Console Output

Started by user Claire Carouge
Checking out git https://github.com/coecms/wrf-testing into /cloudvolume/jenkins/WRF/WRF-Core/workspace@script to read WRF-Core.groovy
The recommended git tool is: NONE
No credentials specified
 > /usr/bin/git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
 > /usr/bin/git config remote.origin.url https://github.com/coecms/wrf-testing # timeout=10
Fetching upstream changes from https://github.com/coecms/wrf-testing
 > /usr/bin/git --version # timeout=10
 > git --version # 'git version 1.8.3.1'
 > /usr/bin/git fetch --tags --progress https://github.com/coecms/wrf-testing +refs/heads/*:refs/remotes/origin/* # timeout=10
 > /usr/bin/git rev-parse refs/remotes/origin/4.3^{commit} # timeout=10
Checking out Revision 198929a6179e182443b55ae1761d5ce73c8282c3 (refs/remotes/origin/4.3)
 > /usr/bin/git config core.sparsecheckout # timeout=10
 > /usr/bin/git checkout -f 198929a6179e182443b55ae1761d5ce73c8282c3 # timeout=10
Commit message: "Modifications for the restart test"
 > /usr/bin/git rev-list --no-walk 21d0e82bcb30bfe8c5b76563a0e6bc407b629cfa # timeout=10
Running in Durability level: MAX_SURVIVABILITY
[Pipeline] Start of Pipeline
[Pipeline] node
Still waiting to schedule task
‘ccc561.gadi’ is offline
Running on ccc561.gadi in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core
[Pipeline] {
[Pipeline] stage
Using the ‘stage’ step without a block argument is deprecated
Entering stage extract
Proceeding
[Pipeline] sh
+ rm -rf tests
[Pipeline] git
The recommended git tool is: NONE
No credentials specified
Fetching changes from the remote Git repository
 > /usr/bin/git rev-parse --is-inside-work-tree # timeout=10
 > /usr/bin/git config remote.origin.url https://github.com/coecms/WRF.git # timeout=10
Fetching upstream changes from https://github.com/coecms/WRF.git
 > /usr/bin/git --version # timeout=10
 > git --version # 'git version 2.27.0'
 > /usr/bin/git fetch --tags --force --progress -- https://github.com/coecms/WRF.git +refs/heads/*:refs/remotes/origin/* # timeout=10
Checking out Revision 32b7e3ff006d990fcf65cac8e6d4d7d44b6e3e60 (refs/remotes/origin/V4.3)
 > /usr/bin/git rev-parse refs/remotes/origin/V4.3^{commit} # timeout=10
 > /usr/bin/git config core.sparsecheckout # timeout=10
 > /usr/bin/git checkout -f 32b7e3ff006d990fcf65cac8e6d4d7d44b6e3e60 # timeout=10
 > /usr/bin/git branch -a -v --no-abbrev # timeout=10
 > /usr/bin/git branch -D V4.3 # timeout=10
 > /usr/bin/git checkout -b V4.3 32b7e3ff006d990fcf65cac8e6d4d7d44b6e3e60 # timeout=10
Commit message: "Updates on NCI files"
[Pipeline] sh
+ git clone https://github.com/coecms/wrf-testing.git tests
Cloning into 'tests'...
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/tests
[Pipeline] {
[Pipeline] sh
+ git branch --track 4.3 origin/4.3
Branch '4.3' set up to track remote branch '4.3' from 'origin'.
[Pipeline] sh
+ git checkout 4.3
Switched to branch '4.3'
Your branch is up to date with 'origin/4.3'.
[Pipeline] }
[Pipeline] // dir
[Pipeline] pwd
[Pipeline] stage
Using the ‘stage’ step without a block argument is deprecated
Entering stage clean_WRF
Proceeding
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/WRF
[Pipeline] {
[Pipeline] }
[Pipeline] // dir
[Pipeline] stage
Using the ‘stage’ step without a block argument is deprecated
Entering stage clean_WPS
Proceeding
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/WPS
[Pipeline] {
[Pipeline] }
[Pipeline] // dir
[Pipeline] stage
Using the ‘stage’ step without a block argument is deprecated
Entering stage compile_WRF
Proceeding
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/WRF
[Pipeline] {
[Pipeline] sh
+ ./run_compile -t
checking for perl5... no
checking for perl... found /bin/perl (perl)
Will use NETCDF in dir: /apps/netcdf/4.7.1
NETCDF_classic:  
HDF5 not set in environment. Will configure WRF for use without.
PHDF5 not set in environment. Will configure WRF for use without.
Will use 'time' to report timing information


If you REALLY want Grib2 output from WRF, modify the arch/Config.pl script.
Right now you are not getting the Jasper lib, from the environment, compiled into WRF.

------------------------------------------------------------------------
Please select from among the following Linux x86_64 options:

  1. (serial)   2. (smpar)   3. (dmpar)   4. (dm+sm)   PGI (pgf90/gcc)
  5. (serial)   6. (smpar)   7. (dmpar)   8. (dm+sm)   PGI (pgf90/pgcc): SGI MPT
  9. (serial)  10. (smpar)  11. (dmpar)  12. (dm+sm)   PGI (pgf90/gcc): PGI accelerator
 13. (serial)  14. (smpar)  15. (dmpar)  16. (dm+sm)   INTEL (ifort/icc)
                                         17. (dm+sm)   INTEL (ifort/icc): Xeon Phi (MIC architecture)
 18. (serial)  19. (smpar)  20. (dmpar)  21. (dm+sm)   INTEL (ifort/icc): Xeon (SNB with AVX mods)
 22. (serial)  23. (smpar)  24. (dmpar)  25. (dm+sm)   INTEL (ifort/icc): SGI MPT
 26. (serial)  27. (smpar)  28. (dmpar)  29. (dm+sm)   INTEL (ifort/icc): IBM POE
 30. (serial)               31. (dmpar)                PATHSCALE (pathf90/pathcc)
 32. (serial)  33. (smpar)  34. (dmpar)  35. (dm+sm)   GNU (gfortran/gcc)
 36. (serial)  37. (smpar)  38. (dmpar)  39. (dm+sm)   IBM (xlf90_r/cc_r)
 40. (serial)  41. (smpar)  42. (dmpar)  43. (dm+sm)   PGI (ftn/gcc): Cray XC CLE
 44. (serial)  45. (smpar)  46. (dmpar)  47. (dm+sm)   CRAY CCE (ftn $(NOOMP)/cc): Cray XE and XC
 48. (serial)  49. (smpar)  50. (dmpar)  51. (dm+sm)   INTEL (ftn/icc): Cray XC
 52. (serial)  53. (smpar)  54. (dmpar)  55. (dm+sm)   PGI (pgf90/pgcc)
 56. (serial)  57. (smpar)  58. (dmpar)  59. (dm+sm)   PGI (pgf90/gcc): -f90=pgf90
 60. (serial)  61. (smpar)  62. (dmpar)  63. (dm+sm)   PGI (pgf90/pgcc): -f90=pgf90
 64. (serial)  65. (smpar)  66. (dmpar)  67. (dm+sm)   INTEL (ifort/icc): HSW/BDW
 68. (serial)  69. (smpar)  70. (dmpar)  71. (dm+sm)   INTEL (ifort/icc): KNL MIC
 72. (serial)  73. (smpar)  74. (dmpar)  75. (dm+sm)   INTEL (ifort/icc): CL/SL
 76. (serial)  77. (smpar)  78. (dmpar)  79. (dm+sm)   INTEL (ifort/icc): CL/SL less opt
 80. (serial)  81. (smpar)  82. (dmpar)  83. (dm+sm)   FUJITSU (frtpx/fccpx): FX10/FX100 SPARC64 IXfx/Xlfx

Enter selection [1-83] : ------------------------------------------------------------------------
Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]: 
Configuration successful! 
------------------------------------------------------------------------
testing for fseeko and fseeko64
fseeko64 is supported
------------------------------------------------------------------------

# Settings for    Linux CL/SLcons x86_64 ppc64le i486 i586 i686  (dm+sm)
#
DESCRIPTION     =       INTEL ($SFC/$SCC): CL/SL less opt
DMPARALLEL      =        1
OMPCPP          =        -D_OPENMP
OMP             =        -qopenmp -fpp -auto
OMPCC           =        -qopenmp -fpp -auto
SFC             =       ifort
SCC             =       icc
CCOMP           =       icc
DM_FC           =       mpif90 -f90=$(SFC)
DM_CC           =       mpicc -cc=$(SCC)
FC              =       time $(DM_FC)
CC              =       $(DM_CC) -DFSEEKO64_OK 
LD              =       $(FC)
RWORDSIZE       =       $(NATIVE_RWORDSIZE)
PROMOTION       =       -real-size `expr 8 \* $(RWORDSIZE)` -i4
ARCH_LOCAL      =       -DNONSTANDARD_SYSTEM_FUNC -DWRF_USE_CLM $(NETCDF4_IO_OPTS)
CFLAGS_LOCAL    =       -w -O2 -ip -xHost -fp-model fast=2 -no-prec-div -no-prec-sqrt -ftz -no-multibyte-chars
LDFLAGS_LOCAL   =       -ip -xHost -fp-model fast=2 -no-prec-div -no-prec-sqrt -ftz -align all -fno-alias -fno-common
CPLUSPLUSLIB    =       
ESMF_LDFLAG     =       $(CPLUSPLUSLIB)
FCOPTIM         =       -O2
FCREDUCEDOPT	=       $(FCOPTIM)
FCNOOPT		=       -O0 -fno-inline -no-ip
FCDEBUG         =       # -g $(FCNOOPT) -traceback # -fpe0 -check noarg_temp_created,bounds,format,output_conversion,pointers,uninit -ftrapuv -unroll0 -u
FORMAT_FIXED    =       -FI
FORMAT_FREE     =       -FR
FCSUFFIX        =
BYTESWAPIO      =       -convert big_endian
RECORDLENGTH    =       -assume byterecl
FCBASEOPTS_NO_G =       -ip -fp-model precise -w -ftz -align all -fno-alias $(FORMAT_FREE) $(BYTESWAPIO) -xHost -fp-model fast=2 -no-heap-arrays -no-prec-div -no-prec-sqrt -fno-common -xCORE-AVX512
FCBASEOPTS      =       $(FCBASEOPTS_NO_G) $(FCDEBUG)
MODULE_SRCH_FLAG =     
TRADFLAG        =      -traditional-cpp $(NETCDF4_IO_OPTS)
CPP             =      /lib/cpp -P -nostdinc
AR              =      ar
ARFLAGS         =      ru
M4              =      m4
RANLIB          =      ranlib
RLFLAGS		=	
CC_TOOLS        =      $(SCC) 

###########################################################
######################
# POSTAMBLE

FGREP = fgrep -iq

ARCHFLAGS       =    $(COREDEFS) -DIWORDSIZE=$(IWORDSIZE) -DDWORDSIZE=$(DWORDSIZE) -DRWORDSIZE=$(RWORDSIZE) -DLWORDSIZE=$(LWORDSIZE) \
                     $(ARCH_LOCAL) \
                     $(DA_ARCHFLAGS) \
                      -DDM_PARALLEL \
                       \
                      -DNETCDF \
                       \
                       \
                       \
                       \
                       \
                       \
                       \
                       \
                       -DLANDREAD_STUB=1 \
                       \
                       \
                      -DUSE_ALLOCATABLES \
                      -Dwrfmodel \
                      -DGRIB1 \
                      -DINTIO \
                      -DKEEP_INT_AROUND \
                      -DLIMIT_ARGS \
                      -DBUILD_RRTMG_FAST=0 \
                      -DBUILD_RRTMK=0 \
                      -DBUILD_SBM_FAST=1 \
                      -DSHOW_ALL_VARS_USED=0 \
                      -DCONFIG_BUF_LEN=$(CONFIG_BUF_LEN) \
                      -DMAX_DOMAINS_F=$(MAX_DOMAINS) \
                      -DMAX_HISTORY=$(MAX_HISTORY) \
		      -DNMM_NEST=$(WRF_NMM_NEST)
CFLAGS          =    $(CFLAGS_LOCAL) -DDM_PARALLEL  \
                      -DLANDREAD_STUB=1 \
                      -DMAX_HISTORY=$(MAX_HISTORY) -DNMM_CORE=$(WRF_NMM_CORE)
FCFLAGS         =    $(FCOPTIM) $(FCBASEOPTS)
ESMF_LIB_FLAGS  =    
# ESMF 5 -- these are defined in esmf.mk, included above
 ESMF_IO_LIB     =    -L$(WRF_SRC_ROOT_DIR)/external/esmf_time_f90 -lesmf_time
ESMF_IO_LIB_EXT =    -L$(WRF_SRC_ROOT_DIR)/external/esmf_time_f90 -lesmf_time
INCLUDE_MODULES =    $(MODULE_SRCH_FLAG) \
                     $(ESMF_MOD_INC) $(ESMF_LIB_FLAGS) \
                      -I$(WRF_SRC_ROOT_DIR)/main \
                      -I$(WRF_SRC_ROOT_DIR)/external/io_netcdf \
                      -I$(WRF_SRC_ROOT_DIR)/external/io_int \
                      -I$(WRF_SRC_ROOT_DIR)/frame \
                      -I$(WRF_SRC_ROOT_DIR)/share \
                      -I$(WRF_SRC_ROOT_DIR)/phys \
                      -I$(WRF_SRC_ROOT_DIR)/wrftladj \
                      -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \
                      -I$(NETCDFPATH)/include/Intel \
                       
REGISTRY        =    Registry
CC_TOOLS_CFLAGS = -DNMM_CORE=$(WRF_NMM_CORE)

LIB             =    $(LIB_BUNDLED) $(LIB_EXTERNAL) $(LIB_LOCAL) $(LIB_WRF_HYDRO)  $(NETCDF4_DEP_LIB)
LDFLAGS         =    $(OMP) $(FCFLAGS) $(LDFLAGS_LOCAL) 
ENVCOMPDEFS     =    
WRF_CHEM	=	0 
CPPFLAGS        =    $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) 
NETCDFPATH      =    /apps/netcdf/4.7.1
HDF5PATH        =    
WRFPLUSPATH     =    
RTTOVPATH       =    
PNETCDFPATH     =    

bundled:  io_only 
external: io_only $(WRF_SRC_ROOT_DIR)/external/RSL_LITE/librsl_lite.a gen_comms_rsllite module_dm_rsllite $(ESMF_TARGET)
io_only:  esmf_time wrfio_nf   \
	  wrf_ioapi_includes wrfio_grib_share wrfio_grib1 wrfio_int fftpack


######################
------------------------------------------------------------------------
Settings listed above are written to configure.wrf.
If you wish to change settings, please edit that file.
If you wish to change the default options, edit the file:
     arch/configure.defaults
NetCDF users note:
 This installation of NetCDF supports large file support.  To DISABLE large file
 support in NetCDF, set the environment variable WRFIO_NCD_NO_LARGE_FILE_SUPPORT
 to 1 and run configure again. Set to any other value to avoid this message.
  
newer location of RPC
*****************************************************************************
This build of WRF will use NETCDF4 with HDF5 compression
*****************************************************************************
 
Submitting the compilation to the express queue. Allow for about 40min to finish. Use the qstat command to check status.
22685012.gadi-pbs
[Pipeline] }
[Pipeline] // dir
[Pipeline] stage
Using the ‘stage’ step without a block argument is deprecated
Entering stage compile_WPS
Proceeding
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/WPS
[Pipeline] {
[Pipeline] sh
+ ./run_compile -t
Will use NETCDF in dir: /apps/netcdf/4.7.1
Found what looks like a valid WRF I/O library in ../WRF
Found Jasper environment variables for GRIB2 support...
  $JASPERLIB = /usr/lib64
  $JASPERINC = /usr/include
------------------------------------------------------------------------
Please select from among the following supported platforms.

   1.  Linux x86_64, gfortran    (serial)
   2.  Linux x86_64, gfortran    (serial_NO_GRIB2)
   3.  Linux x86_64, gfortran    (dmpar)
   4.  Linux x86_64, gfortran    (dmpar_NO_GRIB2)
   5.  Linux x86_64, PGI compiler   (serial)
   6.  Linux x86_64, PGI compiler   (serial_NO_GRIB2)
   7.  Linux x86_64, PGI compiler   (dmpar)
   8.  Linux x86_64, PGI compiler   (dmpar_NO_GRIB2)
   9.  Linux x86_64, PGI compiler, SGI MPT   (serial)
  10.  Linux x86_64, PGI compiler, SGI MPT   (serial_NO_GRIB2)
  11.  Linux x86_64, PGI compiler, SGI MPT   (dmpar)
  12.  Linux x86_64, PGI compiler, SGI MPT   (dmpar_NO_GRIB2)
  13.  Linux x86_64, IA64 and Opteron    (serial)
  14.  Linux x86_64, IA64 and Opteron    (serial_NO_GRIB2)
  15.  Linux x86_64, IA64 and Opteron    (dmpar)
  16.  Linux x86_64, IA64 and Opteron    (dmpar_NO_GRIB2)
  17.  Linux x86_64, Intel compiler    (serial)
  18.  Linux x86_64, Intel compiler    (serial_NO_GRIB2)
  19.  Linux x86_64, Intel compiler    (dmpar)
  20.  Linux x86_64, Intel compiler    (dmpar_NO_GRIB2)
  21.  Linux x86_64, Intel compiler, SGI MPT    (serial)
  22.  Linux x86_64, Intel compiler, SGI MPT    (serial_NO_GRIB2)
  23.  Linux x86_64, Intel compiler, SGI MPT    (dmpar)
  24.  Linux x86_64, Intel compiler, SGI MPT    (dmpar_NO_GRIB2)
  25.  Linux x86_64, Intel compiler, IBM POE    (serial)
  26.  Linux x86_64, Intel compiler, IBM POE    (serial_NO_GRIB2)
  27.  Linux x86_64, Intel compiler, IBM POE    (dmpar)
  28.  Linux x86_64, Intel compiler, IBM POE    (dmpar_NO_GRIB2)
  29.  Linux x86_64 g95 compiler     (serial)
  30.  Linux x86_64 g95 compiler     (serial_NO_GRIB2)
  31.  Linux x86_64 g95 compiler     (dmpar)
  32.  Linux x86_64 g95 compiler     (dmpar_NO_GRIB2)
  33.  Cray XE/XC CLE/Linux x86_64, Cray compiler   (serial)
  34.  Cray XE/XC CLE/Linux x86_64, Cray compiler   (serial_NO_GRIB2)
  35.  Cray XE/XC CLE/Linux x86_64, Cray compiler   (dmpar)
  36.  Cray XE/XC CLE/Linux x86_64, Cray compiler   (dmpar_NO_GRIB2)
  37.  Cray XC CLE/Linux x86_64, Intel compiler   (serial)
  38.  Cray XC CLE/Linux x86_64, Intel compiler   (serial_NO_GRIB2)
  39.  Cray XC CLE/Linux x86_64, Intel compiler   (dmpar)
  40.  Cray XC CLE/Linux x86_64, Intel compiler   (dmpar_NO_GRIB2)

Enter selection [1-40] : ------------------------------------------------------------------------
Configuration successful. To build the WPS, type: compile
------------------------------------------------------------------------
22685096.gadi-pbs
[Pipeline] }
[Pipeline] // dir
[Pipeline] stage
Using the ‘stage’ step without a block argument is deprecated
Entering stage compile_UPP
Proceeding
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/tests
[Pipeline] {
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/tests/oct16
[Pipeline] {
[Pipeline] }
[Pipeline] // dir
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/tests/oct16-nesting
[Pipeline] {
[Pipeline] }
[Pipeline] // dir
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/tests/oct16-diagnostics
[Pipeline] {
[Pipeline] }
[Pipeline] // dir
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/tests/oct16-quilting
[Pipeline] {
[Pipeline] }
[Pipeline] // dir
[Pipeline] dir
Running in /home/561/ccc561/scratch/jenkins/workspace/WRF/WRF-Core/tests/oct16-restart
[Pipeline] {
[Pipeline] stage
Using the ‘stage’ step without a block argument is deprecated
Entering stage oct16-restart
Proceeding
[Pipeline] sh
+ qsub -W block=true -v PROJECT,WRF_ROOT runtest.sh
22685169.gadi-pbs
[Pipeline] sh
+ ./compare_output.sh
ncks: ERROR file wrfout_d01_2016-10-07_00:00:00 not found. It does not exist on the local filesystem, nor does it match remote filename patterns (e.g., http://foo or foo.bar.edu:file).
ncks: HINT file-not-found errors usually arise from filename typos, incorrect paths, missing files, or capricious gods. Please verify spelling and location of requested file. If the file resides on a High Performance Storage System (HPSS) accessible via the 'hsi' command, then add the --hpss option and re-try command.
cdo    diffn: Open failed on >restart_out.nc<
              No such file or directory
[Pipeline] }
[Pipeline] // dir
[Pipeline] }
[Pipeline] // dir
[Pipeline] }
[Pipeline] // node
[Pipeline] End of Pipeline
ERROR: script returned exit code 1
Finished: FAILURE