Problem with porting CESM 1.2.2 on Unix machine

[dana_lapides@berkeley_edu]

Hi, I'm trying to build a case, and it fails at building csm_share. I can't figure our what's going wrong. Any ideas? csm_share.bldlog is as follows: Wed Sep 7 16:47:34 PDT 2016 /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/csm_share.bldlog.160907-164729mpif90  -c -I.  -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/models/csm_share/shr -I. -I/Users/Dana/cesm1_2_2/case1/SourceMods/src.share -I/Users/Dana/cesm1_2_2/models/drv/shr -I/Users/Dana/cesm1_2_2/models/dead_share -I/Users/Dana/cesm1_2_2/models/csm_share/shr -I/Users/Dana/cesm1_2_2/models/utils/esmf_wrf_timemgr -I/Users/Dana/cesm1_2_2/case1/bld/lib/include  -O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none -fno-range-check -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_WAV=1 -DNUM_COMP_INST_ROF=1 -Ddarwin  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Ddarwin -DCPRGNU  -ffree-form   /Users/Dana/cesm1_2_2/models/drv/shr/seq_io_mod.F90/Users/Dana/cesm1_2_2/models/drv/shr/seq_io_mod.F90:1170:58:        rcode = pio_def_dim(cpl_io_file,'time',PIO_UNLIMITED,dimid(1))                                                          1Error: Symbol 'pio_unlimited' at (1) has no IMPLICIT typemake: *** [seq_io_mod.o] Error 1gmake  complib -j 1 MODEL=csm_share COMPLIB=libcsm_share.a USER_CPPDEFS="  -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_WAV=1 -DNUM_COMP_INST_ROF=1" -f /Users/Dana/cesm1_2_2/case1/Tools/Makefile  returned non-zero exit status 2  

 

[jedwards]

it's actually failing in the pio bld - look in that bldlog for details

 

[dana_lapides@berkeley_edu]

Thanks for replying. I don't see anything there. Can you tell what's going on? Wed Sep 7 16:59:27 PDT 2016 /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio.bldlog.160907-165924set pio_dir=/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/piocd /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pioset cmake_opts= -D USER_CMAKE_MODULE_PATH=/Users/Dana/cesm1_2_2/scripts/ccsm_utils/CMakeset cmake_opts= -D USER_CMAKE_MODULE_PATH=/Users/Dana/cesm1_2_2/scripts/ccsm_utils/CMake -D GENF90_PATH=/Users/Dana/cesm1_2_2/tools/cprnc/genf90gmake /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/Makefile MODEL=pio USER_CMAKE_OPTS= -D USER_CMAKE_MODULE_PATH=/Users/Dana/cesm1_2_2/scripts/ccsm_utils/CMake -D GENF90_PATH=/Users/Dana/cesm1_2_2/tools/cprnc/genf90 PIO_LIBDIR=/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio -f /Users/Dana/cesm1_2_2/case1/Tools/Makefilemake: `/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/Makefile' is up to date.gmake -j 1/usr/local/Cellar/cmake/3.6.1/bin/cmake -H/Users/Dana/cesm1_2_2/models/utils/pio -B/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio --check-build-system CMakeFiles/Makefile.cmake 0/usr/local/Cellar/cmake/3.6.1/bin/cmake -E cmake_progress_start /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/CMakeFiles /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/CMakeFiles/progress.marks/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/Makefile2 all/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/dependcd /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio && /usr/local/Cellar/cmake/3.6.1/bin/cmake -E cmake_depends "Unix Makefiles" /Users/Dana/cesm1_2_2/models/utils/pio /Users/Dana/cesm1_2_2/models/utils/pio /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/CMakeFiles/pio.dir/DependInfo.cmake --color=/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/requires/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_kinds.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pio_kinds.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_support.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pio_support.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_types.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pio_types.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/calcdecomp.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/calcdecomp.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/alloc_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/alloc_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_msg_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pio_msg_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_utils.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pio_utils.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/nf_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/nf_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/iompi_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/iompi_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pionfread_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pionfread_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pionfwrite_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pionfwrite_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/calcdisplace_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/calcdisplace_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_spmd_utils.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pio_spmd_utils.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/box_rearrange.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/box_rearrange.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/rearrange.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/rearrange.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/piodarray.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/piodarray.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/ionf_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/ionf_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_mpi_utils.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pio_mpi_utils.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/piolib_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/piolib_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pionfatt_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pionfatt_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pionfget_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pionfget_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pionfput_mod.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pionfput_mod.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio.F90.o.provides.buildmake[3]: `CMakeFiles/pio.dir/pio.F90.o.provides.build' is up to date./Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/buildmake[2]: Nothing to be done for `CMakeFiles/pio.dir/build'.[100%] Built target pio/usr/local/Cellar/cmake/3.6.1/bin/cmake -E cmake_progress_start /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/CMakeFiles 0cp -p libpio.a /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/../libcp -p dtypes.h alloc_mod.mod box_rearrange.mod calcdecomp.mod calcdisplace_mod.mod iompi_mod.mod ionf_mod.mod nf_mod.mod pio.mod pio_kinds.mod pio_mpi_utils.mod pio_msg_mod.mod pio_nf_utils.mod pio_spmd_utils.mod pio_support.mod pio_types.mod pio_utils.mod piodarray.mod piolib_mod.mod pionfatt_mod.mod pionfget_mod.mod pionfput_mod.mod pionfread_mod.mod pionfwrite_mod.mod rearrange.mod /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/../include  exit 0

 

[jedwards]

I'm not seeing the problem here either - but the problem in csm_share was that PIO_UNLIMITED was undefined - this variable should have been included from the use pio statement.Erase directory  /Users/Dana/cesm1_2_2/case1/bld/gnu  and try the build again and look at the new pio.bldlog 

 

[dana_lapides@berkeley_edu]

Aha! That did reveal an error. I'm not sure what to do about it. I installed pnetcdf, but I can't find the file pnetcdf.inc...I defined the P_NETCDF_PATH variable correctly. Thu Sep 8 09:24:48 PDT 2016 /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio.bldlog.160908-092425set pio_dir=/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/piocd /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pioset cmake_opts= -D USER_CMAKE_MODULE_PATH=/Users/Dana/cesm1_2_2/scripts/ccsm_utils/CMakeset cmake_opts= -D USER_CMAKE_MODULE_PATH=/Users/Dana/cesm1_2_2/scripts/ccsm_utils/CMake -D GENF90_PATH=/Users/Dana/cesm1_2_2/tools/cprnc/genf90gmake /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/Makefile MODEL=pio USER_CMAKE_OPTS= -D USER_CMAKE_MODULE_PATH=/Users/Dana/cesm1_2_2/scripts/ccsm_utils/CMake -D GENF90_PATH=/Users/Dana/cesm1_2_2/tools/cprnc/genf90 PIO_LIBDIR=/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio -f /Users/Dana/cesm1_2_2/case1/Tools/Makefilecat: Filepath: No such file or directorycat: Srcfiles: No such file or directory/Users/Dana/cesm1_2_2/case1/Tools/mkSrcfilescp -f /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/Filepath /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/Deppath/Users/Dana/cesm1_2_2/case1/Tools/mkDepends  Deppath Srcfiles > /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/Dependscd /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio;        CC=mpicc   CXX=mpicxx  FC=mpif90  LDFLAGS=""  cmake  -D CMAKE_Fortran_FLAGS:STRING="-O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none -fno-range-check  -Ddarwin  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Ddarwin -DCPRGNU  -I.  -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/models/csm_share/shr" -D CMAKE_C_FLAGS:STRING=" -Ddarwin  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Ddarwin -DCPRGNU  -I.  -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/models/csm_share/shr" -D CMAKE_CXX_FLAGS:STRING=" -Ddarwin  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Ddarwin -DCPRGNU  -I.  -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/models/csm_share/shr" -D CMAKE_VERBOSE_MAKEFILE:BOOL=ON -D NETCDF_DIR:STRING=/usr/local -D USER_CMAKE_MODULE_DIR:STRING=/Users/Dana/cesm1_2_2/scripts/ccsm_utils/CMake -D PNETCDF_DIR:STRING="/usr/local/Cellar/parallel-netcdf/1.7.0"  -D USER_CMAKE_MODULE_PATH=/Users/Dana/cesm1_2_2/scripts/ccsm_utils/CMake -D GENF90_PATH=/Users/Dana/cesm1_2_2/tools/cprnc/genf90 /Users/Dana/cesm1_2_2/models/utils/pio-- The C compiler identification is AppleClang 7.3.0.7030031-- The Fortran compiler identification is GNU 6.2.0-- Check for working C compiler: /usr/local/bin/mpicc-- Check for working C compiler: /usr/local/bin/mpicc -- works-- Detecting C compiler ABI info-- Detecting C compiler ABI info - done-- Detecting C compile features-- Detecting C compile features - done-- Checking whether Fortran compiler has -isysroot-- Checking whether Fortran compiler has -isysroot - yes-- Checking whether Fortran compiler supports OSX deployment target flag-- Checking whether Fortran compiler supports OSX deployment target flag - yes-- Check for working Fortran compiler: /usr/local/bin/mpif90-- Check for working Fortran compiler: /usr/local/bin/mpif90  -- works-- Detecting Fortran compiler ABI info-- Detecting Fortran compiler ABI info - done-- Checking whether /usr/local/bin/mpif90 supports Fortran 90-- Checking whether /usr/local/bin/mpif90 supports Fortran 90 -- yesNETCDF built without MPIIO-- HDF5: Using hdf5 compiler wrapper to determine C configuration-- Found HDF5: /usr/local/lib/libhdf5.dylib;/usr/local/lib/libsz.dylib;/usr/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib (found version "1.8.16") found components:  C HL-- Adding hdf5 libraries-- Found NETCDF: -L/usr/local/lib -lnetcdff -L/usr/local/lib  -lnetcdfBuilding PIO with netcdf support-- Found pnetcdf: /usr/local/Cellar/parallel-netcdf/1.7.0/lib/libpnetcdf.a-- MPIIO detected and enabled.-- MPI Fortran module detected and enabled.-- Configuring done-- Generating doneCMake Warning:  Manually-specified variables were not used by the project:     CMAKE_CXX_FLAGS    USER_CMAKE_MODULE_DIR  -- Build files have been written to: /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/piogmake -j 1/usr/local/Cellar/cmake/3.6.1/bin/cmake -H/Users/Dana/cesm1_2_2/models/utils/pio -B/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio --check-build-system CMakeFiles/Makefile.cmake 0/usr/local/Cellar/cmake/3.6.1/bin/cmake -E cmake_progress_start /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/CMakeFiles /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/CMakeFiles/progress.marks/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/Makefile2 all/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/depend[  2%] Generating pio_msg_getput_callbacks.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/pio_msg_getput_callbacks.F90.in > pio_msg_getput_callbacks.F90[  5%] Generating pionfatt_mod.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/pionfatt_mod.F90.in > pionfatt_mod.F90[  7%] Generating pionfread_mod.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/pionfread_mod.F90.in > pionfread_mod.F90[ 10%] Generating pionfwrite_mod.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/pionfwrite_mod.F90.in > pionfwrite_mod.F90[ 12%] Generating pionfput_mod.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/pionfput_mod.F90.in > pionfput_mod.F90[ 15%] Generating pionfget_mod.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/pionfget_mod.F90.in > pionfget_mod.F90[ 17%] Generating alloc_mod.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/alloc_mod.F90.in > alloc_mod.F90[ 20%] Generating box_rearrange.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/box_rearrange.F90.in > box_rearrange.F90[ 22%] Generating rearrange.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/rearrange.F90.in > rearrange.F90[ 25%] Generating iompi_mod.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/iompi_mod.F90.in > iompi_mod.F90[ 27%] Generating piodarray.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/piodarray.F90.in > piodarray.F90[ 30%] Generating pio_spmd_utils.F90/Users/Dana/cesm1_2_2/tools/cprnc/genf90/genf90.pl /Users/Dana/cesm1_2_2/models/utils/pio/pio_spmd_utils.F90.in > pio_spmd_utils.F90cd /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio && /usr/local/Cellar/cmake/3.6.1/bin/cmake -E cmake_depends "Unix Makefiles" /Users/Dana/cesm1_2_2/models/utils/pio /Users/Dana/cesm1_2_2/models/utils/pio /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio /Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio/CMakeFiles/pio.dir/DependInfo.cmake --color=Scanning dependencies of target pio/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/requires/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_kinds.F90.o.provides.build[ 32%] Building Fortran object CMakeFiles/pio.dir/pio_kinds.F90.o/usr/local/bin/mpif90  -DUSEMPIIO -D_NETCDF -D_NOUSEMCT -D_PNETCDF -D_USEBOX -I/Users/Dana/cesm1_2_2/models/utils/pio -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include  -O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none -fno-range-check  -Ddarwin  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Ddarwin -DCPRGNU  -I.  -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/models/csm_share/shr -ffree-line-length-none   -c /Users/Dana/cesm1_2_2/models/utils/pio/pio_kinds.F90 -o CMakeFiles/pio.dir/pio_kinds.F90.of951: Warning: Nonexistent include directory '/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share' [-Wmissing-include-dirs]/usr/local/Cellar/cmake/3.6.1/bin/cmake -E cmake_copy_f90_mod pio_kinds CMakeFiles/pio.dir/pio_kinds.mod.stamp GNU/usr/local/Cellar/cmake/3.6.1/bin/cmake -E touch CMakeFiles/pio.dir/pio_kinds.F90.o.provides.build/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_support.F90.o.provides.build[ 35%] Building Fortran object CMakeFiles/pio.dir/pio_support.F90.o/usr/local/bin/mpif90  -DUSEMPIIO -D_NETCDF -D_NOUSEMCT -D_PNETCDF -D_USEBOX -I/Users/Dana/cesm1_2_2/models/utils/pio -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include  -O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none -fno-range-check  -Ddarwin  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Ddarwin -DCPRGNU  -I.  -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/models/csm_share/shr -ffree-line-length-none   -c /Users/Dana/cesm1_2_2/models/utils/pio/pio_support.F90 -o CMakeFiles/pio.dir/pio_support.F90.of951: Warning: Nonexistent include directory '/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share' [-Wmissing-include-dirs]/usr/local/Cellar/cmake/3.6.1/bin/cmake -E cmake_copy_f90_mod pio_support CMakeFiles/pio.dir/pio_support.mod.stamp GNU/usr/local/Cellar/cmake/3.6.1/bin/cmake -E touch CMakeFiles/pio.dir/pio_support.F90.o.provides.build/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_types.F90.o.provides.build[ 37%] Building Fortran object CMakeFiles/pio.dir/pio_types.F90.o/usr/local/bin/mpif90  -DUSEMPIIO -D_NETCDF -D_NOUSEMCT -D_PNETCDF -D_USEBOX -I/Users/Dana/cesm1_2_2/models/utils/pio -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/pio -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include  -O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none -fno-range-check  -Ddarwin  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Ddarwin -DCPRGNU  -I.  -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/models/csm_share/shr -ffree-line-length-none   -c /Users/Dana/cesm1_2_2/models/utils/pio/pio_types.F90 -o CMakeFiles/pio.dir/pio_types.F90.of951: Warning: Nonexistent include directory '/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share' [-Wmissing-include-dirs]/Users/Dana/cesm1_2_2/models/utils/pio/pio_types.F90:294:0:  #include   /* _EXTERNAL */ Fatal Error: pnetcdf.inc: No such file or directorycompilation terminated.make[3]: *** [CMakeFiles/pio.dir/pio_types.F90.o] Error 1make[2]: *** [CMakeFiles/pio.dir/pio_types.F90.o.provides] Error 2make[1]: *** [CMakeFiles/pio.dir/all] Error 2make: *** [all] Error 2exit 2

 

[jedwards]

The file pnetcdf.inc should be in directory /usr/local/Cellar/parallel-netcdf/1.7.0/include   is it not there?   Maybe the pnetcdf install had a problem?

 

[dana_lapides@berkeley_edu]

ok. i reinstalled pnetcdf manually, and it exists now. It looks like i'm missing files, but i don't know where to get them. Thu Sep 8 11:57:03 PDT 2016 /Users/Dana/cesm1_2_2/case1/bld/lnd.bldlog.160908-115659mpif90  -c -I.  -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/models/csm_share/shr -I. -I/Users/Dana/cesm1_2_2/case1/SourceMods/src.clm -I/Users/Dana/cesm1_2_2/models/lnd/clm/src/cpl_share -I/Users/Dana/cesm1_2_2/models/lnd/clm/src/util_share -I/Users/Dana/cesm1_2_2/models/lnd/clm/src/clm4_0/main -I/Users/Dana/cesm1_2_2/models/lnd/clm/src/clm4_0/biogeophys -I/Users/Dana/cesm1_2_2/models/lnd/clm/src/clm4_0/biogeochem -I/Users/Dana/cesm1_2_2/models/lnd/clm/src/cpl_mct -I/Users/Dana/cesm1_2_2/case1/bld/lib/include  -O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none -fno-range-check -DMAXPATCH_PFT=17 -Ddarwin  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Ddarwin -DCPRGNU  -ffree-form   /Users/Dana/cesm1_2_2/models/lnd/clm/src/clm4_0/main/clm_initializeMod.F90/Users/Dana/cesm1_2_2/models/lnd/clm/src/clm4_0/main/clm_initializeMod.F90:71:8:      use clmtypeInitMod  , only : initClmtype        1Fatal Error: Can't open module file 'clmtypeinitmod.mod' for reading at (1): No such file or directorycompilation terminated.make: *** [clm_initializeMod.o] Error 1

 

[jedwards]

Good progress - now you need to look further up in the clm.bldlog to find the error building module clmtypeInitMod 

 

[dana_lapides@berkeley_edu]

I deleted the gnu folder again, and now I have a colossal error for the cesm build. Seems like I'm missing linkers or something? I'm not sure what, though. ...mpif90  -c -I.  -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/usr/local/include -I/usr/local/Cellar/parallel-netcdf/1.7.0/include -I/Users/Dana/cesm1_2_2/case1/bld/atm/obj -I/Users/Dana/cesm1_2_2/case1/bld/lnd/obj -I/Users/Dana/cesm1_2_2/case1/bld/ice/obj -I/Users/Dana/cesm1_2_2/case1/bld/ocn/obj -I/Users/Dana/cesm1_2_2/case1/bld/glc/obj -I/Users/Dana/cesm1_2_2/case1/bld/rof/obj -I/Users/Dana/cesm1_2_2/case1/bld/wav/obj -I/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/include -I/Users/Dana/cesm1_2_2/models/csm_share/shr -I. -I/Users/Dana/cesm1_2_2/case1/SourceMods/src.drv -I/Users/Dana/cesm1_2_2/models/drv/driver -I/Users/Dana/cesm1_2_2/case1/bld/lib/include  -O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none -fno-range-check -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_WAV=1 -Ddarwin  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Ddarwin -DCPRGNU  -ffree-form   /Users/Dana/cesm1_2_2/models/drv/driver/ccsm_driver.F90mpif90  -o /Users/Dana/cesm1_2_2/case1/bld/cesm.exe ccsm_comp_mod.o ccsm_driver.o mrg_mod.o seq_avdata_mod.o seq_diag_mct.o seq_domain_mct.o seq_flux_mct.o seq_frac_mct.o seq_hist_mod.o seq_map_esmf.o seq_map_mod.o seq_mctext_mod.o seq_rest_mod.o  -L/Users/Dana/cesm1_2_2/case1/bld/lib/ -latm  -L/Users/Dana/cesm1_2_2/case1/bld/lib/ -lice  -L/Users/Dana/cesm1_2_2/case1/bld/lib/ -llnd  -L/Users/Dana/cesm1_2_2/case1/bld/lib/ -locn  -L/Users/Dana/cesm1_2_2/case1/bld/lib/ -lrof  -L/Users/Dana/cesm1_2_2/case1/bld/lib/ -lglc  -L/Users/Dana/cesm1_2_2/case1/bld/lib/ -lwav -L/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -lcsm_share -L/Users/Dana/cesm1_2_2/case1/bld/gnu/openmpi/nodebug/nothreads/lib -lpio -lgptl -lmct -lmpeu  -L/usr/local -lnetcdff -lnetcdf -L/usr/local/Cellar/parallel-netcdf/1.7.0/lib -lpnetcdfUndefined symbols for architecture x86_64:  "_isnanf", referenced from:      _shr_sisnan_ in libcsm_share.a(shr_isnan.o)ld: symbol(s) not found for architecture x86_64collect2: error: ld returned 1 exit statusmake: *** [/Users/Dana/cesm1_2_2/case1/bld/cesm.exe] Error 1

 

[jedwards]

This error suggests an incompatibility between the compiler or compiler options used to build netcdf vs those used to build cesm.   

 

[dana_lapides@berkeley_edu]

actually, i just found another post you responded to with the same issue. i just replaced inanf with inan in the file, and the build just finished successfully! Thanks for the help.