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CAM 5.3 - Error while building CAM

S

sendtopruthvi@gmail_com

New Member
I'm trying to run CAM 5.3 on a Linux Cluster. I have configured CAM for parallel execution. Upon issuing the make command using - gmake -j2 >& make.outthe cam executable is not being created. This is my make.out file - mpif90 -c -Mfree -I. -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/chemistry/pp_trop_mam3 -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/chemistry/modal_aero -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/chemistry/mozart -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/chemistry/bulk_aero -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/chemistry/utils -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/physics/rrtmg -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/physics/rrtmg/ext/rrtmg_mcica -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/physics/rrtmg/ext/rrtmg_lw -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/physics/rrtmg/ext/rrtmg_sw -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/physics/cam -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/dynamics/fv -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/utils/pilgrim -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/cpl_mct -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/cpl_share -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/control -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/utils -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/utils/timing -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/utils/pio -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/utils/esmf_wrf_timemgr -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/drv/driver -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/drv/shr -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/ocn/docn -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/ocn/docn/cpl_mct -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/lnd/clm/src/cpl_mct -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/lnd/clm/src/cpl_share -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/lnd/clm/src/clm4_0/main -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/lnd/clm/src/clm4_0/biogeochem -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/lnd/clm/src/clm4_0/biogeophys -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/lnd/clm/src/util_share -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/ice/cice/src/drivers/cpl_mct -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/ice/cice/src/drivers/cpl_share -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/ice/cice/src/mpi -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/ice/cice/src/source -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/glc/sglc/cpl_mct -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/rof/rtm/src/cpl_mct -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/rof/rtm/src/cpl_share -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/rof/rtm/src/riverroute -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/wav/swav/cpl_mct -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/csm_share/shr -I/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/csm_share/dshr -I/N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/include/ -I/N/soft/rhel6/openmpi/intel/1.8.4/include/  -I/N/dc2/projects/atmos/shettypr/cam_test7/bld/mct/mct -I/N/dc2/projects/atmos/shettypr/cam_test7/bld/mct/mpeu -I/N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/include/  -DNO_SHR_VMATH -DSEQ_MCT -DNO_C_SIZEOF -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -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_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED  -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=2 -DBLCKY=19 -DMXBLCKS=2  -DMODAL_AERO -DMODAL_AERO_3MODE  -D_USEBOX -D_NETCDF   -DSPMD -DLINUX -DNO_R16 -DCPRPGI -i4 -Mdalign -Mextend -byteswapio -gopt -O2 -Mvect=nosse -Kieee   /N/dc2/projects/atmos/shettypr/cesm1_2_2/models/atm/cam/src/chemistry/mozart/chemistry.F90ifort: command line warning #10006: ignoring unknown option '-Mfree'ifort: command line warning #10006: ignoring unknown option '-Mdalign'ifort: command line warning #10006: ignoring unknown option '-Mextend'ifort: command line warning #10006: ignoring unknown option '-byteswapio'ifort: command line warning #10006: ignoring unknown option '-gopt'ifort: command line warning #10006: ignoring unknown option '-Mvect=nosse'ifort: command line remark #10148: option '-Kieee' not supportedtouch /N/dc2/projects/atmos/shettypr/cam_test7/bld/Filepath This is my Makefile: # Make macros for CAM. UNAMES       := LinuxROOTDIR      := /N/dc2/projects/atmos/shettypr/cesm1_2_2EXENAME      := camMODEL_EXEDIR := /N/dc2/projects/atmos/shettypr/cam_test7/bldINC_NETCDF   := /N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/include/LIB_NETCDF   := /N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/lib/NC_LDFLAGS   := -L/N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/lib -lnetcdff -lnetcdf -lnetcdf -Wl,-rpath=/N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/lib/MOD_NETCDF   := /N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/include/INC_PNETCDF  :=LIB_PNETCDF  :=INC_MPI      := /N/soft/rhel6/openmpi/intel/1.8.4/include/LIB_MPI      := /N/soft/rhel6/openmpi/intel/1.8.4/lib/MPI_LIB_NAME := mpiLAPACK_LIBDIR:=ESMF_LIBDIR  :=DEBUG        := FALSESPMD         := TRUESMP          := FALSEFC           := mpif90FC_TYPE      := pgiCC           := mpiccUSER_LINKER  :=USER_CPPDEFS :=    -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -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_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED  -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=2 -DBLCKY=19 -DMXBLCKS=2  -DMODAL_AERO -DMODAL_AERO_3MODE  -D_USEBOX -D_NETCDFUSER_CFLAGS  :=USER_FFLAGS  :=F_OPTIMIZATION_OVERRIDE :=USER_LDFLAGS :=  -L/N/dc2/projects/atmos/shettypr/cam_test7/bld/mct/mct -lmct -L/N/dc2/projects/atmos/shettypr/cam_test7/bld/mct/mpeu -lmpeuCOSP_LIBDIR  :=MCT_LIBDIR   := /N/dc2/projects/atmos/shettypr/cam_test7/bld/mct What would be the best way to resolve this? 
Thanks 
 
E

eaton

CSEG and Liaisons
You need to set the configure argument "-fc_type intel".  It appears that you've let configure use the default value which is pgi and hence you're getting messages from ifort about the pgi options that it doesn't recognize.
 
S

sendtopruthvi@gmail_com

New Member
Hi, I've set the configure arguement to "-fc_type intel".  [shettypr@h3 bld]$ $camcfg/configure -fc mpif90 -fc_type intel -cc mpicc -dyn fv -hgrid 10x15 -ntasks 6 -nosmp -testIssuing command to the CICE configure utility:  /N/dc2/projects/atmos/shettypr/cesm1_2_2/models/ice/cice/bld/configure -hgrid 10x15 -cice_mode prescribed -ntr_aero 0 -nx 24 -ny 19 -bsizex 2 -bsizey 19 -maxblocks 2 -decomptype blkrobin -cache config_cache_cice.xml -cachedir /N/dc2/projects/atmos/shettypr/cam_test7/bldCICE configure done.MCT configure is done.creating /N/dc2/projects/atmos/shettypr/cam_test7/bld/Filepathcreating /N/dc2/projects/atmos/shettypr/cam_test7/bld/Makefilecreating /N/dc2/projects/atmos/shettypr/cam_test7/bld/config.hcreating /N/dc2/projects/atmos/shettypr/cam_test7/bld/config_cache.xmlLooking for a valid GNU make... using gmakeTesting for Fortran 90 compatible compiler... using mpif90Test linking to NetCDF library... okTest linking to MPI library... okCAM configure done.[shettypr@h3 bld]$ gmake -j2  >& make.out Upon issuing the make command, the cam executable is not being created.  This is make make.out file:  touch /N/dc2/projects/atmos/shettypr/cam_test7/bld/Filepathshr_spfn_mod.o: In function `shr_spfn_mod_mp_shr_spfn_erf_r4_':/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/csm_share/shr/shr_spfn_mod.F90:(.text+0x12): undefined reference to `erf_'shr_spfn_mod.o: In function `shr_spfn_mod_mp_shr_spfn_erf_r8_':/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/csm_share/shr/shr_spfn_mod.F90:(.text+0x22): undefined reference to `derf_'shr_spfn_mod.o: In function `shr_spfn_mod_mp_shr_spfn_erfc_r4_':/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/csm_share/shr/shr_spfn_mod.F90:(.text+0x32): undefined reference to `erfc_'shr_spfn_mod.o: In function `shr_spfn_mod_mp_shr_spfn_erfc_r8_':/N/dc2/projects/atmos/shettypr/cesm1_2_2/models/csm_share/shr/shr_spfn_mod.F90:(.text+0x42): undefined reference to `derfc_'gmake: *** [/N/dc2/projects/atmos/shettypr/cam_test7/bld/cam] Error 1  What would be the best way to resolve this?  This is my Makefile:  # Make macros for CAM. UNAMES       := LinuxROOTDIR      := /N/dc2/projects/atmos/shettypr/cesm1_2_2EXENAME      := camMODEL_EXEDIR := /N/dc2/projects/atmos/shettypr/cam_test7/bldINC_NETCDF   := /N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/include/LIB_NETCDF   := /N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/lib/NC_LDFLAGS   := -L/N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/lib -lnetcdff -lnetcdf -lnetcdf -Wl,-rpath=/N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/lib/MOD_NETCDF   := /N/soft/rhel6/netcdf_fortran/intel/mpi/4.4.1/include/INC_PNETCDF  :=LIB_PNETCDF  :=INC_MPI      := /N/soft/rhel6/openmpi/intel/1.8.4/include/LIB_MPI      := /N/soft/rhel6/openmpi/intel/1.8.4/lib/MPI_LIB_NAME := mpiLAPACK_LIBDIR:=ESMF_LIBDIR  :=DEBUG        := FALSESPMD         := TRUESMP          := FALSEFC           := mpif90FC_TYPE      := intelCC           := mpiccUSER_LINKER  :=USER_CPPDEFS :=    -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -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_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED  -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=2 -DBLCKY=19 -DMXBLCKS=2  -DMODAL_AERO -DMODAL_AERO_3MODE  -D_USEBOX -D_NETCDFUSER_CFLAGS  :=USER_FFLAGS  :=F_OPTIMIZATION_OVERRIDE :=USER_LDFLAGS :=  -L/N/dc2/projects/atmos/shettypr/cam_test7/bld/mct/mct -lmct -L/N/dc2/projects/atmos/shettypr/cam_test7/bld/mct/mpeu -lmpeuCOSP_LIBDIR  :=MCT_LIBDIR   := /N/dc2/projects/atmos/shettypr/cam_test7/bld/mct Thanks 
 
E

eaton

CSEG and Liaisons
The externals that aren't being found; erf_, erfc_, etc, are Fortran intrinsics that should be known to newer intel compilers.  So either your intel compiler is old or misconfigured.  The best solution is to fix or update the compiler.  If you want to work around the compiler problem you'll need to go into the file csm_share/shr/shr_spfn_mod.F90 and comment out the lines the define the macros HAVE_GAMMA_INTRINSICS and HAVE_ERF_INTRINSICS.  That should allow the use of the error function source code in that module rather than attempting to use the intrinsics.
 
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