Logging in to HPCI using Docker (macOS)

0. Change Log

0.1 Major changes

2024.09.09

• Updated Docker image to gsi-openssh-20240902.tar.xz.

2024.04.05

• The wording of the login procedure has been partially changed to match the user’s environment.

2024.03.29

• Fixed “2. Installing Docker Desktop for Mac” based on the behavior of the Docker Desktop 4.27.2 installer.

• Updated Docker image to gsi-openssh-20240209.tar.xz.

• Add a new Docker image for Mac with Apple Silicon.

2023.12.28

• Fixed “2. Installing Docker Desktop for Mac” based on the behavior of the Docker Desktop 4.26.0 installer.

• Updated Docker image to gsi-openssh-20231128.tar.xz.

2023.07.31

• The wording and structure of some items have been arranged.

• The text version of this document has been discontinued.

2023.06.16

• Fixed “2. Installing Docker Desktop for Mac” based on the behavior of the Docker Desktop 4.17.0 installer.

• Updated Docker image to gsi-openssh-20230322.tar.xz.

2023.04.28

• Corrected the URL of the referenced document.

2022.12.19

• Revised to conform with Docker Desktop for Mac with Apple silicon 4.14.1

2022.07.15

• Created an English version of the document.

• Fixed “2. Installing Docker Desktop for Mac” based on the behavior of the Docker Desktop 4.10.1 installer.

• Updated Docker image to gsi-openssh-20220325.tar.xz.

2022.01.06

• Updated headline of referenced HPCI login manual in line with version 22.

2021.07.15

• Added comment about Mac with Apple silicon to “1.2 Operating environment”.

• Added “5. How to use run an X11 client.”

• Updated Docker image to gsi-openssh-20210607.tar.xz.

2021.01.22

• Added comment about macOS version to 1.2 Operating environment.

• Revised installation procedure to accompany changes in Docker Desktop installer operations.

• Added notice regarding problems with docker load occurring with the latest Docker Desktop at time of document publication.

• Updated Docker image to gsi-openssh-20201215.tar.bz2.

2020.07.13

• Revised procedure for getting Docker Desktop installer (because signing in with Docker ID is no longer needed).

• Added “4. Updating Docker images”.

• Added “5. Notes on container environments”.

• Updated Docker image to gsi-openssh-20200713.tar.xz.

2019.10.24

• Initial release

1. Overview

This document is for those using macOS and explains how to log in to the HPCI environment using Docker.

There are two versions of Docker Desktop for MacOS, for the two different chip architectures that Macs use:

• Mac with Intel chip

• Mac with Apple silicon

When it needs to distinguish between the two, this documentation will refer to “Mac with Intel chip” and “Mac with Apple Silicon”, as the Docker Desktop documentation Install Docker Desktop on Mac does.

1.1 Terminology

Image

The foundation for a container.

Container

An entity that executes an image.

Repository

A collection of Docker images.

Tag

An identifying label used to distinguish images in a repository.

1.2 Operating environment

To install Docker Desktop for Mac, your Mac must satisfy the following requirements.

• For up-to-date information on prerequisites, see the Docker Desktop documentation System requirements .

Mac with Intel Chip

• macOS 12 or newer (Monterey, Ventura, Sonoma)

  • Compatible with older versions up to two versions before the latest major version

  • We recommend using upgrading macOS to the current version.

  • HPCI has used Monterey (version 12.7.1) for operational tests in its test environment.

• 4 GB RAM or more.

• VirtualBox version 4.3.30 or newer is needed for compatibility with Docker Desktop for Mac.

Mac with Apple Silicon

• These are Mac with Apple Silicon CPUs.

  • HPCI has used Monterey for operational tests in its test environment.

• About Rosetta 2

  • HPCI has not tested operations with Rosetta 2 installed in its test environment.

2. Installing Docker Desktop for Mac

2.1 Download the installer

Download the Docker.dmg installer.

Attention

As of Apr 8, 2020, you do not need to sign in with a Docker ID in order to download the Docker Desktop installer.

1. Visit https://www.docker.com in your web browser.

2. Click the [ Get Started ] button.

3. Select the appropriate button for the device you are using from the download button pull-down menu ([ Download for XXXX | v ]) on the displayed page to download the installer Docker.dmg.

• [ Download for Mac - Intel Chip ]

• [ Download for Mac - Apple Chip ]

2.2 Installation procedure

See also the description Install and run Docker Desktop on Mac on the Docker official site.

1. Log in as a user with administrator privileges and double-click on the installer Docker.dmg.

2. A window with a “Docker” title will be displayed. Drag the Docker icon and drop it into the Applications folder in the same window.

3. Copy progress is displayed.

4. After the progress display finishes, double-click the Applications icon in the “Docker” window to open the Applications folder.

5. Open the Applications folder and double-click the Docker icon within it.

6. The verification progress will be displayed on the screen.

7. A dialog will be displayed asking, “”Docker” is an app downloaded from the Internet. Are you sure you want to open it?” Click the [Open ] button.

8. The whale icon will appear in the status bar.

9. The Docker Subscription Service Agreement window is displayed. Check the contents and perform the following operations to accept.

• Click the [ Accept ] button.

10. A window with the heading “Finish setting up Docker Desktop” will appear.

• Select one according to the on-screen instructions.

  • Use recommended settings (requires password)

  • Use advanced settings

• Click the [ Finish ] button.

11. A dialog box appears asking for permission for privileged access.

Follow the instructions “Enter your password to allow this.”, enter your password in the password field, and press the [ OK ] button.

12. The Docker Desktop Dashboard will be displayed. When executing for the first time, perform the following operations.

• Welcome to Docker Desktop

  The following buttons and links will be displayed. Select the “Continue without signing in” link.

  • Button : [ Sign up ]

  • Link : Already have an account? Sign in

  • Link : Continue without signing in

• “Welcome Survey”

  • Click the [ Skip surbey → ] button at the bottom of the window.

• When the “Container” tab is displayed, the operation is complete.

2.3 Uninstallation procedure

See also the description Uninstall Docker Desktop on the Docker official site.

When it is no longer needed, follow the procedure below to uninstall Docker Desktop for Mac.

1. Click the whale icon representing Docker in the status menu.

2. Select Troubleshoot from the resulting menu.

3. This will open a window from which you can click [Uninstall ].

4. This will open an “Uninstall Docker Desktop” window. Click the [Uninstall ] button.

5. “Docker Desktop uninstalled successfully” will be displayed,

• followed by the message “You can move the Docker Desktop application to the trash.

• Click the [ Quit ] button to close the window.

6. In the Finder’s Applications folder, find the Docker icon and move it to the trash.

3. Log in to the HPCI environment

This section describes the procedure for logging in to the HPCI environment using Docker Desktop for Mac.

The operation flow is as follows.

1. Launch Docker Desktop

2. Launch the Terminal

3. Load the Docker image (only when installing)

4. Launch the Docker container

5. Run bash

6. Log in to the login server

7. Shut down the Docker container

3.1 Launching Docker Desktop

Normally you will not need to manually launch this, as it would have been installed so as to start automatically when logging in.

If it was set so as not to start automatically when logging in, you will need to perform the following:

1. In the Finder, double-click on the Docker Desktop application in the Applications folder.

It will take a little while for Docker Desktop to launch.

1. Check the status with the whale icon displayed in the status menu.

• The whale icon will be animated while the launch process is underway.

• Once the launch process is finished, the whale icon will stop moving, indicating that it is ready to receive docker commands.

3.2 Launching the Terminal

To run docker commands, launch the Terminal application.

3.3 Loading the Docker image (only when installing)

You will need to store the Docker image in the local-storage domain on the Docker host.

Download

1. Download the latest Docker image:

• Docker image for Mac with Intel Chip

  • gsi-openssh-20240902.tar.xz

• Docker image for Mac with Apple Silicon

  • gsi-openssh-20240902.tar.xz

Load the Docker image

1. Execute the docker load command to load the Docker image.

$ docker load -i gsi-openssh-20240902.tar.xz
Loaded image: hpci/gsi-openssh:20240902
$

2. To confirm that it is stored in local storage, execute the docker images command. Check that the REPOSITORY is hpci/gsi-openssh, and that the value for TAG matches the date in the docker image file name.

$ docker images hpci/gsi-openssh
REPOSITORY         TAG        IMAGE ID       CREATED      SIZE
hpci/gsi-openssh   20240902   b3c96bb6283d   8 days ago   310MB
$

Launching the Docker container

1. Execute the docker run command to run the Docker image you loaded in Step 3.3.

$ docker run -d --rm --name gsi-openssh -v /Users/username/Documents:/home/hpciuser/work hpci/gsi-openssh:20240902
9ef07e5a6b3d067c037c52bb1717b2e8d6509017b58f83fb99998d8a0e0c73d8
$

The long string is the container ID (UUID). When running or stopping this container, you will use this ID (or its short form).

The options used in this command are:

-d

Run the container in the background

--rm

Automatically delete the container after shutdown.

--name NAME

Sets the name of the container. In the above example, it is named gsi-openssh. To identify this container when running it in the future, you can use the container name gsi-openssh instead of the container ID.

-v LIST

Mounts the host OS directory HOST-DIR in the container directory CONTAINER-DIR. Here, LIST is expressed as HOST-DIR:CONTAINER-DIR.

In the above example, the Documents folder under the username account in macOS (/Users/username/Documents) is paired with the container directory /home/hpciuser/work.

Attention

When running on a Mac with Apple Silicon, you previously needed to specify the argument –platform linux/amd64.This argument is not required when using the Docker image for Mac with Apple Silicon.

Without the -d option, Docker will not return you to the terminal prompt. If this happens, you will need to open another Terminal window, and execute the command docker stop gsi-openssh, which will shut down the container and return you to the terminal prompt from which docker run was executed. From that point, you can execute docker run again.

—The name set using the –name option must not conflict with any existing containers. If there is already a container with the same name, either use a different name or delete the existing container (if it is no longer needed).

If you fail to give a name when using the –name option, the container’s name will be set to a random string of characters. You can check the name using the docker ps command, explained later.

You need to use the -v option to set a directory that the container user can access from CONTAINER-DIR. The Docker image gsi-openssh-20240902.tar.xz has the container user fixed to “hpciuser,” so specify a directory under /home/hpciuser.

Attention

With MacOS 10.14 (Mojave) and newer versions, applications may have restricted access to the Documents folder. If so, you will either need to permit access via System Settings > Privacy & Security, or you will need to create a new folder in your home directory to use as your working folder.

2. To confirm that docker is running correctly, execute the docker ps command. Check that the parameters below are correct.

CONTAINER ID

The container ID (first 12 characters) displayed when executing docker run

IMAGE

The Docker repository name:tag name specified in the option

NAMES

The name specified by the –name option.

$ docker ps
CONTAINER ID   IMAGE                       COMMAND                   CREATED         STATUS         PORTS     NAMES
9ef07e5a6b3d   hpci/gsi-openssh:20240902   "sudo /usr/sbin/cron…"   2 minutes ago   Up 2 minutes             gsi-openssh
$

If the output from docker ps does not look like the above, the container may have failed to launch.

The types of information displayed and their order can be changed using the –format option. To show only NAMES, CONTAINER ID, and IMAGE, you will need to execute the following command:

$ docker ps --format "{{.Names}} {{.ID}} {{.Image}}"
gsi-openssh 9ef07e5a6b3d hpci/gsi-openssh:20240902
$

3.5 Running bash

Bash environment

The bash environment’s settings are as follows. These are all fixed values in the gsi-openssh-20240902.tar.xz Docker image.

• Username (user ID)

  hpciuser (2000)

• Group name (group ID)

  hpciuser (2000)

• Home directory

  /home/hpciuser

• Time zone (“TZ” environment variable setting)

  JST-9

Run bash

1. Use the docker exec command to run /bin/bash in the container launched in Step 3.4. Here, this is gsi-openssh.

$ docker exec -i -t gsi-openssh /bin/bash
[hpciuser@XXXXXXXXXXXX ~]$

The options -i and -t are needed to run bash interactively; you can combine these as “-it”.

-i

Keep standard input (STDIN) open.

-t

Allocate a pseudo-terminal (pseudo TTY) to the container process.

After the bash process starts, you will see the following.

• The prompt will be a bash prompt running in the container.

• The “XXXXXXXXXXXX” part is the short form of the container ID.

3.6 Log in to the login server

This section provides an overview of the login procedure. See User’s Guide, HPCI Login Manual for details.

Issue a proxy certificate

First, a proxy certificate must be issued using HPCI Certificate Issuing System and stored in the proxy certificate repository.

Attention

• Proxy certificates are valid for up to 168 hours.

• It should be issued (stored) each time it expires.

• Refer to the following document for the issuing (storing) procedure.

  • User’s Guide, HPCI Login Manual, “2.2. Storing the Proxy Certifdicate”

Download a proxy certificate

Download the proxy certificate to the Docker container.

• For details on the procedure, refer to the following document.

  • User’s Guide, HPCI Login Manual , “2.3.2. Download with myproxy-logon”

• If you are unable to download a proxy certificate, refer to the following document.

  • User’s Guide, HPCI Login Manual , “2.3.2.2. Troubleshooting”

  • トラブルシューティング - GSI-SSHシステム管理関連 in the HPCI information-sharing CMS. (Note: There is no English translation page.)

1. Download the proxy certificate using the myproxy-logon command.

[hpciuser@XXXXXXXXXXXX ~]$ myproxy-logon -s portal.hpci.nii.ac.jp -l [HPCI-ID]
Enter MyProxy pass phrase: ********
A credential has been received for user <HPCI-ID> in /tmp/x509up_up2000.
[hpciuser@XXXXXXXXXXXX ~]$

2. Verify the information in the resulting proxy certificate using the grid-proxy-info command.

[hpciuser@XXXXXXXXXXXX ~]$ grid-proxy-info
subject  : /C=JP/O=NII/OU=HPCI/CN=user/CN=proxy/CN=proxy/CN=proxy/CN=proxy
issuer   : /C=JP/O=NII/OU=HPCI/CN=user/CN=proxy/CN=proxy/CN=proxy
identity : /C=JP/O=NII/OU=HPCI/CN=user
type     : RFC 3820 compliant impersonation proxy
strength : 2048 bits
path     : /tmp/x509up_u2000
timeleft : 12:01:15
[hpciuser@XXXXXXXXXXXX ~]$

Log in to the login server

• For details on the procedure, refer to the following document.

  • User’s Guide, HPCI Login Manual , “2.4. Login to the Login Server”

• If you are unable to log in to the login server, refer to the following document.

  • User’s Guide, HPCI Login Manual , “2.4.2. Troubleshooting”

  • トラブルシューティング - GSI-SSHシステム管理関連 in the HPCI information-sharing CMS. (Note: There is no English translation page.)

1. Log in to the login server. In the following example, we are logging in to the login server at the Tokyo Institute of Technology, login.t3.gsic.titech.ac.jp.

[hpciuser@XXXXXXXXXXXX ~]$ gsissh -p 2222 login.t3.gsic.titech.ac.jp
Last login: Tue Jan 24 11:09:13 2023 from xxx.xxx.xxx.xxx
--------------------------------------------------------------------
Last modified: 2023-04-06 17:00:00 JST

 ** Do not run heavy programs like ISVs on login nodes login[01]. **

    (The current TSUBAME 3.0 operational status)
    https://www.t3.gsic.titech.ac.jp/      Twitter:@Titech_TSUBAME
--------------------------------------------------------------------
<HPCI-ID>@login1:~>

2. When you exit the login server, you will return to the container’s bash shell .

<HPCI-ID>@login1:~> exit
logout
Connection to login.t3.gsic.titech.ac.jp closed.
[hpciuser@XXXXXXXXXXXX ~]$

3.7 Exiting bash

1. To return to the terminal from the container, execute exit in bash.

[hpciuser@XXXXXXXXXXXX ~]$ exit
exit
$

The exit command shuts down the bash process, but the container has not stopped. You can run bash as in Step 3.5 to use the gsissh command again. If you do this while the proxy certificate is valid, you will not need to re-download the proxy certificate.

3.8 Shutting down the Docker container

1. To shut down the container, execute the docker stop command. The container you shut down will be the one you launched in Step 3.4, in this case, gsi-openssh

$ docker stop gsi-openssh
gsi-openssh
$

Attention

When you shut down a container, it is deleted. Any files created and saved in that container will also be deleted. Before shutting down, you should transfer any important files to the directory /home/hpciuser/work (the directory mounted with the -v option to docker run).

3.9 About file sharing

If you mount a folder with file-sharing enabled using the -v LIST option to the docker run command, you will be able to share files between the container and macOS.

The files in the directory in the container mounted as a folder with file-sharing enabled will have the owner and group set as follows:

owner	hpciuser
group	hpciuser

In macOS, the owner and group of files created in the container will be set to the user who executed docker run.

4. Updating Docker images

This section will explain how to update an old version of a Docker image to a new version.

We will be using the following Docker image names in these instructions. Substitute the version you are using as appropriate.

	Docker image names
New version	hpci/gsi-openssh:20240902
Old version	hpci/gsi-openssh:20240209

4.1 About storing different versions of Docker images

You can use tag identifiers to differentiate multiple versions of Docker images, making it possible to store multiple versions of hpci/gsi-openssh in local storage. To save both versions, load the new version (hpci/gsi-openssh:20240902) into an environment where the old version (hpci/gsi-openssh:20240209) is already loaded.

$  docker images hpci/gsi-openssh
REPOSITORY         TAG        IMAGE ID       CREATED        SIZE
hpci/gsi-openssh   20240902   b3c96bb6283d   8 days ago     310MB
hpci/gsi-openssh   20240209   dd8e64a66353   7 months ago   320MB
$

In other words, even loading the new version does not automatically erase the already-loaded old version. If the old version of the image is no longer needed, you will need to explicitly erase it.

4.2 Installing the new version of the Docker image

To install the new version of the Docker image, follow the same instructions you used for the initial deployment in 3.3 Loading the Docker image (only when installing)

4.3 Deleting an old version of a Docker image

If the old version of the Docker image is no longer needed, follow these instructions to delete it from local storage.

Shut down the Docker container

If the Docker image you want to delete is running as a container, you will need to first shut down that container.

1. Check what Docker container is running using the docker ps command.

$ docker ps
CONTAINER ID   IMAGE                       COMMAND                   CREATED         STATUS         PORTS     NAMES
dea437f1788a   hpci/gsi-openssh:20240209   "sudo /usr/sbin/cron…"   2 minutes ago   Up 2 minutes             gsi-openssh
$

You can see that the container gsi-openssh generated by the old version of the Docker image (hpci/gsi-openssh:20240209) is running.

2. Shut down the running container using the docker stop command.

   To shut down the container named gsi-openssh, execute the following command.

$ docker stop gsi-openssh
gsi-openssh
$

If you used the –rm option when you executed the docker run command, the container will be deleted when it is shut down.

Delete the Docker container

If you did not use the –rm option when you executed the docker run command, the container will not be deleted when it is just shut down. Perform the following steps to delete the container.

1. Check all the containers, including stopped ones, using the docker ps -a command.

$ docker ps -a
CONTAINER ID   IMAGE                       COMMAND                   CREATED         STATUS                     PORTS     NAMES
dea437f1788a   hpci/gsi-openssh:20240209   "sudo /usr/sbin/cron…"   4 minutes ago   Exited (0) 2 minutes ago             gsi-openssh
$

You can see that the container gsi-openssh generated by the old version of the Docker image (hpci/gsi-openssh:20240209) exists and is in an “Exited” state.

2. To delete the Docker container, use the docker rm command.

   Here, we are deleting the container named gsi-openssh

$ docker rm gsi-openssh
gsi-openssh
$

Delete the Docker image

1. To delete the Docker image, execute the docker rmi command.

   Here, we are deleting the image named hpci/gsi-openssh:20240209.

$ docker rmi hpci/gsi-openssh:20240209
Untagged: hpci/gsi-openssh:20240209
Deleted: sha256:dd8e64a66353987d617cf242913b2145a7d19cbc80c1fec01329d29997fe6fe0
Deleted: sha256:02d45363cf7630d18dc82f0561ad606a5371b31d21401bcee8d66b5d3cfe5475
Deleted: sha256:53a8a85090e505fae2ed361790bfde3e3fe35e25d5e513827be6dbe76e0aadc0
Deleted: sha256:a0d6a1a8cc9943689acd24e6402aaf89bdf3bb0c32a0af6d8761e316cc999c8c
Deleted: sha256:ebfcbccf216ba5ac337f2d2a04909a7e6fa8ce69ab4adc19b39203efd04183d5
Deleted: sha256:8b72ea9dbe57bf486c9a45f5be486cb0d6a2172838e117894af48c34ee79d505
Deleted: sha256:bb077eef2bb1df3d5cd9dee745744763984d88397026509020f9fa7ff9697619
$

Attention

If you attempt to delete a container generated from an image while it still exists, you will get the following error message.

$ docker rmi hpci/gsi-openssh:20240209
Error response from daemon: conflict: unable to remove repository reference "hpci/gsi-openssh:20240209" (must force) - container dea437f1788a is using its referenced image dd8e64a66353
$

5. How to run an X11 client

Attention

This has not been verified on Mac with Apple silicon.

This explains the procedure for running an X11 client on a remote host for local display on macOS when connected by gsissh.

For the X server running on macOS, we will use XQuartz.

5.1 Installing XQuartz

5.1.1 Download

Download the XQuartz installer from the XQuartz website. As of this writing, the current version is 2.8.5.

https://www.xquartz.org/

5.1.2 Install

1. Run the downloaded XQuartz installer.

• A window with a “XQuartz-2.8.5” title will open.

• Double-click the “XQuartz.pkg” icon within it.

2. A warning window is displayed.

• “The package will run a program to determine if the software can be installed.”

• Click the [ Accept ] button.

3. A window with a “Install” title will be displayed.

   • Seven items are listed.

     • Introduction

     • Read Me

     • License

     • Destination Select

     • Installation Type

     • Installation

     • Summary

   • Follow the order displayed by the installer.

4. Introduction

• Check the contents.

• Click the [ Continue ] button.

5. Read Me

• Check the contents.

• Click the [ Continue ] button.

6. License

• Check the contents.

• Click the [ Continue ] button.

• The software license agreement dialog is displayed.

  • “To continue installing the software you must agree to the terms of the software license agreement.”

  • Click the [ Agree ] button.

7. Destination Select

• If you agree to the “License”, the next item to be displayed is not “Destination Select” but the next “Installation type”. The contents of “Destination Select” are displayed only when the [ Change Install Location … ] button is pressed in “Installation type”.

  • Select the installation destination.

  • Click the [ Continue ] button.

  • Go back to “Installation Type”.

8. Installation Type

• Initially, “Macintosh HD” is selected as the installation destination.

  • Click the [ Change Install Location… ] button if you need to make changes.

  • Go back to “Destination Select”.

  • When the “Destination Select” is finished, the process returns here.

• Click the [ Install ] button.

9. Installation

• A dialog will be displayed asking, “Installer is trying to install new software.”

• Enter the password in the [ Password:] field and click the [ Install Softoware ] button.

• The installation progress will be displayed on the screen.

10. Summary

• The message “The installation was successful.” is displayed.

• Click the [ Log Out ] button.

• A dialog about disposing of the installer is displayed.

  • “Do you want to move the “” Installer to the Trash?”

  • Select either [ Keep ] or [ Move to Trash ] .

• If selected, you will be automatically logged out.

11. Log in again.

• This completes the installation work.

5.1.3 Set up

• Launch XQuartz.

• Select Preferences under the XQuartz menu.

  • Click on the Security tab in the Preferences window.

  • Check the following two checkboxes:

    • Authenticate connections

    • Allow connections from network clients

  • Relaunch XQuartz for these settings to take effect.

    • Select Quit X11 from the XQuartz menu.

    • Launch XQuartz.

5.2 Run the X client

This explains how to run the X client xeyes on the remote host connected by gsissh in the Docker container.

In this example, you will be logging into das.r-ccs.riken.jp, the login server for the large-memory/GPGPU-equipped client environment at the RIKEN Center for Computational Science (R-CCS).

With XQuartz running, follow the below procedure in the terminal.

1. Append 127.0.0.1 to the access control list with the xhost command.

$ xhost
access control enabled, only authorized clients can connect
$ xhost +127.0.0.1
127.0.0.1 being added to access control list
$ xhost
access control enabled, only authorized clients can connect
INET:localhost
$

2. Run the Docker image with the docker run command.

$ docker run -d --rm --name gsi-openssh -v /Users/username/Documents:/home/hpciuser/work -e DISPLAY=host.docker.internal:0 hpci/gsi-openssh:20240902

Be sure to add the -e DISPLAY=host.docker.internal:0 option to the command.

-e LIST

Sets environment variables that are available for the process that will be launched inside of the container. In the above example, we have set the DISPLAY environment variable to the value host.docker.internal:0.

3. Connect to the container with the docker exec command.

$ docker exec -it gsi-openssh /bin/bash

4. Download the proxy certificate using the myproxy-logon command.

[hpciuser@XXXXXXXXXXXX ~]$ myproxy-logon -s portal.hpci.nii.ac.jp -l [HPCI-ID]
Enter MyProxy pass phrase: ********
A credential has been received for user <HPCI-ID> in /tmp/x509up_up2000.
[hpciuser@XXXXXXXXXXXX ~]$

5. Log in to the login server. In the below example, you will be logging into das.r-ccs.riken.jp, the login server for the large-memory/GPGPU-equipped client environment at the RIKEN Center for Computational Science (R-CCS).

[hpciuser@XXXXXXXXXXXX ~]$ gsissh -Y -p 2222 das.r-ccs.riken.jp
*****************************************************************
Gfarm clients with large memory and GPGPU is ready.

  R-CCS provides 4 compute nodes equipped with large-capacity memory (1,024 GB) and GPGPU (NVIDIA Tesla P100) as  HPCI shared storage clients.
  You can use exclusively one of these 4 compute nodes by using pbs pro job scheduler on the login server(das.r-ccs.riken.jp).
  The followings can be used on each compute node.

   Singularity, Container execution environment
   ParaView, Visualization environment
   HPCI shared storage from Singularity container
   Intel compiler and PGI compiler

    For details, please visit : https://www.hpci-office.jp/info/pages/viewpage.action?pageId=133667887
*****************************************************************
Last login: Wed Jun 30 15:15:17 2021 from XXX.XXX.XXX.XXX
[hpci00xxxx@das ~]$

To enable “X Forwarding”, add the -Y option.

-Y

This results in more dependable X11 transfers.

6. Run xeyes

[hpci00xxxx@das ~]$ xeyes

6. Notes on container environments

6.1 sudo

sudo(8) can be run as NOPASSWD. For details, refer to the following file.

• /etc/sudoers.d/hpciuser