AMBER Archive (2009)

Subject: RE: [AMBER] mpirun

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jan 08 2009 - 17:28:12 CST

Dear Wen,

> setenv PATH @AMBERHOME/exe:$PATH

I think the @ here should be a $.

> setenv MPI_HOME AMBERHOME

I assume the missing $ on AMBERHOME is a typo in the email here and not in your .cshrc file?
 
> /home/liw> source .cshrc
> /home/liw> echo $PATH
> @AMBERHOME/exe:/opt/amber10//exe/:/usr/bin:/bin:/usr/sbin:/sbin:/usr/games
> :/opt/gnome/bin:opt/kde3/bin:/usr/bin/X11:usr/lib/mit/bin:/usr/lib/mit/sbi
> n:/usr/lib/qt3/bin:/opt/amber10/bin:/opt/amber10/exe
> /home/liw> setenv DO_PARALLEL 'mpirun -np 4'
> /home/liw> cd /opt/amber10/test
> amber10/test> lamhalt
>
> LAM 7.1.3 - Indiana University
>
> amber10/test> lamboot
>
> LAM 7.1.3 - Indiana University

Can you try running

which lamboot
which mpirun

And see what it reports.

> cd cytosine && ./Run.cytosine
> in.md: Permission denied.
>
> Unit 6 Error on OPEN: cytosine.out
> --------------------------------------------------------------------------
> ---

This still suggests that you don't have write permission to $AMBERHOME/test and its sub directories.

try

whoami
ls -la $AMBERHOME

If the directory is not owned by you will need to get the user that owns it to either chown it to you or adjust the permissions so that you can write to it.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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