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[farmshare-discuss] Stata on corn

Jason Bishop bishopj at stanford.edu
Fri Nov 1 15:51:42 PDT 2013


Hi Susan, Yes, licensed software such as Matlab, Stata, etc are managed via modules command.  There is an easy way to customize your module environment though.  I've added documentation here: https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/FarmShare_software#automatic_loading_of_packages_at_login

If you load the modules that you commonly use you can save this as a "default".  Then when you login again they are automatically loaded for you.

This has a nice feature as it can automatically load the latest matlab/stata, or a specific version of matlab/stata, at your choosing.


Jason
Research Computing


----- Original Message -----
From: "Susan Biancani" <biancani at stanford.edu>
To: "Open discussion for users of FarmShare" <farmshare-discuss at lists.stanford.edu>
Sent: Thursday, October 31, 2013 9:17:36 PM
Subject: Re: [farmshare-discuss] Stata on corn

Hi Jason,
Ok, I'll send a note to research computing about changing my shell. Why did this just recently become a problem? I've had the bash line in my .cshrc file for 3 or 4 years now without incident. 
Also, this came up because I was trying to show a friend how to use stata on corn. Is module load now the new way to do this? I.e., do we have to use module load now for everything on corn?
Thanks for all the help!
Susan

----- Original Message -----
From: "Jason Bishop" <bishopj at stanford.edu>
To: "Open discussion for users of FarmShare" <farmshare-discuss at lists.stanford.edu>
Sent: Thursday, October 31, 2013 11:19:14 AM
Subject: Re: [farmshare-discuss] Stata on corn


Hi Susan, When you login to a system your shell will load a bunch of settings from scripts in /etc/profile.d.   It does this because it knows it is the first shell and it therefore needs to setup your environment.  For you, these settings were loaded into csh because this is your default shell.  Then you did an exec bash from your .cshrc which changed your shell to bash, but none of those settings were loaded because this bash shell is not a "login shell".

One reason why you are seeing this is because profile.d scripts are in wide use for user environment settings these days.

Jason

----- Original Message -----
From: "Susan Biancani" <biancani at stanford.edu>
To: "Open discussion for users of FarmShare" <farmshare-discuss at lists.stanford.edu>
Sent: Thursday, October 31, 2013 10:59:24 AM
Subject: Re: [farmshare-discuss] Stata on corn

I do have exec bash in my .cshrc. The last two lines are:
setenv SHELL bash
exec bash

Just so I understand better, why is this causing a problem (and why is it a new problem)?

----- Original Message -----
From: "Ravi Pillai" <pillai at stanford.edu>
To: "Open discussion for users of FarmShare" <farmshare-discuss at lists.stanford.edu>
Sent: Wednesday, October 30, 2013 8:00:49 PM
Subject: Re: [farmshare-discuss] Stata on corn

One more thing to add to this thread ... for the benefit of folks who may be looking for a not-so-proper fix (e.g., if you don't want to change your shell). 

I use tcsh as my shell, but occasionally need to call matlab from inside a bash script (which I launch from my tcsh shell). 
The following lines do the trick in those bash scripts ... 

lmod_dir_parent=`dirname ${LMOD_DIR}` 
source ${lmod_dir_parent}/init/bash 
module load matlab 

(after which you can add one or more lines for running matlab batch jobs). 

Best, 

RAVI 
3-9258 




On Wed, Oct 30, 2013 at 6:25 PM, Jason Bishop < bishopj at stanford.edu > wrote: 



Hi Susan, do you have any code in your .cshrc that does something like "exec bash"? A number of users have reported problems who are running bash from their .cshrc's. 

The fix (and this is a proper fix) is we set your shell to bash. Then the problem goes away. 

Jason 
Research Computing 


----- Original Message ----- 
From: "Susan Biancani" < biancani at stanford.edu > 
To: "Open discussion for users of FarmShare" < farmshare-discuss at lists.stanford.edu > 
Sent: Wednesday, October 30, 2013 4:56:58 PM 
Subject: Re: [farmshare-discuss] Stata on corn 

Hi Yizheng, 
Thanks for getting back to me. 

I actually did load the module first, and it looked like it ran. But then when I tried the command, it still said command not found. 

I just tried again now, and here is what happened: 
biancani at corn14:~$ module load stata 
module: command not found 

biancani at corn14:~$ module load statase 
module: command not found 

So now, I don't seem to be able to use module...? 
Susan 


----- Original Message ----- 
From: "Yizheng Liao" < yzliao at stanford.edu > 
To: "Open discussion for users of FarmShare" < farmshare-discuss at lists.stanford.edu > 
Sent: Wednesday, October 30, 2013 4:30:43 PM 
Subject: Re: [farmshare-discuss] Stata on corn 

Hi, Susan: 

I think you need to load the module before calling the command. 

Please see 

http://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/FarmShare_software 

Thanks, 
yizheng 

Best wishes, 
Yizheng 


On Wed, Oct 30, 2013 at 4:23 PM, Susan Biancani < biancani at stanford.edu > wrote: 


Hi All, 
I'm trying to use Stata on corn, and I get a "command not found" error. Both stata and xstata give me this error, whereas they worked fine this summer. Any advice on how to access it? 
Thanks, 
Susan 
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_______________________________________________
farmshare-discuss mailing list
farmshare-discuss at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
_______________________________________________
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farmshare-discuss at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
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farmshare-discuss at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
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farmshare-discuss at lists.stanford.edu
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