Macros fixes and diag_type fix (#396)

* Macros fixes and diag_type fix

* update ICE_RUNLENGTH documentation

* update cheyenne job launch, add omplace

* update cheyenne, cleanup Macros, update run checking for diag_type

* retrigger checks

* retrigger checks

configuration/scripts/cice.launch.csh

@@ -29,7 +29,7 @@ cat >> ${jobfile} << EOFR
 EOFR
 else
 cat >> ${jobfile} << EOFR
-mpiexec_mpt -n ${ntasks} ./cice >&! \$ICE_RUNLOG_FILE
+mpiexec_mpt -np ${ntasks} omplace ./cice >&! \$ICE_RUNLOG_FILE
 EOFR
 endif
 

configuration/scripts/cice.run.setup.csh

@@ -46,7 +46,11 @@ cd \${ICE_RUNDIR}
 setenv OMP_NUM_THREADS ${nthrds}
 
 cp -f \${ICE_CASEDIR}/ice_in \${ICE_RUNDIR}
+set diagtype = \`grep -i diag_type \${ICE_CASEDIR}/ice_in | grep -i stdout | wc -l\`
+set diagfile = \`grep -i diag_file \${ICE_CASEDIR}/ice_in | sed -e "s/.* = '\(.*\)'/\1/"\`
+
 echo " "
+echo "CICE case directory is \${ICE_CASEDIR}"
 echo "CICE rundir is \${ICE_RUNDIR}"
 echo "CICE log file is \${ICE_RUNLOG_FILE}"
 echo "CICE run started : \`date\`"
@@ -71,16 +75,33 @@ echo " "
 #--------------------------------------------
 
 if !(-d \${ICE_LOGDIR}) mkdir -p \${ICE_LOGDIR}
+
+set checkfile = \${ICE_RUNLOG_FILE}
 cp -p \${ICE_RUNLOG_FILE} \${ICE_LOGDIR}
+echo "CICE output file is \${ICE_LOGDIR}/\${ICE_RUNLOG_FILE}"
+echo "\`date\` \${0}: CICE output file is \${ICE_LOGDIR}/\${ICE_RUNLOG_FILE}" >> \${ICE_CASEDIR}/README.case
+
+if ( \${diagtype} == 0) then
+  set checkfile = \${diagfile}
+  cp -p \${diagfile} \${ICE_LOGDIR}
+  echo "CICE output file is \${ICE_LOGDIR}/\${diagfile}"
+  echo "\`date\` \${0}: CICE output file is \${ICE_LOGDIR}/\${diagfile}" >> \${ICE_CASEDIR}/README.case
+endif
+
+grep ' CICE COMPLETED SUCCESSFULLY' \${checkfile}
+if ( \$status == 0 ) then
+  echo "CICE run completed successfully"
+  echo "\`date\` \${0}: CICE run completed successfully"  >> \${ICE_CASEDIR}/README.case
+else
+  echo "CICE run did NOT complete"
+  echo "\`date\` \${0}: CICE run did NOT complete"  >> \${ICE_CASEDIR}/README.case
+  exit -1
+endif
 
-grep ' CICE COMPLETED SUCCESSFULLY' \${ICE_RUNLOG_FILE}
-if ( \$status != 0 ) then
-  echo "CICE run did not complete - see \${ICE_LOGDIR}/\${ICE_RUNLOG_FILE}"
-  echo "\`date\` \${0}: \${ICE_CASENAME} run did NOT complete \${ICE_RUNLOG_FILE}"  >> \${ICE_CASEDIR}/README.case
+if ( \${diagtype} == 0) then
   exit -1
 endif
 
-echo "\`date\` \${0}: \${ICE_CASENAME} run completed \${ICE_RUNLOG_FILE}"  >> \${ICE_CASEDIR}/README.case
 echo "done \${0}"
 
 EOFE

configuration/scripts/machines/Macros.brooks_intel

@@ -65,14 +65,9 @@ ifeq ($(ICE_THREADED), true)
 endif
 
 ### if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/lib
    INCLDIR += -I/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/include
    SLIBS   := $(SLIBS) -L$(PIO_PATH) -lpiof
-
-   CPPDEFS :=  $(CPPDEFS) -Dncdf
 endif
 
-ifeq ($(IO_TYPE), netcdf)
-   CPPDEFS :=  $(CPPDEFS) -Dncdf
-endif

configuration/scripts/machines/Macros.cesium_intel

@@ -52,21 +52,16 @@ LIB_MPI := $(IMPILIBDIR)
 #SLIBS   := -L$(LIB_NETCDF) -lnetcdff -lnetcdf -L$(LIB_PNETCDF) -lpnetcdf -lgptl
 SLIBS   := -L$(LIB_NETCDF) -lnetcdff -lnetcdf
 
-ifeq ($(compile_threaded), true) 
+ifeq ($(ICE_THREADED), true) 
    LDFLAGS += -openmp 
    CFLAGS += -openmp 
    FFLAGS += -openmp 
 endif
 
 ### if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/lib
    INCLDIR += -I/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/include
    SLIBS   := $(SLIBS) -L$(PIO_PATH) -lpiof
-
-   CPPDEFS :=  $(CPPDEFS) -Dncdf
 endif
 
-ifeq ($(IO_TYPE), netcdf)
-   CPPDEFS :=  $(CPPDEFS) -Dncdf
-endif

configuration/scripts/machines/Macros.cheyenne_intel

@@ -47,14 +47,14 @@ LIB_MPI := $(IMPILIBDIR)
 #SLIBS   := -L$(LIB_NETCDF) -lnetcdf -lnetcdff -L$(LIB_PNETCDF) -lpnetcdf -lgptl
 SLIBS   := -L$(LIB_NETCDF) -lnetcdf -lnetcdff
 
-ifeq ($(compile_threaded), true) 
+ifeq ($(ICE_THREADED), true) 
    LDFLAGS += -qopenmp 
    CFLAGS += -qopenmp 
    FFLAGS += -qopenmp 
 endif
 
 ### if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/lib
    INCLDIR += -I/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/include
    SLIBS   := $(SLIBS) -L$(PIO_PATH) -lpiof

configuration/scripts/machines/Macros.fram_intel

@@ -52,21 +52,16 @@ LIB_MPI := $(IMPILIBDIR)
 #SLIBS   := -L$(LIB_NETCDF) -lnetcdff -lnetcdf -L$(LIB_PNETCDF) -lpnetcdf -lgptl
 SLIBS   := -L$(LIB_NETCDF) -lnetcdff -lnetcdf
 
-ifeq ($(compile_threaded), true) 
+ifeq ($(ICE_THREADED), true) 
    LDFLAGS += -openmp 
    CFLAGS += -openmp 
    FFLAGS += -openmp 
 endif
 
 ### if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/lib
    INCLDIR += -I/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/include
    SLIBS   := $(SLIBS) -L$(PIO_PATH) -lpiof
-
-   CPPDEFS :=  $(CPPDEFS) -Dncdf
 endif
 
-ifeq ($(IO_TYPE), netcdf)
-   CPPDEFS :=  $(CPPDEFS) -Dncdf
-endif

configuration/scripts/machines/Macros.hobart_intel

@@ -41,7 +41,7 @@ LIB_MPI := $(IMPILIBDIR)
 SLIBS   := -L$(LIB_NETCDF) -lnetcdf -lnetcdff -L/usr/lib64 -llapack -mkl=cluster
 
 ## if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=
    INCLDIR += -I
    SLIBS   := $(SLIB) -L$(PIO_PATH) -lpiofS

configuration/scripts/machines/Macros.hobart_nag

@@ -41,7 +41,7 @@ LIB_MPI := $(IMPILIBDIR)
 SLIBS   := -L/usr/local/nag-6.2/lib/NAG_Fortran -L$(LIB_NETCDF) -lnetcdf -lnetcdff -L/usr/lib64 -llapack -lblas
 
 ## if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=
    INCLDIR += -I
    SLIBS   := $(SLIB) -L$(PIO_PATH) -lpiof

configuration/scripts/machines/Macros.izumi_gnu

@@ -44,7 +44,7 @@ ifeq ($(ICE_THREADED), true)
 endif
 
 ## if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=
    INCLDIR += -I
    SLIBS   := $(SLIB) -L$(PIO_PATH) -lpiofS

configuration/scripts/machines/Macros.izumi_intel

@@ -44,7 +44,7 @@ ifeq ($(ICE_THREADED), true)
 endif
 
 ## if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=
    INCLDIR += -I
    SLIBS   := $(SLIB) -L$(PIO_PATH) -lpiofS

configuration/scripts/machines/Macros.izumi_nag

@@ -46,7 +46,7 @@ else
 endif
 
 ## if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=
    INCLDIR += -I
    SLIBS   := $(SLIB) -L$(PIO_PATH) -lpiof

configuration/scripts/machines/Macros.izumi_pgi

@@ -44,7 +44,7 @@ ifeq ($(ICE_THREADED), true)
 endif
 
 ## if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=
    INCLDIR += -I
    SLIBS   := $(SLIB) -L$(PIO_PATH) -lpiofS

configuration/scripts/machines/Macros.millikan_intel

@@ -52,21 +52,16 @@ LIB_MPI := $(IMPILIBDIR)
 #SLIBS   := -L$(LIB_NETCDF) -lnetcdff -lnetcdf -L$(LIB_PNETCDF) -lpnetcdf -lgptl
 SLIBS   := -L$(LIB_NETCDF) -lnetcdff -lnetcdf
 
-ifeq ($(compile_threaded), true) 
+ifeq ($(ICE_THREADED), true) 
    LDFLAGS += -openmp 
    CFLAGS += -openmp 
    FFLAGS += -openmp 
 endif
 
 ### if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/lib
    INCLDIR += -I/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/include
    SLIBS   := $(SLIBS) -L$(PIO_PATH) -lpiof
-
-   CPPDEFS :=  $(CPPDEFS) -Dncdf
 endif
 
-ifeq ($(IO_TYPE), netcdf)
-   CPPDEFS :=  $(CPPDEFS) -Dncdf
-endif

configuration/scripts/machines/Macros.phase2_intel

@@ -43,14 +43,14 @@ LIB_MPI := $(IMPILIBDIR)
 
 SLIBS   := -L$(LIB_NETCDF) -lnetcdf -lnetcdff 
 
-ifeq ($(compile_threaded), true) 
+ifeq ($(ICE_THREADED), true) 
    LDFLAGS += -qopenmp 
    CFLAGS += -qopenmp 
    FFLAGS += -qopenmp 
 endif
 
 ### if using parallel I/O, load all 3 libraries.  PIO must be first!
-#ifeq ($(IO_TYPE), pio)
+#ifeq ($(ICE_IOTYPE), pio)
 #   PIO_PATH:=/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/lib
 #   INCLDIR += -I/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/include
 #   SLIBS   := $(SLIBS) -L$(PIO_PATH) -lpiof

configuration/scripts/machines/Macros.phase3_intel

@@ -44,14 +44,14 @@ LIB_MPI := $(IMPILIBDIR)
 
 SLIBS   := -L$(LIB_NETCDF) -lnetcdf -lnetcdff 
 
-ifeq ($(compile_threaded), true) 
+ifeq ($(ICE_THREADED), true) 
    LDFLAGS += -qopenmp 
    CFLAGS += -qopenmp 
    FFLAGS += -qopenmp 
 endif
 
 ### if using parallel I/O, load all 3 libraries.  PIO must be first!
-#ifeq ($(IO_TYPE), pio)
+#ifeq ($(ICE_IOTYPE), pio)
 #   PIO_PATH:=/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/lib
 #   INCLDIR += -I/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/include
 #   SLIBS   := $(SLIBS) -L$(PIO_PATH) -lpiof

configuration/scripts/machines/Macros.testmachine_intel

@@ -46,14 +46,14 @@ LIB_MPI := $(IMPILIBDIR)
 
 SLIBS   := -L$(LIB_NETCDF) -lnetcdf -lnetcdff -L$(LIB_PNETCDF) -lpnetcdf -lgptl
 
-ifeq ($(compile_threaded), true) 
+ifeq ($(ICE_THREADED), true) 
    LDFLAGS += -qopenmp 
    CFLAGS += -qopenmp 
    FFLAGS += -qopenmp 
 endif
 
 ### if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/lib
    INCLDIR += -I/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/include
    SLIBS   := $(SLIBS) -L$(PIO_PATH) -lpiof

doc/source/user_guide/ug_case_settings.rst

@@ -58,7 +58,8 @@ to support the CICE model.
    "ICE_BFBCOMP", "string", "location of case for comparison, associated with cice.setup -td", "set by cice.setup"
    "ICE_SPVAL", "string", "special value for cice.settings strings", "set by cice.setup"
    "ICE_RUNLENGTH", "integer (see below)", "batch run length default", "set by cice.setup"
-   " ", "0", "15 minutes (default)", " "
+   " ", "-1", "15 minutes (default)", " "
+   " ", "0", "30 minutes", " "
    " ", "1", "59 minutes", " "
    " ", "2", "2 hours", " "
    " ", "other :math:`2 < N < 8`", "N hours", " "