rb-gsl underlinking narray?

[gengor]

Hi Mr. Wille,

I believe the build system is underlinking narray when final linking rb_gsl.so. The gem builds and installs fine as long as ldflags in the Makefile does not include -Wl,--no-undefined. ldflags is (partially) derived from the underlying OS. Some Linux OSes enforce this check, Gentoo being one of them. If --no-undefined is enforced on the linker, it fails with the following:

linking shared-object rb_gsl.so
multiroots.o: In function `rb_gsl_multiroot_fdjacobian':
multiroots.c:(.text+0x14f1): undefined reference to `cNArray'
multiroots.o: In function `rb_gsl_multiroot_fsolver_set':
multiroots.c:(.text+0x2013): undefined reference to `cNArray'
multiroots.o: In function `rb_gsl_multiroot_fdfsolver_set':
multiroots.c:(.text+0x228b): undefined reference to `cNArray'
multiroots.o: In function `rb_gsl_multiroot_function_solve':
multiroots.c:(.text+0x25cb): undefined reference to `cNArray'
vector_double.o: In function `rb_gsl_vector_decimate':
vector_double.c:(.text+0x1243): undefined reference to `cNArray'
vector_double.o:vector_double.c:(.text+0x165f): more undefined references to `cNArray' follow
vector_double.o: In function `rb_gsl_vector_filescan_na':
vector_double.c:(.text+0x1676): undefined reference to `na_make_object'
vector_double.o: In function `rb_gsl_vector_normalize_bang':
vector_double.c:(.text+0x17c2): undefined reference to `cNArray'
vector_double.o: In function `rb_gsl_vector_normalize':
vector_double.c:(.text+0x1914): undefined reference to `cNArray'
vector_double.o: In function `Init_gsl_vector':
vector_double.c:(.text+0x646f): undefined reference to `cNArray'
dht.o: In function `rb_gsl_dht_xk_sample':
dht.c:(.text+0xc47): undefined reference to `cNArray'
dht.c:(.text+0xc88): undefined reference to `na_make_object'
...<snip - continues on quite a ways>

If we don't enforce --no-undefined and let the build succeed we get the following final linking:

# scanelf -n rb_gsl.so
 TYPE   NEEDED FILE
ET_DYN libgsl.so.0,libm.so.6,libruby19.so.1.9,libc.so.6 rb_gsl.so

The build error can be fixed by changing this line in extconf.rb:

$LOCAL_LIBS = " -L#{File.join(narray_config, 'src')}" + $LOCAL_LIBS

To:

$LOCAL_LIBS = " -L#{File.join(narray_config, 'src')} -l:narray.so" + $LOCAL_LIBS

This allows the final linking phase to succeed when -Wl,--no-undefined is in ldflags in the Makefile. Installation completes successfully. Now we get:

# scanelf -n rb_gsl.so
 TYPE   NEEDED FILE
ET_DYN /usr/local/lib64/ruby/gems/1.9.1/gems/narray-0.6.0.8/src/narray.so,libgsl.so.0,libm.so.6,libruby19.so.1.9,libc.so.6 rb_gsl.so

[blackwinter]

Done. Thanks!

Could you check before I'm going to release a new version?

[gengor]

Thanks for the quick response! Your fix appears to work just fine.

Cheers!

[dsedivec]

I think this fix (a8ce8f0cec5e688ec51332d5e225a7f14ead777a) broke the build for me on OS X. I make a gem from HEAD with rake gem and then try to install it with gem install. Here's the significant-looking parts near the end of the gem install failure:

linking shared-object gsl/gsl_native.bundle
ld: library not found for -l:narray.so
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [gsl_native.bundle] Error 1

I'm on OS X. Looks like it's using clang to build. Versions:

$ clang --version
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
Target: x86_64-apple-darwin12.5.0
Thread model: posix
$ sw_vers
ProductName:    Mac OS X
ProductVersion: 10.8.5
BuildVersion:   12F45
$ ruby --version
ruby 2.1.1p76 (2014-02-24 revision 45161) [x86_64-darwin12.0]

I've never seen a -l option in the format -l:narray.so. Perhaps clang doesn't support that?

[blackwinter]

Clang just passes the option to ld, which also seems to accept it. But the file is probably named narray.bundle instead of narray.so on your platform.

@gengor Is there a reason you made the file extension explicit? Would -lnarray work for you?

[dsedivec]

If I check out a8ce8f0cec5e688ec51332d5e225a7f14ead777a, replace -l:narray.so with -lnarray in ext/gsl/extconf.rb, make the gem with rake gem, and then try to install that gem into a directory where bundler has installed narray for me, I get the following error:

linking shared-object gsl/gsl_native.bundle
ld: library not found for -lnarray

I also tried -l:narray and -l:narray.bundle. They all produced the same error as above (with -lnarray replaced with whatever switch I was trying in that iteration).

I don't know anything about OS X .bundle files, but for what it's worth, I found this excerpt from a relatively old book called Mac OS X for Unix Geeks: "WARNING: You cannot link directly against a bundle. Instead, bundles must be dynamically loaded and unloaded by the dyld APIs."

[blackwinter]

Ok, thanks. I guess the easiest way out would be to add darwin to the guard and skip that flag on OS X altogether. Or maybe even the other way around and only add it on linux platforms.

[blackwinter]

I opted for the latter. It would be great if the two of you could test it one more time.

[dsedivec]

fa9ab3d2e031500832c2b31d9230fc9892fbfe03 seems to build and run for me fine on OS X 10.8.5, Ruby 2.1.1p76. Thanks!

[blackwinter]

Thanks for checking. Version 1.16.0.1 was released a few days ago.

[blackwinter]

FYI, I had to change the guard for adding narray.so to the list of files to link (see c2b4939 and #5). This will be released as 1.16.0.2 soon, unless someone objects.

[rubyist2016]

There are no similar lines in the extconf.rb for this case http://stackoverflow.com/questions/35950494/rails-loaderror-undefined-symbol-cnarray-when-using-gsl