install

mfold

June 2005.

                       INSTALLATION of mfold 3.2

NB: Starting with version 3.2, plotting and secondary structure
drawing software is NO LONGER PART OF mfold. These programs are part
of mfold_util. You must setup the mfold_util software before
installing mfold. You do not require most of the programs in
mfold_util. The interactive graphics programs that require OpenGl are
not required. However, boxplot_ng, sir_graph_ng, tgd, tgd_png and
tgd_jpg are all essential.

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A. The makefile
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The file, "Makefile", contains instructions for compiling the
programs.  The first portion of "Makefile" must be edited. A number of
parameters should be set.

1. FFLAGS: This must be set. At the least, the Fortran compiler must
be able to accept lines longer that the standard 80 columns, and a
"static" option must be selected so that variables do not change
in functions or subroutines between calls. A number of options have
been made available, including one for "Gnu Fortran", g77. The level
of optimization should be as high as possible.

2. CFLAGS: Choose the highest level of optimization that works.

3. FTN, CC and C++: Define the Fortran, C and C++ compilers,
respectively. For example, 'CC' could be gcc (Gnu C), or 'C++' could
be C++.

4. BINDIR, DATDIR: These are optional. If defined, BINDIR is where
the binaries and scripts will be copied, and DATDIR is where the
energy files, images, and other data will be copied.

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B. Environment variables and Path
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1. Define MFOLDDAT to point to DATDIR as defined in "Makefile". 
   If the command

make install

is not issued, then DATDIR is not used. In this case, MFOLDDAT should
point to the 'dat' subdirectory of where the mfold package is stored.

2. Make sure that all binaries are on your path. If you wish, you can
   define an environment variable, MFOLD, that points to where the
   mfold package is stored. In this case, you should add $MFOLD/bin
   to your path. This can be accompished (for example) by adding:

export PATH=$MFOLD/bin:$PATH

to your $HOME/.profile file, or to the system /etc/profile file.

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C. Compilation
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Assuming that you have not downloaded ready-to-run binaries, you must
compile the programs in the package.

In general, the command:

make all

will create all binaries and place them in the bin subdirectory, where
they will be stripped.  If you set FFLAGS to create statically linked
binaries, then you should remove the "strip" statement from
"Makefile".  You may compile individual programs if you wish.

The command:

make install

will do the same as 'make all' and will copy the contents of the bin
subdirectory into BINDIR as defined in Makefile. 
The command:

make clean

will perform a cleanup by erasing object modules and binaries in
the bin subdirectory.

Please report bugs, other problems or suggestions to [e-mail]
Look at the files in the "doc" directory, especially the manual, which
is in PostScript, pdf and HTML form.

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