Following on Mark’s answer for your main question re: using relative paths (which does seem your best bet), if you’re on a Mac you can also be creative with symbolic links. If you create some links for directories on your local machine that mimic the cluster machine’s path, that may work too. We’ve not found a comparable solution on the PC.
the last solution worked! the batchrunner now submitted the jobs. Just to be sure: all OUT.mat files will now be saved in a “status” folder, together with the DONE.mat files. This is a bit counterintuitive, since they are actually not “status” but output (of course, I can change the BatchRunner file, I just want to understand how this is supposed to work). [/quote]
Glad it’s working. And yes, the OUT.mat files’ placement is counterintuitive, and perhaps we should make a separate output folder for them. In practice however, these OUT.mat files are only needed if you want to use, say, Excel or Matlab to inspect the output, and are not useful if you ExportToDatabase. So in most cases in which you need to utilize a computing cluster, and hence CreateBatchFiles, the output will be large enough that a database is necessary to handle the output, and you can opt to not output these files at all. Though I understand that there are some intermediate cases in which it is useful to use these OUT.mat files.
One more question: no matter how the outputfile is called, there is always a “Batch_data.mat” file and all “…OUT.mat” file are called “Batch…something”. That way one is completely missing any information about the analysis in the filenames, I miss a bit the option to enter the name of the Batch-files which was in place in the CreateBatchFiles-module with CP 6 months ago (I am just trying to give friendly feedback).[/quote]
We do appreciate the feedback, but we felt that there were too many options in CreateBatchFiles. And around the same time, we added a new feature (see the DataTool “SubmitBatch”) which simplifies the whole batch submission process substantially anyway, using a GUI and webserver to submit and handle jobs. You (or your IT dept) would need to set up the webserver for your image files first however, so there is some overhead cost. But for new users, we have found that this process is much more straightforward and user-friendly than resorting to the command-line (as much as this is preferable in many cases).