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cesm.exe build failed with error related to Netcdf and HDF5 linkers

rakeshtejak@gmail_com

Rakesh Teja Konduru
Member
Hi,
I am trying to port cesm1.2.2 on the Linux machine X86_64 with the Intel compiler (version 19.0.2.187). I have installed all libraries like hdf5 (v1.10.6), NetCDF-c (4.7.6), NetCDF-FORTRAN (v4.5.2), and pnetcdf (v1.12.1) in the static mode. I have utilized the following linkers to link them all before proceeding with the cesm1.2.2 installation.

SLIBS:=-L/home/rakesh/libraries/cesm/env1/netcdf_4/lib -lnetcdff -lnetcdf -L/home/rakesh/libraries/cesm/env1/pnetcdf_1.12.1/lib -lpnetcdf -L/home/rakesh/libraries/cesm/env1/hdf_1.10.6/lib -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz -ldl -lm

The build of cesm1.2.2 went well for several components with the above settings, but it failed near cesm component. The log of the experiment build is attached and the log of the cesm build is as follows. I have tried several combinations of the linkers to link Netcdf and hdf5, but still this error prevails. It would be great and I would highly appreciate your help to solve this error.

mpif90 -c -I. -I/home/rakesh/run/cesm1/scratch/exp8/bld/intel/mpich/nodebug/nothreads/include -I/home/rakesh/run/cesm1/scratch/exp8/bld/intel/mpich/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/home/rakesh/libraries/cesm/env1/netcdf_4/include -I/home/rakesh/libraries/mpich_3.0.4/include -I/home/rakesh/libraries/cesm/env1/pnetcdf_1.12.1/include -I/home/rakesh/run/cesm1/scratch/exp8/bld/atm/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/lnd/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/ice/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/ocn/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/glc/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/rof/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/wav/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/intel/mpich/nodebug/nothreads/include -I/home/rakesh/models/cesm1_2_2/models/csm_share/shr -I. -I/home/rakesh/run/cesm1/scratch/exp8/SourceMods/src.drv -I/home/rakesh/models/cesm1_2_2/models/drv/driver -I/home/rakesh/run/cesm1/scratch/exp8/bld/lib/include -O2 -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 -DLINUX -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL -DHAVE_SLASHPROC -free /home/rakesh/models/cesm1_2_2/models/drv/driver/ccsm_comp_mod.F90
mpif90 -c -I. -I/home/rakesh/run/cesm1/scratch/exp8/bld/intel/mpich/nodebug/nothreads/include -I/home/rakesh/run/cesm1/scratch/exp8/bld/intel/mpich/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/home/rakesh/libraries/cesm/env1/netcdf_4/include -I/home/rakesh/libraries/mpich_3.0.4/include -I/home/rakesh/libraries/cesm/env1/pnetcdf_1.12.1/include -I/home/rakesh/run/cesm1/scratch/exp8/bld/atm/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/lnd/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/ice/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/ocn/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/glc/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/rof/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/wav/obj -I/home/rakesh/run/cesm1/scratch/exp8/bld/intel/mpich/nodebug/nothreads/include -I/home/rakesh/models/cesm1_2_2/models/csm_share/shr -I. -I/home/rakesh/run/cesm1/scratch/exp8/SourceMods/src.drv -I/home/rakesh/models/cesm1_2_2/models/drv/driver -I/home/rakesh/run/cesm1/scratch/exp8/bld/lib/include -O2 -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 -DLINUX -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL -DHAVE_SLASHPROC -free /home/rakesh/models/cesm1_2_2/models/drv/driver/ccsm_driver.F90
mpif90 -o /home/rakesh/run/cesm1/scratch/exp8/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/home/rakesh/run/cesm1/scratch/exp8/bld/lib/ -latm -L/home/rakesh/run/cesm1/scratch/exp8/bld/lib/ -lice -L/home/rakesh/run/cesm1/scratch/exp8/bld/lib/ -llnd -L/home/rakesh/run/cesm1/scratch/exp8/bld/lib/ -locn -L/home/rakesh/run/cesm1/scratch/exp8/bld/lib/ -lrof -L/home/rakesh/run/cesm1/scratch/exp8/bld/lib/ -lglc -L/home/rakesh/run/cesm1/scratch/exp8/bld/lib/ -lwav -L/home/rakesh/run/cesm1/scratch/exp8/bld/intel/mpich/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -lcsm_share -L/home/rakesh/run/cesm1/scratch/exp8/bld/intel/mpich/nodebug/nothreads/lib -lpio -lgptl -lmct -lmpeu -L/home/rakesh/libraries/cesm/env1/netcdf_4/lib -lnetcdff -lnetcdf -L/home/rakesh/libraries/cesm/env1/pnetcdf_1.12.1/lib -lpnetcdf -L/home/rakesh/libraries/cesm/env1/hdf_1.10.6/lib -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz -ldl -lm -L/home/rakesh/libraries/cesm/env1/pnetcdf_1.12.1/lib -lpnetcdf -L/home/rakesh/libraries/mpich_3.0.4/lib -lmpich
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-hdf5open.o): In function `NC4_open':
hdf5open.c:(.text+0xc74): undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-hdf5var.o): In function `nc4_reopen_dataset':
hdf5var.c:(.text+0x4b): undefined reference to `H5P_CLS_DATASET_ACCESS_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-hdf5var.o): In function `NC4_put_vara':
hdf5var.c:(.text+0x29c4): undefined reference to `H5P_CLS_DATASET_XFER_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-hdf5var.o): In function `NC4_get_vara':
hdf5var.c:(.text+0x39a6): undefined reference to `H5P_CLS_DATASET_XFER_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-hdf5var.o): In function `NC4_put_vars':
hdf5var.c:(.text+0x42b0): undefined reference to `H5P_CLS_DATASET_XFER_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-hdf5var.o): In function `NC4_get_vars':
hdf5var.c:(.text+0x522b): undefined reference to `H5P_CLS_DATASET_XFER_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-hdf5var.o): In function `NC4_HDF5_set_var_chunk_cache':
hdf5var.c:(.text+0x589f): undefined reference to `H5P_CLS_DATASET_ACCESS_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-hdf5var.o): In function `nc_set_var_chunk_cache_ints':
hdf5var.c:(.text+0x5abb): undefined reference to `H5P_CLS_DATASET_ACCESS_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-nc4hdf.o): In function `nc4_create_dim_wo_var':
nc4hdf.c:(.text+0x8ef): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-nc4hdf.o): In function `write_dim':
nc4hdf.c:(.text+0x17f3): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-nc4hdf.o): In function `var_create_dataset':
nc4hdf.c:(.text+0x298f): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
nc4hdf.c:(.text+0x2a67): undefined reference to `H5P_CLS_DATASET_ACCESS_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-nc4hdf.o): In function `nc4_rec_write_groups_types':
nc4hdf.c:(.text+0x3899): undefined reference to `H5P_CLS_GROUP_CREATE_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-nc4memcb.o): In function `NC4_image_init':
nc4memcb.c:(.text+0x3d7): undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'
/home/rakesh/libraries/cesm/env1/netcdf_4/lib/libnetcdf.a(libnchdf5_la-hdf5create.o): In function `NC4_create':
hdf5create.c:(.text+0x24b): undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'
hdf5create.c:(.text+0x2f7): undefined reference to `H5P_CLS_FILE_CREATE_ID_g'
gmake: *** [/home/rakesh/run/cesm1/scratch/exp8/bld/cesm.exe] Error 1


Thank you.

Rakesh
 

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