I searched on the openmpi archives to see if any one else has seen this.. and this is what I found, but it is related to another processor (same error though) and solves specifically for it.
The configure is complaining about the missing atomic directives for your processor. We have the MIPS atomic calls but not the MIPS64. We just have to add them in the opal/asm/base.
Unfortunately, there is no opal directory associated with the cross compiler and I am not sure what lib might contain the atomic primitives or where the configure program is looking for them. Both could be an issue. i assume the atomic primitives are particular to the ppc7448 processor and the Linux OS that runs on it but the cross compiler tool chain should contain them.
The configure works fine for the local compiler / machine, it hits this error only for cross compiling. I did modiify the config.sub file to add the ppc74xx host. Here is the configure command I am using.
/home/MPI/openmpi-1.2.6/configure --prefix=/home/MPI/openmpi-1.2.6/openmpi-1.2.6-install-7448 --host=ppc74xx-linux --build=i686-pc-linux-gnu
configure finds and checks the c and c++ crosscompilers without any problems and does quite alot until it hits this error and stops thus not producing any Makefiels or finishing.