Hello, the automake stuff seems to work fine now in the normal case, but I had some trouble with the --enable-mpqc option of the configure script. I have a solution but tell me if you know it has any problems. So at src/Makefile.am there was (and still is) a line libghemical_INCLUDES = -I$(top_builddir)/src @SC_CPPFLAGS@ but it does not add SC_CPPFLAGS into the commandline. Looking at Makefile.in it is seen that CXXCOMPILE will contain all the stuff that goes into the commandline: CXXCOMPILE = $(CXX) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) I found out that a one way to add something in Makefile.in with automake is a Makefile.include file that is included at Makefile.am ; my Makefile.include is INCLUDES += @SC_CPPFLAGS@ that adds SC_CPPFLAGS into INCLUDES and eventually into CXXCOMPILE, which is enough to make libghemical compile. Then, linking the final ghemical executable has some other issues. It appears that only the static library has the MPQC code added ; perhaps that is how the shared libs are inteded to work but now the executable linked into libghemical.so won't contain all of the MPQC code. Trying to use it will crash the program and pop out an error message like this one: writing MPQC-input file /tmp/mpqc0000.in using ProcMessageGrp as MessageGroup... using ProcThreadGrp as ThreadGroup... ClassDesc::load_class looking for "./classes" ClassDesc::load_class("CLHF"): load failed Either "CLHF" is an invalid class name or the code for "CLHF" was not linked into the executable. Ok, this is a good start anyway, need to look at this later. Regards, Tommi