FW: ../src/liboctinterp.so: undefined reference to `__cxa_guard_acquire'

[Letizia MAZZURCO]

 Hi Thomas,

I have not received answer yet.
For me is very urgent.

Thanks.
Regards,
Letizia M.

-----Original Message-----
From: letizia mazzurco [mailto:address@hidden 
Sent: Monday, May 21, 2007 11:26 AM
To: 'Thomas Treichl'
Cc: 'address@hidden'
Subject: RE: ../src/liboctinterp.so: undefined reference to
`__cxa_guard_acquire'

 Hi Thomas,

I try, but the message is the same :

........
Octave is now configured for i686-pc-linux-gnu

  Source directory:     .
  Installation prefix:  /sw/foss/octave/octave-2.9.10/Linux.i686/
  C compiler:           gcc  -mieee-fp  -Wall -W -Wshadow -g -O2
  C++ compiler:         g++  -mieee-fp  -Wall -W -Wshadow -Wold-style-cast
-g -O2
  Fortran compiler:     gfortran -O -mieee-fp
  Fortran libraries:
-L/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0
-L/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc
-L/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/
../../.. -lhdf5 -lz -lgfortranbegin -lgfortran -lm
  BLAS libraries:       
  FFTW libraries:       -lfftw3
  GLPK libraries:       -lglpk
  UMFPACK libraries:    
  AMD libraries:        -lamd
  CAMD libraries:       -lcamd
  COLAMD libraries:     -lcolamd
  CCOLAMD libraries:    -lccolamd
  CHOLMOD libraries:    
  CXSPARSE libraries:   -lcxsparse
  ARPACK libraries:     
  HDF5 libraries:       -lhdf5
  CURL libraries:       -lcurl
  REGEX libraries:      -lpcre
  LIBS:                 -lreadline  -lncurses -ldl -lhdf5 -lz -lm 
  Default pager:        less
  gnuplot:              gnuplot

  Do internal array bounds checking:  false
  Build static libraries:             false
  Build shared libraries:             true
  Dynamic Linking:                    true (dlopen)
  Include support for GNU readline:   true
  64-bit array dims and indexing:     false

configure: WARNING: UMFPACK not found.  This will result in some lack of
functionality for sparse matrices.
configure: WARNING: CHOLMOD not found. This will result in some lack of
functionality for sparse matrices.
configure:

NOTE: libraries may be skipped if a library is not found OR
      if the library on your system is missing required features.

I sent a block of config.log file :

..........
configure:15796: checking for cholmod_start in -lcholmod
configure:15839: gcc -o conftest -g -O2   conftest.c -lcholmod -lcamd -lamd
-lcolamd -lccolamd   -L/misc/sw1/foss/gfortran/
linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0
-L/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc -L/misc/sw1/foss/gfor
tran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/../../.. -lhdf5 -lz
-lgfortranbegin -lgfortran -lm -lmetis -lhdf5 -l z -lm  >&5
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `d gemv_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `z herk_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `z trsv_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `z potrf_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `d gemm_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `z gemv_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `d trsm_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `d potrf_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `d syrk_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `d trsv_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `z gemm_'
/misc/sw1/foss/gfortran/linux/irun/bin/../lib/gcc/i386-pc-linux-gnu/4.3.0/..
/../../libcholmod.so: undefined reference to `z trsm_'
collect2: ld returned 1 exit status
configure:15845: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define OCTAVE_SOURCE 1
| #define _GNU_SOURCE 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define SEPCHAR ':'
| #define SEPCHAR_STR ":"
| #define __NO_MATH_INLINES 1
| #define CXX_NEW_FRIEND_TEMPLATE_DECL 1 #define 
| CXX_ISO_COMPLIANT_LIBRARY 1 #define CXX_ABI gnu_v3 #define HAVE_LIBM 1 
| #define HAVE_PCRE 1 #define HAVE_REGEXEC 1 #define HAVE_REGEX 1 
| #define HAVE_ZLIB_H 1 #define HAVE_ZLIB 1 #define HAVE_HDF5_H 1 
| #define HAVE_HDF5 1 #define HAVE_H5GGET_NUM_OBJS 1 #define HAVE_FFTW3 
| 1 #define GLPK_PRE_4_14 1 #define HAVE_GLPK_H 1 #define HAVE_GLPK 1 
| #define HAVE_CURL_CURL_H 1 #define HAVE_CURL 1 #define 
| HAVE_IEEE754_DATA_FORMAT 1 #define F77_FUNC(name,NAME) name ## _ 
| #define F77_FUNC_(name,NAME) name ## _ #define 
| HAVE_SUITESPARSE_UMFPACK_H 1 #define HAVE_SUITESPARSE_COLAMD_H 1 
| #define HAVE_COLAMD 1 #define HAVE_SUITESPARSE_CCOLAMD_H 1 #define 
| HAVE_CCOLAMD 1 #define HAVE_SUITESPARSE_CHOLMOD_H 1 #define 
| HAVE_SUITESPARSE_METIS_H 1 #define HAVE_METIS 1
| /* end confdefs.h.  */
|
| /* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */ 
| #ifdef __cplusplus extern "C"
| #endif
| char cholmod_start ();
| #ifdef F77_DUMMY_MAIN
|
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
|
| #endif
| int
| main ()
| {
| return cholmod_start ();
|   ;
|   return 0;
| }
configure:15863: result: no
configure:15870: checking for cholmod_start in -lcholmod
configure:15937: result: no
configure:16114: WARNING: CHOLMOD not found. This will result in some lack
of functionality for sparse matrices.
configure:16153: checking suitesparse/cs.h usability
configure:16170: gcc -c -g -O2  conftest.c >&5 ........

I don't understand, The reference for libcholmod.so library are present.
This happens when I use gfortran compiler (4.3.0 20070514), no by g77 (3.2.3
20030502).

Thanks a lot.
Regards.
Letizia M.


-----Original Message-----
From: Thomas Treichl [mailto:address@hidden
Sent: Friday, May 18, 2007 3:26 PM
To: Letizia MAZZURCO
Cc: address@hidden
Subject: Re: ../src/liboctinterp.so: undefined reference to
`__cxa_guard_acquire'

Please try something like this on your environment

   export LDFLAGS="$LDFLAGS -L/usr/local/lib -lmetis"
   ./configure

It seems that you've installed all the headers and libraries needed to
include UMFPACK and others, but you are missing a linker-option. Maybe the
above line does help, sometimes systems are missing the -lmetis flag.

Thomas

PS. Please always also reply to the list, so that others with similar
problems can have a look how we solved your problems.

Letizia MAZZURCO schrieb:
 > Thomas,
 >
 > I have this libraries, It are installed under /usr/lib/suitesparse, but
the  > warning message is  :
 >
 > ...
 > checking for camd_postorder in -lcamd... yes  > checking
suitesparse/umfpack.h usability... yes  > checking suitesparse/umfpack.h
presence... yes  > checking for suitesparse/umfpack.h... yes  > checking for
umfpack_zi_get_determinant in -lumfpack... no  > checking for
umfpack_zi_get_determinant in -lumfpack... no  > checking for
umfpack_zi_get_determinant in -lumfpack... no  > configure: WARNING: UMFPACK
not found.  This will result in some lack of  > functionality for sparse
matrices.
 > checking suitesparse/colamd.h usability... yes  > checking
suitesparse/colamd.h presence... yes  > checking for suitesparse/colamd.h...
yes  > checking for colamd in -lcolamd... yes  > checking
suitesparse/ccolamd.h usability... yes  > checking suitesparse/ccolamd.h
presence... yes  > ...
 >
 > Also for CHOLMOD library.
 >
 > Letizia M.
 >
 >
 > -----Original Message-----
 > From: Thomas Treichl [mailto:address@hidden  > Sent: Friday, May
18, 2007 2:40 PM  > To: Letizia MAZZURCO  > Subject: Re:
../src/liboctinterp.so: undefined reference to  > `__cxa_guard_acquire'
 >
 >>   Installation prefix:  /sw/foss/octave/octave-2.9.10/Linux.i686
 >>   C compiler:           gcc  -mieee-fp  -Wall -W -Wshadow -g -O2
 >>   C++ compiler:         g++  -mieee-fp  -Wall -W -Wshadow
-Wold-style-cast
 >> -g -O2
 >>   Fortran compiler:     gfortran -O -mieee-fp
 >
 > Looks better now ;o)
 >
 >>   UMFPACK libraries:
 >>   CHOLMOD libraries:
 >>   ARPACK libraries:
 >
 > UMFPACK and CHOLMOD are necessary if you want to work with
sparse-matrices.
 > Otherwise you won't need it and you should do fine with compilation
without  > using them.
 >
 > ARPACK is not needed anymore and has also been removed in the current
CVS.
 > When
 > octave-2.9.11 is out you won't see this anymore.
 >
 >> configure: WARNING: UMFPACK not found.  This will result in some lack
>> of functionality for sparse matrices.
 >> configure: WARNING: CHOLMOD not found. This will result in some lack  >>
of functionality for sparse matrices.
 >> configure:
 >>
 >> NOTE: libraries may be skipped if a library is not found OR
 >>       if the library on your system is missing required features.
 >>
 >>
 >> All packages (UMFPACK, CHOLMOD,...) are compile with g77.
 >> Do I must recompile all packages using gfortran ?
 >
 > No you don't need to recompile these packages. Once you've created  >
dynamic-libraries you can use them nearly forever ;)  >  > - Thomas