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auto3dem:install [2015/07/07 18:52] gcardone |
auto3dem:install [2015/07/07 19:00] 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. | ||
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===== Perl requirements ===== | ===== Perl requirements ===== | ||
- | |||
//auto3dem// and the auxilliary routines //setup_rmc//, //handflip//, | //auto3dem// and the auxilliary routines //setup_rmc//, //handflip//, | ||
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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 ==== | ||
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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. | ||
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% 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. | ||