On Tue, 03 Dec 2013, Jonathan Brooks wrote: > I’m trying to run some randomise_parallel jobs on our cluster (SGE, running > on Ubuntu/Debian) and although the SEED images are being generated, they are > not being defragmented. If I look in LAc30_logs/LAc30.defragment.e1332 I see > a whole load of these errors:
> /rdsfhome/om7253/Documents/Group/RANDOMISE/OUTPUT/LAc30/LAc30.defragment: 1: > /rdsfhome/om7253/Documents/Group/RANDOMISE/OUTPUT/LAc30/LAc30.defragment: Bad > substitution > …. > …. > lots and lots…. > Any tips on how to over-come this? FYI we’re using the neurodebian FSL > repositories (5.0.4 - I think). there was a recent report which is probably of relevance to you (about bashisms in fsl's scripts while ubuntu -- I bet that is what you have -- using dash as bin/sh). so try just changing your shell to be bash across nodes and see if helps. Date: Thu, 31 Oct 2013 13:55:52 +0000 From: "Shpaner, Marina" <[email protected]> To: "'[email protected]'" <[email protected]> Subject: Re: [Neurodebian-users] FSL randomise not finishing the job The problem turned out to be on the randomise side. We had to change sh to bash, and it worked like a charm. Thank you for your reply, and sorry for the trouble. -- Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Senior Research Associate, Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik _______________________________________________ Neurodebian-users mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
