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CAM5 stand alone with SMPD

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CAM5 stand alone with SMPD


I am trying to build the stand alone version of CAM5 on a linux system with CentOS6, intel fortran 12.1.3, netcdf 4.1.3 built with ifort , mpich2 1.4.1p1  - the serial CAM5 builds and runs fine. I am having problems building the mpich2 version. I issue the following command but get errors related to Fortan 90 compatibility. Any help is greatly appreciated. Cheers, Charles Jones.

$camcfg/configure -v -fc mpif90 -fc_type intel -cc mpicc -nc_inc /home/curiosity/netcdf/include  -nc_lib /home/curiosity/netcdf/lib \
? -mpi_inc /usr/local/mpich2/include  -mpi_lib /usr/local/mpich2/lib  -dyn fv -hgrid 10x15 -ntasks 6 -nosmp -test

Physics package: cam5
Chemistry package: trop_mam3
CAM configuration script directory: /home/discoverya/cesm1_2_1/models/atm/cam/bld
Configuration defaults file: config_files/defaults_fv.xml
CAM root directory: /home/discoverya/cesm1_2_1
CAM build directory: /home/discoverya/cam_test/bld2/configure-tests
CAM executable will be created in: /home/discoverya/cam_test/bld2/configure-tests
User source directories:
Configuration cache file: /home/discoverya/cam_test/bld2/configure-tests/config_cache.xml
Target OS: linux
SPMD parallelism: ON
Number of MPI tasks: 6
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:
/home/discoverya/cesm1_2_1/models/ice/cice/bld/configure -hgrid 10x15 -cice_mode prescribed -ntr_aero 0 -nx 24 -ny 19 -bsizex 2 -bsizey 19 -maxblocks 2 -decomptype blkrobin -cache config_cache_cice.xml -cachedir /home/discoverya/cam_test/bld2/configure-tests
CICE configure done.
Name of CAM executable: cam
Fortran compiler: mpif90
Fortran compiler type: intel
C compiler: mpicc
Compiler debugging options: OFF
Will look for NetCDF include file in: /home/curiosity/netcdf/include
Will look for netCDF library in: /home/curiosity/netcdf/lib
Found netCDF module files in: /home/curiosity/netcdf/include
Found MPI include file in: /usr/local/mpich2/include
Found MPI library in: /usr/local/mpich2/lib
checking for cc... cc
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... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking how to run the C preprocessor... cc -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... yes
checking whether mpif90 accepts -g... yes
checking for Fortran flag to compile .F90 files... none
checking for mpif90... mpif90
checking for MPI_Init... yes
checking for mpif.h... yes
Checking Compiler Version
checking how to get the version output from mpif90... --version
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 mpif90... -v
checking for Fortran libraries of mpif90... -L/usr/local/mpich2/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64 -L/opt/intel/composer_xe_2011_sp1.9.293/ipp/../compiler/lib/intel64 -L/opt/intel/composer_xe_2011_sp1.9.293/ipp/lib/intel64 -L/opt/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64 -L/opt/intel/composer_xe_2011_sp1.9.293/tbb/lib/intel64//cc4.1.0_libc2.4_kernel2.6.16.21 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread -lgfortranbegin -lgfortran -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore

Output Variables: {CC=cc} {CFLAGS=-g -O2} {FC=mpif90} {FCFLAGS=-g -O2} {PROGFCFLAGS=}{CPPDEFS= -DSYSLINUX -DCPR} {OPT=} {DEBUG=} {REAL8=} {BIT64=} {ENDIAN=} {MPIFC=mpif90} {MPILIBS=} {MPIHEADER=-I/usr/local/mpich2/include} {INCLUDEFLAG=-I} {INCLUDEPATH=} {AR=ar cq} {BABELROOT=} {COMPILER_ROOT=} {PYTHON=} {PYTHONOPTS=} {FORT_SIZE=} {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 /home/discoverya/cam_test/bld2/configure-tests/Filepath
creating /home/discoverya/cam_test/bld2/configure-tests/Makefile
creating /home/discoverya/cam_test/bld2/configure-tests/config.h
creating /home/discoverya/cam_test/bld2/configure-tests/config_cache.xml
Looking for a valid GNU make... using gmake
Testing for Fortran 90 compatible compiler... **** FAILED ****
Issued the command:
gmake -f /home/discoverya/cam_test/bld2/configure-tests/Makefile test_fc 2>&1

The output was:
/home/discoverya/cesm1_2_1/models/atm/cam/bld/mkSrcfiles > /home/discoverya/cam_test/bld2/configure-tests/configure-tests/Srcfiles
/home/discoverya/cesm1_2_1/models/atm/cam/bld/mkDepends Filepath Srcfiles > /home/discoverya/cam_test/bld2/configure-tests/configure-tests/Depends
mpif90 -c -I. -I/home/discoverya/cam_test/bld2/configure-tests/configure-tests -I/home/curiosity/netcdf/include -I/usr/local/mpich2/include -I/home/discoverya/cam_test/bld2/configure-tests/mct/mct -I/home/discoverya/cam_test/bld2/configure-tests/mct/mpeu -I/home/curiosity/netcdf/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=2 -DBLCKY=19 -DMXBLCKS=2 -DMODAL_AERO -DMODAL_AERO_3MODE -D_USEBOX -D_NETCDF -DNO_SIZEOF -DSPMD -DLINUX -DCPRINTEL -ftz -convert big_endian -fp-model precise -O2 test_fc.F90
f95: big_endian: No such file or directory
f95: precise: No such file or directory
f95: unrecognized option '-convert'
f951: error: unrecognized command line option "-ftz"
f951: error: unrecognized command line option "-fp-model"
gmake: *** [test_fc.o] Error 1


The error from the test for the fortran compiler is coming from "f95" which is not an intel compiler.  The error messages indicate that f95 does not recognize the compiler options that we use with the intel compiler (ifort).  The test was executed using mpif90, which implies that the mpif90 in your path (i.e., PATH environment variable) is not invoking ifort.  Looking through the previous diagnostic output it appears that f95 is the gfortran compiler and that your mpich2 installation was built using gfortran.  To get a successful build of CAM using MPI you'll need netCDF and MPI libs that are built with the same fortran compiler.  We've done a lot of testing with intel, not so much with gfortran, so the former is the best bet.


Thanks Eaton,

i rebuilt mpich2 with FC=ifort and the CAM5 stand alone builds and runs fine.




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