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ABINIT
How to build Abinit under Scientific Linux 5.5 ?
The procedure below describes how to build Abinit 6.8.2 under Scientific Linus 5.5. The results of the different build processes will be installed in the software area, whose path is supposed to be /swmgrs/beappss/abinit. These commands should be run on a workernode.
su - beappss cd /swmgrs/beappss/abinit mkdir install mkdir install/gmp-4.3.2 mkdir install/mpfr-2.4.2 mkdir install/gcc-4.4.5 mkdir install/abinit-6.8.2 wget ftp://ftp.gmplib.org/pub/gmp-4.3.2/gmp-4.3.2.tar.bz2 tar xjvf gmp-4.3.2.tar.bz2 cd gmp-4.3.2 ./configure --prefix=/swmgrs/beappss/abinit/install/gmp-4.3.2 make make check make install cd.. wget http://www.mpfr.org/mpfr-2.4.2/mpfr-2.4.2.tar.bz2 tar xjvf mpfr-2.4.2.tar.bz2 cd mpfr-2.4.2 ./configure --prefix=/swmgrs/beappss/abinit/install/mpfr-2.4.2 --with-gmp=/swmgrs/beappss/abinit/install/gmp-4.3.2 make make check make install cd .. wget ftp://ftp.irisa.fr/pub/mirrors/gcc.gnu.org/gcc/releases/gcc-4.4.5/gcc-4.4.5.tar.gz tar xvzf gcc-4.4.5.tar.gz mkdir gcc-4.4.5-build cd gcc-4.4.5-build export LD_LIBRARY_PATH=/swmgrs/beappss/abinit/install/gmp-4.3.2/lib:/swmgrs/beappss/abinit/install/mpfr-2.4.2/lib:$LD_LIBRARY_PATH ../gcc-4.4.5/configure --prefix=/swmgrs/beappss/abinit/install/gcc-4.4.5 --enable-bootstrap --enable-shared --enable-threads=posix --with-system-zlib --enable-languages=c,c++,fortran --with-cpu=generic --with-mpfr=/swmgrs/beappss/abinit/install/mpfr-2.4.2 --with-gmp=/swmgrs/beappss/abinit/install/gmp-4.3.2 make make install cd .. export PATH=/swmgrs/beappss/abinit/install/gcc-4.4.5/bin:$PATH export LD_LIBRARY_PATH=/swmgrs/beappss/abinit/install/gcc-4.4.5/lib:$LD_LIBRARY_PATH wget http://ftp.abinit.org/abinit-6.8.2.tar.gz tar xvzf abinit-6.8.2.tar.gz cd abinit-6.8.2 ./configure --prefix=/swmgrs/beappss/abinit/install/abinit-6.8.2 make make install
Useful links
- http://forum.abinit.org/viewtopic.php?f=3&t=858
- http://samritmaity.wordpress.com/2010/06/20/cannot-compute-suffix-of-object-files-gcc-4-4-3-installation-problem-solved/
- http://gcc.gnu.org/bugzilla/show_bug.cgi?id=375
Usage
Abinit should be used with the same environment as the one that was set during the build. So, before using Abinit, you should type the following in your shell :
export LD_LIBRARY_PATH=/swmgrs/beappss/abinit/install/gmp-4.3.2/lib:/swmgrs/beappss/abinit/install/mpfr-2.4.2/lib:$LD_LIBRARY_PATH export PATH=/swmgrs/beappss/abinit/install/gcc-4.4.5/bin:$PATH export LD_LIBRARY_PATH=/swmgrs/beappss/abinit/install/gcc-4.4.5/lib:$LD_LIBRARY_PATH
Update : how to build Abinit with MPI support ?
In the following procedure, we suppose that you've already build a newer version of gcc as described above. We also suppose that you want to use the openmpi MPI flavour.
# Never build an app as root : su - beappss # Remove the previous build cd /swmgrs/beappss/abinit mv abinit-6.8.2 abinit-6.8.2_old tar xvzf abinit-6.8.2.tar.gz # With these exports, we will use a newer version of gcc than the one that was initially available. # (We have already built ourself this new version previously.) export LD_LIBRARY_PATH=/swmgrs/beappss/abinit/install/gmp-4.3.2/lib:/swmgrs/beappss/abinit/install/mpfr-2.4.2/lib:$LD_LIBRARY_PATH export PATH=/swmgrs/beappss/abinit/install/gcc-4.4.5/bin:$PATH export LD_LIBRARY_PATH=/swmgrs/beappss/abinit/install/gcc-4.4.5/lib:$LD_LIBRARY_PATH # Now that we are using a new gcc, we must also build a new MPI wget http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.3.tar.bz2 tar xjvf openmpi-1.4.3.tar.bz2 mkdir install/openmpi-1.4.3_gcc-4.4.5 cd openmpi-1.4.3 ./configure --prefix=/swmgrs/beappss/abinit/install/openmpi-1.4.3_gcc-4.4.5 CC=/swmgrs/beappss/abinit/install/gcc-4.4.5/bin/gcc CXX=/swmgrs/beappss/abinit/install/gcc-4.4.5/bin/g++ F77=/swmgrs/beappss/abinit/install/gcc-4.4.5/bin/gfortran FC=/swmgrs/beappss/abinit/install/gcc-4.4.5/bin/gfortran CPP=/swmgrs/beappss/abinit/install/gcc-4.4.5/bin/cpp make make check make install # We adapt our environment to use the new MPI we've just built : export LD_LIBRARY_PATH=/swmgrs/beappss/abinit/install/openmpi-1.4.3_gcc-4.4.5/lib:$LD_LIBRARY_PATH mkdir install/abinit-6.8.2_mpi cd abinit-6.8.2/ ./configure --prefix=/swmgrs/beappss/abinit/install/abinit-6.8.2_mpi --enable-mpi=yes --with-mpi-prefix=/swmgrs/beappss/abinit/install/openmpi-1.4.3_gcc-4.4.5 make mj4 make install
Useful links
Usage
Abinit should be used with the same environment as the one that was set during the build. So, before using Abinit, you should type the following in your shell :
export LD_LIBRARY_PATH=/swmgrs/beappss/abinit/install/gmp-4.3.2/lib:/swmgrs/beappss/abinit/install/mpfr-2.4.2/lib:$LD_LIBRARY_PATH export PATH=/swmgrs/beappss/abinit/install/gcc-4.4.5/bin:$PATH export LD_LIBRARY_PATH=/swmgrs/beappss/abinit/install/gcc-4.4.5/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/swmgrs/beappss/abinit/install/openmpi-1.4.3_gcc-4.4.5/lib:$LD_LIBRARY_PATH
