and see if that fixes it?

rtzui · 2012-03-07T21:50:17Z

That sounds very strange. No, i haven't changed anything in the makefile.

GMP_LIB = -L$(EXTROOTLIB)/ -lgmp
$(CC) -O2 -shared -fPIC $(GMP_INC) $(GMP_LIB) gmp_wrapper.c -o $(EXTROOTLIB)/libgmp_wrapper.$(SHLIB_EXT) -Wl,-rpath,$(EXTROOTLIB)

building it again looks fine for me: http://paste.ubuntu.com/873664/

But the tests still fail.

nolta · 2012-03-07T21:56:59Z

Strange indeed. I don't know what to say at this point, except that -Wl,-rpath,$(EXTROOTLIB) wasn't part of the 2126420 commit, so something is out-of-sync somewhere.

rtzui · 2012-03-07T22:16:55Z

I'll clone it again. But building that will take 2 hours. I'll report tomorrow.

ViralBShah · 2012-03-08T02:56:06Z

We should also include a USE_SYSTEM_GMP option, if GMP is available on the system.

ViralBShah · 2012-03-08T04:24:58Z

On 32-bit linux (Ubuntu 11.10), tests are failing:

$ make test
    JULIA test/default
     * default
     * core
     * numbers
     * strings
     * corelib
     * hashing
     * arrayops
     * sparse
     * lapack
     * fft
     * arpack
     * random
     * amos
     * functional
     * bigint
/home/viral/julia/lib/libgmp_wrapper.so: undefined symbol: __gmpz_get_si
could not load module libgmp_wrapper
 in dlopen at /home/viral/julia/jl/base.jl:97
 in include at src/boot.jl:192
 in load at /home/viral/julia/jl/util.jl:174
 in include at src/boot.jl:192
 in load at /home/viral/julia/jl/util.jl:174
 in runtests at ./runtests.jl:3
 in include at src/boot.jl:192
 in load at /home/viral/julia/jl/util.jl:174
 in load at /home/viral/julia/jl/util.jl:186
 in runtests at ./runtests.jl:3
 in include at src/boot.jl:192
 in process_options at /home/viral/julia/jl/client.jl:166
 in _start at /home/viral/julia/jl/client.jl:204
at ../jl/bigint.jl:1
 in include at src/boot.jl:192
 in load at /home/viral/julia/jl/util.jl:174
 in include at src/boot.jl:192
 in load at /home/viral/julia/jl/util.jl:174
 in runtests at ./runtests.jl:3
 in include at src/boot.jl:192
 in load at /home/viral/julia/jl/util.jl:174
 in load at /home/viral/julia/jl/util.jl:186
 in runtests at ./runtests.jl:3
 in include at src/boot.jl:192
 in process_options at /home/viral/julia/jl/client.jl:166
 in _start at /home/viral/julia/jl/client.jl:204
at bigint.jl:2
 in include at src/boot.jl:192
 in load at /home/viral/julia/jl/util.jl:174
 in runtests at ./runtests.jl:3
 in include at src/boot.jl:192
 in load at /home/viral/julia/jl/util.jl:174
 in load at /home/viral/julia/jl/util.jl:186
 in runtests at ./runtests.jl:3
 in include at src/boot.jl:192
 in process_options at /home/viral/julia/jl/client.jl:166
 in _start at /home/viral/julia/jl/client.jl:204
at default.jl:14
 in load at /home/viral/julia/jl/util.jl:197
 in runtests at ./runtests.jl:3
 in include at src/boot.jl:192
 in process_options at /home/viral/julia/jl/client.jl:166
 in _start at /home/viral/julia/jl/client.jl:204
at ./runtests.jl:48
 in include at src/boot.jl:192
 in process_options at /home/viral/julia/jl/client.jl:166
 in _start at /home/viral/julia/jl/client.jl:204

nolta · 2012-03-08T04:29:35Z

Probably because mpz_get_si returns long?

ViralBShah · 2012-03-08T04:35:16Z

Why would that lead to the undefined symbol error? This error is due to julia being unable to load gmp_wrapper, presumably because it cannot find libmp and resolve the symbols. Would it be related to your rpath fix, which I thought would have solved this?

I think we need the julia binary to be compiled with the correct rpath and fix this once and for all (#353).

-viral

On 08-Mar-2012, at 9:59 AM, Mike Nolta wrote:

Probably because mpz_get_si returns long?

Reply to this email directly or view it on GitHub:
#539 (comment)

on 32-bit (#539)

nolta · 2012-03-08T04:40:46Z

Why would that lead to the undefined symbol error?

Sorry, i'm exhausted.

Would it be related to your rpath fix, which I thought would have solved this?

That's what i'm worried about. Do the tests succeed if you take it out?

aviks · 2012-03-08T12:33:07Z

I tried this with a fresh gmp build on a 32 bit ubuntu 11.4, and everything seems to load correctly. (One of the asserts failed on 32 bits, which I'll fix, but the load was fine)

2.6.38-13-generic-pae #54-Ubuntu SMP Tue Jan 3 15:11:05 UTC 2012 i686 i686 i386 GNU/Linux

So one possible problem is path's etc, which should be easy to check via ldd. eg, I have:

aviks@asterix:~/dev/julia$ ldd external/root/lib/libgmp_wrapper.so 
    linux-gate.so.1 =>  (0xb7783000)
    libgmp.so.10 => /home/aviks/dev/julia/external/root/lib/libgmp.so.10 (0xb7717000)
    libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb75ac000)
    /lib/ld-linux.so.2 (0xb7784000)
aviks@asterix:~/dev/julia$ 2.6.38-13-generic-pae #54-Ubuntu SMP Tue Jan 3 15:11:05 UTC 2012 i686 i686 i386 GNU/Linux

However, gmp has some smarts in how it exposes function names. While clients call functions like mpz_get_si , libgmp exported functions are of the type __gmpz_get_si which are mapped via the .h files. So one possible explanation would be that when the wrapper is compiled, its using a different include from the one used when libgmp was compiled (maybe due to system vs downloaded gmp's?)

So it would make sense to check the exported symbols from any libgmp on the system against what the wrapper is trying to load.

rtzui · 2012-03-08T14:51:10Z

Started with a fresh clone, build it and now i got:

 $ ldd external/root/lib/libgmp_wrapper.so 
    linux-vdso.so.1 =>  (0x00007fff02881000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc355aca000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fc356093000)
 $ uname -a
 Linux kyon 3.0.0-16-generic #28-Ubuntu SMP Fri Jan 27 17:44:39 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

nolta · 2012-03-08T16:31:40Z

Thanks for double checking. I may try replicating your system -- which version of Ubuntu are you running? And is the gmp package installed?

Started with a fresh clone, build it and now i got:

$ ldd external/root/lib/libgmp_wrapper.so 
   linux-vdso.so.1 =>  (0x00007fff02881000)
   libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc355aca000)
   /lib64/ld-linux-x86-64.so.2 (0x00007fc356093000)
$ uname -a
Linux kyon 3.0.0-16-generic #28-Ubuntu SMP Fri Jan 27 17:44:39 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

Reply to this email directly or view it on GitHub:
#539 (comment)

ViralBShah · 2012-03-08T16:53:52Z

BTW, this is how libsuitesparse_wrapper also looks, but it loads just fine.

-viral

On 08-Mar-2012, at 10:01 PM, Mike Nolta wrote:

Thanks for double checking. I may try replicating your system -- which version of Ubuntu are you running? And is the gmp package installed?
Started with a fresh clone, build it and now i got:
$ ldd external/root/lib/libgmp_wrapper.so 
  linux-vdso.so.1 =>  (0x00007fff02881000)
  libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc355aca000)
  /lib64/ld-linux-x86-64.so.2 (0x00007fc356093000)
$ uname -a
Linux kyon 3.0.0-16-generic #28-Ubuntu SMP Fri Jan 27 17:44:39 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
Reply to this email directly or view it on GitHub:
#539 (comment)
Reply to this email directly or view it on GitHub:
#539 (comment)

rtzui · 2012-03-08T17:23:15Z

Ubuntu 11.10, the downloaded libgmp.

ViralBShah · 2012-03-08T17:30:13Z

Removing -rpath does not change anything for me. I am on ubuntu 11.10 as well.

-viral

On 08-Mar-2012, at 10:53 PM, rtzui wrote:

Ubuntu 11.10, the downloaded libgmp.

Reply to this email directly or view it on GitHub:
#539 (comment)

nolta · 2012-03-08T19:28:09Z

Ok, success (of a sort): i can reproduce this bug on Ubuntu 11.10.

nolta · 2012-03-08T20:04:30Z

I've pushed a fix for both @rtzui and @aviks bugs.

rtzui · 2012-03-08T22:27:56Z

works for me.

Fix for #538

ghost assigned nolta Mar 8, 2012

ViralBShah added a commit that referenced this issue Mar 8, 2012

Disable bigint tests yet again, this time because of issues

0be57b7

on 32-bit (#539)

rtzui closed this as completed Mar 8, 2012

KristofferC added a commit that referenced this issue Aug 4, 2018

only look for Project files in installed (#539)

ebdefc1

KristofferC added a commit that referenced this issue Aug 4, 2018

only look for Project files in installed (#539)

9540687

KristofferC added a commit that referenced this issue Aug 4, 2018

only look for Project files in installed (#539)

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KristofferC added a commit that referenced this issue Aug 4, 2018

only look for Project files in installed (#539)

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KristofferC added a commit that referenced this issue Feb 11, 2019

only look for Project files in installed (#539)

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Keno pushed a commit that referenced this issue Oct 9, 2023

Fix is_doc_expr by constraining number of args (#539)

75bc4fb

Fix for #538

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bigint do not work #539

bigint do not work #539

rtzui commented Mar 7, 2012

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rtzui commented Mar 8, 2012

bigint do not work #539

bigint do not work #539

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