Cross-compiling to s390x from x86_64 host with this configuration:

sh ./configure --disable-warnings-as-errors --with-debug-level=fastdebug --openjdk-target=s390x-linux-gnu --with-boot-jdk=/home/shade/jdk --with-sysroot=/pool/chroots/s390x/ --with-toolchain-path=/pool/chroots/s390x/ --with-freetype-include=/pool/chroots/s390x/usr/include/freetype2/ --with-freetype-lib=/pool/chroots/s390x/usr/lib/s390x-linux-gnu

The build succeeds normally, but s390x binary fails:

#
# A fatal error has been detected by the Java Runtime Environment:
#
# Internal Error (/pool/buildbot/slaves/sobornost/jdkX/build/src/hotspot/share/classfile/classLoader.cpp:874), pid=19091, tid=19092
# assert(new_entry != __null && new_entry->is_modules_image()) failed: No java runtime image present

Looking at module header, it looks like endianness is mismatched. s390x is big-endian:

     s390x)
      VAR_CPU=s390x
      VAR_CPU_ARCH=s390
      VAR_CPU_BITS=64
      VAR_CPU_ENDIAN=big
      ;;

Re-running the build with LOG=debug yields:

$ grep endian build.log
...
/home/shade/shenandoah-jdk/build/linux-s390x-normal-server-fastdebug/buildjdk/jdk/bin/jlink ... --endian little ...
...
( /home/shade/shenandoah-jdk/build/linux-s390x-normal-server-fastdebug/buildjdk/jdk/bin/jlink ... --endian little ...

Some configuration got borked along the way. Since native s390x seem to be fine, it looks like cross-compilation issue.