Error compiling Abinit-7-10-2 on x86_64-unknown-linux-gnu

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physguy78
Posts: 4
Joined: Mon Feb 02, 2015 4:48 am

Error compiling Abinit-7-10-2 on x86_64-unknown-linux-gnu

Post by physguy78 » Mon Feb 02, 2015 4:56 am

Hello everyone,

i am a new user and I am trying to compile the latest version of Abinit 7.10.2 on an x86_64-unknown-linux-gnu system. when entering the Abinit directory and hitting ./configure, I get the error:

configure: error: Fortran compiler does not provide iso_c_binding module. Use a more recent version or a different compiler

The output file is below. Thanks for your help in advance.

Elio
University of Rondonia
Brazil.

Code: Select all

 ==============================================================================
 === 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 how to create a ustar tar archive... gnutar
checking whether make sets $(MAKE)... (cached) yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for gawk... (cached) gawk
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for realpath,readlink... no
configure: not loading options (no config file available)

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

configure: ABINIT version 7.10.2
configure: M4 010413 - Autoconf 026300 - Automake 011101 - Libtool 020206
configure: reporting user interface changes:

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

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

 ==============================================================================
 === Multicore architecture startup                                         ===
 ==============================================================================

configure: Initializing MPI support
configure: compiler checks deferred
configure: GPU support disabled from command-line

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

checking for sh... /bin/sh
checking for mv... /bin/mv
checking for perl... /usr/bin/perl
checking for rm... /bin/rm
checking for patch... patch
checking for tar... tar

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

checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 4.1
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 4.1

 ==============================================================================
 === 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 4.1
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/opt/intel/Compiler/11.1/069/lib/intel64 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -lgfortranbegin -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/python2.4 -I/usr/lib64/python2.4/site-packages/numpy/core/include
checking for bzr... no
checking Python.h usability... yes
checking Python.h presence... yes
checking for Python.h... yes
checking for numpy/arrayobject.h... yes

 ==============================================================================
 === 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/default/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 whether to activate debug verbosity 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/default/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... no
checking stddef.h presence... yes
configure: WARNING: stddef.h: present but cannot be compiled
configure: WARNING: stddef.h:     check for missing prerequisite headers?
configure: WARNING: stddef.h: see the Autoconf documentation
configure: WARNING: stddef.h:     section "Present But Cannot Be Compiled"
configure: WARNING: stddef.h: proceeding with the preprocessor's result
configure: WARNING: stddef.h: in the future, the compiler will take precedence
configure: WARNING:     ## ------------------------------------------------- ##
configure: WARNING:     ## Report this to https://bugs.launchpad.net/abinit/ ##
configure: WARNING:     ## ------------------------------------------------- ##
checking for stddef.h... yes
checking stdarg.h usability... no
checking stdarg.h presence... yes
configure: WARNING: stdarg.h: present but cannot be compiled
configure: WARNING: stdarg.h:     check for missing prerequisite headers?
configure: WARNING: stdarg.h: see the Autoconf documentation
configure: WARNING: stdarg.h:     section "Present But Cannot Be Compiled"
configure: WARNING: stdarg.h: proceeding with the preprocessor's result
configure: WARNING: stdarg.h: in the future, the compiler will take precedence
configure: WARNING:     ## ------------------------------------------------- ##
configure: WARNING:     ## Report this to https://bugs.launchpad.net/abinit/ ##
configure: WARNING:     ## ------------------------------------------------- ##
checking for stdarg.h... yes
checking stdio.h usability... no
checking stdio.h presence... yes
configure: WARNING: stdio.h: present but cannot be compiled
configure: WARNING: stdio.h:     check for missing prerequisite headers?
configure: WARNING: stdio.h: see the Autoconf documentation
configure: WARNING: stdio.h:     section "Present But Cannot Be Compiled"
configure: WARNING: stdio.h: proceeding with the preprocessor's result
configure: WARNING: stdio.h: in the future, the compiler will take precedence
configure: WARNING:     ## ------------------------------------------------- ##
configure: WARNING:     ## Report this to https://bugs.launchpad.net/abinit/ ##
configure: WARNING:     ## ------------------------------------------------- ##
checking for stdio.h... yes
checking math.h usability... no
checking math.h presence... yes
configure: WARNING: math.h: present but cannot be compiled
configure: WARNING: math.h:     check for missing prerequisite headers?
configure: WARNING: math.h: see the Autoconf documentation
configure: WARNING: math.h:     section "Present But Cannot Be Compiled"
configure: WARNING: math.h: proceeding with the preprocessor's result
configure: WARNING: math.h: in the future, the compiler will take precedence
configure: WARNING:     ## ------------------------------------------------- ##
configure: WARNING:     ## Report this to https://bugs.launchpad.net/abinit/ ##
configure: WARNING:     ## ------------------------------------------------- ##
checking for math.h... yes
checking termios.h usability... no
checking termios.h presence... yes
configure: WARNING: termios.h: present but cannot be compiled
configure: WARNING: termios.h:     check for missing prerequisite headers?
configure: WARNING: termios.h: see the Autoconf documentation
configure: WARNING: termios.h:     section "Present But Cannot Be Compiled"
configure: WARNING: termios.h: proceeding with the preprocessor's result
configure: WARNING: termios.h: in the future, the compiler will take precedence
configure: WARNING:     ## ------------------------------------------------- ##
configure: WARNING:     ## Report this to https://bugs.launchpad.net/abinit/ ##
configure: WARNING:     ## ------------------------------------------------- ##
checking for termios.h... yes
checking errno.h usability... no
checking errno.h presence... yes
configure: WARNING: errno.h: present but cannot be compiled
configure: WARNING: errno.h:     check for missing prerequisite headers?
configure: WARNING: errno.h: see the Autoconf documentation
configure: WARNING: errno.h:     section "Present But Cannot Be Compiled"
configure: WARNING: errno.h: proceeding with the preprocessor's result
configure: WARNING: errno.h: in the future, the compiler will take precedence
configure: WARNING:     ## ------------------------------------------------- ##
configure: WARNING:     ## Report this to https://bugs.launchpad.net/abinit/ ##
configure: WARNING:     ## ------------------------------------------------- ##
checking for errno.h... yes
checking malloc.h usability... no
checking malloc.h presence... yes
configure: WARNING: malloc.h: present but cannot be compiled
configure: WARNING: malloc.h:     check for missing prerequisite headers?
configure: WARNING: malloc.h: see the Autoconf documentation
configure: WARNING: malloc.h:     section "Present But Cannot Be Compiled"
configure: WARNING: malloc.h: proceeding with the preprocessor's result
configure: WARNING: malloc.h: in the future, the compiler will take precedence
configure: WARNING:     ## ------------------------------------------------- ##
configure: WARNING:     ## Report this to https://bugs.launchpad.net/abinit/ ##
configure: WARNING:     ## ------------------------------------------------- ##
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... no
checking mcheck.h presence... yes
configure: WARNING: mcheck.h: present but cannot be compiled
configure: WARNING: mcheck.h:     check for missing prerequisite headers?
configure: WARNING: mcheck.h: see the Autoconf documentation
configure: WARNING: mcheck.h:     section "Present But Cannot Be Compiled"
configure: WARNING: mcheck.h: proceeding with the preprocessor's result
configure: WARNING: mcheck.h: in the future, the compiler will take precedence
configure: WARNING:     ## ------------------------------------------------- ##
configure: WARNING:     ## Report this to https://bugs.launchpad.net/abinit/ ##
configure: WARNING:     ## ------------------------------------------------- ##
checking for mcheck.h... yes
checking sys/time.h usability... no
checking sys/time.h presence... yes
configure: WARNING: sys/time.h: present but cannot be compiled
configure: WARNING: sys/time.h:     check for missing prerequisite headers?
configure: WARNING: sys/time.h: see the Autoconf documentation
configure: WARNING: sys/time.h:     section "Present But Cannot Be Compiled"
configure: WARNING: sys/time.h: proceeding with the preprocessor's result
configure: WARNING: sys/time.h: in the future, the compiler will take precedence
configure: WARNING:     ## ------------------------------------------------- ##
configure: WARNING:     ## Report this to https://bugs.launchpad.net/abinit/ ##
configure: WARNING:     ## ------------------------------------------------- ##
checking for sys/time.h... yes
checking sys/resource.h usability... no
checking sys/resource.h presence... yes
configure: WARNING: sys/resource.h: present but cannot be compiled
configure: WARNING: sys/resource.h:     check for missing prerequisite headers?
configure: WARNING: sys/resource.h: see the Autoconf documentation
configure: WARNING: sys/resource.h:     section "Present But Cannot Be Compiled"
configure: WARNING: sys/resource.h: proceeding with the preprocessor's result
configure: WARNING: sys/resource.h: in the future, the compiler will take precedence
configure: WARNING:     ## ------------------------------------------------- ##
configure: WARNING:     ## Report this to https://bugs.launchpad.net/abinit/ ##
configure: WARNING:     ## ------------------------------------------------- ##
checking for sys/resource.h... yes
checking for abort... no
checking for mallinfo... no
checking size of char... 0
checking size of short... 0
checking size of int... 0
checking size of long... 0
checking size of long long... 0
checking size of unsigned int... 0
checking size of unsigned long... 0
checking size of unsigned long long... 0
checking size of float... 0
checking size of double... 0
checking size of long double... 0
checking size of size_t... 0
checking size of ptrdiff_t... 0
checking for an ANSI C-conforming const... no
checking for size_t... no
checking whether the Fortran compiler accepts the ASYNCHRONOUS attribute... no
checking whether the Gfortran compiler supports BACKTRACE... no
checking whether the Fortran compiler supports GET_COMMAND_ARGUMENT... yes
checking whether the Fortran compiler supports EXECUTE_COMMAND_LINE... no
checking whether the Fortran compiler supports SYSTEM... yes
checking whether the Fortran compiler accepts the CONTIGUOUS attribute... no
checking whether the Fortran compiler supports allocatable arrays in datatypes... no
checking whether the Fortran compiler supports IEEE_EXCEPTIONS... no
checking whether the Fortran compiler supports IOMSG... yes
checking whether the Fortran compiler provides the iso_c_binding module... configure: error: Fortran compiler does not provide iso_c_binding module. Use a more recent version or a different compiler
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pouillon
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Re: Error compiling Abinit-7-10-2 on x86_64-unknown-linux-g

Post by pouillon » Mon Feb 02, 2015 12:55 pm

GCC 4.1 (published in 2006) is way too old to be able to build Abinit.

Please use a more recent version of GCC (e.g. 4.8 or 4.9) or specify another compiler on the command line, e.g.:

Code: Select all

../configure ... options ... FC="ifort"
Yann Pouillon
Simune Atomistics
Donostia-San Sebastián, Spain
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physguy78
Posts: 4
Joined: Mon Feb 02, 2015 4:48 am

Re: Error compiling Abinit-7-10-2 on x86_64-unknown-linux-g

Post by physguy78 » Mon Feb 02, 2015 3:23 pm

Thanks very much for your help. In fact I have tried this and I got the error:
checking whether to use C clock for timings... no

==============================================================================
=== Multicore architecture support ===
==============================================================================

checking whether to enable OpenMP support... no
checking whether to build MPI code... yes
checking whether MPI is usable... no
configure: error: MPI support is broken - please fix your config parameters and/or MPI installation

I have seen a few posts about this; however I could not resolve. What I did is the following:

which mpif90 and I got
/usr/bin/mpif90

so I have executed : ./configure FC=ifort --enable-mpi="yes" --with-mpi-prefix=/usr/bin/mpif90

But i still get the same error (I have also tried to compile without FC=ifort but i got the previous error: use another compiler!)

Please can you help me in resolving this. The config.log file is attached..
Attachments
config.log
(159.03 KiB) Downloaded 380 times
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physguy78
Posts: 4
Joined: Mon Feb 02, 2015 4:48 am

Re: Error compiling Abinit-7-10-2 on x86_64-unknown-linux-g

Post by physguy78 » Mon Feb 02, 2015 5:51 pm

Hello a quick update:

I have used the following configure line: ./configure --enable-mpi --enable-mpi-fft --enable-mpi-io --with-mpi-prefix=/usr FC=ifort
On one hand I got:

==============================================================================
=== Multicore architecture startup ===
==============================================================================

configure: Initializing MPI support
configure: looking for MPI in /usr
checking for a MPI C compiler... /usr/bin/mpicc
checking for a MPI C++ compiler... /usr/bin/mpicxx
checking for a MPI Fortran compiler... /usr/bin/mpif90
configure: creating wrapper for MPI Fortran compiler
configure: GPU support disabled from command-line

which I guess means Abinit found the compilers but on the other hand, I got the same first error: (although compiler is ifort!!)

checking whether the Fortran compiler provides the iso_c_binding module... configure: error: Fortran compiler does not provide iso_c_binding module. Use a more recent version or a different compiler


How come?

Regards

Elio
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admin
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Joined: Thu Sep 17, 2009 9:49 am

Re: Error compiling Abinit-7-10-2 on x86_64-unknown-linux-g

Post by admin » Sat Feb 14, 2015 10:12 pm

HI,

What the version of ifort ?

only versions >= 12.1 of ifort are supported with Abinit > 7.x

jmb
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