building with oneAPI fails

[manodeep]

With the latest oneAPI compiler (and leaving netcdf and openmpi as is), I get the following error when I try to compile the oasis3-mct package. Same error also occurs upstream, but is not caught and the compile continues past this error. This happens because there is an extra -loopopt=0/1 option that is not correctly parsed and interpreted as a linking flag. The linker then looks for a non-existent file and borks.

Intel says this is an autoconf issue (see release notes for 2025 oneAPI) and can be fixed by using autoconf>=2.70 and using autoupdate. I have tried that but that does not fix the issue.

access-nri/oasis3-mct (from config.log in the build directory):

configure:4580: mpicc -o conftest -O2   conftest.c   -L/apps/openmpi/4.0.2/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -loopopt=1 -L/apps/openmpi/4.0.2/lib/Intel -L/apps/openmpi/4.0.2/lib/profilers -L/apps/netcdf/4.7.4/lib/Intel -L/apps/netcdf/4.7.4/lib -L/apps/intel-tools/intel-compiler-llvm/2024.2.1/lib -L/apps/intel-tools/.packages/2024.2.1/compiler/2024.2/lib -L/apps/intel-tools/.packages/2024.2.1/compiler/2024.2/lib/clang/19/lib/x86_64-unknown-linux-gnu -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8/ -L/half-root/usr/bin/../lib/gcc/ -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../../../lib64 -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../../../lib64/ -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/ -L/apps/openmpi/4.0.2/lib/Intel/ -L/apps/openmpi/4.0.2/lib/ -L/apps/netcdf/4.7.4/lib/Intel/ -L/apps/netcdf/4.7.4/lib/ -L/apps/intel-tools/intel-compiler-llvm/2024.2.1/lib/ -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -lifport -lifcoremt -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl >&5
/bin/ld: cannot find -loopopt=1
icx: error: linker command failed with exit code 1 (use -v to see invocation)
configure:4580: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "MCT"
| #define PACKAGE_TARNAME "mct"
| #define PACKAGE_VERSION "2.8"
| #define PACKAGE_STRING "MCT 2.8"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_MPI 1
| /* end confdefs.h.  */
| #define FC_DUMMY_MAIN _main
| #ifdef FC_DUMMY_MAIN
| #ifndef FC_DUMMY_MAIN_EQ_F77
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int FC_DUMMY_MAIN() { return 1; }
| #endif
| #endif
| int
| main ()
| {
| 
|   ;
|   return 0;
| }
configure:4596: result: unknown
configure:4613: error: in `/home/593/ms2335/codes/access-nri/oasis3-mct/compile_oa3-mct/build/lib/mctdir':
configure:4616: error: linking to Fortran libraries from C fails
See `config.log' for more details.

COSIMA/oasis3-mct: Same error in config.log but the build continues as demonstrated by the output from make:

checking how to get verbose linking output from mpifort... -v
checking for Fortran libraries of mpifort...  -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -loopopt=1 -L/apps/openmpi/5.0.5/lib/Intel -L/apps/openmpi/5.0.5/lib -L/apps/openmpi/5.0.5/lib/profilers -L/apps/netcdf/4.9.2/lib/Intel -L/apps/netcdf/4.9.2/lib -L/apps/intel-tools/intel-compiler-llvm/2024.2.1/lib -L/apps/intel-tools/.packages/2024.2.1/compiler/2024.2/lib -L/apps/intel-tools/.packages/2024.2.1/compiler/2024.2/lib/clang/19/lib/x86_64-unknown-linux-gnu -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8/ -L/half-root/usr/bin/../lib/gcc/ -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../../../lib64 -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../../../lib64/ -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/ -L/apps/openmpi/5.0.5/lib/Intel/ -L/apps/openmpi/5.0.5/lib/ -L/apps/netcdf/4.9.2/lib/Intel/ -L/apps/netcdf/4.9.2/lib/ -L/apps/intel-tools/intel-compiler-llvm/2024.2.1/lib/ -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -lifport -lifcoremt -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
checking for dummy main to link with Fortran libraries... unknown
configure: error: in `/home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/Linux/build/lib/mctdir':
configure: error: linking to Fortran libraries from C fails
See `config.log' for more details.
make[3]: Entering directory '/home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/Linux/build/lib/mctdir'
make[4]: Entering directory '/home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/Linux/build/lib/mctdir/mpeu'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/Linux/build/lib/mctdir/mpeu'
make[4]: Entering directory '/home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/Linux/build/lib/mctdir/mct'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/Linux/build/lib/mctdir/mct'
make[3]: Leaving directory '/home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/Linux/build/lib/mctdir'
make[2]: Leaving directory '/home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/util/make_dir'
/usr/bin/make -f TopMakefileOasis3 makelibs
make[2]: Entering directory '/home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/util/make_dir'
make[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
=> Compiling library scrip
(cd /home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/Linux/build/lib/scrip; cp -f /home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/lib/scrip/src/Makefile .;\
         ( echo 'include /home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/util/make_dir/make.inc' > infile; cat Makefile >> infile ; cp -f infile Makefile ) ; /usr/bin/make all > >(tee -a /home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/util/make_dir/COMP.log) 2> >(tee -a /home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/util/make_dir/COMP.err >&2) )
make[3]: Entering directory '/home/593/ms2335/codes/climate_models/COSIMA/oasis3-mct/Linux/build/lib/scrip'

...

[manodeep]

Adding the update here as well. I managed to get around the configure error (treating loopopt=1 as a linker flag) by replacing the autoconf files (configure.ac, config.sub and config.guess and possibly configure) from the upstream cerfacs/oasis3-mct library from gitlab. This also required adding module load autoconf/2.72 into the relevant script for building on gadi

Once this was done, running make causes an Internal Compiler Error (ICE) with ifx - which has already been documented previously by Paul (ACCESS-NRI/spack-packages#101 (comment)).

I have added a fix for the ICE in this comment - ACCESS-NRI/spack-packages#52 (comment)