# Failure building fv3-jedi on Orion **URL:** \ **Category:** JEDI\ **Created:** [January 26, 2021, 1:39am UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64 "2021-01-26T01:39:25Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![mpagowski](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/mpagowski/32/61_2.png) [@mpagowski](https://forums.jcsda.org/u/mpagowski)\ **Post date:** [January 26, 2021, 1:39am UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/1 "2021-01-26T01:39:25Z")
Hello, following advice from [JEDI Modules on selected HPC systems — JEDI Documentation 1 documentation](https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest/using/jedi_environment/modules.html?highlight=orion) with intel-impi and the fresh clone is not successful. Can someone advise how to proceed? Thanks, Mariusz /work/noaa/gsd-fv3-dev/pagowski/jedi/code/fv3-bundle/fms/exchange/xgrid.F90(4866): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [D] subroutine get\_side1\_from\_xgrid\_ug(d, grid\_id, x, xmap, complete) -----------------------------------^ /work/noaa/gsd-fv3-dev/pagowski/jedi/code/fv3-bundle/fms/exchange/xgrid.F90(3346): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [D] subroutine get\_side1\_from\_xgrid(d, grid\_id, x, xmap, complete) --------------------------------^ [13%] Building Fortran object fms/CMakeFiles/fms.dir/coupler/atmos\_ocean\_fluxes.F90.o [13%] Linking Fortran shared library …/lib/libfms.so [13%] Built target fms make: \*\*\* [all] Error 2 ---
**Author:** ![rickgrubin](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/rickgrubin/32/11_2.png) [@rickgrubin](https://forums.jcsda.org/u/rickgrubin)\ **Post date:** [January 26, 2021, 4:22pm UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/2 "2021-01-26T16:22:25Z")
Hi Mariusz Are you using the Intel or GNU modules to build fv3-jedi? Orion is currently down for maintenance, we’ll have a look when it’s back up. ---
**Author:** ![mpagowski](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/mpagowski/32/61_2.png) [@mpagowski](https://forums.jcsda.org/u/mpagowski)\ **Post date:** [January 26, 2021, 4:39pm UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/3 "2021-01-26T16:39:01Z")
Rick, the failure is with intel, haven’t tried gnu, Mariusz ---
**Author:** ![DengShunChen](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/dengshunchen/32/51_2.png) [@DengShunChen](https://forums.jcsda.org/u/DengShunChen)\ **Post date:** [January 27, 2021, 9:04am UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/4 "2021-01-27T09:04:07Z")
Mariusz, I think you are not showing the error message. for example: > make[2]: \*\*\* [bin/soca\_ensvariance.x] Error 1 > make[1]: \*\*\* [soca/src/mains/CMakeFiles/soca\_ensvariance.x.dir/all] Error 2 > make: \*\*\* [all] Error 2 ---
**Author:** ![mpagowski](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/mpagowski/32/61_2.png) [@mpagowski](https://forums.jcsda.org/u/mpagowski)\ **Post date:** [January 27, 2021, 2:31pm UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/5 "2021-01-27T14:31:40Z")
Yes, you are right, I just mistakenly grabbed stdout before the compilation aborted (because of parallel make it showed some unrelated warnings) ---
**Author:** ![mmiesch](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/mmiesch/32/39_2.png) [@mmiesch](https://forums.jcsda.org/u/mmiesch)\ **Post date:** [January 28, 2021, 10:18pm UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/6 "2021-01-28T22:18:18Z")
@mpagowski - how is it going with this? Are you still having problems? Also - are you building in debug mode? I have seen problems with fms and crtm when built with intel 19 in debug mode. ---
**Author:** ![mpagowski](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/mpagowski/32/61_2.png) [@mpagowski](https://forums.jcsda.org/u/mpagowski)\ **Post date:** [January 28, 2021, 10:34pm UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/7 "2021-01-28T22:34:43Z")
I haven’t tried it since there were no updates on this topic. The flag is -DNDEBUG. Were there any updates to the modules and should I try again? ---
**Author:** ![mmiesch](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/mmiesch/32/39_2.png) [@mmiesch](https://forums.jcsda.org/u/mmiesch)\ **Post date:** [January 28, 2021, 11:21pm UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/8 "2021-01-28T23:21:15Z")
The problem I referred to is independent of the modules. So there is no need to rebuild the modules. Where do you use `-NDEBUG`? Do you build with `ecbuild --build=Debug` or do you specify the compiler options differently? If the failure is with a debug build of fms, then one immediate way around it is to just not build fms in debug mode with intel 19. If that is indeed the problem, we could put a temporary fix in our fork of fms but a longer-term solution would require a bug report to NOAA-GFDL, where the fms repo originates. Would you mind trying again? After it gets to the build failure, enter `make` again (with no -j option) to continue with a serial build and then post the error message here. In the mean time, I’ll see if I can reproduce the error. ---
**Author:** ![mpagowski](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/mpagowski/32/61_2.png) [@mpagowski](https://forums.jcsda.org/u/mpagowski)\ **Post date:** [January 28, 2021, 11:35pm UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/9 "2021-01-28T23:35:36Z")
No, no debug in ecbuild ```auto ecbuild -DMPIEXEC_EXECUTABLE=/opt/slurm/bin/srun -DMPIEXEC_NUMPROC_FLAG="-n" $SRC ``` ```auto That produces -DNDEBUG flag for the compiler ``` ```auto Ok, I will try it again ``` ```auto ``` ---
**Author:** ![mpagowski](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/mpagowski/32/61_2.png) [@mpagowski](https://forums.jcsda.org/u/mpagowski)\ **Post date:** [January 29, 2021, 12:02am UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/10 "2021-01-29T00:02:33Z")
I recloned it and ran ecbuild/make. Long error message [3%] Linking Fortran executable fckit\_test\_shared\_ptr …/…/…/lib/libfckit.so: undefined reference to `eckit::BackTrace::dump()' ../../../lib/libfckit.so: undefined reference to `eckit::Main::displayName() const’ …/…/…/lib/libfckit.so: undefined reference to `eckit::Abort::Abort(std::string const&, eckit::CodeLocation const&)' ../../../lib/libfckit.so: undefined reference to `eckit::AssertionFailed::AssertionFailed(std::string const&, eckit::CodeLocation const&)’ /work/noaa/da/grubin/opt/modules/intel-2020/impi-2020/eckit/jcsda-1.11.6.jcsda2/lib64/libeckit\_mpi.so: undefined reference to `std::basic\_ostream\& std::operator\<\< \(std::basic\_ostream\&, std::\_\_cxx11::basic\_string\ const&)@GLIBCXX\_3.4.21’ … make[2]: \*\*\* [fckit/src/tests/fckit\_test\_shared\_ptr] Error 1 make[1]: \*\*\* [fckit/src/tests/CMakeFiles/fckit\_test\_shared\_ptr.dir/all] Error 2 make: \*\*\* [all] Error 2 ---
**Author:** ![mmiesch](https://yyz1.discourse-cdn.com/flex031/user_avatar/forums.jcsda.org/mmiesch/32/39_2.png) [@mmiesch](https://forums.jcsda.org/u/mmiesch)\ **Post date:** [February 9, 2021, 7:13pm UTC](https://forums.jcsda.org/t/failure-building-fv3-jedi-on-orion/64/11 "2021-02-09T19:13:20Z")
I believe this is solved now, thanks to @mpagowski and @rickgrubin. The problem appeared to be one or more module files, specifically gcc, were not readable for general users. So, the intel compiler was not able to access compatible gcc headers. This has been corrected for all users. Thanks for the report!