Modularised and tested MATLAB code (ustar_cp)

.gitattributes

@@ -0,0 +1 @@
+

.gitignore

@@ -106,7 +106,7 @@ tramp
 
 
 # csvs
-*.csv
+#*.csv
 
 # mac files
 *.DS_Store

oneflux_steps/ustar_cp/cpdBootstrapUStarTh4Season20100901.m

@@ -143,4 +143,3 @@
 		end; % for iBoot
 
 	end; % if ntNee>=ntN;
-

oneflux_steps/ustar_cp/cpdEvaluateUStarTh4Season20100901.m

@@ -178,7 +178,7 @@
 		end; % for iStrata
 
 	end; % for iSeason
-		
+
 %	========================================================================
 %	========================================================================
 

oneflux_steps/ustar_cp_refactor_wip/bin/MCR.txt

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+http://www.mathworks.com/products/compiler/mcr/
+
+$ export MCR_HOME="/home/gilberto/bin/MATLAB_Compiler_Runtime/v717" && export MCR_JRE="/home/gilberto/bin/MATLAB_Compiler_Runtime/v717/sys/java/jre/glnxa64/jre/lib/amd64" && export LD_LIBRARY_PATH="/home/gilberto/bin/MATLAB_Compiler_Runtime/v717/runtime/glnxa64:/home/gilberto/bin/MATLAB_Compiler_Runtime/v717/bin/glnxa64:/home/gilberto/bin/MATLAB_Compiler_Runtime/v717/sys/os/glnxa64:/home/gilberto/bin/MATLAB_Compiler_Runtime/v717/sys/java/jre/glnxa64/jre/lib/amd64/server:/home/gilberto/bin/MATLAB_Compiler_Runtime/v717/sys/java/jre/glnxa64/jre/lib/amd64/client:/home/gilberto/bin/MATLAB_Compiler_Runtime/v717/sys/java/jre/glnxa64/jre/lib/amd64"
+
+$ export XAPPLRESDIR=/home/gilberto/bin/MATLAB_Compiler_Runtime/v717/X11/app-defaults
+

oneflux_steps/ustar_cp_refactor_wip/bin/README_MCR.txt

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+Download MCR (latest version used for USTAR_CP: 2018a)
+http://www.mathworks.com/products/compiler/mcr/

oneflux_steps/ustar_cp_refactor_wip/bin/ustar_cp_linux64_2018a_readme.txt

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+launch Executable
+
+1. Prerequisites for Deployment 
+
+Verify that version 9.4 (R2018a) of the MATLAB Runtime is installed.   
+If not, you can run the MATLAB Runtime installer.
+To find its location, enter
+
+    >>mcrinstaller
+
+at the MATLAB prompt.
+
+Alternatively, download and install the Linux version of the MATLAB Runtime for R2018a 
+from the following link on the MathWorks website:
+
+    http://www.mathworks.com/products/compiler/mcr/index.html
+
+For more information about the MATLAB Runtime and the MATLAB Runtime installer, see 
+Package and Distribute in the MATLAB Compiler documentation  
+in the MathWorks Documentation Center.
+
+2. Files to Deploy and Package
+
+Files to Package for Standalone 
+================================
+-launch 
+-run_launch.sh (shell script for temporarily setting environment variables and executing 
+                the application)
+   -to run the shell script, type
+
+       ./run_launch.sh <mcr_directory> <argument_list>
+
+    at Linux or Mac command prompt. <mcr_directory> is the directory 
+    where version 9.4 of the MATLAB Runtime is installed or the directory where 
+    MATLAB is installed on the machine. <argument_list> is all the 
+    arguments you want to pass to your application. For example, 
+
+    If you have version 9.4 of the MATLAB Runtime installed in 
+    /mathworks/home/application/v94, run the shell script as:
+
+       ./run_launch.sh /mathworks/home/application/v94
+
+    If you have MATLAB installed in /mathworks/devel/application/matlab, 
+    run the shell script as:
+
+       ./run_launch.sh /mathworks/devel/application/matlab
+-MCRInstaller.zip
+    Note: if end users are unable to download the MATLAB Runtime using the
+    instructions in the previous section, include it when building your 
+    component by clicking the "Runtime included in package" link in the
+    Deployment Tool.
+-This readme file 
+
+
+
+3. Definitions
+
+For information on deployment terminology, go to
+http://www.mathworks.com/help and select MATLAB Compiler >
+Getting Started > About Application Deployment >
+Deployment Product Terms in the MathWorks Documentation
+Center.
+
+4. Appendix 
+
+A. Linux systems:
+In the following directions, replace MR/v94 by the directory on the target machine where 
+   MATLAB is installed, or MR by the directory where the MATLAB Runtime is installed.
+
+(1) Set the environment variable XAPPLRESDIR to this value:
+
+MR/v94/X11/app-defaults
+
+
+(2) If the environment variable LD_LIBRARY_PATH is undefined, set it to the following:
+
+MR/v94/runtime/glnxa64:MR/v94/bin/glnxa64:MR/v94/sys/os/glnxa64:MR/v94/sys/opengl/lib/glnxa64
+
+If it is defined, set it to the following:
+
+${LD_LIBRARY_PATH}:MR/v94/runtime/glnxa64:MR/v94/bin/glnxa64:MR/v94/sys/os/glnxa64:MR/v94/sys/opengl/lib/glnxa64
+
+    For more detailed information about setting the MATLAB Runtime paths, see Package and 
+   Distribute in the MATLAB Compiler documentation in the MathWorks Documentation Center.
+
+
+
+        NOTE: To make these changes persistent after logout on Linux 
+              or Mac machines, modify the .cshrc file to include this  
+              setenv command.
+        NOTE: The environment variable syntax utilizes forward 
+              slashes (/), delimited by colons (:).  
+        NOTE: When deploying standalone applications, you can
+              run the shell script file run_launch.sh 
+              instead of setting environment variables. See 
+              section 2 "Files to Deploy and Package".    
+
+
+
+
+
+

oneflux_steps/ustar_cp_refactor_wip/bin/ustar_cp_linux64_2018a_requiredMCRProducts.txt

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+35000	35010	

oneflux_steps/ustar_cp_refactor_wip/bin/ustar_cp_linux64_2018a_run_launch.sh

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+#!/bin/sh
+# script for execution of deployed applications
+#
+# Sets up the MATLAB Runtime environment for the current $ARCH and executes 
+# the specified command.
+#
+exe_name=$0
+exe_dir=`dirname "$0"`
+echo "------------------------------------------"
+if [ "x$1" = "x" ]; then
+  echo Usage:
+  echo    $0 \<deployedMCRroot\> args
+else
+  echo Setting up environment variables
+  MCRROOT="$1"
+  echo ---
+  LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/opengl/lib/glnxa64;
+  export LD_LIBRARY_PATH;
+  echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
+  shift 1
+  args=
+  while [ $# -gt 0 ]; do
+      token=$1
+      args="${args} \"${token}\"" 
+      shift
+  done
+  eval "\"${exe_dir}/ustar_cp_linux64_2018a\"" $args
+fi
+exit
+

oneflux_steps/ustar_cp_refactor_wip/bin/ustar_cp_run.sh

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+#!/bin/sh
+# script for execution of deployed applications
+#
+# Sets up the MATLAB Runtime environment for the current $ARCH and executes 
+# the specified command.
+#
+exe_name=$0
+exe_dir=`dirname "$0"`
+echo "------------------------------------------"
+if [ "x$1" = "x" ]; then
+  echo Usage:
+  echo    $0 \<deployedMCRroot\> args
+else
+  echo Setting up environment variables
+  MCRROOT="$1"
+  echo ---
+  LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/opengl/lib/glnxa64;
+  export LD_LIBRARY_PATH;
+  echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
+  shift 1
+  args=
+  while [ $# -gt 0 ]; do
+      token=$1
+      args="${args} \"${token}\"" 
+      shift
+  done
+  eval "\"${exe_dir}/ustar_cp\"" $args
+fi
+exit
+