New User Guide

This guide is intended for new or first-time users using HPC resources for their research computing. If you have more questions after going through this guide, please also take a look at our FAQs and Other User Guides pages. If you have a more specific question, whether it be an application installation or a troubleshooting problem, please submit a ticket to the HPC Help Desk

Introduction

In this new users guide, we will go through the basics of using the HPC systems at Mines. This includes logging into the systems via ssh, navigating the filesystem and learning how job submission works using the SLURM scheduler. If you need more help after this guide, please refer to the FAQ and User Guide pages. Additionally, you can also request help through the Mines Help Center by submitting a ticket.

Connecting to an HPC System via ssh

Linux and MacOS

Connecting to and using Mines’ HPC systems requires knowledge of the command line. The first step will be opening the terminal on your operating system. On Mac systems, the quickest way is to use the ‘Spotlight’ search by pressing ‘Command + Space’ on your keyboard and typing ‘Terminal’. Most Linux systems will also have a terminal app preinstalled. Once you have the terminal open, you can login using the ssh command. If you are on the Mines network, either on-campus, or connected to the Mines VPN, you can type the command

$ ssh username@name-of-hpc-system.mines.edu

and enter your Mines Multipass password.

For example, if you have an account on Wendian and your username is janedoe,

$ ssh janedoe@wendian.mines.edu 

Mines’ IT infrastructure allows one into Mines HPC systems through an ssh ‘jumpbox’ if you’re not connected to the Mines Network. To do so, you first need to ssh into jumpbox by typing:

$ ssh username@pvm-jumpbox.mines.edu 

If you have multi-factor authentication (MFA) enabled, you will be asked for your one-time password (OTP) here as well in addition to your Mines MultiPass password. Once logged in, you can log into a Mines HPC system as normal.

Windows

On Windows, we either recommend using mobaxterm or setting up Windows Subsystem for Linux (WSL) so you can follow the Linux/Mac instructions above. Note that WSL requires administrator privileges on your Windows machine to set it up.

Introduction to Command Line and Filesystem

In this section, we will go through the basics of how to use the command line to navigate the filesystem. We will also briefly describe aspects of the filesystem that are important to keep your work organized and adhere to HPC policy.

Filesystem Basics

For both HPC systems, there is a basic filesystem structure with designated paths for various types of files. Upon login to either Wendian or Mio, typing ls, you should see the following too directories: bins and scratch.

Useful Environment Variables
Directory 	Environmental variable
Home directory 	$HOME
$HOME/bins 	$BINS
$HOME/scratch 	$SCRATCH

Your home directory is where you can store any personal files, scripts, and programs that you need to keep long term. The bins is a place to store compiled programs and executables that you need to run for jobs. As the name implies, scratch is the scratch directory used for temporary files needed for running jobs.

It is HPC policy to make sure that job data is run under your scratch directory. Users who do not follow this may receive notice or warnings from HPC staff.

 

Command Line Basics for Navigating the Filesystem

In order to manage, edit and run files on an HPC system, you will need to learn the basics of the Unix/Linux command line. There are many guides online on learning how to do this, but we will provide some basic commands in the tables below. For more information, please take a look at the guides mentioned below:

The table below summarizes all the basic commands you need to navigaate the file system:

Command Description
ls -lah shows list (-l) of all files/directories, including hidden ones (-a), in current directory with human-readable (-h) file sizes
pwd prints out the path of the current working directory
cd changes your directory to your home directory (on most Linux/Mac machines, this will be /home/username)
cd .. changes your directory down one directory on the path, e.g. if you're at /home/username, "cd .." will take you to /home
cd $directory-path changes to directory at $directory-path
mkdir $directory-name creates a directory in your current working directory called $directory-name
mkdir -p $directory-path creates a directory located at $directory-path (e.g. $directory-path="/home/Documents/" would move you to /home/Documents as your current working directory)
cp $filename $new_file_location copies $filename (e.g. $filename="/home/Documents/foo.txt" would copy the file to $new_file_location (e.g. $new_file_location="/home/Documents/New/foo.txt")
mv $filename $new_file_location moves $filename (e.g. $filename="/home/Documents/foo.txt" would copy the file to $new_file_location (e.g. $new_file_location="/home/Documents/New/foo.txt")

Choosing a Text Editor

When using the command line, a text editor becomes a powerful tool to create and edit job scripts, as well as modify codes on the system. There are 3 text editors that we recommend:

  • nano – recommended for beginners new to command line-based text editors. A guide and shortcuts can be found on their website.
  • vim – A keyboard-centric highly customizable text editor. Recommended for advanced users who want to customize how they edit their files on the commandline. Documentation can be found here.
  • emacs – Another power user-friendly text editor. Documentation can be found here.

Running Jobs

SLURM: HPC Job Scheduler

Access to compute resources on Mines’ HPC platforms in managed through a job scheduler. The job scheduler manages HPC resources by having users send jobs using scripts, asking for resources, what commands to run, and how to run them. The scheduler will launch the script on compute resources when they are available. The script consists of two parts, instructions for the scheduler and the commands that the user wants to run.

A sample script is shown below:

#!/bin/bash
#SBATCH --job-name="sample"
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --ntasks=8
#SBATCH --exclusive
#SBATCH --export=ALL
#SBATCH --time=01:00:00

cd $HOME
ls > myfiles
srun hostname

The lines that begin with #SBATCH are instructions to the scheduler. In order:

      1. #SBATCH –-job-name=”sample” – You are naming the job
      2. #SBATCH –-nodes=2 – You are telling the scheduler that you want to run on two nodes
      3. #SBATCH –-ntasks-per-node=4 – You want to run four tasks per node for a total of 8 tasks. (The —ntasks-per-node line is redundant in this case.)
      4. #SBATCH –-exclusive – When the job runs you will have exclusive access to the nodes, i.e. no other jobs can run on that node.
      5. #SBATCH –-export=ALL – All your environmental variables setting will passed to the compute nodes.
      6. #SBATCH –-time=01:00:00– You will run no longer than 1 hr.

The last three lines are normal commands:

  1. cd $HOME – You will be put in your home directory.
  2. ls > myfiles – A directory listing will be put in the file myfiles.
  3. srun hostname – The srun command will launch the program hostname in parallel, in this case 8 copies will be started simultaneously. Note that the ls command is not run in parallel; only a single instance will be launched.

The script is launched using the sbatch command. By default the standard output and standard error will be put in files with the names slurm-######.out and slurm-######.err where ###### is a job number. For example running this script on Wendian produces:

[username@wendian001 ~]$ sbatch dohost
Submitted batch job 363541

After some time…

[username@wendian001 ~]$ ls -lt | head
total 88120
-rw-rw-r--  1 joeuser joeuser        64 Sep 24 16:28 slurm-363541.out
-rw-rw-r--  1 joeuser joeuser      2321 Sep 24 16:28 myfiles
...

[username@wendian001 ~]$ cat slurm-363541.out
c001
c002
c001
c001
c001
c002
c002
c002

There are several user level commands available for managing jobs on the HPC resources. These are discussed briefly by the How do I manage jobs? on the HPC FAQs page.

SLURM Job Management and Policy

SLURM manages job priority based on variety of factors, including but not limited to: resources requested (number of nodes, memory, etc), length of job time, and prior number of jobs submitted. Mio and Wendian both have their own job policies, which you can learn more about on our FAQ page.

Running your first compiled job – Hello World!

Now that you can login, navigate the filesystem and understand the basics of the SLURM job scheduler, we are ready to send our first job to the scheduler. For the first example, we are going to show how to send a job using the simple C++ program for “Hello World”:

// Source: https://devblogs.microsoft.com/cppblog/cpp-tutorial-hello-world/
#include "stdio.h"
int main()
{
  std::cout << "Hello, World!" << std::endl;
  return 0;
}

For this program hello_world.cpp, we can compile it using the system’s C++ compiler g++:

$ g++ hello_world.cpp -o hello_world.exe

Now, to send this job using a job script, we need to write one using the SLURM preamble definitions. A sample job script run.slurm for our Hello Program is below:

#!/bin/bash
#SBATCH --nodes=1 # number of nodes
#SBATCH --ntasks-per-node=1 # number of tasks per node
#SBATCH --ntasks=1 # redundant; total number of tasks: ntasks = nodes * ntasks-per-node
#SBATCH --time=00:00:01 # time in HH:MM:SS
#SBATCH -o output.%j # standard print output labeled with SLURM job id %j
#SBATCH -e error.%j  # standard print error  labeled with SLURM job id %j

echo "Job has started!"
srun hello_world.exe
echo "Job has finished!"

We will highlight some aspects of this SLURM script. First, the lines starting with #SBATCH are part of a SLURM script’s preamble. There are a multitude of options for the preamble, where you read more about on the SLURM sbatch documentation page here.

The command srun tells SLURM what executable to run (in this case hello_world) and how to run it using all the SLURM preamble options above.

 

NOTE: For most cases, it is required to send your job’s executable using srun. There are a few exceptions for this rule and will be advised on a case by case basis.

Now to send the job to SLURM we use sbatch:

$ sbatch run.slurm

You should see the following printed to the screen:

Submitted batch job $JOB_ID

where $JOB_ID will look something like 5711043.

An introduction to the module system

Software required for high performance computing is complex due to its web of dependencies of libraries and other scientifc software programs. Furthermore, each piece of scientific software may require dependencies that may conflict with existing libraries, or require a different version of a library completely. Hence, a modular system allows one to load and unload dependencies as needed, depending on what is required from the software.

On Linux systems, paths for software and their libraries are determined by setting environmental variables. You can see the settings of all variables by running the command printenv. In most cases, the most important environment variables are PATH and LD_LIBRARY_PATH. PATH is an environment variable that sets a list of directories that can be searched for finding applications. Similarly, LD_LIBRARY_PATH defines a list of directories that will be searched to find libraries used by applications. If you enter a command and see “command not found” then it is possible the directory containing the application is not in PATH; a similar error occurs for LD_LIBRARY_PATH when it cannot find a required library. The module system is designed to easily set and unset collections of environment variables. On Mines HPC systems, this is done using the lmod module system. We will briefly describe some common important module commands and also how to use it in context of setting up and submitting a job.

Important Module Commands

  • module spider – Lists all available modules in a cascading tree format
  • module -r spider mpi – Lists all modules related to “mpi” in a cascading tree format
  • module keyword gromacs – List modules related to the gromacs program
  • module load Apps/gromacs/5.1.2 – Loads the Gromacs v5.1.2. module
  • module unload Apps/gromacs/5.1.2 – Unoads the Gromacs v5.1.2. module
  • module purge – Unloads all currenty loaded modules
  • module list – Lists all currently loaded modules
  • Not all applications are accessible by all HPC users. Some codes are commercial and require licensing, and hence PI approval. Some require PI approval for other reasons. If you are unable to load a module, or see permission errors when executing a job, and would like to know how you might obtain access, please submit a help request.
  • Some modules have dependencies that need to be manually entered. For example, the gromacs module requires that modules for the compiler and MPI be loaded first. If there is an unsatisfied dependency you will be notified.

Running jobs with modules

Hello World using MPI

// Reference:  https://mpi.deino.net/mpi_functions/MPI_Init.html
#include "mpi.h"
#include "stdio.h"
using namespace std;
int main(int argc, char* argv[])
{
  int rank, np;
  MPI_Init(&argc,&argv); // initialize MPI
  MPI_Comm_size(MPI_COMM_WORLD, &np); // get total number of processors
  MPI_Comm_rank(MPI_COMM_WORLD, &rank); // get current rank  
  cout << "Hello World from rank " << rank << " out of " << np << " processors!" << endl;
  MPI_Finalize(); // finalize MPI
  return 0;
}

For the second program, we wanted to demonstrate how to use the system’s module system. This program initializes MPI, defines integer variables to store the number of processors np and the current processor/”rank”, rank, and then prints “Hello World from rank rank out of np processors!”, followed by finalizing MPI.

To compile this code, we need to load modules from the module system.

On Wendian:

$ module load compilers/devtoolset/7  mpi/openmpi/3.1.3-gnu-7.3.1

On Mio:

$ module load PrgEnv/devtoolset-6 MPI/openmpi/3.0.0/gcc

This will load a newer GCC compiler that is required for our OpenMPI library we’re going to use with the code. To compile the code, we will use the MPI-wrapped C++ compiler mpicxx:

$ mpicxx  hello_world.cpp -o hello_world.exe

A sample job script (which we will call run.slurm) to use the executable will look like:

#!/bin/bash
#SBATCH --nodes=1 # number of nodes
#SBATCH --ntasks-per-node=12 # number of tasks per node
#SBATCH --ntasks=12 # redundant; total number of tasks: ntasks = nodes * ntasks-per-node
#SBATCH --time=00:00:01 # time in HH:MM:SS
#SBATCH -o output.%j # standard print output labeled with SLURM job id %j
#SBATCH -e error.%j  # standard print error  labeled with SLURM job id %j

# If on Wendian, uncomment the line below
module load compilers/devtoolset/7  mpi/openmpi/3.1.3-gnu-7.3.1

# If on Mio, uncomment the line below
# module load PrgEnv/devtoolset-6 MPI/openmpi/3.0.0/gcc

echo "Job has started!"
srun hello_world.exe
echo "Job has finished!

As with the last example, we can send the job to the scheduler using the command:

$ sbatch run.slurm

When the job completes, you should see an output file called output.%j where %j is the job ID. The output for this job should look similar to:

Job has started!
Hello, World! from rank 1 out of 12 processors!
Hello, World! from rank 3 out of 12 processors!
Hello, World! from rank 5 out of 12 processors!
Hello, World! from rank 7 out of 12 processors!
Hello, World! from rank 9 out of 12 processors!
Hello, World! from rank 10 out of 12 processors!
Hello, World! from rank 11 out of 12 processors!
Hello, World! from rank 0 out of 12 processors!
Hello, World! from rank 2 out of 12 processors!
Hello, World! from rank 4 out of 12 processors!
Hello, World! from rank 6 out of 12 processors!
Hello, World! from rank 8 out of 12 processors!
Job has finished! 

[Optional] Using Python

For many cases, Python is a popular scientific computing program language with a large library of modules to choose from. There are so many dependencies that managing python modules through the HPC module system alone would become incredibly cumbersome. As an alternative, we recommend HPC users take control of the python modules they need by creating their own environment using Anaconda. We will briefly go over how to do this below.

Python v2.7 was deprecated at the beginning of 2020 which means that it will no longer be updated. Linux operating systems, such as the ones used on Mines HPC systems, while currently supported, will eventually not include Python 2.7 by default. We encourage researchers to make the transition to Python 3.x as soon as they are able.

Creating your own environment using Anaconda

First step is to load the desired version Python version. We will show examples for both Wendian and Mio below.

On Wendian and Mio

$ module load apps/python3/2020.02

On Mio:

$ module load PrgEnv/python/anaconda/2020.02

Then create your own python environment using the following command:

$ conda create --name my_env python=3.7

You should see something similiar to the following print to the screen:

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /u/pa/sh/username/.conda/envs/my_env

  added / updated specs:
    - python=3.7


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2021.1.19  |       h06a4308_0         121 KB
    certifi-2020.12.5          |   py37h06a4308_0         141 KB
    libedit-3.1.20191231       |       h14c3975_1         116 KB
    libffi-3.3                 |       he6710b0_2          50 KB
    ncurses-6.2                |       he6710b0_1         817 KB
    openssl-1.1.1i             |       h27cfd23_0         2.5 MB
    pip-20.3.3                 |   py37h06a4308_0         1.8 MB
    python-3.7.9               |       h7579374_0        45.3 MB
    readline-8.1               |       h27cfd23_0         362 KB
    setuptools-52.0.0          |   py37h06a4308_0         710 KB
    sqlite-3.33.0              |       h62c20be_0         1.1 MB
    tk-8.6.10                  |       hbc83047_0         3.0 MB
    wheel-0.36.2               |     pyhd3eb1b0_0          33 KB
    ------------------------------------------------------------
                                           Total:        56.0 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2021.1.19-h06a4308_0
  certifi            pkgs/main/linux-64::certifi-2020.12.5-py37h06a4308_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libedit            pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1i-h27cfd23_0
  pip                pkgs/main/linux-64::pip-20.3.3-py37h06a4308_0
  python             pkgs/main/linux-64::python-3.7.9-h7579374_0
  readline           pkgs/main/linux-64::readline-8.1-h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-52.0.0-py37h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0
  tk                 pkgs/main/linux-64::tk-8.6.10-hbc83047_0
  wheel              pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Proceed ([y]/n)? 

Proceed by typing “y”, followed by enter. You can then activate your new environment by typing

$ source activate my_env

WARNING: Anaconda will print out to setup the environment using conda activate instead of source activate. Although this will work on the command line, the conda command will not pass the environment in a SLURM job.

You should now see (my_env) to the left on your command line like follows:

(my_env) [username@wendian001 ~]$

You can now add packages you need for your conda environment either using pip or the conda commands. For example, we can install the petsc4py package through conda-forge:

(my_env) [username@wendian ~]$ conda install -c conda-forge petsc4py

You should see something similiar print to the screen:

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /u/pa/sh/username/.conda/envs/my_env

  added / updated specs:
    - petsc4py


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2020.12.5  |       ha878542_0         137 KB  conda-forge
    certifi-2020.12.5          |   py37h89c1867_1         143 KB  conda-forge
    hdf5-1.10.6                |nompi_h7c3c948_1111         3.1 MB  conda-forge
    hypre-2.18.2               |       hc98498a_1         1.7 MB  conda-forge
    krb5-1.17.2                |       h926e7f8_0         1.4 MB  conda-forge
    libblas-3.9.0              |       8_openblas          11 KB  conda-forge
    libcblas-3.9.0             |       8_openblas          11 KB  conda-forge
    libcurl-7.71.1             |       hcdd3856_3         302 KB  conda-forge
    libgfortran-ng-7.5.0       |      h14aa051_18          22 KB  conda-forge
    libgfortran4-7.5.0         |      h14aa051_18         1.3 MB  conda-forge
    liblapack-3.9.0            |       8_openblas          11 KB  conda-forge
    libopenblas-0.3.12         |pthreads_hb3c22a3_1         8.2 MB  conda-forge
    metis-5.1.0                |    h58526e2_1006         4.1 MB  conda-forge
    mpi-1.0                    |            mpich           4 KB  conda-forge
    mpich-3.3.2                |       h846660c_5         6.4 MB  conda-forge
    mumps-include-5.2.1        |      ha770c72_10          23 KB  conda-forge
    mumps-mpi-5.2.1            |      h12930e3_10         3.5 MB  conda-forge
    numpy-1.18.1               |   py37h8960a57_1         5.2 MB  conda-forge
    parmetis-4.0.3             |    h9f7b9cf_1005         290 KB  conda-forge
    petsc-3.13.6               |       h9a2a0d4_1         9.8 MB  conda-forge
    petsc4py-3.13.0            |   py37h66998c9_5         1.3 MB  conda-forge
    ptscotch-6.0.9             |       h294ddb0_1         1.6 MB  conda-forge
    python_abi-3.7             |          1_cp37m           4 KB  conda-forge
    scalapack-2.0.2            |    hfacbc1e_1009         2.2 MB  conda-forge
    suitesparse-5.6.0          |       h717dc36_0         2.4 MB  conda-forge
    superlu-5.2.2              |       hfe2efc7_0         218 KB  conda-forge
    superlu_dist-6.2.0         |       h5e15a89_2         900 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        54.1 MB

The following NEW packages will be INSTALLED:

  hdf5               conda-forge/linux-64::hdf5-1.10.6-nompi_h7c3c948_1111
  hypre              conda-forge/linux-64::hypre-2.18.2-hc98498a_1
  krb5               conda-forge/linux-64::krb5-1.17.2-h926e7f8_0
  libblas            conda-forge/linux-64::libblas-3.9.0-8_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-8_openblas
  libcurl            conda-forge/linux-64::libcurl-7.71.1-hcdd3856_3
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-h14aa051_18
  libgfortran4       conda-forge/linux-64::libgfortran4-7.5.0-h14aa051_18
  liblapack          conda-forge/linux-64::liblapack-3.9.0-8_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.12-pthreads_hb3c22a3_1
  libssh2            conda-forge/linux-64::libssh2-1.9.0-hab1572f_5
  metis              conda-forge/linux-64::metis-5.1.0-h58526e2_1006
  mpi                conda-forge/linux-64::mpi-1.0-mpich
  mpich              conda-forge/linux-64::mpich-3.3.2-h846660c_5
  mumps-include      conda-forge/linux-64::mumps-include-5.2.1-ha770c72_10
  mumps-mpi          conda-forge/linux-64::mumps-mpi-5.2.1-h12930e3_10
  numpy              conda-forge/linux-64::numpy-1.18.1-py37h8960a57_1
  parmetis           conda-forge/linux-64::parmetis-4.0.3-h9f7b9cf_1005
  petsc              conda-forge/linux-64::petsc-3.13.6-h9a2a0d4_1
  petsc4py           conda-forge/linux-64::petsc4py-3.13.0-py37h66998c9_5
  ptscotch           conda-forge/linux-64::ptscotch-6.0.9-h294ddb0_1
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  scalapack          conda-forge/linux-64::scalapack-2.0.2-hfacbc1e_1009
  scotch             conda-forge/linux-64::scotch-6.0.9-h0eec0ba_1
  suitesparse        conda-forge/linux-64::suitesparse-5.6.0-h717dc36_0
  superlu            conda-forge/linux-64::superlu-5.2.2-hfe2efc7_0
  superlu_dist       conda-forge/linux-64::superlu_dist-6.2.0-h5e15a89_2
  tbb                conda-forge/linux-64::tbb-2020.2-hc9558a2_0

The following packages will be UPDATED:

  certifi            pkgs/main::certifi-2020.12.5-py37h06a~ --> conda-forge::certifi-2020.12.5-py37h89c1867_1

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    pkgs/main::ca-certificates-2021.1.19-~ --> conda-forge::ca-certificates-2020.12.5-ha878542_0


Proceed ([y]/n)?

Confirm by typing ‘y’ and pressing enter. You now should have your own Python environment with petsc4py! Once you are done with your environment, you can disable it by issuing the command:

$ conda deactivate

Post-processing & Visualizing data on HPC

After your job completes, you may want to figure out how you want to post-process and visualize your data. In many cases, HPC is not necessary and many users prefer transferring their data and postprocessing & visualizating their data locally. However, you need to leverage the compute or GPU nodes to do visualization, please go to our Visualization page to learn more.

Transferring Data off HPC Systems

For transferring data off Mines HPC systems, we recommend the following command line programs: scp and rsync. Each of these commands serve a similar purpose, but function differently in practice.

The name scp stands for secure copy. The general syntax for scp to transfer a file from an HPC system to a local directory is as follows:

$ scp  

For example, if you wanted to transfer the file ~/scratch/foo.txt from Wendian to your local home directory /home/username, you would type (while not logged into any HPC system in your terminal):

$ scp username@wendian.mines.edu:~/scratch/foo.txt /home/username 

Conversely, if you needed to transfer foo.txt back to Wendian, you would type:

$ scp /home/username/foo.txt  username@wendian.mines.edu:~/scratch 

If you need to send an entire directory, scp provides the recursive flag -r:

$ scp -r  /home/username/foo_bar  username@wendian.mines.edu:~/scratch 

This will transfer the directory foo_bar and its contents to ~/scartch/foo_bar

There are many other options you can use for scp, which can be found here or by typing man scp in your command line.

In some cases, you may want to transfer an entire directory, but know that many of the files in that directory haven’t changed. That is, you want to sync the files incremently based only on the files that changed. For these instances, it is recommended to use rsync. Recommended syntax for using rsync recursively is as follows:

$ rsync --rsh=ssh -rvP username@remote_host:/path/to/source /path/to/destination

The flag --rsh=ssh ensures rsync uses ssh. -rvP will recursively pull files from the directory (-r), with verbose output to the screen (-v) and allow for partial transfers (-P) in case an interruption or a restart. For example, to transfer the directory foo_bar2 from Wendian to your local directory:

$ rsync --rsh=ssh -rvP username@wendian.mines.edu:~/scratch/foo_bar2 /home/username

Transferring on Windows or Without Command Line

For transferring files without the use of the command line, such as on Windows, both Mio and Wendian support the FTP protocol. For FTP transfers, we recommend Filezilla, since it is cross-platform for Windows, MacOS and Linux. Our recommended command line program MobaXterm also supports file transfer within the program.