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Top Forums Shell Programming and Scripting Shell scripting problems - Commands not on local machine Post 302444878 by Sagan on Friday 13th of August 2010 05:02:57 AM
Old 08-13-2010
Lightbulb Shell scripting problems - Commands not on local machine

Hello all-

I have done a lot of searching tonight, but all leads seem to be dead ends. Forgive me if this has been covered, but I've searched the forum and the internet. I am having trouble building a shell script which uses SSH to login to our schools 1024 cluster grid. The issue that I am having is that I need the script to load MATLAB, using the basic functions:

$module load matlab

$matlab -nodisplay -nosplash -r simulations_sep_07

I can SSH into the remote machine just fine, and execute a script. However, I result in:


./Run_Simulation.sh: 8: module: not found
./Run_Simulation.sh: 10: matlab: not found


I have checked my path repeatedly, and know that I am in the working directory on the remote pc, the code appears to check the local pc for command validity.
I can run the script directly on the remote pc, and the script runs fine. Is there any way of getting this to work?

My files are all rsynced from my local machine, to the remote machine, and the command is set to SSH in and run a script to start the algorithm.

Any help would be great, it's about 4 AM, and this problem has beaten me for the day.

Thank you in advance, this forum has been very helpful as a learning tool.
 

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RECON(1)							     LAM TOOLS								  RECON(1)

NAME
recon - Check if LAM can be started. SYNTAX
recon [-abdhv] [<bhost>] OPTIONS
-a Report all host errors. -b Assume local and remote shell are the same. This means that only one remote shell invocation is used to each node. If -b is not used, two remote shell invocations are used to each node. -d Turn on debugging. -h Print the command help menu. -v Be verbose. DESCRIPTION
In order for LAM to be started on a remote UNIX machine, several requirements have to be fulfilled: 1) The machine must be reachable via the network. 2) The user must be able to remotely execute on the machine with the default remote shell program that was chosen when LAM was config- ured. This is usually rsh(1), but any remote shell program is acceptable (such as ssh(1), etc.). Note that remote host permission must be configured such that the remote shell program will not ask for a password when a command is invoked on remote host. 3) The remote user's shell must have a search path that will locate LAM executables. 4) The remote shell's startup file must not print anything to standard error when invoked non-interactively. If any of these requirements is not met for any machine declared in <bhost>, LAM will not be able to start. By running recon first, the user will be able to quickly identify and correct problems in the setup that would inhibit LAM from starting. The local machine where recon is invoked must be one of the machines specified in <bhost>. The <bhost> file is a LAM boot schema written in the host file syntax. See bhost(5). Instead of the command line, a boot schema can be specified in the LAMBHOST environment variable. Otherwise a default file, bhost.def, is used. LAM seaches for <bhost> first in the local directory and then in the installation directory under etc/. recon tests each machine defined in <bhost> by attempting to execute on it the tkill(1) command using its "pretend" option (no action is taken). This test, if successful, indicates that all the requirements listed above are met, and thus LAM can be started on the machine. If the attempt is successful, the next machine is checked. In case the attempt fails, a descriptive error message is displayed and recon stops unless the -a option is used, in which case recon continues checking the remaining machines. If recon takes a long time to finish successfully, this will be a good indication to the user that the LAM system to be started has slow communication links or heavily loaded machines, and it might be preferable to exclude or replace some of the machines in the system. Remote shell invocation Note that the default remote shell command can be overriden at invocation time with the LAMRSH environment variable. The LAMRSH environ- ment variable can be set with a new command and optional command line arguments. For example, the 1.x series of ssh clients require the -x flag to be specified to suppress standard ssh information from being sent to the standard error (which would cause recon to fail). For example (for the C shell and its derrivates): setenv LAMRSH "ssh -x" Normally, recon uses two remote shell invocations to each node. The first remote shell invocation is used to determine the user's shell on the remote node. The second remote shell invocation is used to launch the desired LAM binary on the remote node. If the -b switch is used, recon will assume that the user's shell on all remote nodes is the same as it is on the local node, and therefore only one remote shell invocation is used, which is noticably faster. In either case, on remote nodes, if the user's shell is not csh, tcsh, or bash, .profile is invoked by LAM before invoking any LAM binary. This allows the user to setup paths and any necessary environment before LAM binaries are invoked (csh and tcsh users can put such setup in their $HOME/.cshrc or $HOME/.tcshrc files; bash users can put this setup in their $HOME/.bashrc file). FILES
$LAMHOME/etc/lam-bhost.def default boot schema file EXAMPLES
recon -v mynodes Check if LAM can be started on all the UNIX machines described in the boot schema mynodes. Report about important steps as they are done. recon -v -a Check if LAM can be started on all the UNIX machines described in the default boot schema. Report about important steps as they are done. Check all the machines; do not stop after the first error message. SEE ALSO
rsh(1), tkill(1), bhost(5), lamboot(1), wipe(1), lam-helpfile(5) LAM 6.5.8 November, 2002 RECON(1)
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