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The executables/binaries are now installed in the directory /usr/local/g77/bin/ Download and install GAMIT/GLOBK. Now that you have installed the FORTRAN compiler, download the source files, request your download form here. Create a directory in /usr/local/gamit with:%sudo mkdir /usr/local/gamit%cd /usr/local/gamit. Download GAMIT sources via.

The Mac OS X operating system is a variant of unix (called Darwin, which is a derivative of BSD unix). It is a versatile computing platform suitable both for computational chemistry calculations and for developing and compiling programs.

Although scientific programs use a variety of languages (basic, pascal, c, java, perl, python, ...), a substantial base of scientific code is written in fortran. Most (though not all) computational engines supported by WebMO are written in fortran. This resource concentrates on fortran compilers and the tools needed to support them.

While integrated development environments (IDE's) are useful in supporting program development, this resource concentrates on the command line interface (CLI) using the Terminal application that is supplied with OS X.

The procedures discussed on this page have been designed for Mac OS X 10.5.

SOFTWARE DEVELOPMENT UTILITIES AND c COMPILER

Command line program development often uses unix utilities (cvs, make, ranlib, ...) when developing and compiling a project. These utilities, together with the c compiler for OS X, are available as part of the Xcode Tools that come with OS X. However, they are not installed by default.

1. Insert Mac OS X Installation DVD. Navigate to the Optional Installs: Xcode Tools folder.
   
2. Double-click XcodeTools.mpkg. Follow the prompts, but at Installation Type, click the Customize button.
   
3. Uncheck all the components and check only Unix Development Support. In particular, Developer Tools Essentials should be unchecked (saving you 2.5GB of disk space)!
4. Provide your password for the installation will proceed.
5. Notes:
   
   • The latest version of Xcode Tools can be obtained by registering for a free ADC membership and then downloading the latest version of Xcode from Apple (caution: it is > 1GB!).
     
   • Xcode can be uninstalled by running
     as described in the Xcode Tools Uninstaller
     

g77 COMPILER

g77 is the gnu fortran77 compiler. It was last produced with gnu compiler collection (gcc) 3.4, and has since been supplanted with gfortran which supports fortran95. Because of the free-cost and high quality of the gnu copmpilers, a significant amount of software has been developed for and compiled with the g77 compiler.

A tar file of the final realease of g77 compiled for OS X exists at High Performance Computing for Mac OS X.

1. Download g77-intel-bin.tar.gz (Intel Mac only) or g77-bin.tar.gz (PowerPC only)
   
2. If your browser did not automatically unzip the file, then
   
   $ gunzip g77-bin-intel.tar.gz
   
3. Install the distribution
   which puts everything in /usr/local
   
4. Notes:
   
   • No uninstall script exists, so the install files need to be listed from the tar file and manually deleted. The following command automates the process of deleting all installed files and empty directories:
     
     $ tar -tf g77-bin.tar | sort -r | (cd /; xargs -p -n 1 rm -d)
     
     You may wish to replace the '-p' switch with '-t' so that you are not prompted to delete each file.
     
   • G77 documentation is available at GCC Online Documentation
     

gfortran COMPILER

gfortran is the new gnu fortran compiler, which attempts to follow the fortran95 standard. As such, it should be backward compatible with fortran77 and fortran90. It also promises to attempt following future fortran standards, such as fortran2003. gfortran replaces the gnu g77 compiler and is included with gnu compiler collection (gcc) 4.0 and higher.

Although Apple XCode Tools includes gcc 4.X, it is not a complete implementation and lacks gfortran. However, various implementations of gfortran have been compiled and are available at GCC Wiki GFortranBinaries, Tools - R (and Fortran) for Mac OS X, or High Performance Computing for Mac OS X. These implementations vary by version, platform supported, and integration with XCode Tools. Important: Install only one implementation of gfortran, as each version would overwrite portions of the others!

• The 'GCC Wiki' implementation described in the following procedure is typically the newest binary release of gfortran, but requires that you download a version appropriate for your architecture.
  1. Visit the GCC Wiki GFortranBinaries page and scroll to the MacOS section
  2. Download gfortran-macosx-x86.dmg (Intel) or gfortran-macosx-ppc.dmg (PowerPC)
     
  3. If your browser did not automatically mount the disk image, the double-click the dmg file to mount and open it
     
  4. Open the gfortran-macosx-{architecture}-{version} folder, double-click gfortran.pkg, and follow the prompts to install it
  5. Notes:
     
     • All gfortran files are installed in /usr/local/gfortran, and a single symbloic link /usr/local/bin/gfortran is created. Thus, to uninstall the package, run
       
       $ sudo rm -r /usr/local/gfortran /usr/local/bin/gfortran
       
     • GNU Fortran documentation is available at GCC Online Documentation
       
• The 'sourceforge' implementation described in the following procedure requires that you download a version appropriate for your architecture, does not produce 'fat binaries', and does not come with an uninstall script (although a method is provided below)
  1. Download gfortran-leopard-intel-bin.tar.gz (Intel) or gfortran-leopard-ppc-bin.tar.gz (Power PC)
     
  2. If your browser did not automatically unzip the file, then
     
  3. Install the distribution
     
     $ sudo tar -xvf gcc-leopard-intel-bin.tar -C /
     
     which puts everything in /usr/local
  4. Notes:
     
     • No uninstall script exists, but the following command will delete all installed files and empty directories:
       
       $ tar -tf gfortran-leopard-intel-bin.tar | sort -r | (cd /; xargs -p -n 1 rm -d)
       
       You may wish to replace the '-p' switch with '-t' so that you are not prompted to delete each file.
       
     • GNU Fortran documentation is available at GCC Online Documentation
       
• Note that there is a G95 project, which is completely independent of the gnu gfortran project (despite the similarity with the gnu g77 compiler name). The G95 project is not associated with the gnu compiler collection!

f2c TRANSLATOR / f77 COMPILER f2c is a fortran77-to-c source code translator. Because f2c is written in c and its ouput is c, both of which can be compiled natively on unix operating systems, f2c offers a very transportable compiler solution for compiling fortran programs. f2c also offers a means of converting large fortran libraries, such as LAPACK, into c. f2c is still actively maintained and is available at http://www.netlib.org/f2c/.

f77 was the first complete fortran77 compiler and was written in c. The original f77 program is no longer available for current computer architectures. However, f2c is based on the original f77 program, and the f2c distribution contains a f77 wrapper script that combines the f2c translation and c compilation steps. The f77 script also supports many command line options commonly associated with fortran compilers. Since the f77 script calls f2c, which in turn is based upon the original f77 program, the f77 script within the f2c distribution represents the most current implementation of the original f77 program.

1. Download the installation script install_f2c_osx.csh which is
2. Run installation script
   
   $ chmod +x install_f2c_osx.csh
   $ sudo ./install_f2c_osx.csh
   
   which will produce the following files:
   /usr/local/bin/f2c
   /usr/local/include/f2c.h
   /usr/local/lib/libf2c.a
   /usr/local/man/man1/f2c.1t
   /usr/local/bin/f77
   
3. Translate, compile, link, and run a program
   
   $ f2c hello.f
   $ gcc -c hello.c
   $ gcc -o hello hello.o -lf2c -lm
   $ ./hello
   
   Or combine the first three steps into a single command
   
4. To uninstall f2c, manually delete the five files produced above

A recent question in one of the discussion forum led to the general question of using some of the performance libraries in Mac OS X with a specific emphasis on mixing C and Fortran, as well as implied data types in LAPACK. In this mini-tutorial I’m going to cover some of the basics of mixed C and Fortran using LAPACK (really the clapack interface) from the Accelerate framework. I’ll cover more of Accelerate when I resume that tutorial series.

C and Fortran

Calling functions/subroutines across C and Fortran can be a mixed bag. This is almost always due to name mangling of the routines that occurs at compile time. In general, without user intervention of any kind (such as typdefs) expect the C frontend to preserve the routine symbols in the form defined in the source file (plus a leading underscore). For example:

Will produce symbols in the compiled file that look like this (‘man nm’ for more information on symbol lookup):

You’ll note that in both cases the symbols have a leading underscore. C compilers typically do this to all external scope items to avoid name clashes from the runtime language support mechanisms. However, you’ll want to otherwise note that the case and trailing underscores are preserved as is.

Fortran on the other hand is slightly different. What you type and what you get are often very different. It can be complicated by the fact that the behavior can also be different depending on the compiler you use or the operating system. For example with gfortran:

Will produce the same symbol:

You’ll notice the following. First, a trailing underscore was automatically added. Second, in both cases the code produced a symbol in all lowercase. Now if you actually tried to write a Fortran program with both of those subroutines defined and compiled as is, the compiler would complain and halt. The trailing underscores with Fortran compilers are there for historical reasons and compatibility across compiler vendors. To suppress trailing underscores you would use a flag like -fno-underscoring in gfortran/g77. To use underscores (or to keep a second underscore from getting appended if you decide to name your subroutines with underscores for C compatability) or not depends on the situation. If you decide that you will manually include underscores in your names you may need to use -fno-second underscore. It can be tricky and confusing…

But what about the case sensitivity issue? There are ways to preserve case so that foo and FoO are treated differently although the settings vary depending on the compiler (for example with g77 you can use -fcase-preserve, the same flag does not appear to work with gfortran).

What to Expect

All things being equal, which they never are in practice, my recommendation is to expect that the C compiler will create symbols from routine names exactly as they appear in the source and for Fortran expect the names to be converted to lowercase with a trailing underscore. If you assume that, and depending on the code, mix of C and Fortran sources that may not be a valid assumption.

So let’s create an example, you’ll need gfortran installed on your computer and gcc which comes with Xcode or from here. We will do all of this from terminal for simplicity.

In the folder called part1 are a C and Fortran file. We are going to start from Fortran so open that first.

We’ve got our main program, and a subroutine called foo, foo then calls cfoo. So open the C file. In the C file, there is function called cfoo_ (note the trailing underscore). We’ve added the trailing underscore because, if you’ll recall, we are expecting the Fortran compiler to generate a trailing underscore.

Let’s compile them and see what happens:

Before we run it, let’s check all of the symbols that contain foo:

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And then let’s run the program:

Sweet! We’ve now got a program that will make calls from Fortran to C. Let’s play some ping pong. Look at the C and Fortran files in part2. Basically we added a new subroutine in Fortran and call to it from C. Again, we are relying on the fact (in C) that the Fortran compiler will append a trailing underscore. You can get around having to mangle your functions using typedefs and compiler flags (but I won’t cover that here).

Passing Variables
This is simple. By default, Fortran (77 at least) passes everything by address. In C it’s by value. So, when calling from Fortran to C you either need to explicitly send in a value (typically using %VAL(myVariable)) or more commonly in C, you take the value as a pointer.

Look in the folder called part3. We’ve modified foo (fortran.f) to send in a variable by address and by value. You’ll need g77 for this example as I’m not sure if gfortran supports the %VAL extension yet.

Similarly if you wanted to call the same C function from within C, you’d either pass in the address of the variable. Look at part4 to see more:

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Note in the C code we passed in the address of the variable as the first argument and the variable directly in the second.

Finally you can do pass through from Fortran to C to call another function in C. Loot at part5 for more information:

Note that we passed the first argument straight through (we already have a pointer and we need one for the first argument) and for the second we dereferenced it to send in the value at the address of that pointer.

“That’s great, but what does this have to do with LAPACK”

Ok, Ok… I’m getting to it. Let’s fast forward to LAPACK as implemented in Accelerate using the clapack entry.

The LAPACK header file is located in:

/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Headers/

Open the file clapack.h in that directory.

At the top you’ll see:

So to the first part of the question in the post/thread mentioned above. What are the data types that you need. That’s easy. The data types are typedef’d for you by Apple, so in reality you send in the the data type that corresponds to the normal C type. Some might argue that you should use the data type as it’s typedef’d by Apple. And they may be right. But unless I have to recreate some complex structure, it makes the most sense to simply use the intrinsic type that C (or Fortran provide).

Now the first place to look for the actual usage and implementation is in the documentation:

The documentation will cover in some detail what LAPACK can (and cannot) do. It will also cover issues related to sizing. In particular if you download the source of LAPACK and look at the file for the subroutine of interest you will see information regarding sizing and size dependencies, in addition to information about the variables and function purpose. What I’ll cover is how to access it in Accelerate from Fortran and C.

Look in the folder called part6. You will see a single Fortran source file with a coll to cgeql2. To compile the code and get it to link against Accelerate do the following:

Of course the calculation doesn’t really do anything or print anything out. But if you wanted to use it with your own data, that is how you would.

How does this look from C?

From C you can use either the direct entry to a function if you are using Accelerate. For example a call from C to CGELQ2, can be done as:

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Or as:

Note that in both cases scalar values (m,n,lda and info) are passed in by address. Remember that in C arrays (either static or dynamic) are really pointers to a location in memory, so those don’t need any modification.

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One other note, if you do as I said above and do NOT use the typedef’s in Accelerate for the data types, the compiler will complain. In particular if you define your own complex or double complex data type. Although the warning is harmless (because the data types are actually correct), this is one of those instances where it might be better to use the type defined by the header.

Am I giving mixed advice? Yes. But in the end you need to evaluate what is most important for YOUR code. Clean, self documenting code is important, but not at the expense of compile time errors or checks that can make debugging harder later on. So when in doubt use the typdef in the header, and make a note about that in your code (so someone else looking at your code doesn’t have to dig into the framework headers to see what is going on).

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Ok that’s it for now.