bohrium

name	bohrium
description	Submit and manage computational jobs on Bohrium (bohrium.com) cloud platform using bohr CLI. Recommended for submitting to Bohrium.
metadata	{"tools":["run_bash"],"tags":["bohrium","hpc","job-submission","cloud-computing"]}

Bohrium Cloud Job Management

Submit and manage computational jobs on Bohrium cloud platform via bohr CLI.

Prerequisites

1. Verify bohr CLI installation

Verify: bohr version

If not installed, run the following command to install it:

• Linux/macOS: curl -fsSL https://bohrium.com/download/bohr | sh

2. Verify user access

echo $ACCESS_KEY

If not set, notify the user to provide the access key as an environment variable, or set an environment variable through MatCreator's WebUI.

Tell the users that access key can be found in the Bohrium main dashboard under User Profile -> Access Key.

3. Get your project ID

First, try

echo $BOHRIUM_PROJECT_ID

If not set, then run:

bohr project list --json
# Note the project ID you want to use

And select the first available project ID in the list. If multiple projects are available, notify the users as the first available project ID may not be the one they want to use, and they had better set the environment variable BOHRIUM_PROJECT_ID to the desired project ID.

To the users that the project ID can also be found in the Bohrium Cloud dashboard under Projects.

Machine Types

For available machine types and suggestions for choosing machines (Machine SKU reference), see references/bohrium-machines-ref.md.

Job submission and management

For submitting, managing and downloading a single job and a batch of jobs, see example and bohr CLI usage details in references/bohrium-cli-ref.md.

Tips and Pitfalls

• Always check machine availability before submitting — popular GPU configs may be out of stock
• Use --backward_files to specify outputs — comma-separate values, not making an array
• Set explanatory job names — job name should indicate its type, content and the variation branch (for example, "SiO2-md-1000K-10000steps-repeat-2") to make tracking easier with many jobs.
• Download results promptly — completed jobs are only retained for a limited time on Bohrium cloud!
• Wrap complex commands in a shell script — write a shell script, upload, and replace command with bash script.sh. This is more reliable and maintainable than long inline --command strings.
• GPU jobs need GPU-enabled images — not all images have CUDA/cuDNN.
• MPI jobs — use mpirun -np N where N matches your machine's CPU cores.
• Memory-intensive jobs — pick machines with higher memory ratio (e.g., c8_m64 vs c8_m8)
• bohr commands can be slow — because API endpoint can be slow. Wrap commands with timeout 60-120. When submitting very large directories and files, it may require even longer timeouts. Expect upload speed averaging ~ 1~5 MB/s.
• Never use bohr <whatever> list commands interactively — without --json keyword, bohr <whatever> list opens interactive TUI that hangs in non-terminal. Never do that!
• Error reports — check error messages in STDOUTERR (shell stdout/stderr) that comes with logs, if not redirected to a result file by something like > output.txt 2>&1.
• Extract zip files — Results are downloaded as a zip file to the specified output directory, may need to extract!
• Use --help to explore more options — e.g., bohr job submit --help for all job submission parameters

Troubleshooting

Issue	Solution
Login fails	bohr login again, check credentials
Machine not available	Try a different SKU or wait
Job stuck in pending	Check quota, try other machines
No output files	Check logs for errors, verify command ran
Out of memory	Use machine with more RAM

References

• references/bohrium-cli-ref.md — Bohr CLI command reference
• references/bohrium-machines-ref.md — Machine SKU reference
• Full docs online: https://bohrium.com/docs/cli