01-10-2013
C-program works fine interactively, but not on the SGE server
Greetings, I have a C-program that is made to implement a hidden Markov model on an input file. The program is very memory intensive.
I've installed it on my local server where I have an account and it compiles fine. The way they have the server set up is that you can either work interactively in a special queue or submit the jobs using SGE. The program works great, but slow, interactively and I really need to send it to one of the queues through SGE to have access to multiple and better nodes. The thing is, when I submit it that (or, interestingly enough, just nohup it while I am working on the interactive queue) the program just freezes at the beginning when it allocating the memory once it has read in the input file.
I've run the program before on servers that use batch-queuing software and I've nohup'd it with no problems (on another server). Here, unless the standard output is going to the screen it freezes interminably.
Any ideas?
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qstart(8B) PBS qstart(8B)
NAME
qstart - start pbs batch job processing at a destination
SYNOPSIS
qstart destination ...
DESCRIPTION
The qstart command directs that a destination should process batch jobs. If the destination is an execution queue, the server will begin
to schedule jobs that reside in the queue for execution. If the destination is a routing queue, the server will begin to route jobs from
that queue.
In order to execute qstart, the user must have PBS Operation or Manager privilege.
OPERANDS
The qstart command accepts one or more destination operands. The operands are one of three forms:
queue
@server
queue@server
If queue is specified, the request is to start that queue at the default server. If the @server form is given, the request is to start all
queues at that server. If a full destination identifier, queue@server, is given, the request is to start the named queue at the named
server.
STANDARD ERROR
The qstart command will write a diagnostic message to standard error for each error occurrence.
EXIT STATUS
Upon successful processing of all the operands presented to the qstart command, the exit status will be a value of zero.
If the qstart command fails to process any operand, the command exits with a value greater than zero.
SEE ALSO
pbs_server(8B), qstop(8B), and qmgr(1B)
Local qstart(8B)