ABINIT Discussion Forums

Hello Everybody,

Sorry to bother you one more time about compilation. I face the quite same problem with another person, but the responses did not help me.

Here is the configure I use :
./configure --prefix=/home/bouyer/workdir/abinit --enable-mpi --enable-gui --enable-openmpi --enable-scalapack --with-scalapack-libs="-lscalapack -lblacs" --program-suffix="-64" FC=mpif90 --with-mpi-library=/usr/lib64/openmpi/1.4-gcc/lib --with-mpi-include=/usr/lib64/openmpi/1.4-gcc/include

The LD_LIBRARY_PATH points to /usr/lib64/openmpi/1.4-gcc/lib

With FC=gfortran or mpif90, the compilation does not start. The PATH contains the path that points to the /usr/lib64/openmpi/1.4-gcc/bin .

the output is :
===========================
...
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 build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for style of include used by make... GNU
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 dependency style of gcc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 98304
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking how to run the C preprocessor... gcc -E
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 for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking whether gcc and cc understand -c and -o together... yes
checking for inline... inline
checking for ANSI C header files... (cached) yes
checking for working alloca.h... yes
checking for alloca... yes
checking size of void*... 8
checking for sqrtf in -lm... yes
checking for cbrt in -lm... yes
checking for cbrtf in -lm... yes
checking whether we are using the GNU Fortran compiler... no
checking whether mpif90 accepts -g... yes
checking whether we are using the GNU Fortran compiler... (cached) no
checking whether mpif90 accepts -g... (cached) yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
libtool.m4: error: problem compiling FC test program
checking for mpif90 option to produce PIC...
checking if mpif90 static flag works... no
checking if mpif90 supports -c -o file.o... no
checking if mpif90 supports -c -o file.o... (cached) no
checking whether the mpif90 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for Fortran flag to compile .f90 files... unknown
configure: error: Fortran could not compile .f90 files
make[3]: *** [stamps/libxc-config-stamp] Erreur 1
make[3]: quittant le répertoire « /media/DATA/bouyer/abinit/abinit-7.0.5/fallbacks »
make[2]: [all-local] Erreur 2 (ignorée)
Checking build of libxc fallback
test -e stamps/libxc-install-stamp
make[2]: *** [all-local] Erreur 1
make[2]: quittant le répertoire « /media/DATA/bouyer/abinit/abinit-7.0.5/fallbacks »
make[1]: *** [all-recursive] Erreur 1
make[1]: quittant le répertoire « /media/DATA/bouyer/abinit/abinit-7.0.5 »
make: *** [all] Erreur 2
==========================================================================================

The config.log file is attached.

Many thanks in advance to have a look, and to tell me haw to overcome this trouble. I face to that trouble on my PC and the cluster we have.

Bien cordialement,

Frédéric

Hi Frédéric,

- scalapack is not yet supported
- try first with :



jmb

Hello,

Same problem. The compilation stops at the same point.

Cordialement

Bonjour Frédéric,

la suite en anglais, cela semble être la tradition ici.

Your system has a (very) deprecated gcc/gfortran toolchain (version 4.1.2) that doesn't recognize options I have included to compile fortran code (i.e. -march=native). There are workarounds for the libxc failure but you will face other troubles later on. I suggest to compile a new gcc/gfortran 4.6 or 4.7 toolchain (or install Intel compilers) and the corresponding openmpi.

Kind regards,

Alain

Bonjour,

I have installed all Intel compilers and MKL libraries. The compilation ran fine. Thanks a lot for your help. I have checked abinit on the first small example as I follow the user guide. I did not check abinit with mpi.

I am using the Opium pseudos generator. Is it the best choice, or do you recommend me another generator ?

best regards, and good luck to continue developing abinit

Frédéric

Bonjour Frédéric,

Glad it worked.
I have not enough experience with Opium to do a real features comparison and certainly don't imply that Opium is a bad application. Abinit "friend" generators are the Atomic Pseudopotentials Engine aka APE - http://www.tddft.org/programs/APE/ and atompaw for projector augmented wave kind of pseudo - http://users.wfu.edu/natalie/papers/pwpaw/man.html (the latter even provided as an optional package in Abinit distribution).
And the venerable fhi98pp generator is another classic reference app - http://th.fhi-berlin.mpg.de/th/fhi98md/fhi98PP/.

Kind regards,

Alain