kamingfung@link_cuhk_edu_hk
New Member
Hi, I am trying to run CLM5 on my institute's cluster but I encountered a problem when trying to invoke case.build.This is the error messages when running case.build:
Building case in directory /users/student/$HOME/CLM/clm5.0/test50sharedlib_only is Falsemodel_only is FalseGenerating component namelists as part of buildCreating component namelists Calling /users/student/$HOME/CLM/clm5.0/cime/src/components/data_comps/datm/cime_config/buildnml Calling /users/student/$HOME/CLM/clm5.0/cime_config/buildnml Calling /users/student/$HOME/CLM/clm5.0/cime/src/components/stub_comps/sice/cime_config/buildnml Calling /users/student/$HOME/CLM/clm5.0/cime/src/components/stub_comps/socn/cime_config/buildnml Calling /users/student/$HOME/CLM/clm5.0/components/mosart//cime_config/buildnmlFile not found: frivinp_rtm = "/users/student/$HOME/CESM/input_data/rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc", will attempt to download in check_input_data phase Running /users/student/$HOME/CLM/clm5.0/components/cism//cime_config/buildnml Calling /users/student/$HOME/CLM/clm5.0/cime/src/components/stub_comps/swav/cime_config/buildnml Calling /users/student/$HOME/CLM/clm5.0/cime/src/components/stub_comps/sesp/cime_config/buildnml Calling /users/student/$HOME/CLM/clm5.0/cime/src/drivers/mct/cime_config/buildnmlFile not found: lnd2glc_fmapname = "cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gland4km_aave.170429.nc", will attempt to download in check_input_data phaseFile not found: lnd2glc_smapname = "cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gland4km_blin.170429.nc", will attempt to download in check_input_data phaseFile not found: glc2lnd_fmapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv1.9x2.5_aave.170429.nc", will attempt to download in check_input_data phaseFile not found: glc2lnd_smapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv1.9x2.5_aave.170429.nc", will attempt to download in check_input_data phaseFinished creating component namelistsBuilding gptl with output to file /users/student/$HOME/CLM/run_dir/test50/bld/gptl.bldlog.180213-061727Building mct with output to file /users/student/$HOME/CLM/run_dir/test50/bld/mct.bldlog.180213-061727Building pio with output to file /users/student/$HOME/CLM/run_dir/test50/bld/pio.bldlog.180213-061727Building csm_share with output to file /users/student/$HOME/CLM/run_dir/test50/bld/csm_share.bldlog.180213-061727Component csm_share build complete with 1 warningsERROR: BUILD FAIL: buildlib.csm_share failed, cat /users/student/$HOME/CLM/run_dir/test50/bld/csm_share.bldlog.180213-061727 It looks like something wrong when building csm_share and here is the content in csm_share.bldlog.180213-061727: /users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads /users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads /users/student/$HOME/CLM/clm5.0/test50installdir is /users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1libdir is /users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/csm_sharempif90 -c -I. -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/include -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include -I/opt/share/netcdf-4.3.2.intel/include -I/opt/share/mpich-3.1.1.intel/include -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/include -I/users/student/$HOME/CLM/clm5.0/cime/src/share/util -I/users/student/$HOME/CLM/clm5.0/cime/src/share/include -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/include -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/mct/noesmf/include -I. -I/users/student/$HOME/CLM/clm5.0/test50/SourceMods/src.share -I/users/student/$HOME/CLM/clm5.0/cime/src/drivers/mct/shr -I/users/student/$HOME/CLM/clm5.0/cime/src/components/xcpl_models/xshare -I/users/student/$HOME/CLM/clm5.0/cime/src/components/data_comps/dshare -I/users/student/$HOME/CLM/clm5.0/cime/src/share/util -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/dsfmt_f03 -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/kissvec -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/mt19937 -I/users/student/$HOME/CLM/clm5.0/cime/src/share/esmf_wrf_timemgr -I/users/student/$HOME/CLM/run_dir/test50/bld/lib/include -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -O2 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_WAV=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_ESP=1 -DNDEBUG -DHAVE_MPI -DPIO1 -DFORTRANUNDERSCORE -DNO_R16 -DLinux -DCPRINTEL -free -DUSE_CONTIGUOUS= /users/student/$HOME/CLM/clm5.0/cime/src/share/esmf_wrf_timemgr/ESMF_AlarmClockMod.F90mpif90 -c -I. -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/include -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include -I/opt/share/netcdf-4.3.2.intel/include -I/opt/share/mpich-3.1.1.intel/include -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/include -I/users/student/$HOME/CLM/clm5.0/cime/src/share/util -I/users/student/$HOME/CLM/clm5.0/cime/src/share/include -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/include -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/mct/noesmf/include -I. -I/users/student/$HOME/CLM/clm5.0/test50/SourceMods/src.share -I/users/student/$HOME/CLM/clm5.0/cime/src/drivers/mct/shr -I/users/student/$HOME/CLM/clm5.0/cime/src/components/xcpl_models/xshare -I/users/student/$HOME/CLM/clm5.0/cime/src/components/data_comps/dshare -I/users/student/$HOME/CLM/clm5.0/cime/src/share/util -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/dsfmt_f03 -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/kissvec -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/mt19937 -I/users/student/$HOME/CLM/clm5.0/cime/src/share/esmf_wrf_timemgr -I/users/student/$HOME/CLM/run_dir/test50/bld/lib/include -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -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 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_ESP=1 -DNDEBUG -DHAVE_MPI -DPIO1 -DFORTRANUNDERSCORE -DNO_R16 -DLinux -DCPRINTEL -free -DUSE_CONTIGUOUS= /users/student/$HOME/CLM/clm5.0/cime/src/share/util/shr_strconvert_mod.F90/users/student/$HOME/CLM/clm5.0/cime/src/externals/genf90/genf90.pl /users/student/$HOME/CLM/clm5.0/cime/src/share/util/shr_assert_mod.F90.in > shr_assert_mod.F90mpicc -c -I. -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/include -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include -I/opt/share/netcdf-4.3.2.intel/include -I/opt/share/mpich-3.1.1.intel/include -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/include -I/users/student/$HOME/CLM/clm5.0/cime/src/share/util -I/users/student/$HOME/CLM/clm5.0/cime/src/share/include -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/include -I/users/student/$HOME/CLM/run_dir/test50/bld/intel/mpich/nodebug/nothreads/mct/noesmf/include -I. -I/users/student/$HOME/CLM/clm5.0/test50/SourceMods/src.share -I/users/student/$HOME/CLM/clm5.0/cime/src/drivers/mct/shr -I/users/student/$HOME/CLM/clm5.0/cime/src/components/xcpl_models/xshare -I/users/student/$HOME/CLM/clm5.0/cime/src/components/data_comps/dshare -I/users/student/$HOME/CLM/clm5.0/cime/src/share/util -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/dsfmt_f03 -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/kissvec -I/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/mt19937 -I/users/student/$HOME/CLM/clm5.0/cime/src/share/esmf_wrf_timemgr -I/users/student/$HOME/CLM/run_dir/test50/bld/lib/include -O2 -fp-model precise -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_WAV=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_ESP=1 -DNDEBUG -DHAVE_MPI -DPIO1 -DFORTRANUNDERSCORE -DNO_R16 -DLinux -DCPRINTEL -O3 -fp-model fast /users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/kissvec/kissvec.c/users/student/$HOME/CLM/clm5.0/cime/src/externals/genf90/genf90.pl /users/student/$HOME/CLM/clm5.0/cime/src/share/util/shr_frz_mod.F90.in > shr_frz_mod.F90icc: command line warning #10121: overriding '-fp-model precise' with '-fp-model fast'/users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/kissvec/kissvec.c(21): error: identifier "restrict" is undefined void kiss_rng(uint32_t seed1[restrict], uint32_t seed2[restrict], ^ compilation aborted for /users/student/$HOME/CLM/clm5.0/cime/src/share/RandNum/src/kissvec/kissvec.c (code 2)make: *** [kissvec.o] Error 2make: *** Waiting for unfinished jobs....rm shr_assert_mod.F90 shr_frz_mod.F90make complib -j 4 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 -DNUM_COMP_INST_ESP=1" -f /users/student/$HOME/CLM/clm5.0/test50/Tools/Makefile returned non-zero exit status 2I googled it. I guess one of the possibility is that my compiler is not capable of interpreting the C99-style usage of "restrict" in kissvec.c. Other possible cause maybe I didn't do it right to specify my compilers or I am using wrong compilers in Macros.make under my case folder, i.e. "test50" in this case. I appended my Macros.make below:
CPPDEFS+= -DFORTRANUNDERSCORE -DNO_R16 -DLinux -DCPRINTEL SLIBS+=# USERDEFINED $(shell $(NETCDF_PATH)/bin/nc-config --flibs) CFLAGS:= -O2 -fp-model precise CONFIG_ARGS:= CXX_LDFLAGS:= -cxxlib CXX_LINKER:=FORTRAN ESMF_LIBDIR:= FC_AUTO_R8:= -r8 FFLAGS:= -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs FFLAGS_NOOPT:= -O0 FIXEDFLAGS:= -fixed -132 FREEFLAGS:= -free MPICC:= mpicc MPICXX:= mpicxx MPIFC:= mpif90 MPI_LIB_NAME:= mpich MPI_PATH:= /opt/share/mpich2-1.5rc3 NETCDF_PATH:= /opt/share/netcdf-4.3.2.intel PNETCDF_PATH:= SCC:= icc SCXX:= g++ SFC:= ifort SUPPORTS_CXX:=FALSE ifeq ($(compile_threaded), true) FFLAGS += -openmp LDFLAGS += -openmp CFLAGS += -openmp endif ifeq ($(MODEL), pop2) CPPDEFS += -D_USE_FLOW_CONTROL endif ifeq ($(DEBUG), FALSE) FFLAGS += -O2 endif ifeq ($(DEBUG), TRUE) FFLAGS += -O0 -g -check uninit -check bounds -check pointers -fpe0 endif I have been trying to fix it for two days but still, don't have a clue what went wrong. Would anyone please give some directions/hints on how to solve this issue? Thank you so much. Our machine is running on SUSE Linus version 3.0.1010-0.47.67-default with gcc version 4.3.4.