Stata

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Running stata in batch mode on the barleys:
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Stata is an integrated statistical software package for data analysis, data management, and graphics.
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==Installed Versions==
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Stata/SE and Stata/MP versions 14, 15, and 16 are available on FarmShare:
<pre>
<pre>
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[chekh@corn-image-new.stanford.edu] /mnt/glusterfs/chekh [0]
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$ module spider stata  
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$ cat test.do
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clear
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sysuse auto
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describe
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[chekh@corn-image-new.stanford.edu] /mnt/glusterfs/chekh [0]
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$ echo "/usr/sweet/bin/stata -b do test2.do" | qsub -cwd -l hostname=barley05
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Your job 5725 ("STDIN") has been submitted
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[chekh@corn-image-new.stanford.edu] /mnt/glusterfs/chekh [0]
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$ ls -ltr |tail -n 4
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-rw-r--r-- 1 chekh root      27 Nov  7 17:27 test2.do
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-rw-r--r-- 1 chekh root      0 Nov  7 17:28 STDIN.o5725
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-rw-r--r-- 1 chekh root      0 Nov  7 17:28 STDIN.e5725
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-rw-r--r-- 1 chekh root    2400 Nov  7 17:28 test2.log
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</pre>
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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.
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----------------------------------------------------------------------------
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  stata-mp:
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----------------------------------------------------------------------------
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    Description:
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      Integrated statistical software package for data analysis, data
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      management, and graphics.
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    Versions:
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        stata-mp/14.2
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        stata-mp/15
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        stata-mp/16
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...
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----------------------------------------------------------------------------
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  stata-se:
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----------------------------------------------------------------------------
 +
    Description:
 +
      Integrated statistical software package for data analysis, data
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      management, and graphics.
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==using module==
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    Versions:
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We're trying to move away from /usr/sweet/bin, using [[FarmShare software | modules]] instead.  So your stata session looks more like:
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        stata-se/14.2
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        stata-se/15
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<pre>
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        stata-se/16
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[chekh@barley02.stanford.edu] /mnt/glusterfs [130]
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$ source /mnt/glusterfs/software/free/modules/tcl/init/bash
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+(0):WARN:0: Directory '/afs/ir/users/c/h/chekh/.modules' not found
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[chekh@barley02.stanford.edu] /mnt/glusterfs [0]
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$ module avail
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--------------------- /mnt/glusterfs/software/free/modules/tcl/modulefiles ---------------------
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MATLAB-R2009b    MATLAB-R2011b    R-2.15.0          StatTransfer-11.2 StataSE-12.1     
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MATLAB-R2010b    MATLAB-R2012a    StatTransfer-10.1 StataMP-12.1     
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------------------------------------------- Aliases --------------------------------------------
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------------------------------------------- Versions -------------------------------------------
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[chekh@barley02.stanford.edu] /mnt/glusterfs [0]
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$ module load StataSE-12.1
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[chekh@barley02.stanford.edu] /mnt/glusterfs [0]
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$ stata
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...
...
</pre>
</pre>
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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.
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==Interactive Sessions==
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===Terminal Mode===
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To start an interactive session, load one of the modules and run <code>stata-se</code> (or <code>stata-mp</code>):
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Job script:
 
<pre>
<pre>
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#!/bin/bash
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$ module load stata-se
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source /mnt/glusterfs/software/free/modules/tcl/init/bash
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$ which stata-se
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module load StataSE-12.1
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/farmshare/software/non-free/stata-se/16/stata-se
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stata -b do test
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$ stata-se
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</pre>
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Full session:
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<pre>
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[chekh@barley02.stanford.edu] /mnt/glusterfs/chekh [0]
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$ qsub -cwd -l mem_free=10M script2.submit
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Your job 167221 ("script2.submit") has been submitted
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[chekh@barley02.stanford.edu] /mnt/glusterfs/chekh [0]
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$ qstat
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job-ID  prior  name      user        state submit/start at    queue                          slots ja-task-ID
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-----------------------------------------------------------------------------------------------------------------
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167221 0.00000 script2.su chekh        qw    04/27/2012 15:21:30                                    1       
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...
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...
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[chekh@barley02.stanford.edu] /mnt/glusterfs/chekh [0]
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$ cat test.log
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   ___  ____  ____  ____  ____ (R)
   ___  ____  ____  ____  ____ (R)
  /__    /  ____/  /  ____/
  /__    /  ____/  /  ____/
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___/  /  /___/  /  /___/  12.1  Copyright 1985-2011 StataCorp LP
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___/  /  /___/  /  /___/  16.1  Copyright 1985-2019 StataCorp LLC
   Statistics/Data Analysis            StataCorp
   Statistics/Data Analysis            StataCorp
                                       4905 Lakeway Drive
                                       4905 Lakeway Drive
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                                      College Station, Texas 77845 USA
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    Special Edition                  College Station, Texas 77845 USA
                                       800-STATA-PC        http://www.stata.com
                                       800-STATA-PC        http://www.stata.com
                                       979-696-4600        stata@stata.com
                                       979-696-4600        stata@stata.com
                                       979-696-4601 (fax)
                                       979-696-4601 (fax)
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...
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</pre>
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23-user Stata network perpetual license:
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===Desktop Mode===
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      Serial number: 40120564988
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If you [https://srcc.stanford.edu/farmshare2/connecting connect] using X11 for remote display, you can run <code>xstata-se</code> (or <code>xstata-mp</code>) to start the desktop (graphical) version of the application:
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        Licensed to: Jane Tansuwan
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                      Stanford University
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Notes:
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<pre>
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      1. Command line editing disabled
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$ ssh -Y sunetid@rice.stanford.edu
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      2. Stata running in batch mode
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rice $ module load stata-se
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rice $ xstata-se &
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</pre>
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Note:  Your site can add messages to the introduction by editing the file
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==Non-interactive jobs==
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      stata.msg in the directory where Stata is installed.
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You can also run Stata non-interactively using the <code>do</code> command, producing a <code>.log</code> file containing results:
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. do test  
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<pre>
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$ module load stata-se
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$ cat test.do
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sysuse auto
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describe
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$ stata -b do test.do
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$ cat test.log
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Contains data from /farmshare/software-prod/non-free/stata-se/16/ado/base/a/aut
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> o.dta
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  obs:            74                          1978 Automobile Data
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vars:            12                          13 Apr 2018 17:45
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...
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</pre>
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. clear
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===Batch jobs===
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Or, submit a batch job to run on one of the compute nodes:
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. sysuse auto
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<pre>
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(1978 Automobile Data)
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$ module load stata-se
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$ sbatch --wrap='stata -b do test.do'
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. describe
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Contains data from /mnt/glusterfs/software/non-free/stata-se-12/ado/base/a/auto
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> .dta
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  obs:            74                          1978 Automobile Data
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vars:            12                          13 Apr 2011 17:45
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size:        3,182                          (_dta has notes)
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-------------------------------------------------------------------------------
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              storage  display    value
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variable name  type  format      label      variable label
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-------------------------------------------------------------------------------
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make            str18  %-18s                  Make and Model
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price          int    %8.0gc                Price
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mpg            int    %8.0g                  Mileage (mpg)
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rep78          int    %8.0g                  Repair Record 1978
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headroom        float  %6.1f                  Headroom (in.)
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trunk          int    %8.0g                  Trunk space (cu. ft.)
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weight          int    %8.0gc                Weight (lbs.)
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length          int    %8.0g                  Length (in.)
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turn            int    %8.0g                  Turn Circle (ft.)
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displacement    int    %8.0g                  Displacement (cu. in.)
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gear_ratio      float  %6.2f                  Gear Ratio
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foreign        byte  %8.0g      origin    Car type
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-------------------------------------------------------------------------------
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Sorted by:  foreign
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.
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end of do-file
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</pre>
</pre>
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==stata-mp test==
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You can also write and submit a traditional Slurm job script:
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  cd /mnt/glusterfs/chekh/stata-mp-test
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My test.do :
 
<pre>
<pre>
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clear
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$ cat test.sh
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sysuse auto
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#!/bin/bash
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describe
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module load stata-se
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stata-se -b do test.do
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$ sbatch test.sh
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$ ls test.log
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test.log
</pre>
</pre>

Latest revision as of 14:46, 3 March 2020

Stata is an integrated statistical software package for data analysis, data management, and graphics.

Contents

Installed Versions

Stata/SE and Stata/MP versions 14, 15, and 16 are available on FarmShare:

$ module spider stata 

----------------------------------------------------------------------------
  stata-mp:
----------------------------------------------------------------------------
    Description:
      Integrated statistical software package for data analysis, data
      management, and graphics.

     Versions:
        stata-mp/14.2
        stata-mp/15
        stata-mp/16
...
----------------------------------------------------------------------------
  stata-se:
----------------------------------------------------------------------------
    Description:
      Integrated statistical software package for data analysis, data
      management, and graphics.

     Versions:
        stata-se/14.2
        stata-se/15
        stata-se/16
...

Interactive Sessions

Terminal Mode

To start an interactive session, load one of the modules and run stata-se (or stata-mp):

$ module load stata-se
$ which stata-se
/farmshare/software/non-free/stata-se/16/stata-se
$ stata-se

  ___  ____  ____  ____  ____ (R)
 /__    /   ____/   /   ____/
___/   /   /___/   /   /___/   16.1   Copyright 1985-2019 StataCorp LLC
  Statistics/Data Analysis            StataCorp
                                      4905 Lakeway Drive
     Special Edition                  College Station, Texas 77845 USA
                                      800-STATA-PC        http://www.stata.com
                                      979-696-4600        stata@stata.com
                                      979-696-4601 (fax)
...

Desktop Mode

If you connect using X11 for remote display, you can run xstata-se (or xstata-mp) to start the desktop (graphical) version of the application:

$ ssh -Y sunetid@rice.stanford.edu
rice $ module load stata-se
rice $ xstata-se &

Non-interactive jobs

You can also run Stata non-interactively using the do command, producing a .log file containing results:

$ module load stata-se
$ cat test.do
sysuse auto
describe
$ stata -b do test.do
$ cat test.log
Contains data from /farmshare/software-prod/non-free/stata-se/16/ado/base/a/aut
> o.dta
  obs:            74                          1978 Automobile Data
 vars:            12                          13 Apr 2018 17:45
...

Batch jobs

Or, submit a batch job to run on one of the compute nodes:

$ module load stata-se
$ sbatch --wrap='stata -b do test.do'

You can also write and submit a traditional Slurm job script:

$ cat test.sh
#!/bin/bash
module load stata-se
stata-se -b do test.do
$ sbatch test.sh
$ ls test.log
test.log
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