ABINIT Discussion Forums

This problem has me stumped. I have been trying to build 10.6.3 under OpenSuse 11.3 using the usual gcc with the configuration line

./configure --prefix=/opt --with-mpi-prefix=/usr/lib64/mpi/gcc/openmpi --with-fallbacks-tardir=~/.abinit/tarballs --with-linalg-flavor=mkl --enable-fallbacks

Both curl and wget are installed and work fine (I just downloaded the abinit source using them). The configure script fails when it gets to the netcdf library and even though I have specified the fallback library *and* netcdf is there for some reason the configure script does not see it. As I demonstrate below, listing the directory shows that all of the necessary sources for the plugins are there and then some. Any suggestions on what is going wrong and how to fix it? The configure output is attached below.



~/abinit/abinit-6.10.3> ./configure --prefix=/opt --with-mpi-prefix=/usr/lib64/mpi/gcc/openmpi --with-fallbacks-tardir=~/.abinit/tarballs --with-linalg-flavor=mkl --enable-fallbacks

==============================================================================
=== Overall startup ===
==============================================================================

checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for gawk... (cached) gawk
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
configure: not loading options (no config file available)

==============================================================================
=== Build-system information ===
==============================================================================

configure: ABINIT version 6.10.3
configure: M4 010416 - Autoconf 026800 - Automake 011100 - Libtool 020204
configure: reporting user interface changes:
configure: * new option --enable-gw-openmp is available

==============================================================================
=== Option consistency checking ===
==============================================================================

configure: checking consistency of library-related options
configure: |---> all OK
configure:
configure: checking consistency of plug-in options
configure: |---> all OK
configure:
configure: checking consistency of experimental options
configure: |---> all OK
configure:
configure: |---> all OK
configure:
configure: parsing command-line options

==============================================================================
=== Connector startup ===
==============================================================================

configure: MPI support disabled from command-line
configure: GPU support disabled from command-line

==============================================================================
=== Utilities ===
==============================================================================

checking for sh... /usr/bin/sh
checking for mv... /bin/mv
checking for perl... /usr/bin/perl
checking for rm... /bin/rm
checking for dvips... no
checking for dvipdf... dvipdf
checking for latex... no
checking for markdown... no
checking for patch... patch
checking for ps2pdf... ps2pdf
checking for tar... tar
checking for wget... wget
checking for curl... curl
configure: using internal version of MarkDown

==============================================================================
=== C support ===
==============================================================================

checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking which type of compiler we have... gnu 4.5
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no

==============================================================================
=== C++ support ===
==============================================================================

checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking which type of C++ compiler we have... gnu 4.5

==============================================================================
=== Fortran support ===
==============================================================================

checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking which type of Fortran compiler we have... gnu 4.5
checking fortran 90 modules extension... mod
checking for Fortran flag to compile .F90 files... none
configure: determining Fortran module case
checking whether Fortran modules are upper-case... no
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran... -L/usr/lib64/gcc/x86_64-suse-linux/4.5 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/intel/composerxe-2011.3.174/compiler/lib/intel64 -L/opt/intel/composerxe-2011.3.174/mkl/lib/intel64 -L/opt/intel/composerxe-2011.3.174/ipp/../compiler/lib/intel64 -L/opt/intel/composerxe-2011.3.174/ipp/lib/intel64 -L/opt/intel/composerxe-2011.3.174/tbb/lib/intel64//cc4.1.0_libc2.4_kernel2.6.16.21 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../.. -lgfortran -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore

==============================================================================
=== Python support ===
==============================================================================

checking for python... python
checking for Python CPPFLAGS... -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include
checking for bzr... no
checking for Python NumPy headers... not found
checking numarray/arrayobject.h usability... no
checking numarray/arrayobject.h presence... no
checking for numarray/arrayobject.h... no

==============================================================================
=== Libraries and linking ===
==============================================================================

checking for ar... ar
checking for ranlib... ranlib

==============================================================================
=== Hints ===
==============================================================================

checking for cpp... cpp
checking for a true C preprocessor... cpp
checking which cpp hints to apply... default/default/default
checking which cc hints to apply... gnu/default/default
checking which xpp hints to apply... none/none/none
checking which cxx hints to apply... gnu/default/default
checking which fpp hints to apply... default/default/default
checking which fc hints to apply... gnu/4.5/default
checking which ar hints to apply... none/none/none
checking which Fortran preprocessor to use...
checking which Fortran preprocessor flags to apply...
checking whether to wrap Fortran compiler calls... no

==============================================================================
=== Debugging ===
==============================================================================

checking debugging status... enabled (profile mode: basic)
configure: setting C debug flags to '-g'
configure: setting C++ debug flags to '-g'
configure: setting Fortran debug flags to '-g'
checking whether to activate debug mode in source files... no
checking which cc debug flags to apply... gnu/default/default
checking which cxx debug flags to apply... none/none/none
checking which fc debug flags to apply... gnu/default/default
checking whether to activate design-by-contract debugging... no

==============================================================================
=== Optimizations ===
==============================================================================

checking optimization status... enabled (profile mode: standard)
checking which cc optimizations to apply... gnu/default/default
checking which cxx optimizations to apply... gnu/default/default
checking which fc optimizations to apply... gnu/4.5/default
checking whether to apply per-directory optimizations... yes

==============================================================================
=== 64-bit support ===
==============================================================================

checking for a 64-bit architecture... yes
checking whether to use 64-bit flags... no
checking for user-defined 64-bit flags...

==============================================================================
=== Build flags ===
==============================================================================

configure: static builds may be performed

==============================================================================
=== Advanced compiler features ===
==============================================================================

checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking sys/malloc.h usability... no
checking sys/malloc.h presence... no
checking for sys/malloc.h... no
checking mcheck.h usability... yes
checking mcheck.h presence... yes
checking for mcheck.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking for abort... yes
checking for mallinfo... yes
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of unsigned int... 4
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of size_t... 8
checking size of ptrdiff_t... 8
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether the Fortran compiler supports allocatable arrays in datatypes... yes
checking whether the Fortran compiler provides the iso_c_binding module... yes
checking whether the Fortran compiler accepts exit()... yes
checking whether the Fortran compiler accepts flush()... yes
checking whether the Fortran compiler accepts flush_()... no
checking whether the Fortran compiler accepts gamma()... yes
checking whether the Fortran compiler accepts getenv()... yes
checking whether the Fortran compiler accepts getpid()... no
checking whether the Fortran compiler accepts the null() intrinsic... yes
checking whether the Fortran compiler accepts quadruple integers... yes
checking whether the Fortran compiler accepts long lines... yes
checking whether the Fortran compiler supports stream IO... yes
checking whether the Fortran compiler accepts cpu_time()... yes
checking whether the Fortran compiler accepts etime()... no
checking whether to use C clock for timings... no

==============================================================================
=== Connectors / Fallbacks ===
==============================================================================

checking whether MPI is usable... no
checking whether to build MPI code... no
checking whether the MPI library supports MPI_CREATE_TYPE_STRUCT... no
checking whether to activate GPU support... no
checking for the requested transferable I/O support... netcdf+etsf_io
checking netcdf.h usability... no
checking netcdf.h presence... no
checking for netcdf.h... no
checking for library containing nc_open... no
checking for Fortran module includes... unknown
configure: WARNING: falling back to internal netcdf version
configure: WARNING: ETSF_IO requires missing NetCDF support
configure: WARNING: falling back to internal etsf_io version
checking for the actual transferable I/O support... netcdf-fallback+etsf_io-fallback
checking for the requested timer support... abinit
checking for the actual timer support... abinit
checking for the requested linear algebra support... mkl
checking for library containing zgemm... -lmkl_intel_lp64
checking for library containing zhpev... -lmkl_intel_lp64
checking whether we have a serial linear algebra support... yes
checking whether we have a parallel linear algebra support... no
checking for the actual linear algebra support... mkl
checking for the requested math support... none
checking for the actual math support... none
checking for the requested FFT support... none
checking for the actual FFT support... none
checking for the requested DFT support... atompaw+bigdft+libxc+wannier90
checking xc.h usability... no
checking xc.h presence... no
checking for xc.h... no
checking xc_funcs.h usability... no
checking xc_funcs.h presence... no
checking for xc_funcs.h... no
checking for library containing xc_func_init... no
checking for Fortran module includes... unknown
configure: WARNING: falling back to internal libxc version
configure: WARNING: AtomPAW recommends missing LibXC support
checking for atompaw... no
checking for graphatom... no
configure: WARNING: falling back to internal atompaw version
configure: WARNING: BigDFT requires missing LibXC support
configure: WARNING: falling back to internal bigdft version
checking for wannier.x... no
checking for wannier90.x... no
checking for library containing wannier_run... no
configure: WARNING: falling back to internal wannier90 version
checking for the actual DFT support... libxc-fallback+atompaw-fallback+bigdft-fallback+wannier90-fallback
configure: using former plugins as a temporary workaround
configure: fallbacks to enable => atompaw bigdft etsf_io libxc netcdf wannier90
checking whether to build atompaw... yes
checking whether to build bigdft... yes
checking whether to build etsf_io... yes
checking whether to build fox... no
checking whether to build libxc... yes
checking whether to build linalg... no
checking whether to build netcdf... yes
checking whether to build wannier90... yes
configure: using tarball repository ~/.abinit/tarballs
configure: copying linear algebra tarball to tarball repository
cp: cannot stat `/home/paulfons/abinit/abinit-6.10.3/fallbacks/transient/lapack-abinit_6.0.tar.gz': No such file or directory
checking whether to enable the LINALG fallback... no
checking whether to build the LINALG fallback... no
checking whether to enable the FOX fallback... no
checking whether to build the FOX fallback... no
checking for a source tarball of NETCDF... no
configure: downloading NETCDF - this may take a while
checking availability of NETCDF from URL 1... ~/.abinit/tarballs/netcdf-4.1.1.tar.gz: No such file or directory
no
checking availability of NETCDF from URL 2... ~/.abinit/tarballs/netcdf-4.1.1.tar.gz: No such file or directory
no
configure: WARNING: could not download NETCDF fallback tarball

+--------------------------------------------------------------+
| Fallback availability failure |
+--------------------------------------------------------------+
| The build system of Abinit has not been able to download |
| one or more required external packages. An unstable or |
| absent connection to internet of this computer is the most |
| probable culprit. This means that the build cannot |
| proceed, and the configure script will thus abort now with |
| an error. |
| |
| To address this issue, you may: |
| |
| * use pre-compiled versions of the external packages, |
| through the --with-*-bins, --with-*-incs, and |
| --with-*-libs options of configure; please see |
| the section associated to connectors in |
| ~abinit/doc/config/build-config.ac for available |
| options and details; |
| |
| * manually upload the source tarballs to a dedicated |
| directory, either ~/.abinit/tarballs/ (the default) or |
| any directory of your choice; please see the section |
| associated to fallbacks in |
| ~abinit/doc/config/build-config.ac for details; |
| |
| * disable the corresponding extensions, by using the |
| following options of configure: |
| --with-dft-flavor="none"; |
| --with-trio-flavor="none"; |
| please see the section associated to connectors in |
| ~abinit/doc/config/build-config.ac for details. |
| |
+--------------------------------------------------------------+

configure: error: cannot build Abinit - aborting
paulfons@asccmp177:~/abinit/abinit-6.10.3> curl
curl: try 'curl --help' or 'curl --manual' for more information
paulfons@asccmp177:~/abinit/abinit-6.10.3> wget
wget: missing URL
Usage: wget [OPTION]... [URL]...

Try ‘wget --help’ for more options.
paulfons@asccmp177:~/abinit/abinit-6.10.3> ls -l ~/.abinit/tarballs/
total 48776
-rw-r--r-- 1 paulfons users 140256 Dec 4 19:29 atompaw-3.0.1.2.tar.gz
-rw-r--r-- 1 paulfons users 3785332 Dec 4 19:34 atompaw-3.0.1.tar.gz
-rw-r--r-- 1 paulfons users 561262 Dec 4 19:34 bigdft-1.0-1.tar.gz
-rw-r--r-- 1 paulfons users 944219 Dec 4 19:34 bigdft-1.2.0.2.tar.gz
-rw-r--r-- 1 paulfons users 959861 Mar 29 2011 bigdft-1.2.0.4.tar.gz
-rw-r--r-- 1 paulfons users 382094 Dec 4 19:34 etsf_io-1.0.2.tar.gz
-rw-r--r-- 1 paulfons users 453734 Dec 4 19:34 etsf_io-1.0.3.tar.gz
-rw-r--r-- 1 paulfons users 294042 Dec 4 19:34 FoX-4.1.0.tar.gz
-rw-r--r-- 1 paulfons users 3468332 Dec 4 19:42 lapack-abinit_6.0.tar.gz
-rw-r--r-- 1 paulfons users 3487599 Dec 4 19:45 lapack-abinit_6.10.tar.gz
-rw-r--r-- 1 paulfons users 502757 Dec 4 19:34 libxc-1.0.tar.gz
-rw-r--r-- 1 paulfons users 256149 Dec 4 19:34 libxc-svn-r6071-fixed.tar.gz
-rw-r--r-- 1 paulfons users 11572512 Dec 4 19:34 netcdf-3.6.3.tar.gz
-rw-r--r-- 1 paulfons users 11201096 Dec 13 06:58 netcdf-4.1.1.tar.gz
-rw-r--r-- 1 paulfons users 6259705 Dec 4 19:34 wannier90-1.1.tar.gz
-rw-r--r-- 1 paulfons users 5643731 Dec 4 19:34 wannier90-1.2.tar.gz

For portability reasons, the configure script does not do tilde (~) expansion. You should provide it with "$HOME" instead.