[Beowulf] Confusion about login, non-interactive, interactive shells

Jörg Saßmannshausen j.sassmannshausen at ucl.ac.uk
Wed Sep 26 01:49:41 PDT 2012


Dear all,

whilst I was debugging a MPI problem the other night, I got highly frustrated 
that the program could not find the orted command despite being in the PATH.

A bit of further digging lead to these observations:

$ ssh node4 env | grep PATH
PATH=/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games

$ ssh node4 echo $PATH
/home/sassy/bin:/usr/local/sge6.2u5/bin/lx24-
amd64:/opt/openmpi/gfortran/1.4.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sod/exe

$ ssh node4 which mpirun
$

$ ssh node4 echo $PATH; which mpirun
/home/sassy/bin:/usr/local/sge6.2u5/bin/lx24-
amd64:/opt/openmpi/gfortran/1.4.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sod/exe
/opt/openmpi/gfortran/1.4.5/bin/mpirun

What I cannot work out is:
a) where does the :/usr/bin/X11 come from? I done a grep in /etc and I could 
not find it (but for the PAM but that was commented out)
b) how come there is a difference between echo $PATH and which mpirun ? It 
appears to me that there are different processes involved here which give 
different answers. My question is why?

I had a play around with /etc/profile and /etc/bash.bashrc. I am using Debian 
Squeeze here. OpenMPI as such is working, the queue is using the right 
environment it is only when I need to restart something manually and the 
binaries I am using (ORCA) are then using mpirun for the parallel execution. 
That goes wrong when I am doing it manually but it works when I am doing it 
via the queue. So for that reason I cannot pass over any parameters to mpirun 
or calling it via the complete path. i.e. /path/to/mpirun/mpirun .

Could somebody be so kind to lift the fog in front of my eyes here?

All the best from a wet London

Jörg

-- 
*************************************************************
Jörg Saßmannshausen
University College London
Department of Chemistry
Gordon Street
London
WC1H 0AJ 

email: j.sassmannshausen at ucl.ac.uk
web: http://sassy.formativ.net

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