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auto3dem:install [2015/07/07 18:52] gcardone |
auto3dem:install [2015/07/07 19:06] (current) gcardone |
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| ===== Library dependencies ===== | ===== Library dependencies ===== | ||
| - | |||
| AUTO3DEM does not depend on external programs, but relies on libraries of the operating system that are not necessarily present by default. | AUTO3DEM does not depend on external programs, but relies on libraries of the operating system that are not necessarily present by default. | ||
| Line 25: | Line 24: | ||
| * [[auto3dem:installation:macosx_libraries|Mac OSX]] | * [[auto3dem:installation:macosx_libraries|Mac OSX]] | ||
| - | ===== Perl requirements ===== | + | ===== Python requirements ===== |
| + | The python programs provided should run on Python version 2.3 and older. | ||
| + | The program to plot one or multiple FSC curves, //a3dm_plot_fsc.py//, requires the modules //Numpy// and //Matplotlib//, which usually are not installed by default but are available from the package manager of most Linux distributions. | ||
| + | |||
| + | ===== Perl requirements ===== | ||
| //auto3dem// and the auxilliary routines //setup_rmc//, //handflip//, | //auto3dem// and the auxilliary routines //setup_rmc//, //handflip//, | ||
| Line 39: | Line 42: | ||
| FSC curves. | FSC curves. | ||
| + | ===== Running parallel jobs ===== | ||
| - | ===== Email notification ===== | + | AUTO3DEM currently is capable to run under the PBS and SGE batch schedulers. In |
| + | your job script, you will need to include the flag (-V) that exports | ||
| + | all environment variables to the job. Do not explicitly include a | ||
| + | nodefile in the auto3dem command since it is automatically passed | ||
| + | through the Perl %ENV hash. | ||
| + | If you are running on a system that is not under control of a batch | ||
| + | scheduler, you can specify that particular nodes be used with the | ||
| + | -nodefile flag. Depending on your computing environment, specification | ||
| + | of a nodefile may not be necessary. | ||
| - | auto3dem has the capability to send email notifications at the end of | + | ===== Email notification ===== |
| - | each iteration. Add the following line to your auto3dem input file | + | |
| + | auto3dem has the capability to send email notifications at the end of | ||
| + | each iteration. Add the following line to your auto3dem input file <code> | ||
| auto recipient address1 [address2 ...] | auto recipient address1 [address2 ...] | ||
| + | </code> | ||
| In order for this to work correctly, you will need to have the mutt | In order for this to work correctly, you will need to have the mutt | ||
| email program installed and properly configured. | email program installed and properly configured. | ||
| - | ===== Compiling image reconstruction codes ===== | + | ===== Additional notes ===== |
| + | ==== Compiling image reconstruction codes ==== | ||
| Line 77: | Line 91: | ||
| directory. | directory. | ||
| - | ===== Compiling image preprocessing applications ===== | + | ==== Programs providing a graphical user interface ==== |
| - | //RobEM//, //fixpif//, //oned//, and //ctfdisp// all make use of the Motif graphical | + | //RobEM//, //fixpif//, //oned//, and //ctfdisp// all make use of the **Motif** graphical |
| user interface toolkit. You will need to install the appropriate | user interface toolkit. You will need to install the appropriate | ||
| library if you wish to use these programs. | library if you wish to use these programs. | ||
| Line 109: | Line 123: | ||
| % unsetenv LANG | % unsetenv LANG | ||
| - | ===== Running parallel jobs ===== | ||
| - | |||
| - | AUTO3DEM currently is capable to run under the PBS and SGE batch schedulers. In | ||
| - | your job script, you will need to include the flag (-V) that exports | ||
| - | all environment variables to the job. Do not explicitly include a | ||
| - | nodefile in the auto3dem command since it is automatically passed | ||
| - | through the Perl %ENV hash. | ||
| - | |||
| - | If you are running on a system that is not under control of a batch | ||
| - | scheduler, you can specify that particular nodes be used with the | ||
| - | -nodefile flag. Depending on your computing environment, specification | ||
| - | of a nodefile may not be necessary. | ||