General:

* Build APBS version 0.3.2, because Mark E. says
that more recent versions use different data
structures that are incompatible with ISIM.

* Apply patch to APBS created by Mark Friederichs to 
reduce reported grid errors from ISIM (which is linked
to APBS libraries) See patch file vgrid.patch

* Build static libraries, in order to create standalone
executables for distribution.  Finding a statically linked
libg2c can be tricky.

* Build MALOC, then APBS, then ISIM

* g77 does not accept "-nofor_main" option, though the 
configure script thinks it does.


On Mac OS X:

* Find a fast BLAS library at  
/Developer/SDKs/MacOSX10.4u.sdk/System/Library/
Frameworks/Accelerate.../Versions/A/Frameworks/vecLib.framework/
Versions/A/libBlas.dylib

* Compilation of apbs and isim

   - the shared library 'libg2c.dylib' in '/usr/local/lib' was being 
     loaded into the IntelMac executable; this led to problems if
     the user did not have the library loaded on their machine in the
     same location or the user's 'LD_LIBRARY_PATH' environment variable 
     did not include the directory where the library was installed. 

   - I tried setting the environment variable 'LDFLAGS' to '-static-libgcc' 
     when compiling, but this did not remove the shared library. Note: setting
     'LDFLAGS' to '-static' will not work since there is no static 'crt0.o' available 
     (this is mentioned in the documentation for 'ld'). The solution I employed is inelegant,
     but appears to work: I removed the soft link to 'libg2c.dyliba' in '/usr/local/lib'
     forcing the loaded to use the static library code.

   - the required shared libraries can be viewed by issuing the command:
     '>otool -L isim' on the Macs; 'otool' is similar to 'ldd' available on 
     Linux machines

   - When compiling isim, the error associated w/  '-nofor_main' can be removed by
     commenting out the line 'FLIBS="$FLIBS -nofor_main"' (line ~3772) in the 
     'configure' script

* To create a universal binary that will run on the PowerPc and IntelMacs:
   - compile programs on ppc (binary=isim_ppc) and on IntelMac (binary=isim_i386)
   - update directory w/ both copies
   - to 'glue' executables from two architectures together:
     >lipo -arch ppc isim_ppc -arch i386 isim_386 -create -output isimUniversal
   - Note currently we are not setup to cross-compile the programs on the same machine


On Windows:

* If using cygwin, avoid linking to cygwin.dll, so they can run on 
non-cygwin machines.
	- use "-mno-cygwin" argument in CFLAGS
	- may need to link to GnuWin32 libraries from sourceforge

    > setenv FETK_SRC /home/cmbruns/projects/apbs032nocygwin/src
    > setenv FETK_PREFIX /home/cmbruns/projects/apbs032nocygwin/bin
    > setenv FETK_INCLUDE ${FETK_PREFIX}/include
    > setenv FETK_LIBRARY ${FETK_PREFIX}/lib
    > mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
    > setenv CFLAGS "-mno-cygwin -DMSDOS -DHAVEWINSOCK_H -O3"
    > setenv LDFLAGS "-L/usr/local/no_cygwin/lib -lgw32c -lole32 -luuid -lwsock32"
          

* MALOC:
	- remove "HAVE_XDR" stanza from configure

    > cd ${FETK_SRC}/maloc
    > make distclean
    > ./configure --prefix=${FETK_PREFIX}
    > make
    > make install

* APBS
	- build from version 0.3.2
	- remove tools directory if causing build trouble; we only need the libs to build ISIM

    > cd ${FETK_SRC}/apbs
    > make distclean
    > ./configure --prefix=${FETK_PREFIX}
    > make all
    > make install

* ISIM
	- check out isim2-su package from simtk.org

    > cd ${FETK_SRC}
    > svn checkout https://simtk.org/svn/isim2-su/trunk isim
    > cd ${FETK_SRC}/isim
    > make distclean
    [ edit configure script to prevent FLIBS from adding "-nofor_main" when it erroneously thinks its OK to.]
    > ./configure --prefix=${FETK_PREFIX}
    > make
    > make install


On Linux:

* compiles easily

* get blas library from simtk.org