Problem in building CESM 1.2.2 on CRAY XC40

A

ashutosh348@gmail_com

New Member
Hi,I am trying to build CESM 1.2.2 on CRAY (edison) system and I am getting some error. I am also attaching the Macros file for the reference. Its been more than a month and some errors are always popping up, quite a stressful time! Please help. Error log: Mon Aug 29 08:01:45 CDT 2016 /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/csm_share.bldlog.160829-080140ftn -c -I.  -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/include -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/opt/cray/netcdf/4.3.2/INTEL/140/include -I/opt/cray/mpt/7.3.3/gni/mpich-intel/15.0/include -I/opt/cray/parallel-netcdf/1.4.1/INTEL/140/include -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/include -I/mnt/lustre/cas2/caspande/cesmnew/models/csm_share/shr -I. -I/mnt/lustre/cas2/caspande/cesmnew/scripts/clmcrop/SourceMods/src.share -I/mnt/lustre/cas2/caspande/cesmnew/models/drv/shr -I/mnt/lustre/cas2/caspande/cesmnew/models/dead_share -I/mnt/lustre/cas2/caspande/cesmnew/models/csm_share/shr -I/mnt/lustre/cas2/caspande/cesmnew/models/utils/esmf_wrf_timemgr -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/lib/include  -O1 -fp-model source -convert big_endian -assume byterecl -ftz -traceback -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_WAV=1 -DNUM_COMP_INST_ROF=1 -DCNL  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX  -DCNL -DCPRINTEL -DHAVE_SLASHPROC -free  /mnt/lustre/cas2/caspande/cesmnew/models/drv/shr/seq_io_mod.F90ftn -c -I.  -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/include -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/opt/cray/netcdf/4.3.2/INTEL/140/include -I/opt/cray/mpt/7.3.3/gni/mpich-intel/15.0/include -I/opt/cray/parallel-netcdf/1.4.1/INTEL/140/include -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/include -I/mnt/lustre/cas2/caspande/cesmnew/models/csm_share/shr -I. -I/mnt/lustre/cas2/caspande/cesmnew/scripts/clmcrop/SourceMods/src.share -I/mnt/lustre/cas2/caspande/cesmnew/models/drv/shr -I/mnt/lustre/cas2/caspande/cesmnew/models/dead_share -I/mnt/lustre/cas2/caspande/cesmnew/models/csm_share/shr -I/mnt/lustre/cas2/caspande/cesmnew/models/utils/esmf_wrf_timemgr -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/lib/include  -O1 -fp-model source -convert big_endian -assume byterecl -ftz -traceback -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_WAV=1 -DNUM_COMP_INST_ROF=1 -DCNL  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX  -DCNL -DCPRINTEL -DHAVE_SLASHPROC -free  /mnt/lustre/cas2/caspande/cesmnew/models/csm_share/shr/shr_scam_mod.F90/mnt/lustre/cas2/caspande/cesmnew/models/csm_share/shr/shr_scam_mod.F90(23): remark #6536: All symbols from this module are already visible due to another USE; the ONLY clause will have no effect. Rename clauses, if any, will be honored.   [SHR_KIND_MOD]   use shr_kind_mod  ! defines kinds-------^/mnt/lustre/cas2/caspande/cesmnew/models/drv/shr/seq_io_mod.F90(1170): error #6404: This name does not have a type, and must have an explicit type.   [PIO_UNLIMITED]      rcode = pio_def_dim(cpl_io_file,'time',PIO_UNLIMITED,dimid(1))---------------------------------------------^compilation aborted for /mnt/lustre/cas2/caspande/cesmnew/models/drv/shr/seq_io_mod.F90 (code 1)No supported cpu target is set, CRAY_CPU_TARGET=x86-64 will be used.Load a valid targeting module or set CRAY_CPU_TARGETgmake: *** [seq_io_mod.o] Error 1gmake: *** Waiting for unfinished jobs....No supported cpu target is set, CRAY_CPU_TARGET=x86-64 will be used.Load a valid targeting module or set CRAY_CPU_TARGETgmake  complib -j 24 MODEL=csm_share COMPLIB=libcsm_share.a USER_CPPDEFS="  -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_WAV=1 -DNUM_COMP_INST_ROF=1" -f /mnt/lustre/cas2/caspande/cesmnew/scripts/clmcrop/Tools/Makefile  returned non-zero exit status 2  RegardsAshutosh 
 
A

ashutosh348@gmail_com

New Member
Thanks for the reply. Actually, I dont have any such directory as you mentioned /project/projectdirs/ccsm1/collections/cesm1_2_2I am considering CRAY as Edison machine as it is mentioned to be compatible with CESM on this link http://www.cesm.ucar.edu/models/cesm1.2/cesm/doc/modelnl/machines.html. Also in the env_mach_specific file I have removed all the module related lines as I was using module load command externally (to avoid conflict) before running the build script. Here is the content of my env_mach_specific file: #! /bin/csh -f #-------------------------------------------------------------------------------# Modules and library paths#------------------------------------------------------------------------------- #-------------------------------------------------------------------------------# Runtime environment variables#------------------------------------------------------------------------------- setenv MPICH_ENV_DISPLAY 1setenv MPICH_VERSION_DISPLAY 1 limit coredumpsize unlimitedlimit stacksize unlimited # The environment variable below increase the stack size, which is necessary for# CICE to run threaded on this machine.  setenv OMP_STACKSIZE 64M AND this is the list of modules I have loaded up before running the build script:

Currently Loaded Modulefiles:
  1) modules/3.2.10.4  2) nodestat/2.2-1.0502.60539.1.31.ari  3) sdb/1.1-1.0502.63652.4.25.ari  4) alps/5.2.4-2.0502.9822.32.1.ari  5) lustre-cray_ari_s/2.5_3.0.101_0.46.1_1.0502.8871.20.1-1.0502.21481.23.2  6) udreg/2.3.2-1.0502.10518.2.17.ari  7) ugni/6.0-1.0502.10863.8.29.ari  8) gni-headers/4.0-1.0502.10859.7.8.ari  9) dmapp/7.0.1-1.0502.11080.8.76.ari 10) xpmem/0.1-2.0502.64982.5.3.ari 11) hss-llm/7.2.0 12) Base-opts/1.0.2-1.0502.60680.2.4.ari 13) intel/15.0.1.133 14) craype-network-aries 15) craype/2.5.4 16) nodehealth/5.1-1.0502.65826.9.1.ari 17) cmake/3.5.2 18) cray-hdf5/1.8.13 19) cray-mpich/7.3.3 20) cray-parallel-netcdf/1.4.1 21) modules/3.2.10.3 22) gcc/5.3.0 23) pbs/12.2.404.152084 24) cray-netcdf/4.3.2 25) cray-libsci/16.03.1 26) pmi/5.0.10-1.0000.11050.0.0.ari 27) atp/2.0.1 28) PrgEnv-intel/5.2.82Some of the module files are by default for the system (I dont have much idea for them).Also, I am kind of new to all this so please bear with me if I am not clear here.Please let me know how to proceed here. Thanks.
 
J

jedwards

CSEG and Liaisons
Staff member
Do you have a complete source tree?  Please seehttp://forum.cgd.ucar.edu/googlecode-repositories-are-offline-pio-source-not-found
 
A

ashutosh348@gmail_com

New Member
Hi,I have update the source tree but still the error pops up in the csm_share.bldlog.160831-082645 Wed Aug 31 08:26:53 CDT 2016 /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/csm_share.bldlog.160831-082645ftn -c -I.  -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/include -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/opt/cray/netcdf/4.3.0/INTEL/130/include -I/opt/cray/mpt/7.3.3/gni/mpich-intel/15.0/include -I/opt/cray/parallel-netcdf/1.4.1/INTEL/140/include -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/include -I/mnt/lustre/cas2/caspande/cesmnew/models/csm_share/shr -I. -I/mnt/lustre/cas2/caspande/cesmnew/scripts/clmcrop/SourceMods/src.share -I/mnt/lustre/cas2/caspande/cesmnew/models/drv/shr -I/mnt/lustre/cas2/caspande/cesmnew/models/dead_share -I/mnt/lustre/cas2/caspande/cesmnew/models/csm_share/shr -I/mnt/lustre/cas2/caspande/cesmnew/models/utils/esmf_wrf_timemgr -I/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/lib/include  -O1 -fp-model source -convert big_endian -assume byterecl -ftz -traceback -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_WAV=1 -DNUM_COMP_INST_ROF=1 -DCNL  -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX  -DCNL -DCPRINTEL -DHAVE_SLASHPROC -free  /mnt/lustre/cas2/caspande/cesmnew/models/drv/shr/seq_io_mod.F90/mnt/lustre/cas2/caspande/cesmnew/models/drv/shr/seq_io_mod.F90(1170): error #6404: This name does not have a type, and must have an explicit type.   [PIO_UNLIMITED]      rcode = pio_def_dim(cpl_io_file,'time',PIO_UNLIMITED,dimid(1))---------------------------------------------^compilation aborted for /mnt/lustre/cas2/caspande/cesmnew/models/drv/shr/seq_io_mod.F90 (code 1)No supported cpu target is set, CRAY_CPU_TARGET=x86-64 will be used.Load a valid targeting module or set CRAY_CPU_TARGETgmake: *** [seq_io_mod.o] Error 1gmake  complib -j 24 MODEL=csm_share COMPLIB=libcsm_share.a USER_CPPDEFS="  -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_WAV=1 -DNUM_COMP_INST_ROF=1" -f /mnt/lustre/cas2/caspande/cesmnew/scripts/clmcrop/Tools/Makefile  returned non-zero exit status 2 Please let me know what to do now.
 
A

ashutosh348@gmail_com

New Member
Hi, Here is the pio.bldlog.160831-082409: Wed Aug 31 08:24:13 CDT 2016 /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio.bldlog.160831-082409set pio_dir=/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/piocd /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pioset cmake_opts= -D USER_CMAKE_MODULE_PATH=/mnt/lustre/cas2/caspande/cesmnew/scripts/ccsm_utils/CMakeset cmake_opts= -D USER_CMAKE_MODULE_PATH=/mnt/lustre/cas2/caspande/cesmnew/scripts/ccsm_utils/CMake -D GENF90_PATH=/mnt/lustre/cas2/caspande/cesmnew/tools/cprnc/genf90gmake /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio/Makefile MODEL=pio USER_CMAKE_OPTS= -D USER_CMAKE_MODULE_PATH=/mnt/lustre/cas2/caspande/cesmnew/scripts/ccsm_utils/CMake -D GENF90_PATH=/mnt/lustre/cas2/caspande/cesmnew/tools/cprnc/genf90 PIO_LIBDIR=/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio -f /mnt/lustre/cas2/caspande/cesmnew/scripts/clmcrop/Tools/Makefilegmake: `/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio/Makefile' is up to date.gmake -j 24/ufs/apps/cmake/3.5.2/bin/cmake -H/mnt/lustre/cas2/caspande/cesmnew/models/utils/pio -B/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio --check-build-system CMakeFiles/Makefile.cmake 0/ufs/apps/cmake/3.5.2/bin/cmake -E cmake_progress_start /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio/CMakeFiles /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio/CMakeFiles/progress.marksgmake -f CMakeFiles/Makefile2 allgmake[1]: Entering directory `/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio'gmake -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/dependgmake[2]: Entering directory `/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio'cd /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio && /ufs/apps/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /mnt/lustre/cas2/caspande/cesmnew/models/utils/pio /mnt/lustre/cas2/caspande/cesmnew/models/utils/pio /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio/CMakeFiles/pio.dir/DependInfo.cmake --color=gmake[2]: Leaving directory `/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio'gmake -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/requiresgmake[2]: Entering directory `/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio'gmake -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/pio_kinds.F90.o.provides.buildgmake[3]: Entering directory 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`/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio'gmake -f CMakeFiles/pio.dir/build.make CMakeFiles/pio.dir/buildgmake[2]: Entering directory `/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio'gmake[2]: Nothing to be done for `CMakeFiles/pio.dir/build'.gmake[2]: Leaving directory `/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio'[100%] Built target piogmake[1]: Leaving directory `/mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio'/ufs/apps/cmake/3.5.2/bin/cmake -E cmake_progress_start /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio/CMakeFiles 0cp -p libpio.a /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio/../libcp -p dtypes.h alloc_mod.mod box_rearrange.mod calcdecomp.mod calcdisplace_mod.mod iompi_mod.mod ionf_mod.mod nf_mod.mod piodarray.mod pio_kinds.mod piolib_mod.mod pio.mod pio_mpi_utils.mod pio_msg_mod.mod pionfatt_mod.mod pionfget_mod.mod pionfput_mod.mod pionfread_mod.mod pio_nf_utils.mod pionfwrite_mod.mod pio_spmd_utils.mod pio_support.mod pio_types.mod pio_utils.mod rearrange.mod /mnt/lustre/cas2/caspande/scratch/clmcrop/bld/intel/mpt/nodebug/nothreads/pio/../includeexit 0
 
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