Parallel computation with R & Python on TACC HPC server NSF REU site at UNCW, 2017-2019 Parallel computation with R & Python on TACC HPC server Dr. Cuixian Chen, 10/12/2017 Declaimer: This PPT is modified based on Dr. Yishi Wang’s HPC tutorial on 9/21/2017. Modified from Dr. Patricia Kelley, 06/13/2017

Overview on HPC with R and Python Online resources: https://www.cac.cornell.edu/education/training/StampedeJan2017/Python_R_HPC_Workshop.pdf https://cvw.cac.cornell.edu/python/hpp

follow the instruction for system setups NSF REU site at UNCW, 2017-2019 For first time users: follow the instruction for system setups Modified from Dr. Patricia Kelley, 06/13/2017

Login to your TACC account, as a first-time user https://portal.tacc.utexas.edu/

Login to your TACC account, as a first-time user

Login to your TACC account, as a first-time user https://portal.tacc.utexas.edu/tutorials/multifactor-authentication

Login to your TACC account, as a first-time user Please follow the instruction to obtain the valid Token and get ready for the next step.

Logins and file transferring into Xsede NSF REU site at UNCW, 2017-2019 Logins and file transferring into Xsede Modified from Dr. Patricia Kelley, 06/13/2017

Log into TACC – From Windows From Computer Lab desktops: search for putty From personal Windows laptops: Install and open Putty. Hostname: stampede2.tacc.utexas.edu Saved Sessions: give a name for the future use, such as Stampede2.

Log into TACC – From Windows From Computer Lab desktops: search for putty From personal Windows laptops: Install and open Putty. Username: Use the one such as tg****** Eg: For Chen is tg842131 Then use the same password with your Xsede account. Input your valid Token for the login here.

Log into TACC – From Windows If you can log in successfully, you will see the following message:

Log into TACC – From Mac Start Terminal in Mac; Or you can use xshell from Windows;

Log into TACC – From Mac

To transfer files into Xsede systems To transfer files, use Cyberduck for mac. For windows, you can consider: Xftp5 Winscp (chen’s option) Filezilla

Use Winscp To transfer files into Xsede 1) Hostname: Stampede2.tacc.utexas.edu 2) Username: Use the one such as tg****** Eg: For Chen is tg842131 3) Then use the same password with your Xsede account. 4) Input your valid Token for the login here.

Use Winscp To transfer files into Xsede Once you log into the system: Now you are able to transfer files between your computer and the Xsede system.

Use Cyberduck for mac To transfer files into Xsede dos2unix YTr.sh sbatch -A TG-TRA150002 YTr.sh sbatch -A TG-DMS170019 YTr.sh

Run R in HPC Job submission R tutorials: NSF REU site at UNCW, 2017-2019 Run R in HPC Job submission R tutorials: https://www.cac.cornell.edu/education/training/StampedeJan2017/Python_R_HPC_Workshop.pdf Modified from Dr. Patricia Kelley, 06/13/2017

Load R in both Windows or Mac Type "module load Rstats", then "R” You then can do a lot of things with R Type “library(parallel)” Type ”detectCores()” module load Rstats R library(parallel) detectCores() Right click the mouse to paste the contents.

Log into TACC – From Windows After typing in the following notes, you will see the following message: moduel load Rstats R library(parallel) detectCores()

Useful commands lscpu to see the info about cpu ls to list all files Familiar with UNIX commands, vi? ’showq -u tg831870’, to see any job working? logout to logout

Use Cyberduck for Mac To transfer files into Xsede dos2unix YTr.sh Job submission: sbatch -A TG-TRA150002 YTr.sh sbatch -A TG-DMS170019 YTr.sh

How to submit a job in Windows NSF REU site at UNCW, 2017-2019 How to submit a job in Windows echo $HOME echo $WOKR echo $DATA echo $SCRATCH To submit a job: sbatch ccx.sh

How to submit a job in Windows NSF REU site at UNCW, 2017-2019 How to submit a job in Windows After submitting a job: sbatch ccx.sh

How to submit a job in Windows NSF REU site at UNCW, 2017-2019 How to submit a job in Windows When a job is done, an email will be received: Now go into your winscp to look at the result file “ccx326512.txt” Message Passing Interface (MPI)

How to make parallel computing in R NSF REU site at UNCW, 2017-2019 How to make parallel computing in R Example code for parallel computing in R: library(parallel) workerFunc <- function(n) {message(paste('we are working on the ',n,'th loop')); x<-rnorm(N,5,1); return(mean(x)) } numWorkers <- detectCores(); set.seed(12345); st<-Sys.time() res<-mclapply(c(1:n), workerFunc, mc.cores = numWorkers); Sys.time()-st Message Passing Interface (MPI)

Python Tutorials: https://cvw.cac.cornell.edu/python/hpp NSF REU site at UNCW, 2017-2019 Run Python in HPC Python Tutorials: https://cvw.cac.cornell.edu/python/hpp Modified from Dr. Patricia Kelley, 06/13/2017

How to run python in TACC NSF REU site at UNCW, 2017-2019 How to run python in TACC module load python module load python3* first, type $ module spider python3 to get instructions on other required modules

Multiprocess example from multiprocessing import Pool def f(x): NSF REU site at UNCW, 2017-2019 Multiprocess example from multiprocessing import Pool def f(x): return x*x p=Pool(4) ##starts 4 worker process print(p.map(f, range(10))) #prints[0, 1, 4, ..., 81] # idev -r ## This is only for reservation nodes Run in an interactive session: module load python python python_multiprocessing.py

Use a standard batch file: batch.sh NSF REU site at UNCW, 2017-2019 Use a standard batch file: batch.sh #!/bin/bash #SBATCH -p development #SBATCH -A your_account_name_goes_here #SBATCH -J mpi4py-demo #SBATCH -o mpi4py-demo.o%j #SBATCH -n 16 #SBATCH -t 00:05:00 # Prohibit writing core files on error. ulimit -c 0 set -x python receiver.py & ibrun python sample.py --loghost `hostname` --level debug pkill python

pip install --user line_profiler Time python filename.py NSF REU site at UNCW, 2017-2019 pip install --user line_profiler Time python filename.py