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Cannot build CESM 1.2.2

W

wang_3866@osu_edu

New Member
Hi there,  I am trying to port CESM 1.2.2 on a linux machine. But the building failed with a catastrophic compiler error. The building information is reproduced below:   infile is /nfs/17/osu6925/cesm1_2_2/scripts/test20150623/Buildconf/cplconf/cesm_namelist  CESM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY-------------------------------------------------------------------------------------------------------------------------------------------------- CESM PRESTAGE SCRIPT STARTING - Case input data directory, DIN_LOC_ROOT, is /nfs/17/osu6925/cesm1_2_2/inputdata/ - Checking the existence of input datasets in DIN_LOC_ROOT CESM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY-------------------------------------------------------------------------------------------------------------------------------------------------- CESM BUILDEXE SCRIPT STARTINGrm: No match. COMPILER is intel - Build Libraries: mct gptl pio csm_share Wed Jun 24 10:11:38 EDT 2015 /nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/mct.bldlog.150624-101128Wed Jun 24 10:11:39 EDT 2015 /nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/gptl.bldlog.150624-101128Wed Jun 24 10:11:39 EDT 2015 /nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/pio.bldlog.150624-101128Wed Jun 24 10:11:40 EDT 2015 /nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/csm_share.bldlog.150624-101128ERROR: buildlib.csm_share failed, see /nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/csm_share.bldlog.150624-101128ERROR: cat /nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/csm_share.bldlog.150624-101128  The error file is reproduced below Wed Jun 24 10:11:40 EDT 2015 /nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/csm_share.bldlog.150624-101128mpif90 -c -I.  -I/nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/include -I/nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/usr/local/netcdf/4.1.3-intel/include -I/usr/local/mvapich2/1.7-intel/include -I/nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/include -I/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr -I. -I/nfs/17/osu6925/cesm1_2_2/scripts/test20150623/SourceMods/src.share -I/nfs/17/osu6925/cesm1_2_2/models/drv/shr -I/nfs/17/osu6925/cesm1_2_2/models/dead_share -I/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr -I/nfs/17/osu6925/cesm1_2_2/models/utils/esmf_wrf_timemgr -I/nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//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 -Dlinux  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Dlinux -DCPRINTEL  -free   /nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F900_12456 : catastrophic error: **Internal compiler error: internal abort** Please report this error along with the circumstances in which it occurred in a Software Problem Report.  Note: File and line given may not be explicit cause of this error.compilation aborted for /nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90 (code 1)gmake: *** [shr_dmodel_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 /nfs/17/osu6925/cesm1_2_2/scripts/test20150623/Tools/Makefile  returned non-zero exit status 2 Thank you very much for any suggestions about this problem. 
 
J

jedwards

CSEG and Liaisons
Staff member
This is a compiler error - you didn't tell us the compiler version, but it looks like a very old intel compiler - please request an update from your system administrators.The netcdf version you are using is also quite old, perhaps you should ask for an update of that library as well.
 
W

wang_3866@osu_edu

New Member
Thank you. I changed the intel compiler version to intel/14.0.0.080  and the mpi version to mvapich2/1.9. I also installed locally netcdf-4.3.3.1 with hdf5-1.8.9 and zlib-1.2.8.  Some new errors occurred. I also attached the env_mach_specific and Macros files for information. ------------------------Tue Jun 30 04:22:28 EDT 2015 /nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/csm_share.bldlog.150630-042218mpif90 -c -I.  -I/nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/include -I/nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/include -I/usr/local/mvapich2/1.9-intel/include -I/nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/include -I/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr -I. -I/nfs/17/osu6925/cesm1_2_2/scripts/test20150623/SourceMods/src.share -I/nfs/17/osu6925/cesm1_2_2/models/drv/shr -I/nfs/17/osu6925/cesm1_2_2/models/dead_share -I/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr -I/nfs/17/osu6925/cesm1_2_2/models/utils/esmf_wrf_timemgr -I/nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//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 -Dlinux  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -Dlinux -DCPRINTEL  -free   /nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(15): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [NETCDF]  use pio------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(40): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareXYabs      = 1 ! X,Y  relative error----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(41): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareXYrel      = 2 ! X,Y  absolute error----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(42): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareAreaAbs    = 3 ! area relative error----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(43): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareAreaRel    = 4 ! area absolute error----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(44): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareMaskIdent  = 5 ! masks are identical----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(45): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareMaskZeros  = 6 ! masks have same zeros----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(46): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareMaskSubset = 7 ! mask is subset of other----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(50): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareXYabsMask      = 101 ! X,Y  relative error----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(51): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareXYrelMask      = 102 ! X,Y  absolute error----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(52): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareAreaAbsMask    = 103 ! area relative error----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(53): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareAreaRelMask    = 104 ! area absolute error----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(54): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareMaskIdentMask  = 105 ! masks are identical----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(55): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareMaskZerosMask  = 106 ! masks have same zeros----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(56): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: shr_dmodel_gGridCompareMaskSubsetMask = 107 ! mask is subset of other----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(58): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN),parameter,public :: iotype_std_netcdf = -99 ! non pio option----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(74): error #6683: A kind type parameter must be a compile-time constant.   [IN]    integer(IN)    , intent(in)    :: gsize------------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(75): error #6683: A kind type parameter must be a compile-time constant.   [IN]    integer(IN)    , intent(in)    :: compid------------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(76): error #6683: A kind type parameter must be a compile-time constant.   [IN]    integer(IN)    , intent(in)    :: mpicom------------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(81): error #6683: A kind type parameter must be a compile-time constant.   [IN]    integer(IN) :: n,npes,ierr------------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(82): error #6683: A kind type parameter must be a compile-time constant.   [IN]    integer(IN), pointer :: start(:)     ! for gsmap initialization------------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(83): error #6683: A kind type parameter must be a compile-time constant.   [IN]    integer(IN), pointer :: length(:)    ! for gsmap initialization------------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(84): error #6683: A kind type parameter must be a compile-time constant.   [IN]    integer(IN), pointer :: pe_loc(:)    ! for gsmap initialization------------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(136): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN)    , intent(out)   :: nxgo----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(137): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN)    , intent(out)   :: nygo----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(139): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN)    , intent(in)    :: compid----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(140): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN)    , intent(in)    :: mpicom----------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(149): error #6683: A kind type parameter must be a compile-time constant.   [R8]  real(R8)        ,optional,intent(in)    :: scmlon   ! single column lon-------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(150): error #6683: A kind type parameter must be a compile-time constant.   [R8]  real(R8)        ,optional,intent(in)    :: scmlat   ! single column lat-------^/nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90(153): error #6683: A kind type parameter must be a compile-time constant.   [IN]  integer(IN)   :: n,k,j,i    ! indices----------^/tmp/ifortOTZKn3.i90(1537): catastrophic error: Too many errors, exitingcompilation aborted for /nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90 (code 1)gmake: *** [shr_dmodel_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 /nfs/17/osu6925/cesm1_2_2/scripts/test20150623/Tools/Makefile  returned non-zero exit status 2
 
J

jedwards

CSEG and Liaisons
Staff member
This error just indicates that the pio library didn't build, check for the root error in the pio build log. /nfs/gpfs/PAS0661/scratch_cesm1_2_2/exe//intel/mpich/nodebug/nothreads/pio.bldlog.150624-101128
 
W

wang_3866@osu_edu

New Member
Thank you. The PIO build log file is attached. I found that the hdf5 path was set incorrectly in the original build. So this is the new corrected version. The error seems to happen on this line?/nfs/17/osu6925/cesm1_2_2/models/utils/pio/pio_types.F90(13): error #7013: This module file was not generated by any release of this compiler. [NETCDF]
 
J

jedwards

CSEG and Liaisons
Staff member
You must build the netcdf fortran library with the same compiler that you use to build CESM - this error indicates that this was not the case.   
 
W

wang_3866@osu_edu

New Member
I rebuilt the netcdf with ifort and icc. But the built failed again at csm_share. Is it still a netcdf problem?  /nfs/17/osu6925/cesm1_2_2/models/csm_share/shr/shr_pio_mod.F90(2): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [NETCDF] --------update----------I found the problem. ${LIB_NETCDF} and ${INC_NETCDF} must be set in the environmental variables. Now the model built. export LIB_NETCDF=${NETCDF_PATH}/lib -lnetcdff -lnetcdfexport INC_NETCDF=${NETCDF_PATH}/include 
 
J

jedwards

CSEG and Liaisons
Staff member
You had this before for the netcdf include path - did that change?
-I/nfs/17/osu6925/local/netcdf-4.3.3.1/include

I'm glad that you managed to solve the problem, but the solution doesn't make any sense to me.
 
W

wang_3866@osu_edu

New Member
I am not aware of a place to set netcdf include path in the scripts. The Macros file does not seem to have a line for it. Where do I put the include line?
 
J

jedwards

CSEG and Liaisons
Staff member
Right cprnc should point to the executable, not just the path.  Is it possible that you are not always using the same ifort compiler?   This error is again indicating that the netcdf build is not compatible with the compiler you are using.  
 
W

wang_3866@osu_edu

New Member
No. Actually I found the problem just now so I removed the codes. On line 147 of the Makefile in cprnc folder:     LDFLAGS += -Wl,rpath,$(LIB_NETCDF)should be      LDFLAGS += -Wl,-rpath,$(LIB_NETCDF) for my compiler to recognize it. Sorry for this fuss.   
 
W

wang_3866@osu_edu

New Member
Hello,  I am here with some additional problems running this model. I get run-time errors with the ICLM45 case (but not the I-case). When I built it with one node (* 12 PEs each) it seems to have netcdf error and segfault (cesm.log_.150721-031029.txt). But then I built it with two nodes (*12 PEs each) it just had segfault (cesm.log_.150721-035809.txt). Could you take a look at the attached log files?  Thank you very much.  
 
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