cesm1_0_3 with GNU builde Error

[li_wei@snnu_edu_cn]

Hello, I am now porting cesm1_0_3, I use the gnu compiler,
this step in the builde when problems can not be solved, pointing to the trouble, thank you.
Due to space limitations I only posted part of the error code, error is as follows:

Wed May 12 01:00:28 CST 2010 /home/yin/run/test_ghnode/run/ccsm.bldlog.100512-005930
-------------------------------------------------------------------------
Building a single executable version of CCSM
-------------------------------------------------------------------------
cat: Srcfiles: No such file or directory
/home/yin/cesm1_0_3/scripts/test_ghnode/Tools/mkSrcfiles > /home/yin/run/test_ghnode/ccsm/obj/Srcfiles
cp -f /home/yin/run/test_ghnode/ccsm/obj/Filepath /home/yin/run/test_ghnode/ccsm/obj/Deppath
/home/yin/cesm1_0_3/scripts/test_ghnode/Tools/mkDepends Deppath Srcfiles > /home/yin/run/test_ghnode/ccsm/obj/Depends
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/seq_diag_mct.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/seq_rearr_mod.F90
/usr/local/mpich/include/mpif.h:468.11:
Included at /home/yin/cesm1_0_3/models/drv/driver/seq_rearr_mod.F90:60:

SAVE /MPIPRIV1/,/MPIPRIV2/
1
Warning: SAVE statement at (1) follows blanket SAVE statement
/usr/local/mpich/include/mpif.h:471.11:
Included at /home/yin/cesm1_0_3/models/drv/driver/seq_rearr_mod.F90:60:

SAVE /MPIPRIVC/
1
Warning: SAVE statement at (1) follows blanket SAVE statement
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/map_ocnocn_mct.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/mrg_x2s_mct.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/mrg_x2o_mct.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/seq_avdata_mod.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/seq_hist_mod.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/mrg_x2a_mct.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/map_atmice_mct.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/map_iceocn_mct.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/map_snoglc_mct.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2 /home/yin/cesm1_0_3/models/drv/driver/map_atmlnd_mct.F90
mpif90 -c -I. -I/usr/local/netcdf/include -I/usr/local/netcdf/include -I/usr/local/mpich/include -I. -I/home/yin/cesm1_0_3/scripts/test_ghnode/SourceMods/src.drv -I/home/yin/cesm1_0_3/models/drv/driver -I/home/yin/run/test_ghnode/lib/include -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fconvert=big-endian -ffree-line-length-none -fno-range-check -fcray-pointer -std=gnu -D___G95__ -O2/home/yin/run/test_ghnode/lib/libcsm_share.a(shr_mct_mod.o): In function `__shr_mct_mod_MOD_shr_mct_smatreadnc':
/home/yin/cesm1_0_3/models/csm_share/shr/shr_mct_mod.F90:105: undefined reference to `nf_open_'
/home/yin/cesm1_0_3/models/csm_share/shr/shr_mct_mod.F90:112: undefined reference to `nf_inq_dimid_'
/home/yin/cesm1_0_3/models/csm_share/shr/shr_mct_mod.F90:113: undefined reference to `nf_inq_dimlen_'
/home/yin/cesm1_0_3/models/csm_share/shr/shr_mct_mod.F90:114: undefined reference to `nf_inq_dimid_'
/home/yin/cesm1_0_3/models/csm_share/shr/shr_mct_mod.F90:115: undefined reference to `nf_inq_dimlen_'
/home/yin/cesm1_0_3/models/csm_share/shr/shr_mct_mod.F90:116: undefined reference to `nf_inq_dimid_'
/home/yin/cesm1_0_3/models/csm_share/shr/shr_mct_mod.F90:117: undefined reference to `nf_inq_dimlen_'
/home/yin/cesm1_0_3/models/csm_share/shr/shr_mct_mod.F90:140: undefined reference to `nf_inq_varid_'
collect2: ld returned 1 exit status
gmake: *** [/home/yin/run/test_ghnode/run/ccsm.exe] Error 1

 

[gus@ldeo_columbia_edu]

Hi Li Wei

The build scripts apparently cannot find your NetCDF library functions.
They seem to be trying to find NetCDF in /usr/local/netcdf/.
Do you really have NetCDF there?

Did you set your NetCDF path, lib, and include directories?
The CESM user guide explains how to port the model to new machines and compilers,
how to set the NetCDF and MPI location, etc.
It is worth reading it.

I hope this helps.
Gus Correa

 

[li_wei@snnu_edu_cn]

Thank you, my problem has been solved, carefully check the NETCDF path configuration, found LDFLAGS path is not configured.