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/4.0.2^{commit} # timeout=10
Checking out Revision d90c3878f7ecf7782305570b5ff9c381cf650fbf (refs/remotes/origin/4.0.2)
 > /usr/bin/git config core.sparsecheckout # timeout=10
 > /usr/bin/git checkout -f d90c3878f7ecf7782305570b5ff9c381cf650fbf # timeout=10
Commit message: "Need to run in jenkins-tests"
 > /usr/bin/git rev-list --no-walk d90c3878f7ecf7782305570b5ff9c381cf650fbf # 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 ca0680f8dc4928fae298cc81ae09403c741ec575 (refs/remotes/origin/V4.0.2)
 > /usr/bin/git rev-parse refs/remotes/origin/V4.0.2^{commit} # timeout=10
 > /usr/bin/git config core.sparsecheckout # timeout=10
 > /usr/bin/git checkout -f ca0680f8dc4928fae298cc81ae09403c741ec575 # timeout=10
 > /usr/bin/git branch -a -v --no-abbrev # timeout=10
 > /usr/bin/git branch -D V4.0.2 # timeout=10
 > /usr/bin/git checkout -b V4.0.2 ca0680f8dc4928fae298cc81ae09403c741ec575 # timeout=10
Commit message: "Correction METGRID.TBL.ERAI for SST"
[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 4.0.2 origin/4.0.2
Branch '4.0.2' set up to track remote branch '4.0.2' from 'origin'.
[Pipeline] sh
+ git checkout 4.0.2
Switched to branch '4.0.2'
Your branch is up to date with 'origin/4.0.2'.
[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/WRFV3
[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/WRFV3
[Pipeline] {
[Pipeline] sh
+ ./run_compile -t -a 79
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 x86_64 ppc64le i486 i586 i686  (dm+sm)
#
DESCRIPTION     =       INTEL ($SFC/$SCC): HSW/BDW
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 -O3 -ip -xHost -fp-model fast=2 -no-prec-div -no-prec-sqrt -ftz -no-multibyte-chars -xCORE-AVX2
LDFLAGS_LOCAL   =       -ip -xHost -fp-model fast=2 -no-prec-div -no-prec-sqrt -ftz -align all -fno-alias -fno-common -xCORE-AVX2
CPLUSPLUSLIB    =       
ESMF_LDFLAG     =       $(CPLUSPLUSLIB)
FCOPTIM         =       -O3
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-AVX2
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) \
                     $(DA_ARCHFLAGS) \
                      -DDM_PARALLEL \
                       \
                      -DNETCDF \
                       \
                       \
                       \
                       \
                       \
                       \
                       \
                       \
                       \
                       \
                      -DUSE_ALLOCATABLES \
                      -Dwrfmodel \
                      -DGRIB1 \
                      -DINTIO \
                      -DKEEP_INT_AROUND \
                      -DLIMIT_ARGS \
                      -DBUILD_RRTMG_FAST=1 \
                      -DCONFIG_BUF_LEN=$(CONFIG_BUF_LEN) \
                      -DMAX_DOMAINS_F=$(MAX_DOMAINS) \
                      -DMAX_HISTORY=$(MAX_HISTORY) \
		      -DNMM_NEST=$(WRF_NMM_NEST)
CFLAGS          =    $(CFLAGS_LOCAL) -DDM_PARALLEL  \
                      -DMAX_HISTORY=$(MAX_HISTORY) -DNMM_CORE=$(WRF_NMM_CORE) -I/usr/include/tirpc
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_BUNDLED     = \
                      $(WRF_SRC_ROOT_DIR)/external/fftpack/fftpack5/libfftpack.a \
                      $(WRF_SRC_ROOT_DIR)/external/io_grib1/libio_grib1.a \
                      $(WRF_SRC_ROOT_DIR)/external/io_grib_share/libio_grib_share.a \
                      $(WRF_SRC_ROOT_DIR)/external/io_int/libwrfio_int.a \
                      $(ESMF_IO_LIB) \
                      $(WRF_SRC_ROOT_DIR)/external/RSL_LITE/librsl_lite.a \
                      $(WRF_SRC_ROOT_DIR)/frame/module_internal_header_util.o \
                      $(WRF_SRC_ROOT_DIR)/frame/pack_utils.o 

 LIB_EXTERNAL    = \
                      -L$(WRF_SRC_ROOT_DIR)/external/io_netcdf -lwrfio_nf -L/apps/netcdf/4.7.1/lib -lnetcdff -lnetcdf     

LIB             =    $(LIB_BUNDLED) $(LIB_EXTERNAL) $(LIB_LOCAL) $(LIB_WRF_HYDRO) -ltirpc $(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.
  
*****************************************************************************
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 nqstat command to check status.
24491347.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 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
------------------------------------------------------------------------
24491390.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/UPPV3.2
[Pipeline] {
[Pipeline] sh
+ ./run_compile -t
Will use NETCDF in dir:  /apps/netcdf/4.7.1
Will use WRF in dir: /scratch/w35/ccc561/jenkins/workspace/WRF/WRF-Core/UPPV3.2/../WRFV3
bindir  /scratch/w35/ccc561/jenkins/workspace/WRF/WRF-Core/UPPV3.2/bin
incmod  /scratch/w35/ccc561/jenkins/workspace/WRF/WRF-Core/UPPV3.2/include
libdir  /scratch/w35/ccc561/jenkins/workspace/WRF/WRF-Core/UPPV3.2/lib
JASPER Environent found :: GRIB2 library ::
grib2lib = -L/usr/lib64 -lpng -lz -ljasper
grib2inc = -I/usr/include
-------------------------------------------------------------------------
Please select from among the following supported platforms.

   1.  Linux x86_64, PGI compiler  (serial)
   2.  Linux x86_64, PGI compiler  (dmpar)
   3.  Linux x86_64, Intel compiler	 (serial)
   4.  Linux x86_64, Intel compiler	 (dmpar)
   5.  Linux x86_64, Intel compiler, SGI MPT	 (serial)
   6.  Linux x86_64, Intel compiler, SGI MPT	 (dmpar)
   7.  Linux x86_64, gfortran compiler  (serial)
   8.  Linux x86_64, gfortran compiler  (dmpar)
   9.  Linux x86_64, Intel compiler, IBM POE	 (serial)
  10.  Linux x86_64, Intel compiler, IBM POE	 (dmpar)
  11.  Linux x86_64, gfortran compiler: -f90=gfortran  (serial)
  12.  Linux x86_64, gfortran compiler: -f90=gfortran  (dmpar)
  13.  Linux x86_64, PGI compiler: -f90=pgf90  (serial)
  14.  Linux x86_64, PGI compiler: -f90=pgf90  (dmpar)

Enter selection [1-14] : -------------------------------------------------------------------------
Configuration successful. To build the UPP, type: compile 
-------------------------------------------------------------------------
Submitting compilation to queue.
24491409.gadi-pbs
[Pipeline] }
[Pipeline] // dir
[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/jan00
[Pipeline] {
[Pipeline] stage
Using the ‘stage’ step without a block argument is deprecated
Entering stage jan00
Proceeding
[Pipeline] sh
+ cp ../../WRFV3/run/run_real ../../WRFV3/run/run_mpi ../../WPS/run_WPS.sh .
[Pipeline] sh
+ cp ../../WPS/namelist.wps.jan00 namelist.wps
[Pipeline] sh
+ cp ../../WRFV3/test/em_real/namelist.input.jan00 namelist.input
[Pipeline] sh
+ qsub -W block=true -v PROJECT,WRF_ROOT run_WPS.sh
qsub: Error: Project "$PROJECT" does not appear to be a valid project. Please check your "-l storage" flag is correct.
[Pipeline] }
[Pipeline] // dir
[Pipeline] }
[Pipeline] // dir
[Pipeline] }
[Pipeline] // node
[Pipeline] End of Pipeline
ERROR: script returned exit code 32
Finished: FAILURE