|Subject:||Re: parallel + blast + LSF|
|Date:||Wed, 6 May 2015 13:50:34 +0200|
Work as a counting semaphore. --semaphore will cause GNU parallel to start command in the background. When the number of simultaneous jobs is reached, GNU parallel will wait for one of these to complete before starting another command.
--semaphore implies --bg unless --fg is specified.
--semaphore implies --semaphorename `tty` unless --semaphorename is specified.
Used with --fg, --wait, and --semaphorename.
The command sem is an alias for parallel --semaphore.
On Tue, May 5, 2015 at 10:32 AM, Giuseppe Aprea
> Hi and thank you for your reply.
> -j issue: I used "-j 192" since 192 is the sum of all the slots the queue
> system allocates on the different hosts. Reading again the manual I see why,
> given my options and my server file, GNU parallel could run 192 jobs on the
> same host. Anyway, in my opinion, this point isn't really clear. An user
> could also get the idea that -j is for the total cores which get divided
> among the different hosts as specified by the ncpus in the server file. At
> least, I expected that.
Please help by rephrasing the man page, so you would have understood
the concept the first time. Would this help:
-P N Number of jobslots on each machine. Run up to N jobs
in parallel. 0 means as many as possible. Default is 100% which will
run one job per CPU core on the machine.
> --wait: I am running on a shared cluster; that means the queue system may
> give me 8 slots an a 16-cores host. The other 8 slots could be used by a
> different user at the same time. Resources fair share implies that I don't
> run more than 8 simultaneous blastp instances on that host.
Which means that for that particular host you have to lie about the
number of cores (e.g. by using the ncpu/host syntax).
If you in general only want to use 50% of the cores, then -j 50% will
do the trick.
> That is why,
> when 8 simultaneous blastp are reached, I want GNU parallel to wait for one
> of these to complete before starting another one.
And that is what GNU Parallel does normally. No extra options needed.
> That is what I expect from
> "--semaphore"; I used --wait for that and to be sure the queue system waited
> for all background gnu parallel jobs to be completed before considering the
> whole job finished. Does that make sense now?
I assume that you have understood, that --pipe makes GNU Parallel
behave very differently from not having --pipe. You could even argue
that 'parallel --pipe' would justify being a command on its own.
Have you understood that --semaphore also makes GNU Parallel behave
very differently from both --pipe and no --pipe? (Which is why it does
have its own alias, namely 'sem').
And have you understood why it does not make sense to use --semaphore
in your situation?
If yes: Please help by rephrasing the man page, so you would have
understood it in the first read.
If no: Please walk through the tutorial section on Semaphore.
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