bohrium

name	bohrium
description	Submit and manage computational jobs on Bohrium (bohrium.com) cloud platform using bohr CLI. Recommended for submission methods on 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. Install bohr CLI

• Windows: Download from https://bohrium.com/download, place in PATH
• Linux/macOS: curl -fsSL https://bohrium.com/download/bohr | sh

Verify: bohr version

2. Login

bohr login
# Enter email and password interactively
# Token saved to ~/.bohrium/credentials.yaml

3. Get your project ID

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

Machine Types (Reference)

Bohrium offers CPU and GPU machines. Always check current availability with bohr node list — pricing and inventory change.

CPU Machines

Format: c{cores}_m{mem}_cpu (some have _H suffix for high-performance)

Range	Examples	Price (CNY/h)
2C	c2_m2_cpu ~ c2_m16_cpu	0.16-0.20
4C	c4_m4_cpu ~ c4_m32_cpu	0.32-0.40
8C	c8_m8_cpu ~ c8_m64_cpu	0.64-0.80
12C	c12_m12_cpu ~ c12_m96_cpu	0.96-1.20
16C	c16_m16_cpu ~ c16_m128_cpu	1.28-1.60
24C	c24_m24_cpu ~ c24_m192_cpu	1.92-2.40
32C	c32_m32_cpu ~ c32_m256_cpu	2.56-3.20
48C	c48_m176_cpu ~ c48_m384_cpu	3.84-4.80
52C	c52_m96_cpu ~ c52_m384_cpu	4.16
56C	c56_m160_cpu ~ c56_m224_cpu	4.48
64C	c64_m64_cpu ~ c64_m512_cpu	5.12-7.68
72C	c72_m288_cpu	7.20
96C	c96_m192_cpu ~ c96_m384_cpu	9.60-11.52
128C	c128_m512_cpu	12.80

Check current machines:

bohr node list

GPU Machines

Format: c{cores}_m{mem}_{count} * {GPU_MODEL} or {count} * {GPU_MODEL}_{vram}g (GPU-only)

Available GPU types:

GPU	VRAM	Price Range (CNY/h)	Configs
NVIDIA T4	16GB	2.5-12.0	10
NVIDIA V100	16/32GB	4.5-36.0	18
NVIDIA A100	40/80GB	10.0-80.0	4
NVIDIA 3090	24GB	4.5-36.0	4
NVIDIA 4090	24GB	5.5-44.0	5
NVIDIA 5090	32GB	1.9	1
NVIDIA L4	24GB	5.0-20.0	3
NVIDIA L20	48GB	8.0-64.0	4
NVIDIA P100	16GB	4.0-32.0	4
DCU	16GB	1.2-6.0	8
FPGA	-	8.0	2

GPU-only vs CPU+GPU: Entries like 1 * NVIDIA V100_32g are GPU-only (no CPU/RAM). Entries like c12_m64_1 * NVIDIA L4 bundle CPU+RAM+GPU. Choose based on your workload's CPU needs.

Job Submission

Core command

bohr job submit \
  --project_id "YOUR_PROJECT_ID" \
  --job_name "job-name" \
  --machine_type "c8_m32_cpu" \
  --image_address "registry.dp.tech/dptech/lammps:2023.08.02" \
  --input_directory "./" \
  --backward_files "output.txt,results.log" \
  --command "your command here"

Key parameters

Parameter	Description	Example
--project_id	Your Bohrium project ID	"12345"
--job_name	Job display name	"Cu-EOS-test"
--machine_type	Machine SKU	"c8_m32_cpu"
--image_address	Docker image URI	"registry.dp.tech/dptech/lammps:2023.08.02"
--input_directory	Local dir to upload as job input	"./"
--backward_files	Comma-separated output files to retrieve	"OUTCAR,vasprun.xml"
--job_group_id	Job group ID for batch tracking	"67890"
--command	Command to run	"mpirun -np 8 lmp -in in.lammps"
--log_file	Log file path inside the job	"run.log"
--max_run_time	Max runtime in minutes	120
--nnode	Number of nodes (default 1)	1
--max_reschedule_times	Auto-retry count on failure	3

Common Docker images

Image	Use Case
registry.dp.tech/dptech/lammps:2023.08.02	LAMMPS MD simulations
registry.dp.tech/dptech/deepmd-kit:3.1.3	LAMMPS + DeePMD-kit
registry.dp.tech/dptech/vasp:5.4.4	VASP DFT calculations
registry.dp.tech/dptech/gromacs:2023	GROMACS MD
registry.dp.tech/dptech/python:3.10	General Python
ubuntu:22.04	Base OS, install your own

Find more: https://bohrium.com/docs/images

Batch Submission

For multiple related jobs, create a job group first, then submit all jobs under it. This enables bulk result download and centralized management.

1. Create a job group:

bohr job_group create -n "my-batch" -p "$PROJECT_ID"

2. Submit multiple jobs under the group

for CALC_DIR in <calc_dir_1> <calc_dir_2> ...; do
  bohr job submit \
    --project_id "$PROJECT_ID" \
    --job_name "$(basename $CALC_DIR)"   \
    --machine_type "c32_m128_cpu" \
    --image_address "$IMAGE" \
    --input_directory "$CALC_DIR/" \
    --job_group_id <group_id> \
    --command "your command here"
done

3. Download all results at once

bohr job_group download -j <group_id> -o ./output/

Input/Output Files

Input files are uploaded at submission time via --input_directory. Output files listed in --backward_files are automatically retrieved when the job finishes.

Download results manually

bohr job download -j <jobId> -o ./output/

Results are downloaded as a zip to the specified output directory.

Download logs

bohr job log -j <jobId> -o ./logs/

Job logs include application output (e.g. log.lammps) and shell stdout/stderr (STDOUTERR).

Job Management

# List jobs in a job group (active jobs only by default — completed jobs NOT shown)
bohr job list -j <jobGroupId>
bohr job list -j <jobGroupId> --json     # JSON output
bohr job list -j <jobGroupId> -i         # Finished only  ← use this to detect completion
bohr job list -j <jobGroupId> -r         # Running only
bohr job list -j <jobGroupId> -f         # Failed only
bohr job list -j <jobGroupId> -p         # Pending only

# Job group management
bohr job_group list --json
bohr job_group download -j <groupId> -o ./output/
bohr job_group terminate <groupId>
bohr job_group delete <groupId>

# Kill a single job
bohr job kill -j <jobId>

# List available images
bohr image list

Tracking Long-Running Jobs

Jobs that take hours require explicit state persistence — the agent's context may be compressed or reset before the job finishes.

Step 1: Persist the job ID to disk immediately after submission

JOB_GROUP_ID=$(bohr job_group create -n "my-batch" -p "$PROJECT_ID" | grep -oP '\d+')
echo "$JOB_GROUP_ID" > .bohrium_job_group_id

Step 2: Poll for completion

bohr job list -j <GROUP_ID> --json returns a JSON array — one object per job — each with a status field. Poll until all jobs reach a terminal state.

Terminal statuses: Finished, Failed, Cancelled, Terminated.

GROUP_ID=$(cat .bohrium_job_group_id)
while true; do
  OUTPUT=$(timeout 90 bohr job list -j "$GROUP_ID" --json 2>/dev/null)
  TOTAL=$(echo "$OUTPUT" | jq 'length')
  DONE=$(echo "$OUTPUT" | jq '[.[] | select(.status == "Finished" or .status == "Failed" or .status == "Cancelled" or .status == "Terminated")] | length')
  FAILED=$(echo "$OUTPUT" | jq '[.[] | select(.status == "Failed" or .status == "Cancelled" or .status == "Terminated")] | length')
  echo "[$(date '+%H:%M:%S')] $DONE/$TOTAL jobs done, $FAILED failed"
  if [ "$DONE" -eq "$TOTAL" ] && [ "$TOTAL" -gt 0 ]; then
    [ "$FAILED" -gt 0 ] && echo "$FAILED job(s) failed!" && break
    echo "All $TOTAL jobs finished successfully!" && break
  fi
  sleep 60
done

Step 3: Download results

bohr job_group download -j "$GROUP_ID" -o ./output/

Tips & Pitfalls

• Always check machine availability before submitting — popular GPU configs may be out of stock

• Use --backward_files to specify outputs — comma-separated, not an array

• Set meaningful job names — makes tracking easier with many jobs

• Download results promptly — completed jobs are retained for a limited time

• Wrap complex commands in a shell script — more reliable 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 — use timeout 60-120 wrapper for scripted access

• bohr project list without --json opens interactive TUI that hangs in non-terminal — always use --json

• Use --help to explore more options — e.g., bohr job submit --help for all 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 smaller machine
No output files	Check logs for errors, verify command ran
Out of memory	Use machine with more RAM

References

• references/bohrium-cli-ref.md — CLI command reference
• Full docs: https://bohrium.com/docs/cli