Stata
From FarmShare
We now have Stata version 13 installed. Try the commands 'module avail', 'module load statase':
$ module help statase
-------------------- Module Specific Help for "statase/13" ---------------------
This is Stata/SE version 13
xstata-se (Run windowed version of Stata/SE)
stata-se (Run console version of Stata/SE)
We actually have three versions installed. If you run 'stata', you get Stata/IC, if you run 'stata-se', you get 'Stata/SE', if you 'module load statamp && stata-mp', you get Stata/MP.
batch mode
Running stata in batch mode in general, use the '-b do' parameter.
Running stata in batch mode on the barley via qsub.
[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 "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.
Job script:
#!/bin/bash source /mnt/glusterfs/software/free/modules/tcl/init/bash module load StataSE-12.1 stata -b do test
Full session:
[chekh@barley02.stanford.edu] /mnt/glusterfs/chekh [0]
$ qsub -cwd -l mem_free=10M script2.submit
Your job 167221 ("script2.submit") has been submitted
[chekh@barley02.stanford.edu] /mnt/glusterfs/chekh [0]
$ qstat
job-ID prior name user state submit/start at queue slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
167221 0.00000 script2.su chekh qw 04/27/2012 15:21:30 1
...
...
[chekh@barley02.stanford.edu] /mnt/glusterfs/chekh [0]
$ cat test.log
___ ____ ____ ____ ____ (R)
/__ / ____/ / ____/
___/ / /___/ / /___/ 12.1 Copyright 1985-2011 StataCorp LP
Statistics/Data Analysis StataCorp
4905 Lakeway Drive
College Station, Texas 77845 USA
800-STATA-PC http://www.stata.com
979-696-4600 stata@stata.com
979-696-4601 (fax)
23-user Stata network perpetual license:
Serial number: 40120564988
Licensed to: Jane Tansuwan
Stanford University
Notes:
1. Command line editing disabled
2. Stata running in batch mode
Note: Your site can add messages to the introduction by editing the file
stata.msg in the directory where Stata is installed.
. do test
. clear
. sysuse auto
(1978 Automobile Data)
. describe
Contains data from /mnt/glusterfs/software/non-free/stata-se-12/ado/base/a/auto
> .dta
obs: 74 1978 Automobile Data
vars: 12 13 Apr 2011 17:45
size: 3,182 (_dta has notes)
-------------------------------------------------------------------------------
storage display value
variable name type format label variable label
-------------------------------------------------------------------------------
make str18 %-18s Make and Model
price int %8.0gc Price
mpg int %8.0g Mileage (mpg)
rep78 int %8.0g Repair Record 1978
headroom float %6.1f Headroom (in.)
trunk int %8.0g Trunk space (cu. ft.)
weight int %8.0gc Weight (lbs.)
length int %8.0g Length (in.)
turn int %8.0g Turn Circle (ft.)
displacement int %8.0g Displacement (cu. in.)
gear_ratio float %6.2f Gear Ratio
foreign byte %8.0g origin Car type
-------------------------------------------------------------------------------
Sorted by: foreign
.
end of do-file
stata-mp test
cd /mnt/glusterfs/chekh/stata-mp-test
My test.do :
clear sysuse auto describe
My job.script:
#!/bin/bash # use the current directory #$ -cwd # mail this address #$ -M chekh@stanford.edu # send mail on begin, end, suspend #$ -m bes # copy current env vars to job #$ -V stata-mp -b do test.do
The job script uses '-V' to copy the env vars from your current session, so need to load the right module first:
[chekh@corn13.stanford.edu] /mnt/glusterfs/chekh/stata-mp-test [0] $ module load StataMP-12.1 [chekh@corn13.stanford.edu] /mnt/glusterfs/chekh/stata-mp-test [0] $ which stata-mp /mnt/glusterfs/software/non-free/stata-mp-12/stata-mp
Test that the command works outside of grid engine:
stata-mp -b do test.do
It produces a test.log as expected.
Submit the job:
[chekh@corn13.stanford.edu] /mnt/glusterfs/chekh/stata-mp-test [0]
$ qsub job.script
Your job 416828 ("job.script") has been submitted
The job is sitting there a long time because the cluster is busy and there are no immediately open slots:
$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- 416828 0.37250 job.script chekh qw 09/04/2012 17:04:24
Submit to the test queue instead:
qsub -l testq=1 job.script
It runs immediately and produces the expected test.log file.
[chekh@corn13.stanford.edu] /mnt/glusterfs/chekh/stata-mp-test [0] $ ls -ltr total 16 -rw-r--r-- 1 chekh root 27 Sep 4 16:59 test.do -rw-r--r-- 1 chekh root 199 Sep 4 17:00 job.script -rw-r--r-- 1 chekh root 2434 Sep 4 17:02 test.log.orig -rw-r--r-- 1 chekh root 0 Sep 4 17:06 job.script.o416829 -rw-r--r-- 1 chekh root 0 Sep 4 17:06 job.script.e416829 -rw-r--r-- 1 chekh root 2434 Sep 4 17:06 test.log
troubleshooting
We've had a report of a user having trouble with Stata v14 and they fixed it by modifying their file:
~/.stata14/console/stata14.rc
So double-check your Stata settings files. Probably an easy thing to do is just to delete your .stata14 directory and start fresh, or you can compare to your ~/.stata13/console/stata13.rc
