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porting CESM1_2_0 on bugaboo machine of westgrid

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yaozhixiong@...
porting CESM1_2_0 on bugaboo machine of westgrid

Hi,

I am tring to install cesm1_2_0 on bugaboo machine of westgrid. And, It failed when it was building a case with compset X.  Here is my setting and error information:

 

***.bashrc***

export PATH=/usr/local/mpi/openmpi-1.6.4/bin:$PATH
export PATH=/usr/local/netcdf-4.1.3/bin:$PATH
export PATH=/usr/local/nco-4.3.4/bin:$PATH

 

***env_mach_specific***

set netcdf  = /usr/local/netcdf-4.1.3
set openmpi = /usr/local/mpi/openmpi-1.6.4

setenv INC_NETCDF ${netcdf}/include
setenv LIB_NETCDF ${netcdf}/lib
setenv INC_MPI ${openmpi}/include
setenv LIB_MPI ${openmpi}/lib

 

***Macros***

CPPDEFS+= -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL

SLIBS+= -L$(LIB_NETCDF) -lnetcdf

CFLAGS:= -O2 -fp-model precise

CONFIG_ARGS:=

CXX_LDFLAGS:= -cxxlib

CXX_LINKER:=FORTRAN

ESMF_LIBDIR:=

FC_AUTO_R8:= -r8

FFLAGS:= -O2 -fp-model source -convert big_endian -assume byterecl -ftz -traceback

FFLAGS_NOOPT:= -O0

FIXEDFLAGS:= -fixed -132

FREEFLAGS:= -free

MPICC:= mpicc

MPICXX:= mpicxx

MPIFC:= mpif90

MPI_LIB_NAME:=

MPI_PATH:= /usr/local/mpi/openmpi-1.6.4

NETCDF_PATH:= /usr/local/netcdf-4.1.3

PNETCDF_PATH:=

SCC:= icc

SCXX:= icpc

SFC:= ifort

SUPPORTS_CXX:=TRUE

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

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

***error 1***

pio.bldlog.131123-105539

Copying source to CCSM EXEROOT...
New build of PIO
Running configure...
for OS=LINUX MACH=userdefined
cat: Filepath: No such file or directory
cat: Srcfiles: No such file or directory
/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/Tools/mkSrcfiles
cp -f /global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio/Filepath /global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio/Deppath
/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/Tools/mkDepends  Deppath Srcfiles > /global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio/Depends
cd /global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio; \
         /global/scratch/zhixiong/CESM/cesm1_2_0/models/utils/pio/configure  --enable-timing CC="icc " FC="ifort " MPICC="mpicc  " MPIFC="mpif90 " FCFLAGS="-O2 -fp-model source -convert big_endian -assume byterecl -ftz -traceback  -free  -I.  -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio -I/usr/local/netcdf-4.1.3/include -I/usr/local/mpi/openmpi-1.6.4/include -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/mct -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/mpeu -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/gptl -I/global/scratch/zhixiong/CESM/cesm1_2_0/models/utils/pio -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/lib/include" CPPDEFS=" -DLINUX  -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_SLASHPROC" CFLAGS="-O2 -fp-model precise   -DLINUX  -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_SLASHPROC -I.. -I.  -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio -I/usr/local/netcdf-4.1.3/include -I/usr/local/mpi/openmpi-1.6.4/include -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/mct -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/mpeu -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/gptl -I/global/scratch/zhixiong/CESM/cesm1_2_0/models/utils/pio -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/lib/include" NETCDF_PATH=/usr/local/netcdf-4.1.3 LDFLAGS="" LIBS="-L/usr/local/netcdf-4.1.3/lib -lnetcdf"   --srcdir /global/scratch/zhixiong/CESM/cesm1_2_0/models/utils/pio
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether icc  accepts -g... yes
checking for icc  option to accept ISO C89... none needed
checking how to run the C preprocessor... icc  -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no
checking whether we are using the GNU Fortran compiler... no
checking whether ifort  accepts -g... yes
checking for Fortran flag to compile .F90 files... none
checking for Fortran flag needed to accept free-form source... none
checking for Fortran flag needed to accept 132 column source lines... none
checking for Fortran flag to compile preprocessed .F files... none
checking how to define symbols for preprocessed Fortran... -D
checking for ftn... mpif90
checking for mpif.h... yes
checking for Fortran flag to compile .F90 files... (cached) none
checking for mpi.mod... yes
checking Fortran support for c_sizeof()... yes
checking MPI-IO support in MPI implementation... no
Full hostname= bugaboo.westgrid.ca
Hostname=bugaboo.westgrid.ca
Machine=x86_64
OS=Linux
checking Fortran 90 module extension... mod
checking Fortran 90 module inclusion flag... -I
using NETCDF_PATH from environment
checking for Fortran flag to compile .F90 files... (cached) none
checking for hdf5... yes
checking for H5open in -lhdf5... no
checking for H5Dclose in -lhdf5_hl... no
configure: Fortran not checked for yet
checking for netcdf... /usr/local/netcdf-4.1.3
checking for library containing nc_inq_libvers... -lnetcdf
checking for library containing NF_INQ_LIBVERS... no
configure: error: cannot find netCDF fortran library
gmake: *** [/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio/Makefile.conf] Error 1
cp: cannot stat `Makefile.conf': No such file or directory
Makefile:25: Makefile.conf: No such file or directory
gmake: *** No rule to make target `Makefile.conf'.  Stop.

 

The error is: cannot find netCDF fortran library, so I add "-lnetcdff" in the SLIBS. There are "libnetcdf.a" and "libnetcdff.a" in the /usr/local/netcdf-4.1.3/lib directory.

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

But, it is still wrong. Below is the error.

 

***error 2***

mct.bldlog.131123-110356

Copying source to CCSM EXEROOT...
New build of MCT
Running configure...
for OS=LINUX MACH=userdefined
cat: Filepath: No such file or directory
cat: Srcfiles: No such file or directory
/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/Tools/mkSrcfiles
cp -f /global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/Filepath /global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/Deppath
/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/Tools/mkDepends  Deppath Srcfiles > /global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/Depends
cd /global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct; \
         /global/scratch/zhixiong/CESM/cesm1_2_0/models/utils/mct/configure  CC="icc " FC="ifort " MPICC="mpicc  " MPIFC="mpif90 " FCFLAGS="-O2 -fp-model source -convert big_endian -assume byterecl -ftz -traceback  -free  -I.  -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio -I/usr/local/netcdf-4.1.3/include -I/usr/local/mpi/openmpi-1.6.4/include -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/mct -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/mpeu -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/gptl -I/global/scratch/zhixiong/CESM/cesm1_2_0/models/utils/pio -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/lib/include" CPPDEFS=" -DLINUX  -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_SLASHPROC" CFLAGS="-O2 -fp-model precise   -DLINUX  -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_SLASHPROC -I.. -I.  -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio -I/usr/local/netcdf-4.1.3/include -I/usr/local/mpi/openmpi-1.6.4/include -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/mct -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/mpeu -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/gptl -I/global/scratch/zhixiong/CESM/cesm1_2_0/models/utils/pio -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/lib/include" NETCDF_PATH=/usr/local/netcdf-4.1.3 LDFLAGS="" LIBS="-L/usr/local/netcdf-4.1.3/lib -lnetcdf -lnetcdff"   --srcdir /global/scratch/zhixiong/CESM/cesm1_2_0/models/utils/mct
checking whether the C compiler works... no
configure: error: in `/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct':
configure: error: C compiler cannot create executables
See `config.log' for more details
gmake: *** [/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/Makefile.conf] Error 77
cp: cannot stat `Makefile.conf': No such file or directory
Makefile:4: Makefile.conf: No such file or directory
gmake: *** No rule to make target `Makefile.conf'.  Stop.

 

Now, the error become a problem with C compiler. I do not know how to solve it.

Thank you very much.

Best regards,

zhixiong

 

jedwards

Look in file /global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/config.log to see what the problem is with the c compiler.  

CESM Software Engineer

yaozhixiong@...

Thank you for quickly reply. I go to see file mct/config.log, I think the error is below.

 

## ----------- ##
## Core tests. ##
## ----------- ##

configure:2336: checking for C compiler version
configure:2345: icc  --version >&5
icc (ICC) 13.1.3 20130607
Copyright (C) 1985-2013 Intel Corporation.  All rights reserved.

configure:2356: $? = 0
configure:2345: icc  -v >&5
icc version 13.1.3 (gcc version 4.7.0 compatibility)
ld    /usr/lib/../lib64/crt1.o /usr/lib/../lib64/crti.o /usr/local/gcc-4.8.0/lib/gcc/x86_64-unknown-linux-gnu/4.8.0/crtbegin.o --eh-frame-hdr --build-id -dynamic-linker /lib64/ld-linux-x86-64.so.2 -L/usr/local/intel/composer_xe_2013.5.192/mkl/lib/intel64 -L/usr/local/intel/composer_xe_2013.5.192/compiler/lib/intel64 -L/usr/local/gcc-4.8.0/lib64 -o a.out -L/usr/local/intel/composer_xe_2013.5.192/compiler/lib/intel64 -L/usr/local/gcc-4.8.0/lib/gcc/x86_64-unknown-linux-gnu/4.8.0/ -L/usr/local/gcc-4.8.0/lib/gcc/x86_64-unknown-linux-gnu/4.8.0/../../../../lib64 -L/usr/local/gcc-4.8.0/lib/gcc/x86_64-unknown-linux-gnu/4.8.0/../../../../lib64/ -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/ -L/usr/local/gcc-4.8.0/lib/gcc/x86_64-unknown-linux-gnu/4.8.0/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -rpath /usr/local/intel/composer_xe_2013.5.192/mkl/lib/intel64 -rpath /usr/local/intel/composer_xe_2013.5.192/compiler/lib/intel64 -rpath /usr/local/gcc-4.8.0/lib64 -lirc -limf -lsvml -lirng -lm -lipgo -ldecimal --as-needed -lcilkrts -lstdc++ --no-as-needed -lgcc -lgcc_s -lintlc -lsvml -lc -lgcc -lgcc_s -lirc_s -ldl -lc /usr/local/gcc-4.8.0/lib/gcc/x86_64-unknown-linux-gnu/4.8.0/crtend.o /usr/lib/../lib64/crtn.o
/usr/lib/../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
configure:2356: $? = 1
configure:2345: icc  -V >&5
GNU ld version 2.20.51.0.2-5.36.el6 20100205
Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 13.1.3.192 Build 20130607
Copyright (C) 1985-2013 Intel Corporation.  All rights reserved.

/usr/lib/../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
configure:2356: $? = 1
configure:2345: icc  -V >&5
GNU ld version 2.20.51.0.2-5.36.el6 20100205
Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 13.1.3.192 Build 20130607
Copyright (C) 1985-2013 Intel Corporation.  All rights reserved.

/usr/lib/../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
configure:2356: $? = 1
configure:2345: icc  -qversion >&5
icc: command line warning #10006: ignoring unknown option '-qversion'
/usr/lib/../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
configure:2356: $? = 1
configure:2376: checking whether the C compiler works
configure:2398: icc  -O2 -fp-model precise   -DLINUX  -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_SLASHPROC -I.. -I.  -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio -I/usr/local/netcdf-4.1.3/include -I/usr/local/mpi/openmpi-1.6.4/include -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/mct -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct/mpeu -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/pio -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/gptl -I/global/scratch/zhixiong/CESM/cesm1_2_0/models/utils/pio -I/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/lib/include   conftest.c -L/usr/local/netcdf-4.1.3/lib -lnetcdf -lnetcdff  >&5
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_varm_double_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_var_endian_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vara_real_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_fieldname_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_typeid_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_varm_int1_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_var_chunking_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vars_int1_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_fieldindex_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_att_double_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_var_deflate_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf__create_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_var_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_dim_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_varm_text_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_var_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_strerror_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf__open_mp_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_create_par_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_user_type_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_size_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_varm_real_'

/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_ncid_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_var_fill_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_set_var_chunk_cache_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_open_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vars_int64_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_var1_real_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_var_deflate_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vara_int64_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_dim_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_dimids_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_field_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_varm_double_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_fieldoffset_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_varm_int64_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vara_int64_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vara_int2_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_opaque_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vara_int2_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vars_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_var1_int2_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_varm_text_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_att_int2_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_open_par_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_fieldndims_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_att_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_rename_var_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_att_real_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_libvers_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_set_chunk_cache_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_att_int1_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_var_chunk_cache_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_att_real_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vara_int_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_abort_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_free_vlen_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_sync_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_vlen_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_att_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_var1_int2_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vars_int_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_grp_full_ncid_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_var_par_access_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_var1_double_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vars_double_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_grpname_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_attname_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vara_int1_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_enum_member_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_att_text_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_opaque_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_format_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_att_text_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_fieldtype_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_varid_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vara_int1_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf__create_mp_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_typeids_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_var1_int1_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf__enddef_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_var1_int1_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_attid_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_copy_att_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_att_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_var_fletcher32_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_create_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vars_real_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_enum_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_enddef_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_att_int2_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_varm_int64_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vara_int_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_varm_int2_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vars_int1_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_var_fletcher32_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_enum_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_compound_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vara_double_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_att_double_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vars_int64_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_del_att_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_var1_double_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_var1_int64_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_grpname_full_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_varm_int_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_varm_int1_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_grpname_len_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_base_pe_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_set_base_pe_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vars_text_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_varids_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_rename_dim_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_var1_int_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_grp_parent_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_varm_int_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vara_double_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_nfields_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_chunk_cache_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vars_double_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_var1_real_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_var_chunking_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_grp_ncid_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_insert_array_compound_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_enum_ident_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf__open_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_varm_int2_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_fielddim_sizes_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_insert_enum_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_vlen_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vars_real_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_att_int1_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_varm_real_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_var1_int_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vara_real_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_name_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_var_fill_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_compound_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vars_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vars_int2_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_att_int_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_insert_compound_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_delete_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_type_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_var_endian_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_close_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_grps_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vars_int2_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_set_fill_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_att_int_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_put_vars_text_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_redef_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_def_grp_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_rename_att_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_var1_int64_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_get_vars_int_'
/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to `nf_inq_dimid_'
configure:2402: $? = 1
configure:2440: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "MCT"
| #define PACKAGE_TARNAME "mct"
| #define PACKAGE_VERSION "2.8"
| #define PACKAGE_STRING "MCT 2.8"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
|
| int
| main ()
| {
|
|   ;
|   return 0;
| }
configure:2445: error: in `/global/scratch/zhixiong/CESM/cesm1_2_0/case_output/testx/bld/mct':
configure:2447: error: C compiler cannot create executables
See `config.log' for more details

jedwards

/usr/local/netcdf-4.1.3/lib/libnetcdff.so: undefined reference to

`nf_get_varm_double_' This is a common problem with building the netcdf libraries - the fortran compiler is generating an _ character at the end of fortran function names, but your netcdf c library was built without them.     Fix this by writing a simple fortran based netcdf program such as: 
program tryit
  include 'netcdf.inc'
  integer :: ierr, nf
  ierr = nf_close(nf)
end program
 
(It doesn't do anything, you just need to be able to link it)Rebuild netcdf so that you can link this program or ask your systems group to fix it if that is appropriate.  As long as you're doing this you should consider updating to the latest netcdf 4.3.0.

CESM Software Engineer

yaozhixiong@...

Thank you for reply.

 

I just use other compilers, the compset X can be run successfully. Then I use the same setting to run compset B. It can be built successfully, but fail after job be subbmitted.

 

My setting and error information is showed below.

 

***.bashrc***

export PATH=/usr/local/intel/impi/4.1.1.036/intel64/bin:$PATH
export PATH=/usr/local/bin:$PATH
export PATH=/usr/local/nco-4.3.4/bin:$PATH

 

***env_mach_specific***

set netcdf = /usr/local
set mpich  = /usr/local/intel/impi/4.1.1.036/intel64

setenv INC_NETCDF ${netcdf}/include
setenv LIB_NETCDF ${netcdf}/lib64
setenv INC_MPI ${mpich}/include
setenv LIB_MPI ${mpich}/lib

 

***Macros**

# Makefile Macros generated from /global/scratch/zhixiong/CESM/cesm1_2_0/scripts/ccsm_utils/Machines/config_compilers.xml using
# COMPILER=intel
# OS=LINUX
# MACH=userdefined
#
CPPDEFS+= -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL

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

CFLAGS:= -O2 -fp-model precise

CONFIG_ARGS:=

CXX_LDFLAGS:= -cxxlib

CXX_LINKER:=FORTRAN

ESMF_LIBDIR:=

FC_AUTO_R8:= -r8

FFLAGS:= -O2 -fp-model source -convert big_endian -assume byterecl -ftz -traceback

FFLAGS_NOOPT:= -O0

FIXEDFLAGS:= -fixed -132

FREEFLAGS:= -free

MPICC:= mpicc

MPICXX:= mpicxx

MPIFC:= mpif90

MPI_LIB_NAME:=

MPI_PATH:= /usr/local/intel/impi/4.1.1.036/intel64

NETCDF_PATH:= /usr/local

PNETCDF_PATH:=

SCC:= icc

SCXX:= icpc

SFC:= ifort

SUPPORTS_CXX:=TRUE

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

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

 

***error***

cesm.log.131202-141214

the last several lines of error information

 

forrtl: error (69): process interrupted (SIGINT)
Image              PC                Routine            Line        Source
libmpi.so.4        00002B734D65A85D  Unknown               Unknown  Unknown
libmpi.so.4        00002B734D654AB1  Unknown               Unknown  Unknown
libmpi.so.4        00002B734D741DB7  Unknown               Unknown  Unknown
libmpi.so.4        00002B734D7423FC  Unknown               Unknown  Unknown
libmpi.so.4        00002B734D73B0C3  Unknown               Unknown  Unknown
libmpi.so.4        00002B734D63F1A9  Unknown               Unknown  Unknown
libmpi.so.4        00002B734D63E48E  Unknown               Unknown  Unknown
libmpi.so.4        00002B734D642A5B  Unknown               Unknown  Unknown
libmpi.so.4        00002B734D6424EF  Unknown               Unknown  Unknown
libmpigf.so.4      00002B734DC11532  Unknown               Unknown  Unknown
cesm.exe           0000000000E6DF6C  ice_broadcast_mp_         322  ice_broadcast.F90
cesm.exe           0000000000D874CE  ice_restart_mp_re         722  ice_restart.F90
cesm.exe           0000000000E0F42C  cice_initmod_mp_c         132  CICE_InitMod.F90
cesm.exe           0000000000CD7536  ice_comp_mct_mp_i         254  ice_comp_mct.F90
cesm.exe           00000000004245A4  ccsm_comp_mod_mp_        1152  ccsm_comp_mod.F90
cesm.exe           000000000042AFDC  MAIN__                     90  ccsm_driver.F90
cesm.exe           0000000000407E5C  Unknown               Unknown  Unknown
libc.so.6          0000003E80E1ECDD  Unknown               Unknown  Unknown
cesm.exe           0000000000407CE9  Unknown               Unknown  Unknown
forrtl: error (69): process interrupted (SIGINT)
Image              PC                Routine            Line        Source
libmpi.so.4        00002AB2DE469AE1  Unknown               Unknown  Unknown
libmpi.so.4        00002AB2DE556DB7  Unknown               Unknown  Unknown
libmpi.so.4        00002AB2DE5573FC  Unknown               Unknown  Unknown
libmpi.so.4        00002AB2DE5500C3  Unknown               Unknown  Unknown
libmpi.so.4        00002AB2DE4541A9  Unknown               Unknown  Unknown
libmpi.so.4        00002AB2DE45348E  Unknown               Unknown  Unknown
libmpi.so.4        00002AB2DE457A5B  Unknown               Unknown  Unknown
libmpi.so.4        00002AB2DE4574EF  Unknown               Unknown  Unknown
libmpigf.so.4      00002AB2DEA26532  Unknown               Unknown  Unknown
cesm.exe           0000000000E6DF6C  ice_broadcast_mp_         322  ice_broadcast.F90
cesm.exe           0000000000D874CE  ice_restart_mp_re         722  ice_restart.F90
cesm.exe           0000000000E0F42C  cice_initmod_mp_c         132  CICE_InitMod.F90
cesm.exe           0000000000CD7536  ice_comp_mct_mp_i         254  ice_comp_mct.F90
cesm.exe           00000000004245A4  ccsm_comp_mod_mp_        1152  ccsm_comp_mod.F90
cesm.exe           000000000042AFDC  MAIN__                     90  ccsm_driver.F90
cesm.exe           0000000000407E5C  Unknown               Unknown  Unknown
libc.so.6          0000003C32A1ECDD  Unknown               Unknown  Unknown
cesm.exe           0000000000407CE9  Unknown               Unknown  Unknown
[mpiexec@b137] control_cb (./pm/pmiserv/pmiserv_cb.c:1151): assert (!closed) failed
[mpiexec@b137] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status
[mpiexec@b137] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:430): error waiting for event
[mpiexec@b137] main (./ui/mpich/mpiexec.c:847): process manager error waiting for completion

 

I use mpirun (not mpiexec) in both compset X and B. I think that may be some problem with file testb.run. And the file testb.run and error file cesm_log can be seen it the attachment.

 

Thank you very much.

Best regards,

zhixiong

yaozhixiong@...

Sorry, I am too careless. I know the problem. It's the same error as I met before: lack of one input data.

yaozhixiong@...

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