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Using BMD Compute
Who this page is for. You are new to the BMD Lab and want to run your first calculations. You do not need to know Linux, SSH, the POWER cluster, SLURM, Python, or how to run VASP by hand. BMD Compute takes care of those for you. You can learn them later, when you want to understand and control what BMD Compute does underneath.
BMD Compute is authoritative for how BMD VASP calculations are generated and executed. This page is a first-use walk-through; the pages linked at the end explain the science and the settings in depth.
BMD Compute is the lab's browser-based tool for running VASP calculations on Tel Aviv University's POWER cluster. You give it a crystal structure and tell it what result you want; it builds the calculation, prepares it on the cluster, submits it, lets you follow its progress, and shows you the results.
Everything happens in one web page, arranged as numbered steps from top to bottom:
- Structure
- Structure Summary (including Method Considerations)
- Calculation Definition
- Calculation Summary
- Generated Inputs
- Execution Summary
- Ready for Submission
- Monitoring
- Results
The rest of this page follows those steps.
BMD Compute is a lab-internal service. It is only reachable from the Tel Aviv University network or the TAU VPN, so connect to the VPN first if you are working off campus.
Connect to the TAU network or TAU VPN, then open http://132.66.66.90:8000/
in your browser. No personal BMD Compute login is required.
BMD Compute submits calculations through the lab's shared computing infrastructure.
In Structure, choose the Structure Format (POSCAR or CIF) and paste the text of your structure into the Structure box. Then click Analyze Structure.
If you do not have a structure file yet, ask your supervisor, or download one from a structure database such as the Materials Project, which lets you export a material's structure as a CIF or POSCAR file.
If the structure cannot be read, BMD Compute shows Structure Validation Failed with a reason and a suggestion.
Structure Summary shows what BMD Compute understood: formula, number of atoms, volume, density, lattice parameters and angles, and symmetry (space group and crystal system). Check that this matches the material you intended.
Below it, BMD Compute may show Method Considerations. These are cards that point out features of your structure that matter for the method, for example:
- elements that are often magnetic (spin polarisation);
- heavy elements (spin–orbit coupling, SOC);
- a likely two-dimensional, layered structure (a van der Waals correction);
- transition-metal oxides or fluorides (DFT+U).
In the standard workflows (next step), BMD Compute resolves some of these treatments automatically, according to its methodology, and the card then says so (for example "DFT+U applied" or "Spin Polarisation applied"). In some cases the card instead explains why a treatment was not applied. You do not have to act on these cards, but read them: they tell you what physics your calculation includes. The treatments themselves are explained on BMD Compute Advanced Options.
In Calculation Definition, under Scientific Specification, choose a Desired Output: the result you want. BMD Compute then sets up the complete, multi-stage calculation for you.
| Desired Output (in BMD Compute) | What you get | Explained on the Workflows page as |
|---|---|---|
| Energy only | A PBE static total energy of the structure as supplied | Static Energy |
| Relaxed structure | The relaxed (equilibrium) structure, from two successive PBE geometry optimisations | Relaxed Structure |
| Electronic density of states | An HSE06 density of states at the PBE-relaxed structure | Density of States |
| Electronic band structure | An HSE06 band structure at the PBE-relaxed structure | Band Structure |
| Custom workflow | You choose every stage, level of theory and option yourself | — |
For your first calculations, choose one of the first four. Their stages are shown as a "BMD Compute workflow" and cannot be edited; any treatments BMD Compute has added automatically are listed under Applied Treatments on the stage cards. Custom workflow is for later, when you know which stages and options you want; in a Custom workflow nothing is added automatically, and you set the Advanced Options yourself.
Why each Desired Output uses the stages it does is explained on BMD Compute Workflows.
Execution Resources (CPUs, memory, walltime and queue) control the computational resources requested for the calculation. New users can normally leave these unchanged unless a maintainer or project workflow specifies otherwise.
Click Build Calculation. If the combination is not supported, BMD Compute shows Calculation Validation Failed with a reason and a suggestion. After a successful build, the Calculation Summary shows the plan. If you change something, click Update Calculation.
Generated Inputs shows the VASP input files BMD Compute will use (INCAR,
KPOINTS, POSCAR) and a Submission Summary and SLURM script describing
how the job will run. Execution Summary repeats the key facts: cluster,
resources, POTCARs and VASP executable.
You are not expected to understand every setting yet. At this stage it is enough to notice that:
- the inputs were generated for you, and nothing has been sent to the cluster;
- for multi-stage workflows these are previews made before anything runs; a later stage uses the structure produced by the stage before it.
When you want to understand the settings, read VASP — fundamentals and BMD Compute INCARs.
In Ready for Submission, click Prepare Remote.
This sets up your calculation on the POWER cluster: BMD Compute connects to the cluster, creates a working directory for the job, uploads the calculation and the files needed to run it, links the pseudopotentials (POTCARs), and writes the job script. When it finishes you see Remote Preparation Complete.
Preparation is not submission. After Prepare Remote, everything is in place, but no job has been submitted and nothing is running yet. If preparation fails, BMD Compute shows Remote Preparation Failed with the step that failed, a reason and a suggestion; nothing has been submitted.
Only after a successful preparation does Submit Calculation become available. Click it to submit the job to the cluster's queue.
On success you see Submitted together with a Job ID. Write down the Job ID. It is how you come back to this calculation later, and how you ask for help about it. BMD Compute does not keep a personal list of your calculations.
If submission fails, BMD Compute shows Submission Failed with a reason and a suggestion.
Monitoring shows the job's current state on the cluster. The page does not update by itself: click Refresh Queue Status to check again. The summary you will usually see is:
| Summary | Meaning |
|---|---|
| PENDING | The job is waiting in the queue for computing resources. This can take a while. |
| RUNNING | The job is running. |
| SUCCESS | The job has finished normally (the scheduler reports it as COMPLETED). |
| FAILURE | The job stopped with an error, ran out of time or memory, or was cancelled. |
| UNKNOWN | BMD Compute could not determine the state. Try refreshing later. |
The panel also shows the raw scheduler state (for example COMPLETED) and the job's exit code. Calculations can take from minutes to days, depending on the material and the Desired Output.
Coming back later. You can close the page. To return to a calculation, enter its Job ID under Resume Existing Calculation at the top of the page and click Resume.
When the summary is SUCCESS, click Load Results. Results shows a summary of the completed calculation, for example:
- final formula, final energy and energy per atom;
- whether the electronic and ionic steps converged;
- the density of states or band structure (with band gap) when you asked for one, including a plot you can save with Download PNG;
- the final structure in an interactive viewer.
Check the convergence lines before trusting a result. If you are unsure what a result means, ask your supervisor.
BMD Agent helps you
understand what happened in a calculation, for example when a job is stuck,
fails, finishes without converging, or gives results you did not expect. Given
the Job ID (bmd-agent JOB_ID), it gathers the evidence from the cluster and
summarises it in plain language.
BMD Agent is a command-line tool. If it has not been set up for you, ask a BMD Lab maintainer, and include the Job ID when you ask for help.
When you want to understand what BMD Compute is doing for you, read these in order:
- VASP — fundamentals: the physics and the VASP input files.
- BMD Compute Workflows: why each Desired Output is a sequence of stages.
- BMD Compute INCARs: what the settings in each stage mean.
- BMD Compute Advanced Options: spin polarisation, DFT+U, van der Waals corrections and other treatments.
Later, if you want to work on the cluster directly, the numbered computing tutorials on the Home page teach Linux, connecting to POWER, the SLURM queue and Python. They are not needed to use BMD Compute.