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Bugs in EMAN refine job submission script

Added by Fei Sun over 13 years ago

When I used Appion to submit EMAN refine job to my cluster, I found the errors in the last line of the Appion-generated job file:

...
   cd /leginon/rawimage/Titan/appion/feisun/11apr19f/recon/emanrecon1
   /leginon/appion/binupdateAppionDB.py 44 D 16
   exit
-----------------------------------------------

It should be 

/leginon/appion/bin/updateAppionDB.py 44 D 16

How can I fix this issue in the future?


Replies (3)

RE: Bugs in EMAN refine job submission script - Added by Fei Sun over 13 years ago

Also I found other bugs:

First line of the job file:

/leginon/appion/binupdateAppionDB.py 44 R 16

And the resolution cal line:

/leginon/appion/bingetRes.pl 8 128 2.39963 >! resolution.txt

They should be
/leginon/appion/bin/updateAppionDB.py 44 R 16

and
/leginon/appion/bin/getRes.pl 8 128 2.39963 >! resolution.txt

RE: Bugs in EMAN refine job submission script - Added by Amber Herold over 13 years ago

Hi Fei Sun,
It looks like a path in one of your configuration files is not set correctly.

That path is defined by C_APPION_BIN which is located in your cluster config file.
The cluster configuration file should be named in the format, YOUR_CLUSTER_NAME.php.
This name should have been provided to the Web tools setup wizard at myamiweb/setup in step 4 during appion installation, so if you need to look up the name of the file, just start the setup wizard and click through to step 4.
As an alternative, you can look directly in your config.php file for $CLUSTER_CONFIGS which will list your cluster name.

To fix the problem, open the cluster config file for editing.
Locate C_APPION_BIN.
Ensure the correct path to the location of your appion scripts is listed, taking care to add a / at the end of the path.

Let me know if this does not correct the issue.

Thanks!
Amber

RE: Bugs in EMAN refine job submission script - Added by Fei Sun over 13 years ago

Thanks, Amber! The problem has been fixed according to your suggestion.

Fei

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