From FarmShare

Running stata in batch mode on the barleys:

[chekh@corn-image-new.stanford.edu] /mnt/glusterfs/chekh [0] 
$ cat test.do 
clear
sysuse auto
describe
[chekh@corn-image-new.stanford.edu] /mnt/glusterfs/chekh [0] 
$ echo "/usr/sweet/bin/stata -b do test2.do" | qsub -cwd -l hostname=barley05 
Your job 5725 ("STDIN") has been submitted
[chekh@corn-image-new.stanford.edu] /mnt/glusterfs/chekh [0] 
$ ls -ltr |tail -n 4
-rw-r--r-- 1 chekh root      27 Nov  7 17:27 test2.do
-rw-r--r-- 1 chekh root       0 Nov  7 17:28 STDIN.o5725
-rw-r--r-- 1 chekh root       0 Nov  7 17:28 STDIN.e5725
-rw-r--r-- 1 chekh root    2400 Nov  7 17:28 test2.log

Looks like stata doesn't print anything to stdin or stderr, but does create a .log file with the same name as your .do file.

using module

We're trying to move away from /usr/sweet/bin, using modules instead. So your stata session looks more like:

[chekh@barley02.stanford.edu] /mnt/glusterfs [130] 
$ source /mnt/glusterfs/software/free/modules/tcl/init/bash
+(0):WARN:0: Directory '/afs/ir/users/c/h/chekh/.modules' not found
[chekh@barley02.stanford.edu] /mnt/glusterfs [0] 
$ module avail
--------------------- /mnt/glusterfs/software/free/modules/tcl/modulefiles ---------------------
MATLAB-R2009b     MATLAB-R2011b     R-2.15.0          StatTransfer-11.2 StataSE-12.1      
MATLAB-R2010b     MATLAB-R2012a     StatTransfer-10.1 StataMP-12.1      
------------------------------------------- Aliases --------------------------------------------
------------------------------------------- Versions -------------------------------------------
[chekh@barley02.stanford.edu] /mnt/glusterfs [0] 
$ module load StataSE-12.1
[chekh@barley02.stanford.edu] /mnt/glusterfs [0] 
$ stata 
...

But that also means you need to modify your job script to point to the right MATLAB. So you'll want to add that "module load" command to that job script.