Dear all,
First message here,so please excuse any newbie behaviour.
Because NetCDF (with netcdf4 capabilities) depends on HDF5, I'm trying to build the latest (1.8.11) HDF5 source on a brand new, up-to-date Mac Pro (Mountain Lion, 10.8.3). I didn't have any success, even after reading the documentation. Please allow me to provide some useful information.
My Fortran compiler is:
SOIL201158464:hdf5-1.8.11 dossa013$ which gfortran
/usr/local/bin/gfortran
SOIL201158464:hdf5-1.8.11 dossa013$ gfortran --version
GNU Fortran (GCC) 4.2.3
Copyright (C) 2007 Free Software Foundation, Inc.
GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
And my C compiler is:
SOIL201158464:hdf5-1.8.11 dossa013$ which gcc
/usr/bin/gcc
SOIL201158464:hdf5-1.8.11 dossa013$ gcc --version
i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Also, I have zlib and szlib installed on /Users/dossa013/software. Based on this, I'm trying to build by issuing the following command:
FC=/usr/local/bin/gfortran CC=/usr/bin/gcc ./configure --prefix=/Users/dossa013/software --with-zlib=/Users/dossa013/software --with-szlib=/Users/dossa013/software --enable-fortran --enable-cxx
which apparently goes fine:
SUMMARY OF THE HDF5 CONFIGURATION
config.log (1.02 MB)
make.out (2.3 MB)
ยทยทยท
=================================
General Information:
-------------------
HDF5 Version: 1.8.11
Configured on: Wed May 29 21:06:42 CDT 2013
Configured by: dossa013@SOIL201158464.cfans.umn.edu
Configure mode: production
Host system: i386-apple-darwin12.3.0
Uname information: Darwin SOIL201158464.cfans.umn.edu 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64
Byte sex: little-endian
Libraries: static, shared
Installation point: /Users/dossa013/software
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc ( (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00))
CFLAGS:
H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/Users/dossa013/software/include -I/Users/dossa013/software/include
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS: -L/Users/dossa013/software/lib -L/Users/dossa013/software/lib
Extra libraries: -lsz -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: /usr/local/bin/gfortran ( GNU Fortran (GCC) 4.2.3)
Fortran 2003 Compiler: no
Fortran Flags:
H5 Fortran Flags: -pedantic -Wall -Wconversion -Wunderflow -Wimplicit-interface -W -O2 -s
AM Fortran Flags:
Shared Fortran Library: no
Static Fortran Library: yes
C\+\+: yes
C\+\+ Compiler: /usr/bin/g\+\+ \( \(GCC\) 4\.2\.1 \(Based on Apple Inc\. build 5658\) \(LLVM build 2336\.11\.00\)\)
C\+\+ Flags:
H5 C\+\+ Flags:
AM C\+\+ Flags:
Shared C\+\+ Library: yes
Static C\+\+ Library: yes
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
However, "make >& make.out" yields tons of warnings since the beggining and finishes with an error I couldn't understand. Since the output is too long, I'm attaching (instead of pasting) both make.out (2.3MB) and config.log (1.2MB).
I wonder if someone more experienced could help me figuring out what I'm doing wrong.
Many thanks in advance,
Thiago.
--
Thiago V. dos Santos
PhD student
Land and Atmospheric Science
University of Minnesota
http://www.laas.umn.edu/CurrentStudents/MeettheStudents/ThiagodosSantos/index.htm
Phone: (612) 323 9898