The following error occurs when compiling "x86_64 to powerpc64"
cross compiler, as soon as the libgcc_s.so.1 has appeared in obj/gcc
directory:

...
# Now that we have built all the objects, we need to copy
# them back to the GCC directory.  Too many things (other
# in-tree libraries, and DejaGNU) know about the layout
# of the build tree, for now.
make install-leaf DESTDIR=../.././gcc \
 slibdir= libsubdir= MULTIOSDIR=.
make[5]: Entering directory
`/a/linux/.powerpc/gcc/obj/powerpc64-unknown-linux-gnu/libgcc'
/bin/bash ../../../src/libgcc/../mkinstalldirs ../.././gcc
/usr/bin/install -c -m 644 libgcc_eh.a ../.././gcc/
chmod 644 ../.././gcc/libgcc_eh.a
/a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/bin/ranlib
../.././gcc/libgcc_eh.a
/bin/bash ../../../src/libgcc/../mkinstalldirs ../.././gcc;
/usr/bin/install -c -m 644 ./libgcc_s.so.1 ../.././gcc/libgcc_s.so.1;
rm -f ../.././gcc/libgcc_s.so; ln -s libgcc_s.so.1
../.././gcc/libgcc_s.so
/bin/bash ../../../src/libgcc/../mkinstalldirs ../.././gcc
/usr/bin/install -c -m 644 libgcc.a ../.././gcc/
chmod 644 ../.././gcc/libgcc.a
/a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/bin/ranlib
../.././gcc/libgcc.a
/usr/bin/install -c -m 644 libgcov.a ../.././gcc/
chmod 644 ../.././gcc/libgcov.a
/a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/bin/ranlib
../.././gcc/libgcov.a
parts="crtbegin.o crtbeginS.o crtbeginT.o crtend.o crtendS.o ecrti.o
ecrtn.o ncrti.o ncrtn.o"; \
for file in $parts; do \
 rm -f ../.././gcc/$file; \
 /usr/bin/install -c -m 644 $file ../.././gcc/; \
done
make[5]: Leaving directory
`/a/linux/.powerpc/gcc/obj/powerpc64-unknown-linux-gnu/libgcc'
make[4]: Leaving directory
`/a/linux/.powerpc/gcc/obj/powerpc64-unknown-linux-gnu/libgcc'
Checking multilib configuration for libgomp...
mkdir -p -- powerpc64-unknown-linux-gnu/libgomp
Configuring in powerpc64-unknown-linux-gnu/libgomp
configure: creating cache ./config.cache
checking for --enable-version-specific-runtime-libs... no
checking for --enable-generated-files-in-srcdir... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... powerpc64-unknown-linux-gnu
checking target system type... powerpc64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for powerpc64-unknown-linux-gnu-strip...
/a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/bin/strip
checking for powerpc64-unknown-linux-gnu-gcc...
/a/linux/.powerpc/gcc/obj/./gcc/xgcc
-B/a/linux/.powerpc/gcc/obj/./gcc/
-B/a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/bin/
-B/a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/lib/
-isystem /a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/include
-isystem /a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/sys-include
checking for C compiler default output file name... configure: error:
in `/a/linux/.powerpc/gcc/obj/powerpc64-unknown-linux-gnu/libgomp':
configure: error: C compiler cannot create executables
See `config.log' for more details.
make[3]: *** [configure-target-libgomp] Error 1
make[3]: Leaving directory `/a/linux/.powerpc/gcc/obj'

The obj/powerpc64-unknown-linux-gnu/libgomp/config.log content is:

...
configure:2569: checking for C compiler default output file name
configure:2572: /a/linux/.powerpc/gcc/obj/./gcc/xgcc
-B/a/linux/.powerpc/gcc/obj/./gcc/
-B/a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/bin/
-B/a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/lib/
-isystem /a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/include
-isystem /a/linux/.powerpc/cross-tools/powerpc64-unknown-linux-gnu/sys-include
-g -O2     conftest.c  >&5
/a/linux/.powerpc/gcc/obj/./gcc/cc1: error while loading shared
libraries: /a/linux/.powerpc/gcc/obj/./gcc/libgcc_s.so.1: ELF file
data encoding not little-endian
configure:2575: $? = 1
configure: failed program was:
| /* confdefs.h.  */
|
| #define PACKAGE_NAME "GNU OpenMP Runtime Library"
| #define PACKAGE_TARNAME "libgomp"
| #define PACKAGE_VERSION "1.0"
| #define PACKAGE_STRING "GNU OpenMP Runtime Library 1.0"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "libgomp"
| #define VERSION "1.0"
| /* end confdefs.h.  */
|
| int
| main ()
| {
|
|   ;
|   return 0;
| }
configure:2613: error: in
`/a/linux/.powerpc/gcc/obj/powerpc64-unknown-linux-gnu/libgomp':
configure:2616: error: C compiler cannot create executables
See `config.log' for more details.
...


It seems that host cc1 executable tries to load target libgcc_s.so.1
from obj/gcc directory, rather than host libgcc_s.so.1 from /lib.

I have successfully build the cross-compiler with overriden RPATH_ENVVAR variable, as following:

make RPATH_ENVVAR=MY_LD_LIBRARY_PATH

 So error was indeed caused by changing LD_LIBRARY_PATH environment variable during the build

HOST gcc version is:

Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.4.1-4ubuntu4' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4 --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-mpfr --enable-objc-gc --disable-werror --with-arch-32=i486 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu4) 


gcc versions I was tried to build are 4.4.1 and 4.5.0 (rev 153504)