GENIE Using netCDF - Revision history

Genie-user at 09:30, 23 May 2012

2012-05-23T09:30:02Z

GethinWilliams: /* Compiling the NetCDF libraries */

2008-10-29T10:02:33Z

Compiling the NetCDF libraries

GethinWilliams: /* Compiling the NetCDF libraries */

2008-10-29T10:01:50Z

Compiling the NetCDF libraries

GethinWilliams: /* Compiling the NetCDF libraries */

2008-10-29T09:59:30Z

Compiling the NetCDF libraries

GethinWilliams: /* Obtaining the NetCDF Libraries */

2008-10-29T09:24:29Z

Obtaining the NetCDF Libraries

GethinWilliams: /* Obtaining the NetCDF Libraries */

2008-10-29T09:22:47Z

Obtaining the NetCDF Libraries

GethinWilliams: /* Compiling the NetCDF libraries */

2008-04-02T09:05:24Z

Compiling the NetCDF libraries

GethinWilliams: /* If you get Compilation Errors */

2008-03-05T10:17:41Z

If you get Compilation Errors

Genie-user: /* Compiling the NetCDF libraries */ corrected CPPFLAGS

2007-10-05T10:47:44Z

Compiling the NetCDF libraries: corrected CPPFLAGS

Genie-user: /* Linking with GENIE */

2007-06-19T08:58:48Z

Linking with GENIE

@@ Line 1: / Line 1: @@
 ==What is NetCDF? and why use it?==
@@ Line 15: / Line 24: @@
 </pre>
-==Quickstart==
+==Compiling the NetCDF libraries==
 The Unidata webpage contains links to documentation describing installing and using the libraries.  However, the quickstart below, may be enough to get you going.  Note that it's far easier if you use the same fortran compiler to compile both GENIE and the NetCDF libraries.  If you do not, then you will need to become familiar with compiler options which deal with the topic of "name mangling" (enough said).  Note that you will also most likely fair better with an up-to-date copy of the NetCDF libraries.  The libraries are written in C and Fortran.  You need to set some environment variables to tell the installation process which compilers you are using.  On my Linux system, using gcc to compile the C code and ifort for the Fortran, I typed the following in my bash shell:
@@ Line 24: / Line 31: @@
 tar -xzf netcdf-4.0.tar.gz
 cd netcdf-4.0
-./configure --prefix=/gsb6/ggdagw/netcdf FC=ifort CC=gcc CXX=g++ CPPFLAGS="-DpgiFortran"
+./configure --prefix=${HOME}/netcdf/4.0 FC=gfortran CC=gcc CXX=g++ CPPFLAGS="-DpgiFortran"
 make
 make check
@@ Line 32: / Line 39: @@
 Check that you have the created all the files you need.  You should see '''libnetcdf.a''' in the your installation lib directory.  For Fortran90 support, you will also need '''netcdf.mod''' in the include directory.
-===Linking with GENIE===
+==Linking with GENIE==
 Once you have compiled the NetCDF libraries, you must make them available to GENIE.  To do this, you will need edit '''genie-main/user.mak'''.  If you followed the example above, you should edit the line begining '''NETCDF_DIR=''' to be '''NETCDF_DIR=/opt/local'''.

@@ Line 26: / Line 26: @@
 ./configure --prefix=/gsb6/ggdagw/netcdf FC=ifort CC=gcc CXX=g++ CPPFLAGS="-DpgiFortran"
 make
 make install
 </pre>

@@ Line 19: / Line 19: @@
 ===Compiling the NetCDF libraries===
-The Unidata webpage contains links to documentation describing installing and using the libraries.  However, the quickstart below, may be enough to get you going.  Note that it's far easier if you use the same fortran compiler to compile both GENIE and the NetCDF libraries.  If you do not, then you will need to become familiar with compiler options which deal with the topic of "name mangling" (enough said).  Note that you will also most likely fair better with an upto date copy of the NetCDF libraries.
+The Unidata webpage contains links to documentation describing installing and using the libraries.  However, the quickstart below, may be enough to get you going.  Note that it's far easier if you use the same fortran compiler to compile both GENIE and the NetCDF libraries.  If you do not, then you will need to become familiar with compiler options which deal with the topic of "name mangling" (enough said).  Note that you will also most likely fair better with an up-to-date copy of the NetCDF libraries.  The libraries are written in C and Fortran.  You need to set some environment variables to tell the installation process which compilers you are using.  On my Linux system, using gcc to compile the C code and ifort for the Fortran, I typed the following in my bash shell:
 <pre>
 ./configure --prefix=/gsb6/ggdagw/netcdf FC=ifort CC=gcc CXX=g++ CPPFLAGS="-DpgiFortran"
 make

@@ Line 24: / Line 24: @@
 # Change directory to that containing the source code, e.g. '''cd netcdf-3.6.0-p1/src'''
 # The libraries are written in C and Fortran.  You need to set some environment variables to tell the installation process which compilers you are using.  On my Linux system, using gcc to compile the C code and ifort for the Fortran, I typed the following in my bash shell:
-#*'''export CC=gcc'''
-#*'''export CXX=g++'''
+<pre>
-#*'''export FC=ifort'''
+./configure --prefix=/gsb6/ggdagw/netcdf FC=ifort CC=gcc CXX=g++ CPPFLAGS="-DpgiFortran"
-#*'''export CPPFLAGS="-DpgiFortran"'''
+make
-# Now run the '''configure''' script.  You can use the "--prefix" option to choose where to install the libraries.  For example, "--prefix=/opt/local" will cause files to be placed in /opt/local/lib, opt/local/bin and /opt/local/include.
+make install
-# Finally run '''make''' and then '''make install'''.
+</pre>
-# Check that you have the created all the files you need.  You should see '''libnetcdf.a''' in the your installation lib directory.  For Fortran90 support, you will also need '''netcdf.mod''' in the include directory.
 ===Linking with GENIE===

@@ Line 9: / Line 9: @@
 ==Obtaining the NetCDF Libraries==
-You can download the source code for the NetCDF libraries from the [http://www.unidata.ucar.edu/software/netcdf/ Unidata NetCDF web page].  Note the choice between Fortran77 and Fortran90--there are different libraries for the two languages.
+You can download the source code for the NetCDF libraries from the [http://www.unidata.ucar.edu/software/netcdf/ Unidata NetCDF web page].  '''Note''' for older versions of the libraries, there is a choice of download between Fortran77 and Fortran90--i.e. there were different libraries for the two languages.  For more recent versions however, one downloa fits all:
 <pre>

← Older revision		Revision as of 09:22, 29 October 2008
Line 10:		Line 10:

	You can download the source code for the NetCDF libraries from the [http://www.unidata.ucar.edu/software/netcdf/ Unidata NetCDF web page]. Note the choice between Fortran77 and Fortran90--there are different libraries for the two languages.		You can download the source code for the NetCDF libraries from the [http://www.unidata.ucar.edu/software/netcdf/ Unidata NetCDF web page]. Note the choice between Fortran77 and Fortran90--there are different libraries for the two languages.
		+
		+	<pre>
		+	wget http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.0.tar.gz
		+	</pre>

	==Quickstart==		==Quickstart==

@@ Line 33: / Line 33: @@
 ==If you get Compilation Errors==
-If you have followed the guidelines above and you still find you get errors compiling GENIE, then it is likely that these are due to something called '''name-mangling'''.  When I compiler creates ''object code'' from source code (you will see .o files created from .f files, for example--.o stands for 'object'), it ''mangles'' or decorates the names of functions, subroutines etc. typically with a number of leading or trailing underscores.  This is all fine and dandy and doesn't seem to be an issue.  Now, if you compiled your NetCDF libraries with one compiler and the GENIE source code with another, you will get errors.  In particular, you will get errors about 'unresolved symbols'--decorated subroutine names etc. are often referred to as symbols.  This is because compiler A might expect symbols to look like '''myname_''', wheeras compiler B might expect '''myname__''' and hence you can expect trouble.
+If you have followed the guidelines above and you still find you get errors compiling GENIE, then it is likely that these are due to something called '''name-mangling'''.  When I compiler creates ''object code'' from source code (you will see .o files created from .f files, for example--.o stands for 'object'), it ''mangles'' or decorates the names of functions, subroutines etc. typically with a number of leading or trailing underscores.  This is all fine and dandy--so long as the decorated names, or ''symbols'', match between your program and your library.  If different compilers were used to compile your NetCDF libraries and GENIE, then you will get a mismatch, and errors about '''unresolved symbols''', i.e. compiler A might work with symbols like '''myname_''', wheeras compiler B might expect '''myname__''' and hence we get trouble.
-If you are in this situation, you can do one of two things:
+If you are in this situation, you can do one of several things:
 # Make sure you use the same compiler for both the NetCDF libararies and GENIE.
-# Use an argument to your compiler to change the way it mangles names so that you can match the symbols in your NetCDF libraries to those expected when compiling GENIE.
+# If (1) is true and you are using the '''g95''' compiler, you will need to add '''-fno-second-underscore''' to the Fortran compilation flags for both the NetCDF libs and GENIE
-If you elect for the second approach, you will find the UNIX command line tool '''nm''' useful for examing the contents of object files and libraries, e.g. <tt>nm path_to_netcdf_lib</tt> or <tt>nm path_to_a_genie_object_file</tt>.  Determine the form of decoration and provide the appropriate options to the compiler.
+If you must use different compilers, you will find the UNIX command line tool '''nm''' useful for examing the contents of object files and libraries, e.g. <tt>nm path_to_netcdf_lib</tt> or <tt>nm path_to_a_genie_object_file</tt>.  Determine the form of decoration and provide the appropriate options to the compiler.