Re: [Bug-gsl] [bug #33040] libgsl should be linked against libgslcblas

[Peter Johansson]

Hi Christoph,

On 4/10/11 8:05 AM, Christoph Junghans wrote:
> Details:
>
> $cat main.c
> int gsl_linalg_QR_decomp();
> int main() {
>    return 0;
> }
> $gcc main.c -lgsl
> /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../lib64/libgsl.so: undefined
> reference to `cblas_csyrk'
> (and more)
>
> In gentoo the problem is fixed. (see patch)

IMHO, this is not a problem - it's a feature that allows me as a user to 
choose at build time of my application which cblas to use. GSL documents 
that the way to link against GSL is via

gcc main.c -lgsl -lgslcblas -lm

On one of my systems at work I have no control over how GSL is installed 
and find it useful that GSL by default does not hardwire a specific 
cblas into `libgsl.la'. With your patch the default behavior will be 
different and it will be less flexible in terms of choosing cblas for 
the end user (not for the sysadm who installs GSL).

I think it'd be good if the patch could be modified so the default 
behavior is as it is now, i.e., no cblas is hardwired into `libgsl.la' 
et cetera.

What stops you from hardwire a specific cblas into libgsl as it is now? 
Wouldn't
./configure LIBS=-lcblas
accomplish what you want? [honest question]

If the GSL maintainers accept the patch, I have a few suggestions diff 
-Nur gsl-1.14.orig/acx_cblas.m4 gsl-1.14/acx_cblas.m4
> --- gsl-1.14.orig/acx_cblas.m4    1970-01-01 01:00:00.000000000 +0100
> +++ gsl-1.14/acx_cblas.m4    2010-04-09 02:19:59.000000000 +0100
> @@ -0,0 +1,60 @@
> +AC_DEFUN([ACX_CBLAS],[
> +  use_cblas=no
> +  use_cblas_libs="-lcblas -lblas"
> +  use_cblas_cflags=""
> +
> +  AC_ARG_WITH(cblas,
> +    [AS_HELP_STRING([--with-cblas], [use external CBLAS library 
> (default is no)])])
> +
underquoted:

s/cblas/[cblas]/

> +  case $with_cblas in
> +    yes) use_cblas=yes ;;
> +    no | "" ) use_cblas=no ;;
> +    -* | */* | *.a | *.so | *.so.* | *.o) use_cblas_libs="$with_cblas" ;;
> +    *) use_cblas_libs="-l$with_cblas" ;;
> +  esac
> +
> +  AC_ARG_WITH(cblas-libs,
likewise

> +    [AS_HELP_STRING([--with-cblas-libs=<libs>],
> +     [external cblas libraries to link with (default is 
> "$use_cblas_libs")])],
> +    [use_cblas_libs=$withval], [])
> +
> +  AC_ARG_WITH(cblas-cflags,
likewise
> +    [AS_HELP_STRING([--with-cblas-cflags=<flags>],
> +     [extra cflags to compile with external cblas ("-I<dir>")])],
> +    [use_cblas_cflags=$withval], [])
> +
> +  if test x$use_cblas != xno; then
> +    if test "x$CBLAS_LIBS" = x; then
> +        CBLAS_LIBS="$use_cblas_libs"
> +         fi
> +         if test "x$CBLAS_FLAGS" = x; then
> +               CBLAS_CFLAGS="$use_cblas_cflags"
> +       fi
> +
> +       CFLAGS_sav="$CFLAGS"
> +       CFLAGS="$CFLAGS $CBLAS_CFLAGS"
> +       AC_CHECK_HEADER(cblas.h, ,
likewise
> +        [AC_MSG_ERROR([
> +           *** Header file cblas.h not found.
> +           *** If you installed cblas header in a non standard place,
> +           *** specify its install prefix using the following option
> +           ***  --with-cblas-cflags="-I<include_dir>"])
> +         ])
> +       CFLAGS="$CFLAGS_sav"
> +
> +       LIBS_sav="$LIBS"
> +       LIBS="$LIBS $CBLAS_LIBS -lm"
> +       AC_MSG_CHECKING([for cblas_sgemm in $CBLAS_LIBS])
> +       AC_TRY_LINK_FUNC(cblas_sgemm, [use_cblas=yes],
likewise
> +            [AC_MSG_ERROR([
> +            *** Linking with cblas with $LIBS failed.
> +                   *** If you installed cblas library in a non 
> standard place,
> +               *** specify its install prefix using the following option
> +            ***  --with-cblas-libs="-L<lib_dir> -l<lib>"])
> +         ])
> +       AC_MSG_RESULT($use_cblas)
likewise

> +       LIBS="$LIBS_sav"
> +    AC_SUBST(CBLAS_CFLAGS)
> +    AC_SUBST(CBLAS_LIBS)
> + fi
> +])
> diff -Nur gsl-1.14.orig/bspline/Makefile.am gsl-1.14/bspline/Makefile.am
> --- gsl-1.14.orig/bspline/Makefile.am    2010-04-09 02:04:47.000000000 
> +0100
> +++ gsl-1.14/bspline/Makefile.am    2010-04-09 02:19:59.000000000 +0100
> @@ -12,6 +12,6 @@
>
>  TESTS = $(check_PROGRAMS)
>
> -test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la 
> ../permutation/libgslpermutation.la ../blas/libgslblas.la 
> ../matrix/libgslmatrix.la ../vector/libgslvector.la 
> ../block/libgslblock.la ../complex/libgslcomplex.la 
> ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la  
> ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la 
> ../utils/libutils.la ../statistics/libgslstatistics.la
> +test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la 
> ../permutation/libgslpermutation.la ../blas/libgslblas.la 
> ../matrix/libgslmatrix.la ../vector/libgslvector.la 
> ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ 
> ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la 
> ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la 
> ../statistics/libgslstatistics.la
I prefer $(CBLAS_LINK_LIBS) over @CBLAS_LINK_LIBS@ so Automake has a 
chance to pick up dependencies et cetera.

>  test_SOURCES = test.c
> diff -Nur gsl-1.14.orig/configure.ac gsl-1.14/configure.ac
> --- gsl-1.14.orig/configure.ac    2010-04-09 02:04:47.000000000 +0100
> +++ gsl-1.14/configure.ac    2010-04-09 02:19:59.000000000 +0100
> @@ -185,6 +185,16 @@
>    AC_CHECK_LIB(m, cos)
>  fi
>
> +sinclude(acx_cblas.m4)
This is not needed as GSL uses aclocal, which will create this include 
in `aclocal.m4'.

> +ACX_CBLAS
> +if test "x$CBLAS_LIBS" != "x"; then
> +   CBLAS_LINK_LIBS="$CBLAS_LIBS"
> +else
> +   CBLAS_LINK_LIBS="\$(top_builddir)/cblas/libgslcblas.la"
> +   CBLAS_LIBS="-lgslcblas"
> +fi
> +AC_SUBST(CBLAS_LINK_LIBS)
> +
>  dnl Remember to put a definition in acconfig.h for each of these
>  AC_CHECK_DECLS(feenableexcept,,,[#define _GNU_SOURCE 1
>  #include <fenv.h>])
> diff -Nur gsl-1.14.orig/eigen/Makefile.am gsl-1.14/eigen/Makefile.am
> --- gsl-1.14.orig/eigen/Makefile.am    2010-04-09 02:04:46.000000000 +0100
> +++ gsl-1.14/eigen/Makefile.am    2010-04-09 02:19:59.000000000 +0100
> @@ -11,7 +11,7 @@
>
>  TESTS = $(check_PROGRAMS)
>
> -test_LDADD = libgsleigen.la  ../test/libgsltest.la 
> ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la 
> ../blas/libgslblas.la ../cblas/libgslcblas.la 
> ../matrix/libgslmatrix.la ../vector/libgslvector.la 
> ../block/libgslblock.la  ../complex/libgslcomplex.la 
> ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la 
> ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la 
> ../sort/libgslsort.la
> +test_LDADD = libgsleigen.la  ../test/libgsltest.la 
> ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la 
> ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la 
> ../vector/libgslvector.la ../block/libgslblock.la  
> ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la 
> ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la 
> ../rng/libgslrng.la ../sort/libgslsort.la
likewise prefer $(foo) over @foo@ when possible
>  test_SOURCES = test.c
>
> diff -Nur gsl-1.14.orig/gsl-config.in gsl-1.14/gsl-config.in
> --- gsl-1.14.orig/gsl-config.in    2010-04-09 02:04:47.000000000 +0100
> +++ gsl-1.14/gsl-config.in    2010-04-09 02:19:59.000000000 +0100
> @@ -58,11 +58,11 @@
>      ;;
>
>      --cflags)
> -           echo @GSL_CFLAGS@
> +           echo @GSL_CFLAGS@ @CBLAS_CFLAGS@
>             ;;
>
>      --libs)
> -        : ${GSL_CBLAS_LIB=-lgslcblas}
> +        : address@hidden@}
>             echo @GSL_LIBS@ $GSL_CBLAS_LIB -lm
>             ;;
>
> diff -Nur gsl-1.14.orig/gsl.pc.in gsl-1.14/gsl.pc.in
> --- gsl-1.14.orig/gsl.pc.in    2010-04-09 02:04:46.000000000 +0100
> +++ gsl-1.14/gsl.pc.in    2010-04-09 02:19:59.000000000 +0100
> @@ -6,5 +6,5 @@
>  Name: GSL
>  Description: GNU Scientific Library
>  Version: @VERSION@
> -Libs: @GSL_LIBS@ -lgslcblas @LIBS@
> -Cflags: @GSL_CFLAGS@
> +Libs: @GSL_LIBS@ @CBLAS_LIBS@ @LIBS@
> +Cflags: @GSL_CFLAGS@ @CBLAS_CFLAGS@
> diff -Nur gsl-1.14.orig/interpolation/Makefile.am 
> gsl-1.14/interpolation/Makefile.am
> --- gsl-1.14.orig/interpolation/Makefile.am    2010-04-09 
> 02:04:47.000000000 +0100
> +++ gsl-1.14/interpolation/Makefile.am    2010-04-09 
> 02:19:59.000000000 +0100
> @@ -10,7 +10,7 @@
>
>  TESTS = $(check_PROGRAMS)
>
> -test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la 
> ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la 
> ../blas/libgslblas.la ../matrix/libgslmatrix.la 
> ../vector/libgslvector.la ../block/libgslblock.la 
> ../complex/libgslcomplex.la ../cblas/libgslcblas.la 
> ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la 
> ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
> +test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la 
> ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la 
> ../blas/libgslblas.la ../matrix/libgslmatrix.la 
> ../vector/libgslvector.la ../block/libgslblock.la 
> ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ 
> ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la 
> ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la

likewise
>  test_SOURCES = test.c
>
> diff -Nur gsl-1.14.orig/linalg/Makefile.am gsl-1.14/linalg/Makefile.am
> --- gsl-1.14.orig/linalg/Makefile.am    2010-04-09 02:04:46.000000000 
> +0100
> +++ gsl-1.14/linalg/Makefile.am    2010-04-09 02:19:59.000000000 +0100
> @@ -12,7 +12,7 @@
>
>  check_PROGRAMS = test
>
> -test_LDADD = libgsllinalg.la ../blas/libgslblas.la 
> ../cblas/libgslcblas.la ../permutation/libgslpermutation.la 
> ../matrix/libgslmatrix.la ../vector/libgslvector.la 
> ../block/libgslblock.la ../complex/libgslcomplex.la 
> ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la 
> ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
> +test_LDADD = libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ 
> ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la 
> ../vector/libgslvector.la ../block/libgslblock.la 
> ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la 
> ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la 
> ../utils/libutils.la

likewise
>  test_SOURCES = test.c
>
> diff -Nur gsl-1.14.orig/Makefile.am gsl-1.14/Makefile.am
> --- gsl-1.14.orig/Makefile.am    2010-04-09 02:04:46.000000000 +0100
> +++ gsl-1.14/Makefile.am    2010-04-09 02:20:13.000000000 +0100
> @@ -19,13 +19,12 @@
>
>  lib_LTLIBRARIES = libgsl.la
>  libgsl_la_SOURCES = version.c
> -libgsl_la_LIBADD = $(SUBLIBS)
> +libgsl_la_LIBADD = $(SUBLIBS) @CBLAS_LINK_LIBS@
likewise

>  libgsl_la_LDFLAGS = -version-info $(GSL_LT_VERSION)
>  noinst_HEADERS = templates_on.h templates_off.h build.h
>
>  MINGW32_HOST = @MINGW32_HOST@
>  if MINGW32_HOST
> -libgsl_la_LIBADD += cblas/libgslcblas.la
>  libgsl_la_LDFLAGS += -no-undefined
>  endif
>
> @@ -35,10 +34,10 @@
>  bin_PROGRAMS = gsl-randist gsl-histogram
>
>  gsl_randist_SOURCES = gsl-randist.c
> -gsl_randist_LDADD = libgsl.la cblas/libgslcblas.la
> +gsl_randist_LDADD = libgsl.la
>
>  gsl_histogram_SOURCES = gsl-histogram.c
> -gsl_histogram_LDADD = libgsl.la cblas/libgslcblas.la
> +gsl_histogram_LDADD = libgsl.la
>
>  check_SCRIPTS = test_gsl_histogram.sh
>  TESTS = test_gsl_histogram.sh
> @@ -56,6 +55,8 @@
>      -e 's|@address@hidden|$(includedir)|g' \
>      -e 's|@address@hidden|$(GSL_CFLAGS)|g' \
>      -e 's|@address@hidden|$(GSL_LIBS)|g' \
> +    -e 's|@address@hidden|$(CBLAS_CFLAGS)|g' \
> +    -e 's|@address@hidden|$(CBLAS_LIBS)|g' \
>      -e 's|@address@hidden|$(LIBS)|g' \
>      -e 's|@address@hidden|$(VERSION)|g'
>
> diff -Nur gsl-1.14.orig/multifit/Makefile.am gsl-1.14/multifit/Makefile.am
> --- gsl-1.14.orig/multifit/Makefile.am    2010-04-09 
> 02:04:47.000000000 +0100
> +++ gsl-1.14/multifit/Makefile.am    2010-04-09 02:19:59.000000000 +0100
> @@ -13,8 +13,8 @@
>  TESTS = $(check_PROGRAMS)
>
>  test_SOURCES = test.c
> -test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la 
> ../permutation/libgslpermutation.la ../blas/libgslblas.la 
> ../cblas/libgslcblas.la ../matrix/libgslmatrix.la 
> ../vector/libgslvector.la ../block/libgslblock.la  
> ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la 
> ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la 
> ../sys/libgslsys.la
> +test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la 
> ../permutation/libgslpermutation.la ../blas/libgslblas.la 
> @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la 
> ../block/libgslblock.la  ../complex/libgslcomplex.la 
> ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la 
> ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
likewise
>  #demo_SOURCES = demo.c
> -#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la 
> ../permutation/libgslpermutation.la ../blas/libgslblas.la 
> ../cblas/libgslcblas.la ../matrix/libgslmatrix.la 
> ../vector/libgslvector.la ../block/libgslblock.la 
> ../randist/libgslrandist.la ../rng/libgslrng.la 
> ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la 
> ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la 
> ../sys/libgslsys.la
> +#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la 
> ../permutation/libgslpermutation.la ../blas/libgslblas.la 
> @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la 
> ../block/libgslblock.la ../randist/libgslrandist.la 
> ../rng/libgslrng.la ../complex/libgslcomplex.la 
> ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la 
> ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
likewise
> diff -Nur gsl-1.14.orig/multimin/Makefile.am gsl-1.14/multimin/Makefile.am
> --- gsl-1.14.orig/multimin/Makefile.am    2010-04-09 
> 02:04:47.000000000 +0100
> +++ gsl-1.14/multimin/Makefile.am    2010-04-09 02:19:59.000000000 +0100
> @@ -13,8 +13,8 @@
>  TESTS = $(check_PROGRAMS)
>
>  test_SOURCES = test.c test_funcs.c test_funcs.h
> -test_LDADD = libgslmultimin.la ../min/libgslmin.la 
> ../poly/libgslpoly.la ../blas/libgslblas.la ../cblas/libgslcblas.la 
> ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la 
> ../matrix/libgslmatrix.la ../vector/libgslvector.la 
> ../block/libgslblock.la ../complex/libgslcomplex.la 
> ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la 
> ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
> +test_LDADD = libgslmultimin.la ../min/libgslmin.la 
> ../poly/libgslpoly.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ 
> ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la 
> ../matrix/libgslmatrix.la ../vector/libgslvector.la 
> ../block/libgslblock.la ../complex/libgslcomplex.la 
> ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la 
> ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
likewise
>  #demo_SOURCES = demo.c
> -#demo_LDADD = libgslmultimin.la ../min/libgslmin.la 
> ../blas/libgslblas.la ../cblas/libgslcblas.la 
> ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la 
> ../vector/libgslvector.la ../block/libgslblock.la 
> ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la 
> ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la 
> ../utils/libutils.la
> +#demo_LDADD = libgslmultimin.la ../min/libgslmin.la 
> ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la 
> ../matrix/libgslmatrix.la ../vector/libgslvector.la 
> ../block/libgslblock.la ../complex/libgslcomplex.la 
> ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la 
> ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
likewise
> diff -Nur gsl-1.14.orig/multiroots/Makefile.am 
> gsl-1.14/multiroots/Makefile.am
> --- gsl-1.14.orig/multiroots/Makefile.am    2010-04-09 
> 02:04:46.000000000 +0100
> +++ gsl-1.14/multiroots/Makefile.am    2010-04-09 02:19:59.000000000 +0100
> @@ -15,5 +15,5 @@
>  TESTS = $(check_PROGRAMS)
>
>  test_SOURCES = test.c test_funcs.c test_funcs.h
> -test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la 
> ../blas/libgslblas.la ../cblas/libgslcblas.la 
> ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la 
> ../vector/libgslvector.la ../block/libgslblock.la 
> ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  
> ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la 
> ../utils/libutils.la
> +test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la 
> ../blas/libgslblas.la @CBLAS_LINK_LIBS@ 
> ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la 
> ../vector/libgslvector.la ../block/libgslblock.la 
> ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  
> ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la 
> ../utils/libutils.la
likewise
> diff -Nur gsl-1.14.orig/ode-initval/Makefile.am 
> gsl-1.14/ode-initval/Makefile.am
> --- gsl-1.14.orig/ode-initval/Makefile.am    2010-04-09 
> 02:04:47.000000000 +0100
> +++ gsl-1.14/ode-initval/Makefile.am    2010-04-09 02:19:59.000000000 
> +0100
> @@ -12,7 +12,7 @@
>
>  TESTS = $(check_PROGRAMS)
>
> -test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la 
> ../blas/libgslblas.la ../cblas/libgslcblas.la 
> ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la 
> ../vector/libgslvector.la ../block/libgslblock.la 
> ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  
> ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la 
> ../utils/libutils.la
> +test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la 
> ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la 
> ../permutation/libgslpermutation.la ../vector/libgslvector.la 
> ../block/libgslblock.la ../complex/libgslcomplex.la 
> ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la 
> ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la

likewise

Cheers,
Peter