Hi,
Am 18.01.2010 um 20:53 schrieb madskad...@gmail.com:
2010/1/18 Brian Smith <b...@usf.edu>:
Ah, the RedHat-isms that we take for granted... hah! I forgot
that the
default ~/.bashrc I push out to everyone sources /etc/bashrc by
default.
What distro are you using?
Debian lenny
There's also this bit of goodness from the man page:
"Bash attempts to determine when it is being run with its standard
input
connected to a a network connection, as if by the remote shell
daemon,
usually rshd, or the secure shell daemon sshd.
The Debian bash man page doesn't say the word "sshd" (only "rshd"),
and I'm using ssh as the remote shell, so it may be the case (weird,
but possible).
(...)
a) you could define a starter method in SGE's queue setup to define
the necessary things.
But what functions are these in detail? I checked on one cluster and
to me it looks like it's only one:
module ()
{
eval `/mypath/environment-modules/3.2.6//Modules/$MODULE_VERSION/
bin/modulecmd bash $*`
}
and the eval isn't necessary IMO. It would be necessary if $* would
include something which has to be interpreted again. So an alias is
also working for me (unset module and define it like below):
b) alias module='/cm/local/apps/environment-modules/3.2.6//Modules/
$MODULE_VERSION/bin/modulecmd bash $*'
or c) you could define a wrapper with a script and put it in /user/
local/bin or alike.
-- Reuti
I wonder if sge_shepherd doesn't, in fact, trick shells into beha
ving
this way... I know I'm not using BASH_ENV and my modules environment
works correctly.
Just to be sure we aren't missing something: you can load a module
inside the submit job, correct?
Case 1:
- module load something
- qsub job.sh
- cat job.sh
#!/bin/bash
#(sge config stuff)
mpirun ...
#EOF
Case 2 (what I pretend):
- qsub job.sh
- cat job.sh
#!/bin/bash
#(sge config stuff)
module add something
mpirun ...
#EOF
-Brian
--
Brian Smith
Senior Systems Administrator
IT Research Computing, University of South Florida
4202 E. Fowler Ave. ENB308
Office Phone: +1 813 974-1467
Organization URL: http://rc.usf.edu
On Mon, 2010-01-18 at 14:38 +0000, madskad...@gmail.com wrote:
2010/1/16 Brian Smith <b...@usf.edu>:
I'm using this in our environment. I've simply added the Modules
environment code to /etc/bashrc and /etc/csh.cshrc on all nodes
(I use
puppet to manage everything, so this is easy). This ensures that
Modules is properly integrated with your environment regardless of
whether you are using an interactive or non-interactive
invocation of
these shells. This works for SGE (I'm on 6.2u4, ATM)
But it seems that gridengine spawns like "bash script_name" so no rc
files are read. Reading bash manpage, I found the BASH_ENV
environment
variable:
"""
When bash is started non-interactively, to run a shell script,
for
example, it looks for the variable BASH_ENV in the environment,
expands its value if it appears there, and uses the expanded
value as
the name of a file to read and execute. Bash behaves as if the
following command were executed:
if [ -n "$BASH_ENV" ]; then . "$BASH_ENV"; fi
but the value of the PATH variable is not used to search for the
file name.
"""
(bash manpage)
Right now I'm setting this variable and with the "-V" job submission
flag it's working well (it does not work correctly without it)
Gil
--
"
It can't continue forever. The nature of exponentials is that you push
them out and eventually disaster happens.
"
Gordon Moore (Intel co-founder and author of the Moore's law)
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