HOMME test in acme_developer is no longer building on edison

[ndkeen]

I didn't see anything obviously wrong, but may just need a tweak on how we link with MKL.
I think this test was working a few weeks ago, but I noticed it after updating master.

H5PL.c:(.text+0x5c2): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
CMakeFiles/preqx-nlev20-interp.dir/__/__/src/share/linear_algebra_mod.F90.o: In function `reigen_solver':
/global/cscratch1/sd/ndk/wacmy/master27-cori/components/homme/src/share/linear_algebra_mod.F90:88: undefined reference to `dgeev_'
CMakeFiles/preqx-nlev20-interp.dir/__/__/src/share/prim_si_ref_mod.F90.o: In function `set_vert_struct_mat':
/global/cscratch1/sd/ndk/wacmy/master27-cori/components/homme/src/share/prim_si_ref_mod.F90:390: undefined reference to `dgetrf_'
/global/cscratch1/sd/ndk/wacmy/master27-cori/components/homme/src/share/prim_si_ref_mod.F90:391: undefined reference to `dgetri_'
/global/cscratch1/sd/ndk/wacmy/master27-cori/components/homme/src/share/prim_si_ref_mod.F90:435: undefined reference to `dgetrf_'
/global/cscratch1/sd/ndk/wacmy/master27-cori/components/homme/src/share/prim_si_ref_mod.F90:436: undefined reference to `dgetri_'
/usr/bin/ld: link errors found, deleting executable `preqx'
make[2]: *** [src/preqx/preqx] Error 1
make[1]: *** [src/preqx/CMakeFiles/preqx.dir/all] Error 2
/usr/bin/ld: link errors found, deleting executable `preqx-nlev20-interp'
make[2]: *** [test_execs/preqx-nlev20-interp/preqx-nlev20-interp] Error 1
make[1]: *** [test_execs/preqx-nlev20-interp/CMakeFiles/preqx-nlev20-interp.dir/all] Error 2
make: *** [all] Error 2
e```

[ndkeen]

Saving this information here for later use (or in case someone sees the issue) @amametjanov
HOMME is still failing to build on edison with both Intel and GNU compiler. I also just verified it doesn't build on cori either. Here is partial output of homme build log:

-- HOMME_USE_MKL=TRUE
-- For Edison/Cori at NERSC, MKL included with Intel compiler
NETCDF built with hdf5 MPIIO support
-- nc-config found at /opt/cray/pe/netcdf/4.4.0/bin
-- nc-config: Netcdf does not depend upon Pnetcdf
-- nc-config: Netcdf depends upon HDF5
-- nc-config: Netcdf does not depend upon CURL
-- Found HDF5: /opt/cray/pe/hdf5-parallel/1.8.16/GNU/5.1/lib/libhdf5_hl.a /opt/cray/pe/hdf5-parallel/1.8.16/GNU/5.1/lib/libhdf5.a
-- Looking for H5_HAVE_SZLIB_H
-- Looking for H5_HAVE_SZLIB_H - not found
-- Looking for H5_HAVE_ZLIB_H
-- Looking for H5_HAVE_ZLIB_H - found
-- This HDF5 library requires ZLIB
-- Found ZLIB_LIBRARY: /global/common/cori/software/zlib/1.2.8/hsw/gnu/lib/libz.a
-- ZLIB_LIBRARIES: 
-- Found ZLIB: /global/common/cori/software/zlib/1.2.8/hsw/gnu/lib/libz.a
-- Found Netcdf:
--   Libraries: /opt/cray/pe/netcdf-hdf5parallel/4.4.0/GNU/5.1/lib/libnetcdff.a;/opt/cray/pe/netcdf-hdf5parallel/4.4.0/GNU/5.1/lib/libnetcdf.a;/opt/cray/pe/hdf5-parallel/1.8.16/GNU/5.1/lib/libhdf5_hl.a;/opt/cray/pe/hdf5-parallel/1.8.16/GNU/5.1/lib/libhdf5.a;/global/common/cori/software/zlib/1.2.8/hsw/gnu/lib/libz.a
--   Includes:  /opt/cray/pe/netcdf-hdf5parallel/4.4.0/GNU/5.1/include
-- Found Netcdf and all dependencies
-- Found NetCDF_C: /opt/cray/pe/netcdf-hdf5parallel/4.4.0/GNU/5.1/lib/libnetcdf.a  
-- Checking NetCDF version
-- Checking NetCDF version - 4.4.0./*!<
-- Checking whether NetCDF has parallel support
-- Checking whether NetCDF has parallel support - yes
-- Found NetCDF_Fortran: /opt/cray/pe/netcdf-hdf5parallel/4.4.0/GNU/5.1/lib/libnetcdff.a  
Building PIO with netcdf support 
CMake Error at /global/common/cori/software/cmake/3.3.2/share/cmake-3.3/Modules/FindPackageHandleStandardArgs.cmake:148 (message):
  Could NOT find PnetCDF_C (missing: PnetCDF_C_LIBRARY PnetCDF_C_INCLUDE_DIR)
Call Stack (most recent call first):
  /global/common/cori/software/cmake/3.3.2/share/cmake-3.3/Modules/FindPackageHandleStandardArgs.cmake:388 (_FPHSA_FAILURE_MESSAGE)
  utils/cime/externals/pio2/cmake/LibFind.cmake:302 (find_package_handle_standard_args)
  utils/cime/externals/pio2/cmake/FindPnetCDF.cmake:52 (find_package_component)
  utils/cime/externals/pio1/pio/CMakeLists.txt:49 (FIND_PACKAGE)

-- Configuring incomplete, errors occurred!
See also "/global/cscratch1/sd/ndk/acme_scratch/m30a-gnu/HOMME_P24.f19_g16_rx1.A.cori-knl_gnu.20170329_144450_ywzn5n/bld/CMakeFiles/CMakeOutput.log".
See also "/global/cscratch1/sd/ndk/acme_scratch/m30a-gnu/HOMME_P24.f19_g16_rx1.A.cori-knl_gnu.20170329_144450_ywzn5n/bld/CMakeFiles/CMakeError.log".```

Looking into one of those files:

```Building C object CMakeFiles/cmTC_e5fc3.dir/CheckSymbolExists.c.o
/opt/cray/pe/craype/2.5.7/bin/cc   -O2 -g -fopenmp     -o CMakeFiles/cmTC_e5fc3.dir/CheckSymbolExists.c.o   -c /global/cscratch1/sd/ndk/acme_scratch/m30a-gnu/HOMME_P24.f19_g16_rx1.A.cori-knl_gnu.20170329_144450_ywzn5n/bld/CMakeFiles/CMakeTmp/CheckSymbolExists.c
/global/cscratch1/sd/ndk/acme_scratch/m30a-gnu/HOMME_P24.f19_g16_rx1.A.cori-knl_gnu.20170329_144450_ywzn5n/bld/CMakeFiles/CMakeTmp/CheckSymbolExists.c: In function 'main':
/global/cscratch1/sd/ndk/acme_scratch/m30a-gnu/HOMME_P24.f19_g16_rx1.A.cori-knl_gnu.20170329_144450_ywzn5n/bld/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8:19: error: 'H5_HAVE_SZLIB_H' undeclared (first use in this function)
   return ((int*)(&H5_HAVE_SZLIB_H))[argc];
                   ^~~~~~~~~~~~~~~
/global/cscratch1/sd/ndk/acme_scratch/m30a-gnu/HOMME_P24.f19_g16_rx1.A.cori-knl_gnu.20170329_144450_ywzn5n/bld/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8:19: note: each undeclared identifier is reported only once for each function it appears in
CMakeFiles/cmTC_e5fc3.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_e5fc3.dir/CheckSymbolExists.c.o' failed
make[1]: *** [CMakeFiles/cmTC_e5fc3.dir/CheckSymbolExists.c.o] Error 1
make[1]: Leaving directory '/global/cscratch1/sd/ndk/acme_scratch/m30a-gnu/HOMME_P24.f19_g16_rx1.A.cori-knl_gnu.20170329_144450_ywzn5n/bld/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_e5fc3/fast' failed
gmake: *** [cmTC_e5fc3/fast] Error 2

[jgfouca]

I've fixed HOMME on a number of machines, I should be able to figure this out.

[ndkeen]

Yea I noticed you had made some progress with building HOMME elsewhere and was hoping it would address it here. Note I tagged edison, but it's not building on any NERSC machine with any compiler.

[rljacob]

Consider this a low priority unless its stopping HOMME development work.