Source installation

Compiler variables

First, please look at the "Machine-specific notes" section of this document for appropriate compiler flags, etc. to be set via pre-configuration environmental variables. It's not a big deal if you skip this step, but APBS will run more slowly.

Installation directories

There are two directories you'll need to identify prior to installation. The first, which we'll call FETK_SRC, will contain the APBS and MALOC source code. This directory can be deleted after installation, if you wish. The second directory will be the permanent location for APBS and MALOC; we'll call this FETK_PREFIX. If you have root permission, you could pick a global directory such as /usr/local for this; otherwise, pick a directory for which you have write permission. The following commands set up the directories and environmental which point to them:

            $ export FETK_SRC=/home/soft/src
            $ export FETK_PREFIX=/home/soft
            $ export FETK_INCLUDE=${FETK_PREFIX}/include
            $ export FETK_LIBRARY=${FETK_PREFIX}/lib
            $ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
          

If you're planning to use MPI, you'll need to set some additional environmental variables. The variable FETK_MPI_INCLUDE points to the directory where the MPI header files reside (mpi.h) and the variable FETK_MPI_LIBRARY points to the directory where the MPI libraries are located (libmpi.a or libmpich.a). For example, on my system, I type: $ export FETK_MPI_INCLUDE=/usr/share/mpi/include $ export FETK_MPI_LIBRARY=/usr/share/mpi/lib

Unpacking the source code

You're now ready to unpack the source code:

            $ cd ${FETK_SRC}
            $ gzip -dc maloc.tar.gz | tar xvf -
            $ gzip -dc apbs-0.4.0.tar.gz | tar xvf -
          

Compiling MALOC

Now we need to compile the hardware-abstraction library, MALOC. First, go to the MALOC directory:

            $ cd ${FETK_SRC}/maloc
          

If you are not starting from a freshly-untarred version of MALOC, you need to clean up the previous distribution by: $ make distclean and ignoring any error messages that may result.

1. Sequential execution only (no MPI):

   $ ./configure --prefix=${FETK_PREFIX}

2. With parallel execution (MPI):

   $ ./configure --prefix=${FETK_PREFIX} --enable-mpi

Be sure to keep an eye out for warning messages during the configuration of MALOC, especially if you are using MPI.

              $ make; make install
           

Intel IA32/IA64

In what follows, we're denoting Pentium/Xeon 32-bit Intel machines as "IA32" and Itanium* 64-bit Intel machines as "IA64".

                $ export CC='icc'
                $ export CXX='icc'
                $ export F77='ifort'
              

                $ export LDFLAGS='-static-libcxa'
              

                $ export FFLAGS='-fast -arch pn4'
                $ export CFLAGS='-fast -tpp5'
                $ export CXXFLAGS=${CFLAGS}
              

              $ ./configure --prefix=${FETK_PREFIX} --disable-blas
              $  make; make install 
            

              $ export INTEL_BLAS=/path/to/MKL/lib/directory
              $ ./configure --prefix=${FETK_PREFIX} --with-blas="-L${INTEL_BLAS} -lmkl_lapack -lmkl_ipf -ldl" --with-blas-name="mkl_lapack"
              $  make; make install 
            

Macintosh

We are happy to now provide a Mac install package for G5 OS 10.4 (Tiger). Unfortunately this is the only binary for Mac that we have available, so users on G4s or OS 10.3 may have to compile binaries for themselves - you may want to examine the apbs-users mailing list which has a number of threads which discuss installation on Mac OS platforms. Alternatively you can try using Fink for the installation - please see Bill Scott's excellent guidelines at http://chemistry.ucsc.edu/~wgscott/xtal.

A few notes about compiling on Macintosh:

1. It has become apparent from the mailing lists that some "packages" of the GNU development software available for MacOS contain different major versions of the C and FORTRAN compilers. This is very bad; APBS will not compile with different versions of the C and FORTRAN compilers. If you use GCC 4.0, for instance, gfortran 4.0 will work while g77 3.3 will not. If you see link errors involving "restFP" or "saveFP" this is most likely the cause.

2. In gcc 4.0 (included in Xcode 2.0 and higher) the -fast option turns on the -fast-math flag. This flag optimizes by using rounding, and thus can lead to inaccuate results and should be avoided.

3. As it stands now the autoconf script does not support using the native vecLib framework as an architecture-tuned BLAS replacement. In testing there were only slight timing improvements over using the MALOC-supplied BLAS as it is.

4. We have had success using IBM's XLF for Mac in conjunction with GCC 4.0, although the corresponding XLC compilers do not seem to work under Tiger.

IBM Power3/Power4 AIX

These are various compilation options I experimented with on the NPACI Blue Horizon platform -- we're working on acquiring a Power4 machine for additional notes. However, I expect some of the issues are applicable to other AIX machines. In what follows, I used the mpcc and mpxlf compilers.

In order to use a reasonable amount of memory during runs, you also need to specify -bmaxdata:0x80000000 and -bmaxstack:0x10000000, or whatever values are appropriate to your system. You'll also want to link to the IBM blas, mass, and essl libraries (if available) and optimize as much as possible for the specific machine you're running on. Putting it all together gives:

            $ export CC=mpcc
            $ export CXX=mpcc
            $ export F77=mpxlf
            $ export BLASPATH=/usr/lib
            $ export CFLAGS="-bmaxdata:0x80000000 -bmaxstack:0x10000000 -L/usr/local/apps/mass -lmass -lessl -O3 -qstrict -qarch=pwr3 -qtune=pwr3 -qmaxmem=-1 -qcache=auto"
            $ export FFLAGS="-qfixed=132 -bmaxdata:0x80000000 -bmaxstack:0x10000000 -L/usr/local/apps/mass -lmass -lessl -O3 -qstrict -qarch=pwr3 -qtune=pwr3 -qmaxmem=-1 -qcache=auto"
          

Sun/Solaris

Compilation tips for this system are short and sweet: Whatever you do, don't use the GNU compilers; they result in very slow binaries.

DEC/Compaq/HP/Samsung Alpha

Two tips:

1. Don't use the GNU compilers; they result in very slow binaries.

2. Use the vendor-supplied BLAS library.

AMD Opteron

Since the MALOC BLAS is not 64 bit clean, you must used a third party BLAS for installation on the Opteron. We have had good success using the Portland group compilers and the associated PGI BLAS libraries, although a different third party BLAS (like ATLAS) should work as well. For the Portland compilers:

1. Set the following flags for use with the Portland compilers:

   $ export CC=pgcc $ export CFLAGS='-O2 -fPIC -fastsse -Bstatic' $ export F77=pgf77 $ export FFLAGS='-O2 -fPIC -fastsse -Bstatic'

2. When compiling MALOC, disable the building of the BLAS library:

   $ ./configure --prefix=${FETK_PREFIX} --disable-blas $ make; make install

3. Locate the BLAS library in your PGI installation and configure APBS to use that library, and then finish the installation:

   $ export BLAS_DIR='/path/to/blas' $ ./configure --with-blas="-L${BLAS_DIR} -lblas" $ make; make install