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Porting errors: build.csm_share

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rangel@...
Porting errors: build.csm_share
Hello,

I'm trying to port CESM 1.2.2.

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

In the csm_share log file, there are some warnings like:
/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:
/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 . . .

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 http://parallelio.googlecode.com/svn/ trunk_tags/pio1_8_12/pio add: models/utils/pio https://github.com/NCAR/ParallelIO $ 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.

Some files are attached (error log, env_build, config_machines, config_compilers and our hpc environment variables).

Versions:
netCDF 4.4.1.1
pio 2.3.0
pnetcdf 1.8.1
ifort version 17.0.5
icc version 17.0.5


Any help will be very appreciated!

Regards,
Rafael
jedwards
rangel@...

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:

In $CESM/SVN_EXTERNAL_DIRECTORIES:
remove: models/utils/pio http://parallelio.googlecode.com/svn/
trunk_tags/pio1_8_12/pio
add: models/utils/pio   https://github.com/NCAR/ParallelIO
    $ svn propset svn:externals -F SVN_EXTERNAL_DIRECTORIES ./
    $ svn update

the errors appeared.

About the link:  https://github.com/NCAR/ParallelIO.git/tags/pio1_7_2/pio it isn't available anymore.

Thanks!

 

jedwards
rangel@...

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 line

models/utils/pio       [whatever]

with:

models/utils/pio                   https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio

then type:

svn propset svn:externals -F SVN_EXTERNAL_DIRECTORIES ./
svn update


and it's done! Just build the case!

 

 

rangel@...

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

 

Any help will be very appreciated!

Regards,
Rafael
jedwards

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.

 

rangel@...

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.180102-203024

ERROR: cesm.buildexe.csh failed, see /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v3/bld/cesm.bldlog.180102-203024

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  -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 -lblas

ld: cannot find -llapack

ld: 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-...

I 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)/include

LAPACK_LIBDIR=${MKLROOT}/lib/intel64

SLIBS+= -L$(NETCDF_PATH) -lnetcdff -lnetcdf  -L$(MKLROOT)/lib/intel64/libmkl_blas95_ilp64.a -L$(MKLROOT)/lib/intel64/libmkl_lapack95_ilp64.a -liomp5 -lpthread -lm -ldl

but it didn't work ... is it possible to use intel MKL?

 

jedwards

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  

rangel@...

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_lhs

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

Is 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 -lblas

ld: cannot find -llapack

ld: 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' failed

gmake: *** [/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.

jedwards

Yes it does.  Remove -llapack and -lblas and add -mkl to FFLAGS and CFLAGS.

rangel@...

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_lhs

So, 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 STARTING

rm: 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.180103-182105

Wed Jan 3 18:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/intel//nodebug/nothreads/gptl.bldlog.180103-182105

Wed Jan 3 18:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/intel//nodebug/nothreads/pio.bldlog.180103-182105

Wed Jan 3 18:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/intel//nodebug/nothreads/csm_share.bldlog.180103-182105

Wed Jan 3 18:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/atm.bldlog.180103-182105

Wed Jan 3 18:22:15 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/lnd.bldlog.180103-182105

Wed Jan 3 18:24:09 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/ice.bldlog.180103-182105

Wed Jan 3 18:25:16 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/ocn.bldlog.180103-182105

Wed Jan 3 18:26:39 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v5/bld/glc.bldlog.180103-182105

ERROR: 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' failed

gmake: *** [glc_global_fields.o] Error 1

gmake: *** 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' failed

gmake: *** [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/cism

svn 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

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.

rangel@...

Hi, Bill.

I've attached now the full glc bldlog. 

I'll set up a new case right now and let you know what happened.

Thanks for your help!

rangel@...

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/3.10.0

2) exported variables:

export LIB_NETCDF=$NETCDF_PATH/lib

export INC_NETCDF=$NETCDF_PATH/include

export NETCDF=$NETCDF_PATH

export LAPACK_LIBDIR=${MKLROOT}/lib/intel64

export FC=ifort

export F77=ifort

export F90=ifort

export CC=icc

export CXX=c++

export MPIFC=mpiifort

export MPIF77=mpiifort

export MPIF90=mpiifort

export MPICC=mpiicc

export CASE=BGCN_T31_g37_v6

export CCSMROOT=/scratch/10071a/rafaelrangel/cesm1_2_2

export CSMDATA=/scratch/10071a/cesm/inputdata

export CASEROOT=$CCSMROOT/$CASE

3) created new case:

./create_newcase -case $CASEROOT -res T31_g37 -compset BGCN -mach loboc

4) ./cesm_setup

 

5) removed "-lblas" and "-llpack" from ./Tools/Makefile, which became:

ifdef LAPACK_LIBDIR

   SLIBS += -L$(LAPACK_LIBDIR)

endif

6) Changed four lines (bold) inside the Macros to:

CFLAGS:= -O2 -fp-model precise -mkl

FFLAGS:= -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -mkl

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

LAPACK_LIBDIR=${MKLROOT}/lib/intel64

7)  ./BGCN_T31_g37_v6.build

And now, the problem is with cesm:

CESM BUILDEXE SCRIPT STARTING

rm: 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.180104-141313

Thu Jan 4 14:13:55 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/intel//nodebug/nothreads/gptl.bldlog.180104-141313

Thu Jan 4 14:13:57 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/intel//nodebug/nothreads/pio.bldlog.180104-141313

Thu Jan 4 14:14:19 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/intel//nodebug/nothreads/csm_share.bldlog.180104-141313

Thu Jan 4 14:14:34 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/atm.bldlog.180104-141313

Thu Jan 4 14:15:48 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/lnd.bldlog.180104-141313

Thu Jan 4 14:17:46 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/ice.bldlog.180104-141313

Thu Jan 4 14:18:55 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/ocn.bldlog.180104-141313

Thu Jan 4 14:20:18 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/glc.bldlog.180104-141313

Thu Jan 4 14:21:09 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/wav.bldlog.180104-141313

Thu Jan 4 14:21:10 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/rof.bldlog.180104-141313

Thu Jan 4 14:21:17 BRST 2018 /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/cesm.bldlog.180104-141313

ERROR: cesm.buildexe.csh failed, see /scratch/10071a/rafaelrangel/cesm1_2_2/BGCN_T31_g37_v6/bld/cesm.bldlog.180104-141313

ERROR: 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.

jedwards

I think that you're almost there, try adding -mkl to the LDFLAGS as well.   

rangel@...

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/3.10.0

2) exported variables:

export LIB_NETCDF=$NETCDF_PATH/lib

export INC_NETCDF=$NETCDF_PATH/include

export NETCDF=$NETCDF_PATH

export LAPACK_LIBDIR=${MKLROOT}/lib/intel64

export FC=ifort

export F77=ifort

export F90=ifort

export CC=icc

export CXX=c++

export MPIFC=mpiifort

export MPIF77=mpiifort

export MPIF90=mpiifort

export MPICC=mpiicc

export CASE=BGCN_T31_g37_v7

export CCSMROOT=/scratch/10071a/rafaelrangel/cesm1_2_2

export CSMDATA=/scratch/10071a/cesm/inputdata

export CASEROOT=$CCSMROOT/$CASE

3) created new case:

./create_newcase -case $CASEROOT -res T31_g37 -compset BGCN -mach loboc

4) ./cesm_setup

 

5) removed "-lblas" and "-llpack" from ./Tools/Makefile, which became:

ifdef LAPACK_LIBDIR

   SLIBS += -L$(LAPACK_LIBDIR)

endif

6) Changed five lines (bold) inside the Macros to:

CFLAGS:= -O2 -fp-model precise -mkl

FFLAGS:= -fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -mkl

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

LAPACK_LIBDIR=${MKLROOT}/lib/intel64

LDFLAGS:= -mkl

7)  ./BGCN_T31_g37_v7.build

 CESM BUILDEXE SCRIPT HAS FINISHED SUCCESSFULLY

 

jedwards

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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