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Porting errors: build.csm_share


Code:
Hello,<br /><br />I'm trying to port CESM 1.2.2.<br /><br />When I try to build a case, there is a problem that I can't find the solution here.

The cases are BCN and BGCN, same are presenting build.csm_share errors:

 Wed Dec 13 13:07:40 BRST 2017
/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37/bld/intel//nodebug/nothreads/csm_share.bldlog.171213-130620
ERROR: buildlib.csm_share failed, see
/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37/bld/intel//nodebug/nothreads/csm_share.bldlog.171213-130620
<br /><br />
In the csm_share log file, there are some warnings like:<br />
/scratch/10071a/rafaelrangel/cesm1_2_2/models/utils/esmf_wrf_timemgr/ESMF_BaseMod.F90(672):
warning #6843: A dummy argument with an explicit INTENT(OUT) declaration
is not given an explicit value.   [TYPE]
      subroutine ESMF_AttributeGetbyNumber(anytype, number, name, type,
value, rc)

However, the errors are:<br />
/scratch/10071a/rafaelrangel/cesm1_2_2/models/csm_share/shr/shr_pcdf_mod.F90(32):
error #7002: Error in opening the compiled module file.  Check INCLUDE
paths.   [PIO]
  use pio
------^
/scratch/10071a/rafaelrangel/cesm1_2_2/models/csm_share/shr/shr_pcdf_mod.F90(64):
error #7002: Error in opening the compiled module file.  Check INCLUDE
paths.   [PIO]
  use pio, only : iosystem_desc_t
------^
/scratch/10071a/rafaelrangel/cesm1_2_2/models/csm_share/shr/shr_pcdf_mod.F90(68):
error #6406: Conflicting attributes or multiple declaration of name.  
[IOSYSTEM_DESC_T]
  type(iosystem_desc_t) :: iosystem
.
.
.<br /><br />I've contacted our HPC (called LOBOC - SGI X) admin, and he told me that he properly configured the Pio environment variables. However, before the "build" errors, I was trying to build the case, but there was a PIO and
genf90 problem, which I solved like this (I saw the solution in CESM forum):

In $CESM/SVN_EXTERNAL_DIRECTORIES:
remove: models/utils/pio <a href="http://parallelio.googlecode.com/svn/" target="_blank">http://parallelio.googlecode.com/svn/</a>
trunk_tags/pio1_8_12/pio
add: models/utils/pio   <a href="https://github.com/NCAR/ParallelIO" target="_blank">https://github.com/NCAR/ParallelIO</a>
    $ svn propset svn:externals -F SVN_EXTERNAL_DIRECTORIES ./
    $ svn update

So I don't know if these steps have any influence on the building errors.<br /><br />Some files are attached (error log, env_build, config_machines, config_compilers and our hpc environment variables).<br /><br />Versions:<br />netCDF 4.4.1.1<br />pio 2.3.0<br />pnetcdf 1.8.1<br />ifort version 17.0.5<br />icc version 17.0.5<br /><br /><br />Any help will be very appreciated!<br /><br />Regards,<br />Rafael
 
Hi, Jim.I saw that topic a few day ago, but I didn't understand what to do.Do I have to use an older Pio version?When I did this:
Code:
In $CESM/SVN_EXTERNAL_DIRECTORIES:
remove: models/utils/pio <a href="http://parallelio.googlecode.com/svn/" target="_blank">http://parallelio.googlecode.com/svn/</a>
trunk_tags/pio1_8_12/pio
add: models/utils/pio   <a href="https://github.com/NCAR/ParallelIO" target="_blank">https://github.com/NCAR/ParallelIO</a>
    $ svn propset svn:externals -F SVN_EXTERNAL_DIRECTORIES ./
    $ svn update<br /><br />the errors appeared.<br /><br />About the link:  <a href="https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio" target="_blank">https://github.com/NCAR/ParallelIO.git/tags/pio1_7_2/pio</a> it isn't available anymore.<br /><br />Thanks!<br /><br />
 
 

jedwards

CSEG and Liaisons
Staff member
This has the corrected linkhttps://svn-ccsm-models.cgd.ucar.edu/cesm1/release_tags/cesm1_2_2_1/
 
Thank you very much, Jim.It worked fine!  Just to explain to anyone who could have the same problem as mine:In the top SVN_EXTERNAL_DIRECTORIES replace the linemodels/utils/pio       [whatever] with:
Code:
models/utils/pio                   https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio<br /><br />then type:<br /><br />svn propset svn:externals -F SVN_EXTERNAL_DIRECTORIES ./<br />svn update<br /><br /><br />and it's done! Just build the case!
  
 
After solving the PIO problem, with Jim Edwards' help, there is another problem that I don't know what I'm missing. Now it is a cism.buildexe.csh problem (log file is attached): CESM BUILDEXE SCRIPT STARTING
rm: No match.
 COMPILER is intel
 - Build Libraries: mct gptl pio csm_share
Thu Dec 21 17:24:24 BRST 2017 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/intel//nodebug/nothreads/mct.bldlog.171221-172419
Thu Dec 21 17:24:24 BRST 2017 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/intel//nodebug/nothreads/gptl.bldlog.171221-172419
Thu Dec 21 17:24:24 BRST 2017 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/intel//nodebug/nothreads/pio.bldlog.171221-172419
Thu Dec 21 17:24:24 BRST 2017 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/intel//nodebug/nothreads/csm_share.bldlog.171221-172419
Thu Dec 21 17:24:24 BRST 2017 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/atm.bldlog.171221-172419
Thu Dec 21 17:24:25 BRST 2017 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lnd.bldlog.171221-172419
Thu Dec 21 17:24:25 BRST 2017 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/ice.bldlog.171221-172419
Thu Dec 21 17:24:25 BRST 2017 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/ocn.bldlog.171221-172419
Thu Dec 21 17:24:26 BRST 2017 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/glc.bldlog.171221-172419
ERROR: cism.buildexe.csh failed, see /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/glc.bldlog.171221-172419
ERROR: cat /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/glc.bldlog.171221-172419 It is basically showing this kind of error:/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_global_fields.F90(18): error #7002: Error in opening the
compiled module file.  Check INCLUDE paths.   [GLINT_EXAMPLE_CLIM]
   use glint_example_clim, only: glex_climate
-------^ What am I missing? I don't know what (path) and where to include. The versions that I'm using are:rafaelrangel@service1:/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3> module list
Currently Loaded Modulefiles:
  1) intel/2017.5.239   2) cmake/3.10.0       3) szip/2.1.1         4) phdf5/1.8.19       5) pnetcdf/1.8.1      6) netcdf/4.5.0       7) pio/2.3.0 Macros file content:#
# Makefile Macros generated from /scratch/10071a/rafaelrangel/cesm1_2_2/scripts/ccsm_utils/Machines/config_compilers.xml using
# COMPILER=intel
# OS=LINUX
# MACH=loboc
#
CPPDEFS+= -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL

CFLAGS:= -O2 -fp-model precise

CXX_LDFLAGS:= -cxxlib

CXX_LINKER:=FORTRAN

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:= mpiicc 

MPICXX:= mpiicxx

MPIFC:= mpiifort

NETCDF_PATH:=/sw/apps/suse/intel17/netcdf/4.5.0

SLIBS+= -L$(NETCDF_PATH) -lnetcdff -lnetcdf

LAPACK_LIBDIR=${MKLROOT}/lib/intel64

SCC:= icc

SCXX:= icpc

SFC:= ifort

SUPPORTS_CXX:=TRUE

ifeq ($(compile_threaded), true)
   CFLAGS += -qopenmp
   FFLAGS += -qopenmp
   LDFLAGS += -qopenmp
endif

ifeq ($(MODEL), pop2)
   CPPDEFS += -D_USE_FLOW_CONTROL
endif

ifeq ($(DEBUG), TRUE)
   FFLAGS += -O0 -g -check uninit -check bounds -check pointers -fpe0
endif

ifeq ($(DEBUG), FALSE)
   FFLAGS += -O2
endif 
Code:
<strong>Any help will be very appreciated!</strong><br /><br /><strong>Regards,</strong><br /><strong>Rafael</strong>
 

jedwards

CSEG and Liaisons
Staff member
Maybe the checkout failed to complete?You should have a directory models/glc/cism/glimmer-cism/libglint/if you don't try running svn up again from the cism directory. 
 
I tried the svn update and aparently it is ok now. However, when building CESM, a new problem occured:Tue Jan 2 20:36:55 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/cesm.bldlog.180102-203024ERROR: cesm.buildexe.csh failed, see /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/cesm.bldlog.180102-203024mpiifort  -o /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/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/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -latm  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -lice  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -llnd  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -locn  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -lrof  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -lglc  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -lwav  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/glc/lib/ -lglimmercismfortran -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/intel//nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -lcsm_share -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/intel//nodebug/nothreads/lib -lpio -lgptl -lmct -lmpeu -L/sw/apps/suse/intel17/netcdf/4.5.0 -lnetcdff -lnetcdf  -L/sw/apps/intel17/compilers_and_libraries_2017.5.239/linux/mkl/lib/intel64/libmkl_blas95_ilp64.a -L/sw/apps/intel17/compilers_and_libraries_2017.5.239/linux/mkl/lib/intel64/libmkl_lapack95_ilp64.a -liomp5 -lpthread -lm -ldl -L/sw/apps/intel17/compilers_and_libraries_2017.5.239/linux/mkl/lib/intel64 -llapack -lblasld: cannot find -llapackld: cannot find -lblas/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/Tools/Makefile:625: recipe for target '/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/cesm.exe' failedgmake: *** [/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/cesm.exe] Error 1 Well, I think now the problem is with LAPACK (-llapack and -lblas).Following what was said here: https://bb.cgd.ucar.edu/clm45cn-compilerun-error and here: https://bb.cgd.ucar.edu/math-library-mkl-intel-compiler-applicable-cesm-instead-lapack-and-blas%EF%BC%9FI changed some lines in Macros file:FFLAGS:= -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -L$(MKLROOT)/include/intel64/ilp64 -L$(MKLROOT)/includeLAPACK_LIBDIR=${MKLROOT}/lib/intel64SLIBS+= -L$(NETCDF_PATH) -lnetcdff -lnetcdf  -L$(MKLROOT)/lib/intel64/libmkl_blas95_ilp64.a -L$(MKLROOT)/lib/intel64/libmkl_lapack95_ilp64.a -liomp5 -lpthread -lm -ldlbut it didn't work ... is it possible to use intel MKL? 
 

jedwards

CSEG and Liaisons
Staff member
Yes if you have the mkl library you should use it. but you don't need to explicitly provide any of the link flags,instead you should just add the flag -mkl  
 
Unfortunately, it isn't working yet.I changed the Macros lines to:FFLAGS:= -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhsSLIBS+= -L$(NETCDF_PATH) -lnetcdff -lnetcdf -mklIs this right?The error is still due to -llapack and -lblas:mpiifort  -o /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/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/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -latm  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -lice  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -llnd  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -locn  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -lrof  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -lglc  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/lib/ -lwav  -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/glc/lib/ -lglimmercismfortran -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/intel//nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -lcsm_share -L/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/intel//nodebug/nothreads/lib -lpio -lgptl -lmct -lmpeu -L/sw/apps/suse/intel17/netcdf/4.5.0 -lnetcdff -lnetcdf -mkl -L/sw/apps/intel17/compilers_and_libraries_2017.5.239/linux/mkl/lib/intel64 -llapack -lblasld: cannot find -llapackld: cannot find -lblas/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/Tools/Makefile:625: recipe for target '/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/cesm.exe' failedgmake: *** [/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/cesm.exe] Error 1 Does the MKL has -llapack and -lblas? I tried to find without success.
 
I removed the "-llapack" and "-lblas" from the ./Tools/Makefile. Makefile: # System libraries (netcdf, mpi, pnetcdf, esmf, trilinos, etc.)  ifndef SLIBS    SLIBS := -L$(LIB_NETCDF) -lnetcdf endif ifdef LIB_PNETCDF    SLIBS += -L$(LIB_PNETCDF) -lpnetcdf endif ifdef LAPACK_LIBDIR    SLIBS += -L$(LAPACK_LIBDIR) -llapack -lblas endif ifdef LIB_MPI    ifndef MPI_LIB_NAME       SLIBS += -L$(LIB_MPI) -lmpi    else       SLIBS += -L$(LIB_MPI) -l$(MPI_LIB_NAME)    endif endif  Then added to Macros: CFLAGS:= -O2 -fp-model precise -mkl FFLAGS:= -mkl -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhsSo, the final Macros file is:CPPDEFS+= -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  CFLAGS:= -O2 -fp-model precise -mkl CXX_LDFLAGS:= -cxxlib  CXX_LINKER:=FORTRAN FC_AUTO_R8:= -r8  FFLAGS:= -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -mkl FFLAGS_NOOPT:= -O0  FIXEDFLAGS:= -fixed -132  FREEFLAGS:= -free  MPICC:= mpiicc   MPICXX:= mpiicxx  MPIFC:= mpiifort  NETCDF_PATH:=/sw/apps/suse/intel17/netcdf/4.5.0 LAPACK_LIBDIR=${MKLROOT}/lib/intel64 SLIBS+= -L$(NETCDF_PATH) -lnetcdff -lnetcdf SCC:= icc  SCXX:= icpc  SFC:= ifort  SUPPORTS_CXX:=TRUE ifeq ($(compile_threaded), true)    LDFLAGS += -qopenmp    FFLAGS += -qopenmp    CFLAGS += -qopenmp endif ifeq ($(DEBUG), TRUE)    FFLAGS += -O0 -g -check uninit -check bounds -check pointers -fpe0 endif ifeq ($(DEBUG), FALSE)    FFLAGS += -O2 endif ifeq ($(MODEL), pop2)    CPPDEFS += -D_USE_FLOW_CONTROL endif Tried to build again, and: CESM BUILDEXE SCRIPT STARTINGrm: No match. COMPILER is intel - Build Libraries: mct gptl pio csm_share Wed Jan 3 18:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/intel//nodebug/nothreads/mct.bldlog.180103-182105Wed Jan 3 18:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/intel//nodebug/nothreads/gptl.bldlog.180103-182105Wed Jan 3 18:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/intel//nodebug/nothreads/pio.bldlog.180103-182105Wed Jan 3 18:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/intel//nodebug/nothreads/csm_share.bldlog.180103-182105Wed Jan 3 18:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/atm.bldlog.180103-182105Wed Jan 3 18:22:15 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/lnd.bldlog.180103-182105Wed Jan 3 18:24:09 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/ice.bldlog.180103-182105Wed Jan 3 18:25:16 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/ocn.bldlog.180103-182105Wed Jan 3 18:26:39 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/glc.bldlog.180103-182105ERROR: cism.buildexe.csh failed, see /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/glc.bldlog.180103-182105 glc.bldlog.180103-182105 content:mpiifort  -c -I.  -I/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/intel//nodebug/nothreads/include -I/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/intel//nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/sw/apps/suse/intel17/netcdf/4.5.0/include -I/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/intel//nodebug/nothreads/include -I/scratch/10071a/rafaelrangel/cesm1_2_2/models/csm_share/shr -I. -I/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/SourceMods/src.cism -I/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/drivers/cpl_share -I/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/drivers/cpl_mct -I/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc -I/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/mpi -I/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/lib/include  -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -mkl -O2   -DLINUX  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_SLASHPROC -free   /scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_global_fields.F90/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_global_fields.F90(18): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [GLINT_EXAMPLE_CLIM]   use glint_example_clim, only: glex_climate-------^/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_global_fields.F90(19): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [GLINT_MAIN]   use glint_main, only: glint_params-------^/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_global_fields.F90(61): error #6406: Conflicting attributes or multiple declaration of name.   [GLINT_PARAMS]  type(glint_params) :: ice_sheet   ! Parameters relevant to all model instances,-------^/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_global_fields.F90(64): error #6457: This derived type name has not been declared.   [GLEX_CLIMATE]  type(glex_climate) :: climate     ! Climate parameters and fields-------^/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_global_fields.F90(18): error #6580: Name in only-list does not exist.   [GLEX_CLIMATE]   use glint_example_clim, only: glex_climate---------------------------------^/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_global_fields.F90(19): error #6580: Name in only-list does not exist.   [GLINT_PARAMS]   use glint_main, only: glint_params-------------------------^compilation aborted for /scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_global_fields.F90 (code 1)/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/Tools/Makefile:639: recipe for target 'glc_global_fields.o' failedgmake: *** [glc_global_fields.o] Error 1gmake: *** Waiting for unfinished jobs..../scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_constants.F90(33): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [GLIMMER_PARAMETS]  use glimmer_paramets, only: stdout------^/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_constants.F90(33): error #6580: Name in only-list does not exist.   [STDOUT]  use glimmer_paramets, only: stdout------------------------------^compilation aborted for /scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/source_glc/glc_constants.F90 (code 1)/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/Tools/Makefile:639: recipe for target 'glc_constants.o' failedgmake: *** [glc_constants.o] Error 1/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/mpi/glc_communicate.F90(77): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [PARALLEL]   use parallel, only : parallel_set_info-------^/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/mpi/glc_communicate.F90(106): error #6406: Conflicting attributes or multiple declaration of name.   [PARALLEL_SET_INFO]   call parallel_set_info(MPI_COMM_GLC, master_task)--------^/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/mpi/glc_communicate.F90(77): error #6580: Name in only-list does not exist.   [PARALLEL_SET_INFO]   use parallel, only : parallel_set_info------------------------^/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/mpi/glc_communicate.F90(198): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.   [IERR] subroutine abort_message_environment(ierr)--------------------------------------^/scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/mpi/glc_communicate.F90(165): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.   [IERR] subroutine exit_message_environment(ierr)-------------------------------------^compilation aborted for /scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cism/mpi/glc_communicate.F90 (code 1)/scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/Tools/Makefile:639: recipe for target 'glc_communicate.o' failedgmake: *** [glc_communicate.o] Error 1. Which is the same error that appeared previously!I tried to "svn update" the models/glc/cism/glimmer-cism/libglint/ this way:cd /scratch/10071a/rafaelrangel/cesm1_2_2/models/glc/cismsvn update The result was:Updating '.': Fetching external item into 'glimmer-cism':External at revision 1902. At revision 88194. Is it the right way to do the svn update? If so, what am I missing with this cism.buildexe.csh error?
 

sacks

Bill Sacks
CSEG and Liaisons
Staff member
Are you sure that there aren't earlier errors in the glc bldlog? The contents of cism/glimmer_cism (which includes the glint-related things referenced in the error message you attached) are built using cmake, and I'm wondering if there was an error in the cmake-based build of glimmer_cism. It might be easiest if you set up a fresh case with a fresh build, then examined the glc bldlog from this fresh build. If it's not clear what the error is from that, you could attach the full glc bldlog to this thread.
 
My step-by-step to create a new case:1) loaded necessary modules;Currently Loaded Modulefiles: 1) intel/2017.5.239   2) szip/2.1.1         3) phdf5/1.8.19       4) pnetcdf/1.8.1      5) netcdf/4.5.0       6) pio/2.3.0          7) cmake/3.10.02) exported variables:export LIB_NETCDF=$NETCDF_PATH/libexport INC_NETCDF=$NETCDF_PATH/includeexport NETCDF=$NETCDF_PATHexport LAPACK_LIBDIR=${MKLROOT}/lib/intel64export FC=ifortexport F77=ifortexport F90=ifortexport CC=iccexport CXX=c++export MPIFC=mpiifortexport MPIF77=mpiifortexport MPIF90=mpiifortexport MPICC=mpiiccexport CASE=BGCN_T31_g37_v6export CCSMROOT=/scratch/10071a/rafaelrangel/cesm1_2_2export CSMDATA=/scratch/10071a/cesm/inputdataexport CASEROOT=$CCSMROOT/$CASE3) created new case:./create_newcase -case $CASEROOT -res T31_g37 -compset BGCN -mach loboc4) ./cesm_setup 5) removed "-lblas" and "-llpack" from ./Tools/Makefile, which became:ifdef LAPACK_LIBDIR   SLIBS += -L$(LAPACK_LIBDIR)endif6) Changed four lines (bold) inside the Macros to:CFLAGS:= -O2 -fp-model precise -mklFFLAGS:= -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -mklSLIBS+= -L$(NETCDF_PATH) -lnetcdff -lnetcdfLAPACK_LIBDIR=${MKLROOT}/lib/intel647)  ./BGCN_T31_g37_v6.buildAnd now, the problem is with cesm:CESM BUILDEXE SCRIPT STARTINGrm: No match. COMPILER is intel - Build Libraries: mct gptl pio csm_share Thu Jan 4 14:13:19 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/intel//nodebug/nothreads/mct.bldlog.180104-141313Thu Jan 4 14:13:55 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/intel//nodebug/nothreads/gptl.bldlog.180104-141313Thu Jan 4 14:13:57 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/intel//nodebug/nothreads/pio.bldlog.180104-141313Thu Jan 4 14:14:19 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/intel//nodebug/nothreads/csm_share.bldlog.180104-141313Thu Jan 4 14:14:34 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/atm.bldlog.180104-141313Thu Jan 4 14:15:48 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/lnd.bldlog.180104-141313Thu Jan 4 14:17:46 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/ice.bldlog.180104-141313Thu Jan 4 14:18:55 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/ocn.bldlog.180104-141313Thu Jan 4 14:20:18 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/glc.bldlog.180104-141313Thu Jan 4 14:21:09 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/wav.bldlog.180104-141313Thu Jan 4 14:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/rof.bldlog.180104-141313Thu Jan 4 14:21:17 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/cesm.bldlog.180104-141313ERROR: cesm.buildexe.csh failed, see /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/cesm.bldlog.180104-141313ERROR: cat /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/cesm.bldlog.180104-141313 The cesm.bldlog.180104-141313 is attached. I think this error is due to Lapack (mkl?), and I don't know how to solve it.
 
Thank you very much, Jim! It would not be possible without your precious help.Bill, I followed your suggestion of create another fresh case and start again, and that avoided some strange errors that were happening. Thanks!

Then it is finally complete. Just to register the correct step-by-step:1) loaded necessary modules;Currently Loaded Modulefiles: 1) intel/2017.5.239   2) szip/2.1.1         3) phdf5/1.8.19       4) pnetcdf/1.8.1      5) netcdf/4.5.0       6) pio/2.3.0          7) cmake/3.10.02) exported variables:export LIB_NETCDF=$NETCDF_PATH/libexport INC_NETCDF=$NETCDF_PATH/includeexport NETCDF=$NETCDF_PATHexport LAPACK_LIBDIR=${MKLROOT}/lib/intel64export FC=ifortexport F77=ifortexport F90=ifortexport CC=iccexport CXX=c++export MPIFC=mpiifortexport MPIF77=mpiifortexport MPIF90=mpiifortexport MPICC=mpiiccexport CASE=BGCN_T31_g37_v7export CCSMROOT=/scratch/10071a/rafaelrangel/cesm1_2_2export CSMDATA=/scratch/10071a/cesm/inputdataexport CASEROOT=$CCSMROOT/$CASE3) created new case:./create_newcase -case $CASEROOT -res T31_g37 -compset BGCN -mach loboc4) ./cesm_setup 5) removed "-lblas" and "-llpack" from ./Tools/Makefile, which became:ifdef LAPACK_LIBDIR   SLIBS += -L$(LAPACK_LIBDIR)endif6) Changed five lines (bold) inside the Macros to:CFLAGS:= -O2 -fp-model precise -mklFFLAGS:= -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -mklSLIBS+= -L$(NETCDF_PATH) -lnetcdff -lnetcdfLAPACK_LIBDIR=${MKLROOT}/lib/intel64LDFLAGS:= -mkl7)  ./BGCN_T31_g37_v7.build CESM BUILDEXE SCRIPT HAS FINISHED SUCCESSFULLY 
 

jedwards

CSEG and Liaisons
Staff member
Great, you should be able to move those changes from your case back to the Machines directory so that you can build out of the box. 
 
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