Thanks for posting your questions here where others may find them useful or chip in.
I'd say yes to all three questions as such, but let's go a bit more into detail.
Principally you have only 1GB of storage in your MiG home where your files are hosted but we provide external storage resources when much more than that is needed. The files are not automatically available on compute resources like the cluster. They need to be explicitly transferred as part of the job (INPUTFILES) or made available in a more ad-hoc fashion. The same applies for the results (OUTPUTFILES). I'm sure we can find a suitable setup for your actual file access pattern.
It sounds like your jobs take ~2500 files and produce one output file. Is that about right and approximately how big are those files?
Are the input files overlapping for different runs or do they work on disjunctive sub sets of the complete set of files?
I'd suggest that you upload e.g. a zip file with a single set of job
files and see if you can make a job description file to get it processed on
the Octuplets cluster.
You may find the java example around page 32 in the 'Intro for new users of MiG' pdf onhttps://sites.google.com/site/minimumintrusiongrid/tutorials-and-talks
useful for inspiration.
The runtime environment you want for java jobs is called JAVA-ANY-1 and it is available on the Octuplets cluster now. Do you know if your Java app requires a specific Java flavor and version? We generally have OpenJDK 6 available.
Other dependencies have to be fulfilled either by other runtime environments or with software explicitly included in the job. If you have a set of jar files they can easily be included in the job using INPUTFILES or EXECUTABLES. If they are huge we may prefer to make a runtime environment for them on the resource(s) instead of transferring them for each job, however.
Please feel free to ask ...