Merge pull request #32 from marshallward/update

MOM 5.1 Update

README

@@ -0,0 +1,71 @@
+
+Where to start
+~~~~~~~~~~~~~~
+A good place to start is the "doc" directory, where you
+will find  "user" guides for the MOM.  
+
+How to run the MOM tests
+~~~~~~~~~~~~~~~~~~~~~~~~~
+MOM tests provided in exp directory divide in two types, 
+both using the GFDL shared infrastructure (FMS) :
+
+1. Solo models   : Run stand alone MOM Ocean model.
+2. Coupled models: Run MOM coupled with GFDL ice model 
+                   (besides null versions of atmosphere and land models).
+
+To run Solo models:
+	 a. cd to exp and run mom4p1_solo_compile.csh first.
+         b. Modify the 'name' variable in the script 
+            mom4p1_solo_run.csh to be the name of the test you 
+            want to run. A list of available tests is included in the script.
+         c. Get the required input data for the test from GFDL ftp site.
+            You can get the info by running the script mom4p1_solo_run.csh
+            and following the instructions.
+	 d. Run mom4p1_solo_run.csh
+         e. The results go into subdir name/workdir
+
+To run Coupled models:
+         Do the same steps above to mom4p1_coupled_compile.csh and  mom4p1_coupled_run.csh
+
+To run EBM models:
+         Do the same steps above to mom4p1_ebm_compile.csh and  mom4p1_ebm_run.csh
+
+
+
+Warning: The Solo and Coupled run scripts have been tested only on 10 and 24, ia64 
+         processors respectively. 
+Warning: Some of these tests require a large disk space to save the input data.
+         Choose a partition with enough space (1-2 G) to untar the code and data bundels.
+Warning: If you want to use the same root directory for all three experiments we suggest to
+         compile in the order of increasing complexity: solo -> coupled -> ebm .
+         You may have to remove some of the existing .o and .mod files
+         if you want to compile ebm experiment after the coupled experiment.
+         E.g., you probably have to:   cd ../exec; rm mpp*.o mpp*.mod fms_io*.o fms_io*.mod 
+
+Note:    IBM platform users might want to add the following line to the top of the run scripts 
+             setenv LDR_CNTRL MAXDATA=0xD0000000@DSA 
+
+
+Note:    The compile scripts provide the basic capability to use static memory allocation 
+         which might be faster on some platforms. In that case you need to adjust the values
+         of domain bounds properly according to the number of processors and layout. 
+
+
+Summary of directory contents
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+bin/
+     -- mkmf script for creating Makefiles
+     -- template files for the mkmf script
+     -- assorted other scripts
+
+exp/
+     -- all MOM experiments (test cases)
+
+src/   
+     -- source code for all models
+
+src/postprocessing/
+    -- source code for postprocessing programs
+
+src/preprocessing/
+    -- source code for preprocessing programs

bin/diag_table_chk

@@ -1,8 +1,8 @@
 #! /usr/bin/perl
 
-# $Author: fms $
-# $Revision: 17.0 $
-# $Date: 2009/08/10 20:51:27 $
+# $Author: Niki.Zadeh $
+# $Revision: 1.1.2.1 $
+# $Date: 2013/12/18 17:47:53 $
 
 # Perl script to parse the diag_table.  Count the number of files to
 # be used, and the max number of fields per file used.

bin/environs.ibm.xlf

@@ -0,0 +1,3 @@
+export OMP_NUM_THREADS=1
+export BG_APPTHREADDEPTH=1
+

bin/environs.ncrc2.gnu

@@ -0,0 +1,15 @@
+          source $MODULESHOME/init/csh
+          module use -a /ncrc/home2/fms/local/modulefiles
+          module unload PrgEnv-pgi PrgEnv-pathscale PrgEnv-intel PrgEnv-gnu PrgEnv-cray
+          module unload netcdf fre fre-commands
+          module load PrgEnv-gnu
+          module load hdf5/1.8.8
+          module load netcdf/4.2.0
+          module list
+          setenv MPICH_MAX_SHORT_MSG_SIZE 8000
+          setenv KMP_STACKSIZE 512m
+          setenv NC_BLKSZ 1M
+
+        setenv mpirunCommand   "aprun -n"
+        setenv PATH ${PATH}:.
+

bin/environs.ncrc2.intel

@@ -4,7 +4,7 @@
 #
         source $MODULESHOME/init/csh
         module rm PrgEnv-pgi PrgEnv-pathscale netcdf
-        module load PrgEnv-intel/4.0.30
+        module load PrgEnv-intel
         module swap intel intel/12.0.5.220
 	module load hdf5/1.8.7
         module load netcdf/4.1.3

bin/environs.workstation.gfort

@@ -0,0 +1,2 @@
+         setenv mpirunCommand   "mpirun -np"
+

bin/environs.workstation.intel

@@ -0,0 +1,17 @@
+         source $MODULESHOME/init/csh
+         module use -a /home/fms/local/modulefiles
+         module purge
+         module load ifort.11.0.074
+         module load icc.11.0.074
+         module load idb.10.1.35
+         module load hdf5-1.8.3
+         module load netcdf-4.0.1
+         setenv OMP_NUM_THREADS 1
+#
+         setenv NC_BLKSZ 64K 
+         setenv FMS_ARCHIVE /archive/fms
+         setenv PATH ${PATH}:.
+         setenv netcdf3_inc_dir "/usr/local/netcdf-3.6.2/include"
+         setenv netcdf3_lib_dir "/usr/local/netcdf-3.6.2/lib"
+         setenv mpirunCommand   "mpirun -np"
+

bin/list_files_with_tag

@@ -4,7 +4,7 @@
 #   Returns list of files under CVS control, relative to current 
 #   directory, which can be updated or checked out with the tag tagname.
 #Modified to also list files not currently checked out (arl, 4/2002)
-#Version: $Id: list_files_with_tag,v 10.0 2003/10/27 22:46:40 fms Exp $
+#Version: $Id: list_files_with_tag,v 1.1.2.1 2013/12/18 17:47:54 Niki.Zadeh Exp $
 
 #test that a tagname was given as an argument
 if( "$#ARGV" ne "0" ) {

bin/list_paths

@@ -1,5 +1,5 @@
 #!/bin/csh -ef
-# $Id: list_paths,v 10.1 2010/05/19 18:42:43 fms Exp $
+# $Id: list_paths,v 1.1.2.1 2013/12/18 17:47:54 Niki.Zadeh Exp $
 #-----------------------------------------------------------------------
 #              list_paths: CVS administrative script
 #
@@ -93,6 +93,6 @@ echo "<title>Documentation in current working directory</title>"           > $ou
 echo "<h1>Documentation in current working directory</h1>"                >> $outdoc
 sort -u $doc | awk '{print "<p><a href=\"" $1 "\">" $1 "</a>"}'           >> $outdoc
 echo '<p><hr><small>This file was automatically generated by list_paths.' >> $outdoc
-echo '$Revision: 10.1 $ $Date: 2010/05/19 18:42:43 $'                 >> $outdoc
+echo '$Revision: 1.1.2.1 $ $Date: 2013/12/18 17:47:54 $'                 >> $outdoc
 
 rm -f $doc $src

bin/mkmf

@@ -37,7 +37,7 @@ sub ensureTrailingSlash {
    local $/ = '/'; chomp @_[0]; @_[0] .= '/';
 }
 
-my $version = '$Id: mkmf,v 16.1 2010/05/19 18:49:19 fms Exp $ ';
+my $version = '$Id: mkmf,v 1.1.2.1 2013/12/18 17:47:54 Niki.Zadeh Exp $ ';
 
 # initialize variables: use getopts for these
 getopts( 'a:I:c:dfm:o:l:p:t:vx' ) || die "\aSyntax: $0 [-a abspath] [-c cppdefs] [-d] [-f] [-m makefile] [-o otherflags] ][-p program] [-t template] [-v] [-x] [-I \"space separated include dirs\"] [targets]\n";
@@ -106,8 +106,8 @@ if ( $opt_c ) {
       $cppdefs_xlf =~ s/,/\\,/g; # escape any commas already there
       $cppdefs_xlf =~ s/\s+/,/g; # replace whitespace with commas
       &print_formatted_list("CPPDEFS_XLF = $cppdefs_xlf");
-      $compile_cmd{'.F'}   = q/$(FC) $(CPPDEFS_XLF) $(FFLAGS) -c/;
-      $compile_cmd{'.F90'} = q/$(FC) $(CPPDEFS_XLF) $(FFLAGS) -c/;
+      $compile_cmd{'.F'}   = q/$(FC) $(CPPDEFS_XLF) $(FFLAGS) $(OTHERFLAGS) -c/;
+      $compile_cmd{'.F90'} = q/$(FC) $(CPPDEFS_XLF) $(FFLAGS) $(OTHERFLAGS) -c/;
    }
    &print_formatted_list("CPPDEFS = $opt_c") if $opt_c;
 }

bin/mkmf.html

@@ -1,4 +1,4 @@
-<!--$Id: mkmf.html,v 10.0 2003/10/27 22:46:40 fms Exp $ -->
+<!--$Id: mkmf.html,v 1.1.2.1 2013/12/18 17:47:54 Niki.Zadeh Exp $ -->
 <!-- using template.html
      substitute AAA with the file
      substitute BBB with exact path to RCS/CVS file -->
@@ -286,7 +286,7 @@ <h2>mkmf - a tool for making makefiles</h2>
 following <tt>Makefile</tt>:
 
 <p><pre>
-# Makefile created by mkmf $Id: mkmf.html,v 10.0 2003/10/27 22:46:40 fms Exp $ 
+# Makefile created by mkmf $Id: mkmf.html,v 1.1.2.1 2013/12/18 17:47:54 Niki.Zadeh Exp $ 
 
 
 .DEFAULT:
@@ -348,7 +348,7 @@ <h2>mkmf - a tool for making makefiles</h2>
 The new Makefile looks like this:
 
 <p><pre>
-# Makefile created by mkmf $Id: mkmf.html,v 10.0 2003/10/27 22:46:40 fms Exp $ 
+# Makefile created by mkmf $Id: mkmf.html,v 1.1.2.1 2013/12/18 17:47:54 Niki.Zadeh Exp $ 
 
 
 .DEFAULT:

bin/mkmf.template.gfdl_ws_64.gnu

@@ -1,4 +1,4 @@
-# $Id: gnu.mk,v 1.1.2.1.2.1 2012/03/07 15:08:54 sdu Exp $
+# $Id: mkmf.template.gfdl_ws_64.gnu,v 1.1.2.1 2013/12/18 17:47:54 Niki.Zadeh Exp $
 # template for the Intel fortran compiler
 # typical use with mkmf
 # mkmf -t template.ifc -c"-Duse_libMPI -Duse_netCDF" path_names /usr/local/include

bin/mkmf.template.gfdl_ws_64.gnu.debug

@@ -0,0 +1,184 @@
+# $Id: mkmf.template.gfdl_ws_64.gnu.debug,v 1.1.2.1 2013/12/18 17:47:54 Niki.Zadeh Exp $
+# template for the Intel fortran compiler
+# typical use with mkmf
+# mkmf -t template.ifc -c"-Duse_libMPI -Duse_netCDF" path_names /usr/local/include
+############
+# commands #
+############
+FC = gfortran
+CC = gcc
+LD = gfortran $(MAIN_PROGRAM)
+#########
+# flags #
+#########
+DEBUG = on
+REPRO =
+VERBOSE =
+OPENMP =
+
+MAKEFLAGS += --jobs=$(shell grep '^processor' /proc/cpuinfo | wc -l)
+
+FPPFLAGS := 
+
+FFLAGS := -fcray-pointer -fdefault-real-8 -Waliasing -ffree-line-length-none -fno-range-check
+FFLAGS += -I/net2/nnz/opt/netcdf-4.1.1/include
+#FFLAGS += -I/home/fms/local/opt/netcdf/4.1.1-gnu-4/include
+#The above fails with   USE netcdf, ONLY: NF_FILL_REAL => NF90_FILL_REAL
+#                                                  1
+#                                                  Fatal Error: Parse error when checking module version for file 'netcdf.mod' opened at (1)
+#
+#FFLAGS += $(shell nc-config --fflags)
+#
+FFLAGS += -I/net2/nnz/opt/mpich2-1.3_ifort11_x64/include
+#FFLAGS += -I/usr/local/x64/mpich2-1.2.1p1/include # I do not trust this package, mpirun does not work 
+#$(shell pkg-config --cflags-only-I mpich2-c)
+FFLAGS_OPT = -O2
+FFLAGS_REPRO = 
+FFLAGS_DEBUG = -O0 -g -W -fbounds-check 
+FFLAGS_OPENMP = -fopenmp
+FFLAGS_VERBOSE = 
+
+CFLAGS := -D__IFC 
+CFLAGS += $(shell nc-config --cflags)
+CFLAGS += -I/net2/nnz/opt/netcdf-4.1.1/include -I/net2/nnz/opt/mpich2-1.3_ifort11_x64/include
+#CFLAGS += $(shell pkg-config --cflags-only-I mpich2-c)
+CFLAGS_OPT = -O2
+CFLAGS_OPENMP = -fopenmp
+CFLAGS_DEBUG = -O0 -g 
+
+# Optional Testing compile flags.  Mutually exclusive from DEBUG, REPRO, and OPT
+# *_TEST will match the production if no new option(s) is(are) to be tested.
+FFLAGS_TEST = -O2
+CFLAGS_TEST = -O2
+
+LDFLAGS :=
+LDFLAGS_OPENMP := -fopenmp
+LDFLAGS_VERBOSE := 
+
+ifneq ($(REPRO),)
+CFLAGS += $(CFLAGS_REPRO)
+FFLAGS += $(FFLAGS_REPRO)
+endif
+ifneq ($(DEBUG),)
+CFLAGS += $(CFLAGS_DEBUG)
+FFLAGS += $(FFLAGS_DEBUG)
+else ifneq ($(TEST),)
+CFLAGS += $(CFLAGS_TEST)
+FFLAGS += $(FFLAGS_TEST)
+else
+CFLAGS += $(CFLAGS_OPT)
+FFLAGS += $(FFLAGS_OPT)
+endif
+
+ifneq ($(OPENMP),)
+CFLAGS += $(CFLAGS_OPENMP)
+FFLAGS += $(FFLAGS_OPENMP)
+LDFLAGS += $(LDFLAGS_OPENMP)
+endif
+
+ifneq ($(VERBOSE),)
+CFLAGS += $(CFLAGS_VERBOSE)
+FFLAGS += $(FFLAGS_VERBOSE)
+LDFLAGS += $(LDFLAGS_VERBOSE)
+endif
+
+ifeq ($(NETCDF),3)
+  # add the use_LARGEFILE cppdef
+  ifneq ($(findstring -Duse_netCDF,$(CPPDEFS)),)
+    CPPDEFS += -Duse_LARGEFILE
+  endif
+endif
+
+LIBS := $(shell nc-config --flibs) -L/net2/nnz/opt/mpich2-1.3_ifort11_x64/lib -lmpich -lmpl -lpthread
+#$(shell pkg-config --libs mpich2-f90) #does not work
+LDFLAGS += $(LIBS)
+
+#---------------------------------------------------------------------------
+# you should never need to change any lines below.
+
+# see the MIPSPro F90 manual for more details on some of the file extensions
+# discussed here.
+# this makefile template recognizes fortran sourcefiles with extensions
+# .f, .f90, .F, .F90. Given a sourcefile <file>.<ext>, where <ext> is one of
+# the above, this provides a number of default actions:
+
+# make <file>.opt	create an optimization report
+# make <file>.o		create an object file
+# make <file>.s		create an assembly listing
+# make <file>.x		create an executable file, assuming standalone
+#			source
+# make <file>.i		create a preprocessed file (for .F)
+# make <file>.i90	create a preprocessed file (for .F90)
+
+# The macro TMPFILES is provided to slate files like the above for removal.
+
+RM = rm -f
+SHELL = /bin/csh -f
+TMPFILES = .*.m *.B *.L *.i *.i90 *.l *.s *.mod *.opt
+
+.SUFFIXES: .F .F90 .H .L .T .f .f90 .h .i .i90 .l .o .s .opt .x
+
+.f.L:
+	$(FC) $(FFLAGS) -c -listing $*.f
+.f.opt:
+	$(FC) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.f
+.f.l:
+	$(FC) $(FFLAGS) -c $(LIST) $*.f
+.f.T:
+	$(FC) $(FFLAGS) -c -cif $*.f
+.f.o:
+	$(FC) $(FFLAGS) -c $*.f
+.f.s:
+	$(FC) $(FFLAGS) -S $*.f
+.f.x:
+	$(FC) $(FFLAGS) -o $*.x $*.f *.o $(LDFLAGS)
+.f90.L:
+	$(FC) $(FFLAGS) -c -listing $*.f90
+.f90.opt:
+	$(FC) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.f90
+.f90.l:
+	$(FC) $(FFLAGS) -c $(LIST) $*.f90
+.f90.T:
+	$(FC) $(FFLAGS) -c -cif $*.f90
+.f90.o:
+	$(FC) $(FFLAGS) -c $*.f90
+.f90.s:
+	$(FC) $(FFLAGS) -c -S $*.f90
+.f90.x:
+	$(FC) $(FFLAGS) -o $*.x $*.f90 *.o $(LDFLAGS)
+.F.L:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -listing $*.F
+.F.opt:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.F
+.F.l:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $(LIST) $*.F
+.F.T:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -cif $*.F
+.F.f:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -EP $*.F > $*.f
+.F.i:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -P $*.F
+.F.o:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $*.F
+.F.s:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -S $*.F
+.F.x:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -o $*.x $*.F *.o $(LDFLAGS)
+.F90.L:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -listing $*.F90
+.F90.opt:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.F90
+.F90.l:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $(LIST) $*.F90
+.F90.T:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -cif $*.F90
+.F90.f90:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -EP $*.F90 > $*.f90
+.F90.i90:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -P $*.F90
+.F90.o:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $*.F90
+.F90.s:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -S $*.F90
+.F90.x:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -o $*.x $*.F90 *.o $(LDFLAGS)