Problems with linking GSL / CBLAS

Question

EDIT: Problem resolved, see my answer below.

Is there a problem with the GSL library in Oneiric? I'm having trouble linking and don't understand why -- this works fine in 10.4, 10.10, and 11.4.

EDIT: small test cases first, full problem is below:

Works fine on Natty:

$ cat /etc/issue
Ubuntu 11.04 \n \l

$ cat gsl-test.cpp
#include <gsl/gsl_errno.h>
void handler(const char *, const char *, int, int) { }
int main() { gsl_set_error_handler(handler); }

$ g++ gsl-test.cpp  ## Expect problems since libraries not linked in
/tmp/ccnjUNdv.o: In function `main':
gsl-test.cpp:(.text+0x16): undefined reference to `gsl_set_error_handler'
collect2: ld returned 1 exit status

$ g++ -lgsl -lgslcblas gsl-test.cpp
$ ./a.out
$

Fails on Oneiric:

$ cat /etc/issue
Ubuntu 11.10 \n \l

$ cat gsl-test.cpp
#include <gsl/gsl_errno.h>
void handler(const char *, const char *, int, int) { }
int main() { gsl_set_error_handler(handler); }

$ g++ gsl-test.cpp
/tmp/ccWKJMov.o: In function `main':
gsl-test.cpp:(.text+0x16): undefined reference to `gsl_set_error_handler'
collect2: ld returned 1 exit status

$ g++ -lgsl -lgslcblas -lm gsl-test.cpp
/tmp/ccV0UIx5.o: In function `main':
gsl-test.cpp:(.text+0x16): undefined reference to `gsl_set_error_handler'
collect2: ld returned 1 exit status

But this works on Oneiric:

$ g++ gsl-test.cpp -lgsl -lgslcblas
$ ./a.out

I suspect there's some difference in how g++ is working (4.6.1 vs. 4.5.2).

EDIT:

$ nm /usr/lib/libgslcblas.so
nm: /usr/lib/libgslcblas.so: no symbols
$ nm /usr/lib/libgslcblas.a|grep 'cblas_zher2k\|cblas_dtrsm\|cblas_zhemm'
00000000 T cblas_dtrsm
00000000 T cblas_zhemm
00000000 T cblas_zher2k

And here's the full problem, which seems to have a bit of a different flavor than my test case above, since it still isn't fixed by putting -lgsl -lgslcblas at the end of the line:

/usr/bin/c++   -g -O2  -O2 -g   -Wl,-Bsymbolic-functions CMakeFiles/css.dir/main.cpp.o  -o ../../../bin/css -rdynamic ../../../lib/libtemt.so.5.2.3 -lCoin -lQuarter -lQtOpenGL -lQtWebKit -lQtGui -lQtXml -lQtXmlPatterns -lQtNetwork -lQtCore -lode -lgslcblas -lgsl -lGLU -lGL -lSM -lICE -lX11 -lXext -lz -lreadline -lreadline -ltermcap -Wl,-rpath,/tmp/emergent-5.2.3/build/lib: 
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zher2k'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dtrsm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zhemm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_sgemv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dgemm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_drotg'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_sscal'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cdotc_sub'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ssymm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zherk'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_caxpy'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_scasum'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dgemv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cgemm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_isamax'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dtrsv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_sswap'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cher2'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dasum'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cgeru'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_csscal'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_chemm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ctrsv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_icamax'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_scnrm2'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ctrsm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_drotmg'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dsyrk'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dznrm2'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ssyr2k'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_chemv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dsyr2'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_srotm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dscal'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cdotu_sub'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zswap'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dswap'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zcopy'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ztrmv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_scopy'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_drot'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ssyrk'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zsyr2k'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zaxpy'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zher'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_daxpy'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cscal'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_srotmg'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ssyr'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_strsm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dsymv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zgeru'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dcopy'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_snrm2'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dtrmm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_strsv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zdotc_sub'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_strmm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_csymm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_sger'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zscal'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_srotg'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_strmv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cgerc'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_saxpy'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cherk'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dsdot'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ssymv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zher2'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ddot'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dnrm2'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cgemv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zgemv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ctrmv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cswap'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zgemm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ctrmm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_csyrk'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dsyr2k'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dsyr'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_sgemm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_srot'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dzasum'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_idamax'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_csyr2k'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zhemv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_drotm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dsymm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zsyrk'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_sdsdot'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zgerc'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ssyr2'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cher'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zsymm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ztrsm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_cher2k'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_sasum'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ztrsv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ccopy'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_ztrmm'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dger'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_dtrmv'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_izamax'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zdscal'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_sdot'
/usr/lib/gcc/i686-linux-gnu/4.6.1/../../../../lib/libgsl.so: undefined reference to `cblas_zdotu_sub'
collect2: ld returned 1 exit status

I get the same slew of undefined references if I do this, whether on Natty or Oneiric:

$ g++ gsl-test.cpp -lgsl

Not sure what to make of that yet.

Solution 1

The problem was that libtemt.so.5.2.3 was also linked against the GSL libraries, and in the wrong order. Somehow that link succeeded, but caused the next one to fail. Once I linked libtemt with the ordering: -lgsl -lgslcblas, then I could link the css executable with the same correct ordering, and it succeeded. Now I just need to figure out how to convince CMake to write the correct link.txt file.

Solution 2

Try to write -lgsl before -lgslcblas. I know that's stupid, but for me it works...

Comments

[Dan]

I tried that, since pkg-config --libs gsl reports -lgsl -lgslcblas but it still didn't work. Also tried -lgsl -lgslcblas -lgsl -lgslcblas -lgsl which seems silly but if there were circular dependencies maybe?