Changes between Initial Version and Version 1 of cypress/STATA-Singularity

Timestamp:

09/17/2026 05:09:10 PM (3 days ago)

Author:

fuji

Comment:

--

cypress/STATA-Singularity

@@ +1 @@
+= Run STATA with Singularity =
+The glibc version on CentOS 6.5 nodes is 2.12. The glibc version on CentOS 7.4 nodes is 2.17. The latest STATA requires a more up-to-date glibc version. If you have a newer version of STATA and encounter a [[cypress/glibc-version-problems|glibc version problem]], follow the steps below.
+
+
+== Run on commandline interactively ==
+
+Start an interactive session on the CentOS7 partition,
+{{{#!bash
+[uid@cypress2 ~]$ idev --partition=centos7
+Requesting 1 node(s)  task(s) to normal queue of centos7partition
+1 task(s)/node, 20 cpu(s)/task, 2 MIC device(s)/node
+Time: 0 (hr) 60 (min).
+Submitted batch job 47343
+JOBID=47343 begin on cypress01-066
+--> Creating interactive terminal session (login) on node cypress01-063.
+--> You have 0 (hr) 60 (min).
+Last login: Mon Jun  8 20:18:50 2015 from cypress1.cm.cluster
+}}}
+The default `idev` session reserves a node for '''one hour'''. If you want to work on it for a longer time, use `-t` option. See [[cypress/using#SubmittingInteractiveJobs]].
+
+Load the module
+{{{#!bash
+[uid@cypress01-066 ~]$ module load singularity
+}}}
+Set up the environment and run Rocky Linux with Singularity.
+{{{#!bash
+[uid@cypress01-066 ~]$ source $SingularityImageDir/setup_cypress.sh
+[uid@cypress01-066 ~]$ singularity shell -s /bin/bash $SingularityImageDir/rockylinux-9.2.sif
+}}}
+You will get a command line prompt, `Apptainer>`.
+Assuming `stata` is in your $PATH directory, run STATA on the command line,
+{{{#!bash
+Apptainer> stata
+
+  ___  ____  ____  ____  ____ ®
+ /__    /   ____/   /   ____/      StataNow 19.5
+___/   /   /___/   /   /___/       BE—Basic Edition
+
+ Statistics and Data Science       Copyright 1985-2025 StataCorp LLC
+                                   StataCorp
+                                   4905 Lakeway Drive
+                                   College Station, Texas 77845 USA
+                                   800-782-8272        https://www.stata.com
+                                   979-696-4600        [email protected]
+
+Stata license: Unlimited-user network, expiring 14 Dec 2026
+Serial number: 501909301438
+  Licensed to: Tulane University
+               New Orleans, LA
+
+Notes:
+      1. Unicode is supported; see help unicode_advice.
+. 
+}}}
+
+Use `exit` command to finalize STATA.
+Use `exit` command to finalize Rocky Linux.
+
+'''Note that when `idev` session expires, your STATA session will be killed and all unsaved data will be lost. '''
+
+== Run STATA in batch mode ==
+
+Make sure your do-files work correctly. It is recommended to test your do-files on the local machine or on an interactive session with a small dataset for a short time.
+
+Suppose we have `hello.do` file that contains:
+{{{#!bash
+[uid@cypress2 ~]$ cat hello.do 
+clear
+display "Hello, STATA!!!"
+exit
+}}}
+
+SLURM script will be:
+{{{#!bash
+#!/bin/bash
+#SBATCH --partition=centos7     # Partition
+#SBATCH --qos=normal            # Quality of Service
+#SBATCH --job-name=STATA        # Job Name
+#SBATCH --time=24:00:00         # WallTime
+#SBATCH --nodes=1               # Number of Nodes
+#SBATCH --ntasks-per-node=1     # Number of tasks (MPI processes)
+#SBATCH --cpus-per-task=2       # Number of processors per task OpenMP threads()
+#SBATCH --gres=mic:0            # Number of Co-Processors
+
+# SETUP SINGULARITY
+module load singularity
+source $SingularityImageDir/setup_cypress.sh
+
+# SET YOUR STATA DIRECTORY
+STATA_DIR=/lustre/project/eisaac/opt/stata19
+
+# RUN STATA
+singularity exec $SingularityImageDir/rockylinux-9.2.sif $STATA_DIR/stata -b do hello
+
+}}}
+
+Submit a job
+{{{#!bash
+[uid@cypress2 ~]$ sbatch slurmscript 
+}}}
+
+''''slurmscript'''' is the file name of the above SLURM script. The results will be stored in ''''hello.log''''.
+
+=== STATA-MP ===
+
+
+Stata can run with multiple threads. You can check the license info by 'creturn list' command on stata-window.
+
+{{{
+      c(processors) = 8                          (Stata/MP, set processors)
+      c(processors_lic) = 8
+}}}
+
+The example above shows that the default is 8 cores. So 
+{{{#!bash
+#!/bin/bash
+#SBATCH --partition=defq        # Partition
+#SBATCH --qos=normal            # Quality of Service
+#SBATCH --job-name=STATA        # Job Name
+#SBATCH --time=24:00:00         # WallTime
+#SBATCH --nodes=1               # Number of Nodes
+#SBATCH --ntasks-per-node=1     # Number of tasks (MPI processes)
+#SBATCH --cpus-per-task=8       # Number of processors per task OpenMP threads()
+#SBATCH --gres=mic:0            # Number of Co-Processors
+
+module load stata
+
+stata-mp -b do parappelcode
+}}}