sbasu@iarc_uaf_edu
Member
Hello,I am trying to configure CAM 5.3 on a cray machine. When I am running the configuration command I am getting an error in linking to the netcdf library. When I ran the configure command with -v option it gave me the following output.fish1 % ../cesm1_2_2/models/atm/cam/bld/configure -dyn fv -hgrid 10x15 -nospmd -nosmp -test -v
Physics package: cam5
Chemistry package: trop_mam3
CAM configuration script directory: /import/c/w/basu/cam_5/cesm1_2_2/models/atm/cam/bld
Configuration defaults file: config_files/defaults_fv.xml
CAM root directory: /import/c/w/basu/cam_5/cesm1_2_2
CAM build directory: /import/c/w/basu/cam_5/cam_bld
CAM executable will be created in: /import/c/w/basu/cam_5/cam_bld
User source directories:
Configuration cache file: /import/c/w/basu/cam_5/cam_bld/config_cache.xml
Target OS: linux
SPMD parallelism: OFF
SMP parallelism: OFF
Component interface: mct
Dynamics package: fv
Number of user requested test tracers: 0
Age of air tracer package: OFF
Microphysics package: mg1
Macrophysics package: park
Using uw PBL scheme.
Radiation package: rrtmg
Ocean package: docn
Land package: clm
Sea ice package: cice
Runoff package: rtm
Perturbation growth testing: OFF
CAM single column mode (SCAM): OFF
Produce IOP file for SCAM: OFF
Horizontal grid specifier: 10x15
Maximum number of columns in a chunk: 16
Maximum number of sub-columns per column: 1
Number of vertical levels: 30
Advected constituents added by mg1 microphysics: 4
Advected constituents added by chemistry trop_mam3: 20
Total advected constituents: 25
Issuing command to the CICE configure utility:
/import/c/w/basu/cam_5/cesm1_2_2/models/ice/cice/bld/configure -hgrid 10x15 -cice_mode prescribed -ntr_aero 0 -nx 24 -ny 19 -bsizex 6 -bsizey 19 -maxblocks 4 -decomptype blkrobin -cache config_cache_cice.xml -cachedir /import/c/w/basu/cam_5/cam_bld
CICE configure done.
Name of CAM executable: cam
Fortran compiler: pgf95
Fortran compiler type: pgi
C compiler: pgcc
Compiler debugging options: OFF
Will look for NetCDF include file in: /opt/cray/netcdf/4.2.0/pgi/119/include
Will look for netCDF library in: /opt/cray/netcdf/4.2.0/pgi/119/lib
Found netCDF module files in: /opt/cray/netcdf/4.2.0/pgi/119/include
Found PnetCDF include file in: /opt/cray/parallel-netcdf/1.4.1/PGI/141/include
CPP definitions set by configure: ' -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=6 -DBLCKY=19 -DMXBLCKS=4 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF '
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking how to run the C preprocessor... pgcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 pgf95 accepts -g... yes
checking for Fortran flag to compile .F90 files... none
MPISERIAL ENABLED: BYPASSING MPI CHECK
FORT_SIZE IS PRESET TO real4double8
Checking Compiler Version
checking how to get the version output from pgf95... -V
checking for Fortran flag to compile preprocessed .F files... none
checking how to define symbols for preprocessed Fortran... -D
checking how to get verbose linking output from pgf95... -v
checking for Fortran libraries of pgf95... -L/opt/pgi/12.10.0/linux86-64/12.10/lib -L/usr/lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -lpgmp -lpthread -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lrt -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
Hostname=fish1
Machine=x86_64
OS=Linux
Fortran Compiler is Portland Group
checking for ranlib... ranlib
Output Variables: {CC=pgcc} {CFLAGS=-g} {FC=pgf95} {FCFLAGS=} {PROGFCFLAGS=}{CPPDEFS= -DSYSLINUX -DCPRPGI} {OPT=-O2} {DEBUG=} {REAL8=-r8} {BIT64=-pc 64} {ENDIAN=-byteswapio} {MPIFC=pgf95} {MPILIBS=-L/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -lmpi-serial} {MPIHEADER=-I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial} {INCLUDEFLAG=-I} {INCLUDEPATH=} {AR=ar cq} {RANLIB=ranlib} {BABELROOT=} {COMPILER_ROOT=} {PYTHON=} {PYTHONOPTS=} {FORT_SIZE=real4double8} {prefix=NONE} {SRCDIR=} {FC_DEFINE=-D}
configure: creating ./config.status
config.status: creating Makefile.conf
config.status: creating config.h
config.status: config.h is unchanged
Please check the Makefile.conf
Have a nice day!
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking how to run the C preprocessor... pgcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 pgf95 accepts -g... yes
checking for Fortran flag to compile .F90 files... none
MPISERIAL ENABLED: BYPASSING MPI CHECK
FORT_SIZE IS PRESET TO real4double8
Checking Compiler Version
checking how to get the version output from pgf95... -V
checking for Fortran flag to compile preprocessed .F files... none
checking how to define symbols for preprocessed Fortran... -D
checking how to get verbose linking output from pgf95... -v
checking for Fortran libraries of pgf95... -L/opt/pgi/12.10.0/linux86-64/12.10/lib -L/usr/lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -lpgmp -lpthread -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lrt -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
Hostname=fish1
Machine=x86_64
OS=Linux
Fortran Compiler is Portland Group
checking for ranlib... ranlib
Output Variables: {CC=pgcc} {CFLAGS=-g} {FC=pgf95} {FCFLAGS=} {PROGFCFLAGS=}{CPPDEFS= -DSYSLINUX -DCPRPGI} {OPT=-O2} {DEBUG=} {REAL8=-r8} {BIT64=-pc 64} {ENDIAN=-byteswapio} {MPIFC=pgf95} {MPILIBS=-L/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -lmpi-serial} {MPIHEADER=-I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial} {INCLUDEFLAG=-I} {INCLUDEPATH=} {AR=ar cq} {RANLIB=ranlib} {BABELROOT=} {COMPILER_ROOT=} {PYTHON=} {PYTHONOPTS=} {FORT_SIZE=real4double8} {prefix=NONE} {SRCDIR=} {FC_DEFINE=-D}
configure: creating ./config.status
config.status: creating Makefile.conf
config.status: creating config.h
config.status: config.h is unchanged
Please check the Makefile.conf
Have a nice day!
MCT configure is done.
creating /import/c/w/basu/cam_5/cam_bld/Filepath
creating /import/c/w/basu/cam_5/cam_bld/Makefile
creating /import/c/w/basu/cam_5/cam_bld/config.h
creating /import/c/w/basu/cam_5/cam_bld/config_cache.xml
Looking for a valid GNU make... using gmake
Testing for Fortran 90 compatible compiler... **** PASS ****
Issued the command:
gmake -f /import/c/w/basu/cam_5/cam_bld/Makefile test_fc 2>&1
The output was:
/import/c/w/basu/cam_5/cesm1_2_2/models/atm/cam/bld/mkSrcfiles > /import/c/w/basu/cam_5/cam_bld/configure-tests/Srcfiles
/import/c/w/basu/cam_5/cesm1_2_2/models/atm/cam/bld/mkDepends Filepath Srcfiles > /import/c/w/basu/cam_5/cam_bld/configure-tests/Depends
pgf95 -c -Mfree -I. -I/import/c/w/basu/cam_5/cam_bld/configure-tests -I/opt/cray/netcdf/4.2.0/pgi/119/include -I/opt/cray/parallel-netcdf/1.4.1/PGI/141/include -I/import/c/w/basu/cam_5/cam_bld/mct/mct -I/import/c/w/basu/cam_5/cam_bld/mct/mpeu -I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -I/opt/cray/netcdf/4.2.0/pgi/119/include -DNO_SHR_VMATH -DSEQ_MCT -DNO_C_SIZEOF -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=6 -DBLCKY=19 -DMXBLCKS=4 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF -DLINUX -DNO_R16 -DCPRPGI -i4 -Mdalign -Mextend -byteswapio -gopt -O2 -Mvect=nosse -Kieee -DHIDE_MPI -D_MPISERIAL -DNO_MPIMOD -DNO_MPI2 -DNO_SIZEOF test_fc.F90
pgf95 -o test_fc -I. -I/import/c/w/basu/cam_5/cam_bld/configure-tests -I/opt/cray/netcdf/4.2.0/pgi/119/include -I/opt/cray/parallel-netcdf/1.4.1/PGI/141/include -I/import/c/w/basu/cam_5/cam_bld/mct/mct -I/import/c/w/basu/cam_5/cam_bld/mct/mpeu -I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -I/opt/cray/netcdf/4.2.0/pgi/119/include -DNO_SHR_VMATH -DSEQ_MCT -DNO_C_SIZEOF -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=6 -DBLCKY=19 -DMXBLCKS=4 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF -DLINUX -DNO_R16 -DCPRPGI -i4 -Mdalign -Mextend -byteswapio -gopt -O2 -Mvect=nosse -Kieee -DHIDE_MPI -D_MPISERIAL -DNO_MPIMOD -DNO_MPI2 -DNO_SIZEOF test_fc.o
**** PASS ****
Issued the command:
./test_fc
The output was:
hello world
using pgf95
Test linking to NetCDF library... **** FAILED ****
Issued the command:
gmake -f /import/c/w/basu/cam_5/cam_bld/Makefile test_nc 2>&1
The output was:
cat: Srcfiles: No such file or directory
/import/c/w/basu/cam_5/cam_bld/Makefile:1052: /import/c/w/basu/cam_5/cam_bld/configure-tests/Depends: No such file or directory
/import/c/w/basu/cam_5/cesm1_2_2/models/atm/cam/bld/mkSrcfiles > /import/c/w/basu/cam_5/cam_bld/configure-tests/Srcfiles
/import/c/w/basu/cam_5/cesm1_2_2/models/atm/cam/bld/mkDepends Filepath Srcfiles > /import/c/w/basu/cam_5/cam_bld/configure-tests/Depends
pgf95 -c -Mfree -I. -I/import/c/w/basu/cam_5/cam_bld/configure-tests -I/opt/cray/netcdf/4.2.0/pgi/119/include -I/opt/cray/parallel-netcdf/1.4.1/PGI/141/include -I/import/c/w/basu/cam_5/cam_bld/mct/mct -I/import/c/w/basu/cam_5/cam_bld/mct/mpeu -I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -I/opt/cray/netcdf/4.2.0/pgi/119/include -DNO_SHR_VMATH -DSEQ_MCT -DNO_C_SIZEOF -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=6 -DBLCKY=19 -DMXBLCKS=4 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF -DLINUX -DNO_R16 -DCPRPGI -i4 -Mdalign -Mextend -byteswapio -gopt -O2 -Mvect=nosse -Kieee -DHIDE_MPI -D_MPISERIAL -DNO_MPIMOD -DNO_MPI2 -DNO_SIZEOF test_nc.F90
pgf95 -o test_nc -I. -I/import/c/w/basu/cam_5/cam_bld/configure-tests -I/opt/cray/netcdf/4.2.0/pgi/119/include -I/opt/cray/parallel-netcdf/1.4.1/PGI/141/include -I/import/c/w/basu/cam_5/cam_bld/mct/mct -I/import/c/w/basu/cam_5/cam_bld/mct/mpeu -I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -I/opt/cray/netcdf/4.2.0/pgi/119/include -DNO_SHR_VMATH -DSEQ_MCT -DNO_C_SIZEOF -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=6 -DBLCKY=19 -DMXBLCKS=4 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF -DLINUX -DNO_R16 -DCPRPGI -i4 -Mdalign -Mextend -byteswapio -gopt -O2 -Mvect=nosse -Kieee -DHIDE_MPI -D_MPISERIAL -DNO_MPIMOD -DNO_MPI2 -DNO_SIZEOF test_nc.o -L/opt/cray/netcdf/4.2.0/gnu/46/lib -lnetcdff -Wl,--as-needed,-L/opt/cray/netcdf/4.2.0/gnu/46/lib -lnetcdf -lnetcdf
test_nc.o: In function `main':
/import/c/w/basu/cam_5/cam_bld/configure-tests/./test_nc.F90:5: undefined reference to `netcdf_nf90_create_'
/import/c/w/basu/cam_5/cam_bld/configure-tests/./test_nc.F90:8: undefined reference to `netcdf_nf90_strerror_'
test_nc.o: In function `.C1_283':
test_nc.F90:(.data+0x30): undefined reference to `netcdf_'
test_nc.F90:(.data+0x38): undefined reference to `typesizes_'
gmake: *** [test_nc] Error 2
Can anybody please provide some suggestions on how to fix this issue.Thanks,Soumik
Physics package: cam5
Chemistry package: trop_mam3
CAM configuration script directory: /import/c/w/basu/cam_5/cesm1_2_2/models/atm/cam/bld
Configuration defaults file: config_files/defaults_fv.xml
CAM root directory: /import/c/w/basu/cam_5/cesm1_2_2
CAM build directory: /import/c/w/basu/cam_5/cam_bld
CAM executable will be created in: /import/c/w/basu/cam_5/cam_bld
User source directories:
Configuration cache file: /import/c/w/basu/cam_5/cam_bld/config_cache.xml
Target OS: linux
SPMD parallelism: OFF
SMP parallelism: OFF
Component interface: mct
Dynamics package: fv
Number of user requested test tracers: 0
Age of air tracer package: OFF
Microphysics package: mg1
Macrophysics package: park
Using uw PBL scheme.
Radiation package: rrtmg
Ocean package: docn
Land package: clm
Sea ice package: cice
Runoff package: rtm
Perturbation growth testing: OFF
CAM single column mode (SCAM): OFF
Produce IOP file for SCAM: OFF
Horizontal grid specifier: 10x15
Maximum number of columns in a chunk: 16
Maximum number of sub-columns per column: 1
Number of vertical levels: 30
Advected constituents added by mg1 microphysics: 4
Advected constituents added by chemistry trop_mam3: 20
Total advected constituents: 25
Issuing command to the CICE configure utility:
/import/c/w/basu/cam_5/cesm1_2_2/models/ice/cice/bld/configure -hgrid 10x15 -cice_mode prescribed -ntr_aero 0 -nx 24 -ny 19 -bsizex 6 -bsizey 19 -maxblocks 4 -decomptype blkrobin -cache config_cache_cice.xml -cachedir /import/c/w/basu/cam_5/cam_bld
CICE configure done.
Name of CAM executable: cam
Fortran compiler: pgf95
Fortran compiler type: pgi
C compiler: pgcc
Compiler debugging options: OFF
Will look for NetCDF include file in: /opt/cray/netcdf/4.2.0/pgi/119/include
Will look for netCDF library in: /opt/cray/netcdf/4.2.0/pgi/119/lib
Found netCDF module files in: /opt/cray/netcdf/4.2.0/pgi/119/include
Found PnetCDF include file in: /opt/cray/parallel-netcdf/1.4.1/PGI/141/include
CPP definitions set by configure: ' -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=6 -DBLCKY=19 -DMXBLCKS=4 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF '
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking how to run the C preprocessor... pgcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 pgf95 accepts -g... yes
checking for Fortran flag to compile .F90 files... none
MPISERIAL ENABLED: BYPASSING MPI CHECK
FORT_SIZE IS PRESET TO real4double8
Checking Compiler Version
checking how to get the version output from pgf95... -V
checking for Fortran flag to compile preprocessed .F files... none
checking how to define symbols for preprocessed Fortran... -D
checking how to get verbose linking output from pgf95... -v
checking for Fortran libraries of pgf95... -L/opt/pgi/12.10.0/linux86-64/12.10/lib -L/usr/lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -lpgmp -lpthread -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lrt -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
Hostname=fish1
Machine=x86_64
OS=Linux
Fortran Compiler is Portland Group
checking for ranlib... ranlib
Output Variables: {CC=pgcc} {CFLAGS=-g} {FC=pgf95} {FCFLAGS=} {PROGFCFLAGS=}{CPPDEFS= -DSYSLINUX -DCPRPGI} {OPT=-O2} {DEBUG=} {REAL8=-r8} {BIT64=-pc 64} {ENDIAN=-byteswapio} {MPIFC=pgf95} {MPILIBS=-L/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -lmpi-serial} {MPIHEADER=-I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial} {INCLUDEFLAG=-I} {INCLUDEPATH=} {AR=ar cq} {RANLIB=ranlib} {BABELROOT=} {COMPILER_ROOT=} {PYTHON=} {PYTHONOPTS=} {FORT_SIZE=real4double8} {prefix=NONE} {SRCDIR=} {FC_DEFINE=-D}
configure: creating ./config.status
config.status: creating Makefile.conf
config.status: creating config.h
config.status: config.h is unchanged
Please check the Makefile.conf
Have a nice day!
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking how to run the C preprocessor... pgcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 pgf95 accepts -g... yes
checking for Fortran flag to compile .F90 files... none
MPISERIAL ENABLED: BYPASSING MPI CHECK
FORT_SIZE IS PRESET TO real4double8
Checking Compiler Version
checking how to get the version output from pgf95... -V
checking for Fortran flag to compile preprocessed .F files... none
checking how to define symbols for preprocessed Fortran... -D
checking how to get verbose linking output from pgf95... -v
checking for Fortran libraries of pgf95... -L/opt/pgi/12.10.0/linux86-64/12.10/lib -L/usr/lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -lpgmp -lpthread -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lrt -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
Hostname=fish1
Machine=x86_64
OS=Linux
Fortran Compiler is Portland Group
checking for ranlib... ranlib
Output Variables: {CC=pgcc} {CFLAGS=-g} {FC=pgf95} {FCFLAGS=} {PROGFCFLAGS=}{CPPDEFS= -DSYSLINUX -DCPRPGI} {OPT=-O2} {DEBUG=} {REAL8=-r8} {BIT64=-pc 64} {ENDIAN=-byteswapio} {MPIFC=pgf95} {MPILIBS=-L/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -lmpi-serial} {MPIHEADER=-I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial} {INCLUDEFLAG=-I} {INCLUDEPATH=} {AR=ar cq} {RANLIB=ranlib} {BABELROOT=} {COMPILER_ROOT=} {PYTHON=} {PYTHONOPTS=} {FORT_SIZE=real4double8} {prefix=NONE} {SRCDIR=} {FC_DEFINE=-D}
configure: creating ./config.status
config.status: creating Makefile.conf
config.status: creating config.h
config.status: config.h is unchanged
Please check the Makefile.conf
Have a nice day!
MCT configure is done.
creating /import/c/w/basu/cam_5/cam_bld/Filepath
creating /import/c/w/basu/cam_5/cam_bld/Makefile
creating /import/c/w/basu/cam_5/cam_bld/config.h
creating /import/c/w/basu/cam_5/cam_bld/config_cache.xml
Looking for a valid GNU make... using gmake
Testing for Fortran 90 compatible compiler... **** PASS ****
Issued the command:
gmake -f /import/c/w/basu/cam_5/cam_bld/Makefile test_fc 2>&1
The output was:
/import/c/w/basu/cam_5/cesm1_2_2/models/atm/cam/bld/mkSrcfiles > /import/c/w/basu/cam_5/cam_bld/configure-tests/Srcfiles
/import/c/w/basu/cam_5/cesm1_2_2/models/atm/cam/bld/mkDepends Filepath Srcfiles > /import/c/w/basu/cam_5/cam_bld/configure-tests/Depends
pgf95 -c -Mfree -I. -I/import/c/w/basu/cam_5/cam_bld/configure-tests -I/opt/cray/netcdf/4.2.0/pgi/119/include -I/opt/cray/parallel-netcdf/1.4.1/PGI/141/include -I/import/c/w/basu/cam_5/cam_bld/mct/mct -I/import/c/w/basu/cam_5/cam_bld/mct/mpeu -I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -I/opt/cray/netcdf/4.2.0/pgi/119/include -DNO_SHR_VMATH -DSEQ_MCT -DNO_C_SIZEOF -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=6 -DBLCKY=19 -DMXBLCKS=4 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF -DLINUX -DNO_R16 -DCPRPGI -i4 -Mdalign -Mextend -byteswapio -gopt -O2 -Mvect=nosse -Kieee -DHIDE_MPI -D_MPISERIAL -DNO_MPIMOD -DNO_MPI2 -DNO_SIZEOF test_fc.F90
pgf95 -o test_fc -I. -I/import/c/w/basu/cam_5/cam_bld/configure-tests -I/opt/cray/netcdf/4.2.0/pgi/119/include -I/opt/cray/parallel-netcdf/1.4.1/PGI/141/include -I/import/c/w/basu/cam_5/cam_bld/mct/mct -I/import/c/w/basu/cam_5/cam_bld/mct/mpeu -I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -I/opt/cray/netcdf/4.2.0/pgi/119/include -DNO_SHR_VMATH -DSEQ_MCT -DNO_C_SIZEOF -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=6 -DBLCKY=19 -DMXBLCKS=4 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF -DLINUX -DNO_R16 -DCPRPGI -i4 -Mdalign -Mextend -byteswapio -gopt -O2 -Mvect=nosse -Kieee -DHIDE_MPI -D_MPISERIAL -DNO_MPIMOD -DNO_MPI2 -DNO_SIZEOF test_fc.o
**** PASS ****
Issued the command:
./test_fc
The output was:
hello world
using pgf95
Test linking to NetCDF library... **** FAILED ****
Issued the command:
gmake -f /import/c/w/basu/cam_5/cam_bld/Makefile test_nc 2>&1
The output was:
cat: Srcfiles: No such file or directory
/import/c/w/basu/cam_5/cam_bld/Makefile:1052: /import/c/w/basu/cam_5/cam_bld/configure-tests/Depends: No such file or directory
/import/c/w/basu/cam_5/cesm1_2_2/models/atm/cam/bld/mkSrcfiles > /import/c/w/basu/cam_5/cam_bld/configure-tests/Srcfiles
/import/c/w/basu/cam_5/cesm1_2_2/models/atm/cam/bld/mkDepends Filepath Srcfiles > /import/c/w/basu/cam_5/cam_bld/configure-tests/Depends
pgf95 -c -Mfree -I. -I/import/c/w/basu/cam_5/cam_bld/configure-tests -I/opt/cray/netcdf/4.2.0/pgi/119/include -I/opt/cray/parallel-netcdf/1.4.1/PGI/141/include -I/import/c/w/basu/cam_5/cam_bld/mct/mct -I/import/c/w/basu/cam_5/cam_bld/mct/mpeu -I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -I/opt/cray/netcdf/4.2.0/pgi/119/include -DNO_SHR_VMATH -DSEQ_MCT -DNO_C_SIZEOF -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=6 -DBLCKY=19 -DMXBLCKS=4 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF -DLINUX -DNO_R16 -DCPRPGI -i4 -Mdalign -Mextend -byteswapio -gopt -O2 -Mvect=nosse -Kieee -DHIDE_MPI -D_MPISERIAL -DNO_MPIMOD -DNO_MPI2 -DNO_SIZEOF test_nc.F90
pgf95 -o test_nc -I. -I/import/c/w/basu/cam_5/cam_bld/configure-tests -I/opt/cray/netcdf/4.2.0/pgi/119/include -I/opt/cray/parallel-netcdf/1.4.1/PGI/141/include -I/import/c/w/basu/cam_5/cam_bld/mct/mct -I/import/c/w/basu/cam_5/cam_bld/mct/mpeu -I/import/c/w/basu/cam_5/cam_bld/mct/mpi-serial -I/opt/cray/netcdf/4.2.0/pgi/119/include -DNO_SHR_VMATH -DSEQ_MCT -DNO_C_SIZEOF -DFORTRANUNDERSCORE -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=24 -DPLAT=19 -DNUM_COMP_INST_ATM=1 -DNUM_COMP_INST_LND=1 -DNUM_COMP_INST_OCN=1 -DNUM_COMP_INST_ICE=1 -DNUM_COMP_INST_GLC=1 -DNUM_COMP_INST_ROF=1 -DNUM_COMP_INST_WAV=1 -DPLEV=30 -DPCNST=25 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DCCSMCOUPLED -Dcoupled -Dncdf -DNCAT=1 -DNXGLOB=24 -DNYGLOB=19 -DNTR_AERO=0 -DBLCKX=6 -DBLCKY=19 -DMXBLCKS=4 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF -DLINUX -DNO_R16 -DCPRPGI -i4 -Mdalign -Mextend -byteswapio -gopt -O2 -Mvect=nosse -Kieee -DHIDE_MPI -D_MPISERIAL -DNO_MPIMOD -DNO_MPI2 -DNO_SIZEOF test_nc.o -L/opt/cray/netcdf/4.2.0/gnu/46/lib -lnetcdff -Wl,--as-needed,-L/opt/cray/netcdf/4.2.0/gnu/46/lib -lnetcdf -lnetcdf
test_nc.o: In function `main':
/import/c/w/basu/cam_5/cam_bld/configure-tests/./test_nc.F90:5: undefined reference to `netcdf_nf90_create_'
/import/c/w/basu/cam_5/cam_bld/configure-tests/./test_nc.F90:8: undefined reference to `netcdf_nf90_strerror_'
test_nc.o: In function `.C1_283':
test_nc.F90:(.data+0x30): undefined reference to `netcdf_'
test_nc.F90:(.data+0x38): undefined reference to `typesizes_'
gmake: *** [test_nc] Error 2
Can anybody please provide some suggestions on how to fix this issue.Thanks,Soumik