News and Announcements

[Product Update] A Fresh New Look and New features: Paper Recommendations & Public Databases

Release time: 2024-04-07

This update is version 2.0.0, which mainly includes:

1. Bohrium Gets a Fresh New Look: Bohruim Discovery merged into Main Site for better browsing experience.

2. New Paper Recommendations: The most personalized paper recommendation engine, discovering the most worthwhile papers for you.

3. New Public Databases: With millions of massive data resources, empowering scientific computing with strong support.

[Product Update] Storage System Upgrade: New Personal Storage Space /personal

Release time: 2023-12-27

This update is version 1.9.2, which mainly includes:

Storage system upgrade: new personal storage space /personal.

1. Features of /personal:

   • /personal is a storage space for individual user files, not tied to any specific project.

   • Only the user themselves can access it, and files within can be used across any project.

2. Storage Capacity of /personal:

   • Each user will receive 500GB of free storage space. If you need more storage space, please contact bohrium@dp.tech to apply.

3. Usage Recommendations: It's advised to store personal private files in /personal, while files that belong to a project should be placed in the /share within the project.

Note:

• Due to various disadvantages, the /data is scheduled to be discontinued at the end of January 2024. Please ensure to migrate any data you wish to keep to /personal or the /share within your project in a timely manner.

• We will launch a one-click data migration feature in mid-January 2024 to assist you with the data transfer.

Appendix: Comparison of /personal, /data, and /share:

Difference	/personal	/data	/share
Read/Write Permissions	Only the individual user	User and project admins	All members of the project
Scope of Use	Files can be accessed in any project	Files can only be accessed within the project to which the /data belongs	Files can only be accessed within the project to which the /share belongs
Mounting to Nodes	Supported, can be mounted on any project's nodes	Supported, can only be mounted on nodes of the project to which the /data belongs	Supported, can only be mounted on nodes of the project to which the /share belongs
Automatic Download of Job Results to Drive with -r	Supported	Supported	Supported
Capacity Expansion	Supported	Not supported	Supported

[Product Update] New Job Result Visualization Analysis Module, Files Support Batch Upload and Download

Release time: 2023-11-16

This update is version 1.9.1, which mainly includes:

1. Job results support visualization analysis

   • For DeepMD-kit model training jobs, the job details page automatically displays the training loss chart and learning rate curve, supporting various interactive operations such as mouse wheel zooming and dragging to view

• The "Real-time Files" module in the job details page now supports previews of images and structure files, allowing real-time previews of dynamic trajectories and structural changes during calculations of various software such as VASP, LAMMPS, GROMACS, and also supports a series of interactive operations such as mouse wheel zooming and rotating structures

2. File management page upload and download function updates

   • Files support batch upload and download

   • Added file transfer list, file transfer supports canceling or retrying, and both upload and download have records

   • Downloaded content can be quickly downloaded again in the transfer list, or the download address can be copied with one click and shared with others

3. Notebook experience optimization

   • Notebook page loading speed is greatly improved

   • Code cells display line numbers and indentation, running status indicators during runtime, and support one-click running of code cells and viewing running time

   • The left side directory of the Bohrium Square Notebook supports jumping, and multi-level directories support expansion and collapse

   • When editing a Notebook, you can use the terminal to log in to the Notebook node, perform environment installation and configuration, and take effect in real time

4. Image center upgrade and renovation

   • Public images have been completely revamped, now aggregated according to software, and marked with the various software included

   • Support creating images using Dockerfile and viewing build logs

   • When building images for development institutions, support excluding unnecessary paths to reduce image size and improve image pull speed

   • Deleted image tags now support reuse

5. Other feature updates

   • Added Bohr translation assistant, which can translate the full text of the Notebook in Bohrium Square into Chinese or English with one click

   • During job execution, users are allowed to perform various operations such as adding, deleting, and modifying files on the computing nodes to assist in job result analysis

   • Machine models are fully open, and can be selected as needed in various scenarios such as submitting jobs, opening container nodes, and running Notebooks

   • Support mobile recharge; recharge records can be viewed and invoices can be applied for by yourself

   • Added user ID, which can be viewed in the top navigation bar (including mobile), personal center, and account settings

[Product Update] Comprehensive upgrade of Notebook, supporting collaborative editing and creating Notebook collections; added project shared drive, supporting file sharing within the project; added Bohrium user profile; integrated Bohr code assistant

Release time: 2023-09-25

This update is version 1.9.0, which mainly includes:

1. Comprehensive upgrade of Notebook, now supporting private sharing, public publishing, and collaborative editing; additionally, enabled connections to existing nodes during Notebook editing

   • Visit Bohrium Square, click the "New Notebook" button, and you can quickly create a new Notebook
   • When running a Notebook, in addition to creating a new Notebook node, you can also use the already configured container node through the "Connect to existing node" option
   • If you need to invite others to collaborate on the Notebook, you can click the "Share" button in the upper right corner of the page to enable collaborative editing
   • Completed Notebooks can be privately shared or publicly published, both of which are supported by Bohrium Notebook

2. Allowing browsing or creating Notebook collections

   • On the "All Collections" page, you can freely browse or follow existing Notebook collections, and display reading progress
   • By clicking "Your Profile-Collections", you can view your own created and followed Notebook collections, and support creating new collections
   • When reading a Notebook in Bohrium Square, you can quickly add a single Notebook to a collection

3. Supports file sharing within projects

   • Added a shared drive (/share), where files in this directory can be shared among project members; calculation results, real-time files, and Bohrium Square Notebooks can all be saved to the shared drive

4. Supports mounting datasets when container nodes are powered on

   • When the container node is powered on, you can choose the required dataset for mounting. After mounting is completed, you can access the dataset files through the command line or in the Notebook editing page

5. Added Bohrium user profile, displaying personal created or followed Notebooks and participated competitions

   • On all Bohrium pages, by clicking on the user's avatar, you can quickly jump to the user's homepage. On this page, you can view the user's growth level, followed users, created and followed single Notebooks and Notebook collections, as well as participated competitions.

6. Integrated Bohr code assistant

   • When running a Notebook in Bohrium Square, if a code error occurs, the Bohr code assistant will automatically provide answers for the error cell; in addition, when selecting a portion of code in a code cell, a "Code Interpretation" button will automatically pop up, and clicking it will make the Bohr code assistant interpret the selected code

   • Provides automatic error answering function when editing a Notebook

[Product Update] Added Bohrium Dataset

Release Time: 2023-08-15

This update is version 1.8.1, which mainly includes:

1. Introducing the Bohrium Dataset feature, which allows users to create datasets for job submission, data sharing, version control, and permission management.

   Now, when you encounter the following issues, you can resolve them by creating datasets, such as:

   • When submitting a job, input files are large, resulting in slow job submission.

   • When submitting a job, input files need to be frequently reused.

   • Need to share files with other users or projects.

[Product Update] Home redesign, added Bohr Assistant; new feature to view computing node monitor; support for custom notification sending channels; comments now supported within Bohrium Notebooks.

Release Time: 2023-07-20

This update is version 1.8.0, which mainly includes:

1. The home has been fully redesigned, with the addition of the Bohr Assistant

   • The Bohrium home is now divided into three main sections: User Guide, Recent Usage, and Notebooks.

     • User Guide: Provides usage guidance for different scenarios, helping new users get started quickly, while also serving as a quick access point for experienced users.

     • Recent Usage: Displays the user's recently submitted jobs, used files, and nodes, allowing for quick access to information and actions.

     • Notebooks: Showcases the most popular and latest Notebooks examples.

   • Introducing the new Bohr AI Assistant. This assistant is capable of answering any complex questions, as well as helping you write code, explaining the meaning of code, debug, and much more. It can be used throughout the entire Bohrium.

2. Job status refinement and adjustment, now supports viewing the monitor of computing nodes

   • Job status has been comprehensively refined, allowing you to clearly understand the current progress of your jobs.

   • Identifies common job failure causes, such as OOM (Out of Memory), non-existent commands, and program exceptions.

   • During job running, you can view the monitor of the computing node machine for the job within the Job Details page, allowing for timely detection of any operational anomalies.

3. Custom settings are now available for notifications

   • Click on the profile icon in the top right corner of the page and find Notification Settings to customize the sending channels for various notifications.

4. Bohrium Notebooks now support comments within cells

   • Click on the comment button in the upper right corner of a Notebooks cell to leave a comment on the current cell. Additionally, you can also reply to existing comments.

   • When your published Notebooks receive new comments or your posted comments receive new replies, you will be notified in your Bohrium Notifications.

5. Other detailed experience optimizations and bug fixes

[Product Update] Added support for more software with web submission. Allowing submission of multi-node jobs. All jobs now support clone for efficient submission. Management nodes support domain name connection

Release Time: 2023-05-23

This update is version 1.7.13, which mainly includes:

1. Web Submission feature update:

   • Added support for more software. Now DeepMD-kit, ABACUS, LAMMPS, GROMACS, CP2K, and Quantum Espresso all support job submission via the Web Submission.

   • Input files now support uploading folders.

   • Support for submitting multi-node jobs.

2. All jobs now support one-click clone for resubmission. Have you ever encountered the following situations?

   • You need to submit a new job by only modifying a parameter from a previous job, but you still have to prepare the entire input folder, which is quite troublesome.

   • After submitting a job, you realize the configuration is incorrect and want to quickly modify and resubmit it.

   Now, the clone feature can quickly help you solve the above problems. Simply find the job you want to copy on the "Jobs" page, clone, modify and submit.

3. Supports connecting to management nodes using domain names. After stop and restart, the domain name remains unchanged.

[Product Update] Notebook supports custom images. Web Shell experience is upgraded

Release Time: 2023-05-18

This update is version 1.7.10, which mainly includes:

1. Supports running Notebook with custom images. Click here to learn about image requirements.

2. Optimized the Notebook user experience:

   • The author can preview the shared page, and the author can view the number of page views in the shared pop-up.

   • Renaming or moving a Notebook will no longer affect the shared link.

   • Notebook displays node GPU/CPU utilization, memory, and other information when running.

3. Optimized the Web Shell user experience:

   • Supports collapsing the left-side directory tree, and the terminal zoom and full-screen experience have been improved.

   • Clicking on an opened file will automatically navigate to the corresponding location in the file tree.

   • Material visualization supports more file types, such as common structure files and their variants like .poscar/.contcar/.vasp, as well as common trajectory files and their variants like .dump/.lammps/.lammpstrj/.lmp/.conf.

   • Unknown file types will be opened with the text editor by default.

   • Optimized details such as real-time saving, image scaling, format error checking, and text copy prompts within the terminal for a better user experience.

[Product Update] Added real-time viewing of computing results for running jobs. Support for pulling DockerHub images. New Web Shell online decompression feature

Release Time: 2023-04-04

This update is version 1.7.0, which mainly includes:

1. No need to wait for the job to finish, you can now conveniently view the real-time files generated during the computation on the job details page.

• You can click on the real-time file within the job details to directly view its content。 You can also download the real-time file you want to view to your local device or save it directly to the /data for further processing.

• The real-time files generated during the job execution will be retained for a period of time, so you can view and save them whenever needed.

2. There is no need to manually transfer existing images on the public repository. You can directly pull images from the DockerHub public repository, create Bohrium custom images, and use them directly on Bohrium. Click here to learn the specific creation method.

3. Web Shell now supports online decompression.

[Product Update] Added web job submission, making it simpler and faster. Jobs can be cloned, allowing for direct reuse of the same configuration

Release Time: 2023-02-06

This update is version 1.6.0, which mainly includes:

1. Have you ever encountered this kind of issue:

   Not sure how to get started with Bohrium for the first time?

   Unfamiliar with Linux commands?

   Want to quickly run a simple job, but preparing a job.json file is too cumbersome.

   Using the Web Submission can solve your problem. All you need to do is select the software you want to use, upload input files, and complete the software and hardware configuration to submit a simple job.

2. Jobs submitted via the web can be cloned, allowing you to save frequently used software and hardware configurations as templates. When needed, simply clone the template with one click.

3. For jobs submitted to parallel, you can view the files while they are running. You can go to the job details page and use SSH to connect to the computing node.

[Product Update] Added self-service top-up option

Release Time: 2023-01-17

This update is version 1.5.3, which mainly includes:

1. Introducing Bohrium Self-Service Top-up, which allows users to make small payments within the system, making the top-up process simpler and more convenient.

[Product Update] Added low disk space reminder and optimized the automatic download feature

Release Time: 2022-12-29

This update is version 1.5.2, which mainly includes:

1. Added low disk space reminder: when the usage of your management node's system disk reaches ≥80%, the node will display the current usage and send you a low disk space warning message. Please clean up unnecessary files in a timely manner to avoid issues such as the inability to retrieve computation results due to full disk capacity.

2. Optimized the automatic download feature

• In addition to Bohrium management nodes, for locally submitted jobs, you can also specify the automatic download path for the results when submitting a job using lbg job submit -r /data.

• There's no need to keep the node running. The system will download the results to the specified directory on the data disk after the job is completed.

Notice：Automatic downloads can only be specified to download to a directory on the data disk. The specified path following the -r parameter should start with /data. After the job is completed, you can view the results by entering the corresponding project's data disk.

3. Bohrium Notebook has added code auto-completion (requires the node to be in a running state) and made other user experience improvements.

4. Other detail experience improvements and bug fixes.

[Product Update] Added Bohrium Notebook

Release Time: 2022-11-25

This update is version 1.5.1, which mainly includes:

1. Introducing the Bohrium Notebook feature, providing a one-stop interactive environment for writing and running code, enhancing the development collaboration experience.

[Product Update] Added administrator role and project manager capabilities, allowing for management of member nodes and jobs. Data disk can be accessed without start the node. You can submit jobs while creating images

Release Time: 2022-11-22

This update is version 1.5.0, which mainly includes:

1. Supports setting Project Administrators and Batch Managing Members, effectively improving project management efficiency. For a detailed description of administrator permissions, please refer to Project Roles and Permission Explanation.

2. Project administrators can manage all nodes and jobs within the project, such as logging into member nodes, viewing member job progress, and assisting members in resolving bugs, resulting in higher team collaboration efficiency and more synchronized information.

3. Access the data disk without start the node: When the node is stopeed, you can directly access the data disk by clicking the "SSH Connect" button, making file management more convenient.

4. You can submit jobs using the image address without waiting for the image creation to complete, saving time and increasing efficiency.

[Product Update] New features include automatic stop, member budget, message center, and relaxed command restrictions when logging into compute nodes via Web Shell

Release Time: 2022-09-28

This update is version 1.4.0, which mainly includes:

1. Introducing the Automatic stop of Management Nodes feature, allowing users to specify a stop time according to their needs. The system will send a message reminder about 10 minutes prior to stop.
2. Introducing the Member Budget Feature, allowing project managers to set spending limits for each member, suitable for scenarios such as research group cost management, classroom teaching, and hands-on workshops.
3. Introducing the Message Center feature, which sends notifications when events such as insufficient balance or budget, job failure, or node/snapshot/image creation failure occur. To avoid unnecessary disturbances, if multiple jobs fail within 5 minutes, only the first one will be sent as a notification.
4. When logging into compute nodes via Web Shell, the restriction of only being able to execute commands from a whitelist has been lifted. Now, all commands supported by the compute node environment can be executed.
5. Lebesgue Utility supports command auto-completion. In addition to updating to the latest version, you also need to add auto-completion related configurations in the rc file.

[Product Update] Supports automatic downloading of computation results and introduces job details page

Release Time: 2022-09-05

This update is version 1.3.0, which mainly includes:

1. Supports automatic downloading of computation results to the management node. You can add a line with the result field in the job submission script to specify the directory, for example:

    "result":"./result/"

   You can also specify the directory when submitting the job using the lbg job submit -r ./result parameter.

   Notice：This feature only supports automatic downloading of results to the Bohrium management node, and the node must be in a running state when the job is completed.

2. Introducing a new job details page, which allows you to view information such as the job's lifecycle and the status of compute nodes. It also supports terminating jobs via the web interface.

3. Introducing a new job view, which supports searching by job ID or job name.

4. Introducing online viewing support for structure files in pdb, sdf, mol, and mol2 formats, as well as improved speed when opening trajectory files in Web Shell.

5. Optimized the error message when there are mistakes in the json file used for job submission.

6. Other detailed experience optimizations and bug fixes.

[Product Update] Now you can specify the maximum duration for a job to run

Release Time: 2022-08-11

This update is version 1.2.0, which mainly includes:

1. When submitting a job, you can specify the maximum duration for it to run. For example, by specifying "max_run_time": 1440, in the configuration file, you indicate that the job's maximum runtime is 24 hours (1440 minutes). If the job has not finished after 24 hours, the system will automatically terminate the job and save the generated calculation result files.

2. Optimized the style of the price calculator page.

3. Other detailed experience optimizations and bug fixes.

[Product Update] Supports trajectory file playback

Release Time: 2022-07-27

This update is version 1.1.2, which mainly includes:

1. In the visualization preview feature of the management node's data disk, playback of dump and other trajectory files is supported.

2. Lebesgue Utility introduces the log machine ls command, which allows you to view all available machine configurations.

3. Other detailed experience optimizations and bug fixes.

[Product Update] Supports sharing images across projects.

Release Time: 2022-07-15

This update is version 1.1.1, which mainly includes:

1. Supports sharing images across projects, allowing you to share pre-built software and data with any specified user via images.

2. The number of custom images per project has been increased to 10.

3. Project creators can pause or release nodes created by project members.

4. New images for some commonly used software have been added. You can view them in the public image list on the "Images" page.

5. Other detailed experience optimizations and bug fixes.

[Product Update] The management node now features a 1TB data disk, supporting online previews of common file formats.

Release Time: 2022-07-01

This update is version 1.1.0, which mainly includes:

1. The management node now has a 1TB (1024 GB) data disk, providing persistent storage for your data and files, which will not be deleted when the node is released.

2. Files in the data disk support visualization management, allowing you to preview structures and images, as well as edit scripts and parameter files online.

3. Other detailed experience optimizations and bug fixes.

Notice: Lebesgue Utility has an upgrade. It is recommended for existing users to update to the latest version in the terminal to avoid any impact on usage:

pip install -U lbg

[Product Update] Bohrium 1.0.0 release

Release Time: 2022-06-22

This update is version 1.0.0, which mainly includes:

1. Supports first-principles calculations using ABACUS and CP2K on Bohrium, molecular dynamics simulations with LAMMPS, and training and construction of machine learning potential functions using DeePMD-kit and DP-GEN.

2. Introduces Web Shell, providing one-click connection to the management node without logging in; supports accessing compute nodes via Web Shell, making it easy to view the progress of jobs on compute nodes.

3. Project balance has been upgraded to project budget, so you no longer need to transfer funds into the project. Expenses generated by the project will be directly deducted from your account balance. If you need to control the project budget, you can set it on the project management page.

4. Other improvements include interactive and visual experience enhancements, the addition of a help center, updates to public images, and more.