parallel
[Top][All Lists]
Advanced

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: parallel + blast + LSF


From: Ole Tange
Subject: Re: parallel + blast + LSF
Date: Sun, 10 May 2015 15:44:39 +0200

On Fri, May 8, 2015 at 11:37 AM, Giuseppe Aprea
<giuseppe.aprea@gmail.com> wrote:

> Let's now go to the execution problem. I tried to run your example with both
> ssh and blaunch.sh (the queue system spawn agent) with this script:
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> #!/bin/bash
>
> module load 4.8.3/parallel/20150422
>
> REM=`tail -n 1 ${LSB_DJOB_HOSTFILE}`
> echo -e
> "--------------------------------------------------------------------------------------"
> echo -e
> "--------------------------------------------------------------------------------------"
> 1>&2
> echo -e "local=`hostname`"
> echo -e
> "--------------------------------------------------------------------------------------"
> echo -e
> "--------------------------------------------------------------------------------------"
> 1>&2
> echo -e "remote=${REM}"
> echo -e
> "--------------------------------------------------------------------------------------"
> echo -e
> "--------------------------------------------------------------------------------------"
> 1>&2
> ssh ${REM} echo 1
:
> this is stdout:
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> --------------------------------------------------------------------------------------
> local=cresco3x018.portici.enea.it
> --------------------------------------------------------------------------------------
> remote=cresco3x003.portici.enea.it
> --------------------------------------------------------------------------------------

[ssh should have given 1. It gave nothing]

:
> and this is stderr:
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> --------------------------------------------------------------------------------------
> --------------------------------------------------------------------------------------
> --------------------------------------------------------------------------------------
> Permission denied, please try again.
> Permission denied, please try again.
> Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password).

[ssh gave the above]

> As you can see ssh is returning "Permission denied" error which sounds
> different from the previous one (0 simultaneous logins allowed).

GNU Parallel uses ssh to login to remote machines. If 'ssh remote
echo' fails, GNU Parallel will fail, too. GNU Parallel assumes ssh
works, and when ssh does not, GNU Parallel's error message may be
somewhat confusing.

It seems using 'blaunch.sh' instead of 'ssh' you can login, so you
probably want to use 'blaunch.sh' instead of ssh. To do that each line
for -S should be prepended with 'blaunch.sh ':

4//path/to/blaunch.sh cresco3x046.portici.enea.it


/Ole



reply via email to

[Prev in Thread] Current Thread [Next in Thread]