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Error when running GARD analysis on linux cluster (Read 2945 times)
Kurt Wollenberg
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Error when running GARD analysis on linux cluster
Oct 23rd, 2013 at 9:17am

I have been trying to run a GARD analysis on our linux cluster so that I can use the required mpi environment. I get an error when the program tries to write an output file to the lib/hyphy/TemplateBatchFiles directory. This also happens when I try to run SBP analysis. I have noticed an odd behavior when trying to set up the runs. For GARD I get the prompt

Please select the file you want to use (or press ENTER to return to the list of analysis types):Initialized GARD on 4 MPI nodes.
Population size is 6 models

When I type in the filename and path I get

/usr/local/stow/hyphy/lib/hyphy/TemplateBatchFiles/Nucleotide file to screen::

So I retype the filename and path and things proceed looking like they should (I get prompts for options that make sense). Then when the program tries to run I get the error

/usr/local/stow/hyphy/lib/hyphy/TemplateBatchFiles/Save results to::Error:

Master node received an error:Could not create/open output file at path '/usr/local/stow/hyphy/lib/hyphy/TemplateBatchFiles/1'. in call to fprintf(

Function call stack

Why does the program try to write output to a directory which doesn't exist in /TemplateBatchFiles? Any ideas how I managed to invoke this behavior?

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Re: Error when running GARD analysis on linux cluster
Reply #1 - Oct 31st, 2013 at 3:28pm
Hi Kurt,

The best guess I have is that the prompts and the responses are off by 1:

1). You type the file path twice : HyPhy will prompt for a pathname for a second time if it doesn't find the path specified the first time
2). The path it tries to write to (/usr/local/stow/hyphy/lib/hyphy/TemplateBatchFiles/1) seems to be using the numeric response ('1') from the previous option.

Sometimes this happens with MPI environments (e.g. buffered output to the console etc).

Try this

1). (echo option1; echo option 2; echo option 3...; echo option N) | start HYPHYMPI /path/to/GARD.bf
2). Write a wrapper file for GARD following the steps explained here : Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login and then simply call HyPhy with that script as the command line argument (no inputs should be needed).

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