Re: can't find qhull and HDF5 libs on octave 3.0 installing (need powerful guy's help)

[Tatsuro MATSUOKA]

Hello
> I use intel fortran compiler "ifort" alternatively.
> HDF5 was compiled without --enable-fortran the first time. NO error
> reported when making it. But cannot pass octave configuration. 
> That's why I attach --enable-fortran to see where the question in HDF5.
> here is the config.log output of octave:

HDF5 was compiled without --enable-fortran is OK.
I do not use this option for HDF5.

I guess that the problem MPI-c and Intel fortran incomptible each other.
Please use complible C, C++ and fortran like gcc, g++ and g77.
If you have Intel C and C++, please use them.
If you do not have them, first you build f2c for MPI-c and try to build octave 
by --with-f2c.

http://netlib.sandia.gov/f2c/

Regards
Tatsuro

--- guez offtsing <address@hidden> wrote:

> I use intel fortran compiler "ifort" alternatively.
> HDF5 was compiled without --enable-fortran the first time. NO error
> reported when making it. But cannot pass octave configuration. 
> That's why I attach --enable-fortran to see where the question in HDF5.
> here is the config.log output of octave:
> ============================================
> ============================================
> configure:9216: /opt/intel/cc/9.0/bin/icc -o conftest -g -O2
> -I/usr/local/include  -L/usr/local/lib conftest.c -lhdf5  -lz -lm  >&5
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0x2202): In function
> `H5AC_flush':
> : undefined reference to `MPI_Barrier'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0x2242): In function
> `H5AC_flush':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0x7d92): In function
> `H5AC_broadcast_clean_list':
> : undefined reference to `MPI_Bcast'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0x7dd2): In function
> `H5AC_broadcast_clean_list':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0x82e2): In function
> `H5AC_broadcast_clean_list':
> : undefined reference to `MPI_Bcast'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0x8322): In function
> `H5AC_broadcast_clean_list':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0xa852): In function
> `H5AC_propagate_flushed_and_still_clean_entries_list':
> : undefined reference to `MPI_Barrier'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0xa892): In function
> `H5AC_propagate_flushed_and_still_clean_entries_list':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0xadf2): In function
> `H5AC_receive_and_apply_clean_list':
> : undefined reference to `MPI_Bcast'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0xae32): In function
> `H5AC_receive_and_apply_clean_list':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0xb112): In function
> `H5AC_receive_and_apply_clean_list':
> : undefined reference to `MPI_Bcast'
> /usr/local/lib/libhdf5.a(H5AC.o)(.text+0xb152): In function
> `H5AC_receive_and_apply_clean_list':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5Distore.o)(.text+0x8212): In function
> `H5D_istore_allocate':
> : undefined reference to `MPI_Barrier'
> /usr/local/lib/libhdf5.a(H5Distore.o)(.text+0x8262): In function
> `H5D_istore_allocate':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x3c2): In function
> `H5D_mpio_opt_possible':
> : undefined reference to `MPI_Allreduce'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x402): In function
> `H5D_mpio_opt_possible':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x1232): In function
> `H5D_mpio_get_min_chunk':
> : undefined reference to `MPI_Allreduce'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x1272): In function
> `H5D_mpio_get_min_chunk':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x1452): In function
> `H5D_mpio_get_sum_chunk':
> : undefined reference to `MPI_Allreduce'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x1492): In function
> `H5D_mpio_get_sum_chunk':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x2862): In function
> `H5D_link_chunk_collective_io':
> : undefined reference to `MPI_Type_struct'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x28a2): In function
> `H5D_link_chunk_collective_io':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x2982): In function
> `H5D_link_chunk_collective_io':
> : undefined reference to `MPI_Type_commit'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x29c2): In function
> `H5D_link_chunk_collective_io':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x2ab2): In function
> `H5D_link_chunk_collective_io':
> : undefined reference to `MPI_Type_struct'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x2af2): In function
> `H5D_link_chunk_collective_io':
> : undefined reference to `MPI_Error_string'
> /usr/local/lib/libhdf5.a(H5Dmpio.o)(.text+0x2c02): In function
> `H5D_link_chunk_collective_io':
> : undefined reference to `MPI_Type_commit'
> ...
> ...
> /usr/local/lib/libhdf5.a(H5Smpio.o)(.text+0x2392): more undefined
> references to `MPI_Error_string' follow
> /usr/local/lib/libhdf5.a(H5Smpio.o)(.text+0x2522): In function
> `H5S_obtain_datatype':
> : undefined reference to `MPI_Type_free'
> /usr/local/lib/libhdf5.a(H5Dcontig.o)(.text+0x922): In function
> `H5D_contig_fill':
> : undefined reference to `MPI_Barrier'
> /usr/local/lib/libhdf5.a(H5Dcontig.o)(.text+0x972): In function
> `H5D_contig_fill':
> : undefined reference to `MPI_Error_string'
> configure:9222: $? = 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_QHULL 1
> | #define HAVE_PCRE 1
> | #define HAVE_REGEXEC 1
> | #define HAVE_REGEX 1
> | #define HAVE_ZLIB_H 1
> | #define HAVE_ZLIB 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 H5Pcreate ();
> | int
> | main ()
> | {
> | return H5Pcreate ();
> |   ;
> |   return 0;
> | }
> configure:9241: result: no
> configure:9583: WARNING: HDF5 library not found.  Octave will not be
> able to save or load HDF5 data files.
> ============================================
> ============================================
> 
> It seems MPI not found by HDF5. Maybe my system box is quite out of
> date. I have compiled BLAS, LAPACK,
> FFTW, GLPK, Sparse, CURL, QHULL from source, HDF5 is the only problem
> left to do. I would hack the source code of HDF5 when waiting for 
> Someone's help.
> Thank you for your kindly and patient help.
> 
> Regards.
> 
> 在 2008-03-25二的 15:11 +0900，Tatsuro MATSUOKA写道：
> > Hello 
> > 
> > I have not tried that HDF5-1.8.0.
> > On my cygwin binary, I have used Ver. 1.6.7.
> > There is no definte reason why I do not select ver. 1.8.0.
> > I guessed that octave itself does not change about the HDF5. 
> > I am afraid that HDF5-1.8.0 is too new.  
> > 
> > It is a mere guess.　
> > 
> > However, what fortran complier did use?   
> >  
> > Is the --enable-fortran required ?
> > I did not use this option for the hdf5 for octave.
> > 
> > I do not know how hdf5 is implemented to the octave so that I cannot answer 
> > any longer.
> > 
> > Let us wait a more powerful guy's help.
> > 
> > Regards
> > 
> > Tatsuro
> > 
> > --- guez offtsing <address@hidden> wrote:
> > 
> > > Thank you for your quick reply. I dive into the config.log and qhull is
> > > solved, while hdf5 not.
> > > HDF5-1.8.0 is recompiled with mpicc a second time. A lot of "undefined
> > > reference" appear when approach to "fortranlib". It has taken me several
> > > days seeking the solution. But I don't find any either from Google or
> > > from HDF team.
> > > It is a far question from octave although. I will be more appreciative
> > > if you can give me further advices on hdf5 compiling.
> > > ------------------------------
> > > ------------------------------
> > > My configure option:
> > > CC=/opt/mpich/ch-p4/bin/mpicc ./configure --prefix=/usr/local/hdf5
> > > --enable-fortran
> > > 
> > > AND the error output:
> > > : undefined reference to `MPI_Type_commit'
> > > ../../src/.libs/libhdf5.a(H5Smpio.o)(.text+0x1d22): In function
> > > `H5S_obtain_datatype':
> > > : undefined reference to `MPI_Type_free'
> > > ../../src/.libs/libhdf5.a(H5Smpio.o)(.text+0x1d92): In function
> > > `H5S_obtain_datatype':
> > > : undefined reference to `MPI_Type_struct'
> > > ../../src/.libs/libhdf5.a(H5Smpio.o)(.text+0x1de2): In function
> > > `H5S_obtain_datatype':
> > > : undefined reference to `MPI_Error_string'
> > > ../../src/.libs/libhdf5.a(H5Smpio.o)(.text+0x1f92): In function
> > > `H5S_obtain_datatype':
> > > : undefined reference to `MPI_Error_string'
> > > ../../src/.libs/libhdf5.a(H5Smpio.o)(.text+0x2092): In function
> > > `H5S_obtain_datatype':
> > > : undefined reference to `MPI_Error_string'
> > > ../../src/.libs/libhdf5.a(H5Smpio.o)(.text+0x2192): In function
> > > `H5S_obtain_datatype':
> > > : undefined reference to `MPI_Error_string'
> > > ../../src/.libs/libhdf5.a(H5Smpio.o)(.text+0x2292): In function
> > > `H5S_obtain_datatype':
> > > : undefined reference to `MPI_Error_string'
> > > ../../src/.libs/libhdf5.a(H5Smpio.o)(.text+0x2392): more undefined
> > > references to `MPI_Error_string' follow
> > > ../../src/.libs/libhdf5.a(H5Smpio.o)(.text+0x2522): In function
> > > `H5S_obtain_datatype':
> > > : undefined reference to `MPI_Type_free'
> > > ../../src/.libs/libhdf5.a(H5Dcontig.o)(.text+0x922): In function
> > > `H5D_contig_fill':
> > > : undefined reference to `MPI_Barrier'
> > > ../../src/.libs/libhdf5.a(H5Dcontig.o)(.text+0x972): In function
> > > `H5D_contig_fill':
> > > : undefined reference to `MPI_Error_string'
> > > make[2]: *** [fortranlib_test] Error 1
> > > make[2]: Leaving directory `/home/linux/hdf5-1.8.0/fortran/test'
> > > make[1]: *** [all-recursive] Error 1
> > > make[1]: Leaving directory `/home/linux/hdf5-1.8.0/fortran'
> > > make: *** [all-recursive] Error 1
> > > ---------------------------
> > > ---------------------------
> > > 
> > > Regards
> > > 在 2008-03-22六的 06:39 +0900，Tatsuro MATSUOKA写道： 
> > > > Hello
> > > > 
> > > > Please also check the config.log.
> > > > 
> > > > The configure script of octave does not only check the existence but 
> > > > also check test code
> to
> > > be
> > > > complied correctly.  The detailed results do not appear on the screen.  
> > > > 
> > > > Please open  config.log by an editor and seach the corresponding part 
> > > > by the keywords
> qhull
> > > and hdf5.
> > > > 
> > > > Regards
> > > > 
> > > > Tatsuro
> > > > 
> > > > 
> > > > --- guez offtsing <address@hidden> wrote:
> > > > 
> > > > > hellow, I try to build octave3 from source on Suse Enterprise Server 
> > > > > 9.
> > > > > But octave
> > > > > cannot find the qhull lib, so does HDF5.
> > > > > 
> > > > > linux:~/octave-3.0.0 # uname -a
> > > > > Linux linux 2.6.5-7.191-sn2 #1 SMP Tue Jun 28 14:58:56 UTC 2005 ia64
> > > > > ia64 ia64 GNU/Linux
> > > > > 
> > > > > linux:~/octave-3.0.0 #./configure CPPFLAGS=-I/usr/local/include
> > > > > LDFLAGS=-L/usr/local/lib |grep -E "qhull|hdf5"
> > > > > -------------------------
> > > > > checking qhull/qhull_a.h usability... no
> > > > > checking qhull/qhull_a.h presence... no
> > > > > checking for qhull/qhull_a.h... no
> > > > > configure: WARNING: Qhull library not found --- This will result in 
> > > > > loss
> > > > > of functionality of some geometry functions.
> > > > > checking for H5Pcreate in -lhdf5... no
> > > > > configure: WARNING: HDF5 library not found.  Octave will not be able 
> > > > > to
> > > > > save or load HDF5 data files.
> > > > > --------------------------
> > > > > libqhull.a is compiled and put in /usr/local/lib
> > > > > header files put in dir /usr/local/include/qhull
> > > > > 
> > > > > HDF5 v1.8.0 installed in /usr/local/hdf5, but I copy the .a files and 
> > > > > .h files to /usr/local/lib & include, too.
> > > > > 
> > > > > Why octave cannot find them? Btw, Sparse suite put in the same paths
> > > > > don't have any problems.
> > > > > 
> > > > > 
> > > > > _______________________________________________
> > > > > Help-octave mailing list
> > > > > address@hidden
> > > > > https://www.cae.wisc.edu/mailman/listinfo/help-octave
> > > > > 
> > > > 
> > > > 
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