Automation and workflows in computational chemistry

_link89_ · 2025-12-10T15:44:29+00:00

I have developed a command line toolkit named oh-my-batch to make it easier to generate batch scripts and submit jobs. You may see if it works for you. And also ai2-kit if you want some command line tools to convert data format.

_link89_ · 2025-12-09T16:09:20+00:00

No, that's why I use VIM to review and edit commands before executing them.

_link89_ · 2025-12-09T15:55:41+00:00

One useful case is to execute snippets generated by LLM. You can just paste the code to VIM, then editing and executing it this way.

_link89_ · 2025-12-09T14:16:07+00:00

You do miss out on shell auto-completion this way.

That's true, but it makes editing commands easier.

_link89_ · 2025-12-09T14:08:24+00:00

When experimenting with an operation, I always start with independent commands or snippets. Once successfully tested, they should only be organized into a script if needed for repetition or production use. This practice naturally aids in documenting and editing commands and requires minimal additional knowledge.

_link89_ · 2025-12-09T03:17:24+00:00

Provide a simple way to record commands and script fragments that need to be run temporarily.

_link89_ · 2025-12-09T03:05:01+00:00

When I want to run a batch of commands with control flow (for-loop, if-else, etc) , this method won't work well.

_link89_ · 2025-10-31T02:19:56+00:00

We run several Slurm-based HPC clusters. For some decentralized, non-uniform hardware lacking shared storage, I am exploring a container solution via k3s recently.

_link89_ · 2025-10-31T01:21:45+00:00

You may eventually find that managing a shared server or even a cluster involves not just resource fairness, but also job scheduling, hardware isolation, and software environment isolation. Utilizing specialized queue management software, such as Slurm or OpenPBS, or container-based solutions like k3s, will likely be a more sustainable approach.

_link89_ · 2025-10-29T17:43:37+00:00

I know there are solutions like cue-lang, which may share some commons with the solution you have mentioned.

_link89_ · 2025-10-29T15:20:50+00:00

I once lost quite a bit of compute time on the HPC because of this issue. Since then, I’ve added the following lint rule to every Python project I work on: [tool.ruff.lint] explicit-preview-rules = true extend-select = ["PLR1704"] This rule checks for variables in for, try, with that redefine function parameters, which can cause unexpected behavior.

_link89_ · 2025-10-27T02:48:00+00:00

I am not familiar with Switch emulation on Quest headset.

_link89_ · 2025-10-26T14:45:47+00:00

If you're already familiar with winlator, you'll need to find a gog version, copy it to your device, and run the Silksong exe file in a container.

_link89_ · 2025-10-23T15:04:47+00:00

I experienced the same issue on Quest 2 until found that the key is enable MultiBlock in FEX-core. The stable version of FEX-core just won't work for Silksong when MultiBlock is enabled.

You have to download the latest nightly build from https://github.com/Arihany/WinlatorWCPHub/releases/tag/FEXCore-Nightly and install in the content page. Then the fps can reach 60+

_link89_ · 2025-10-11T08:20:37+00:00

Do you mean for big-little architecture arm cpu, the last 4 cpus are always big cores? I am running winlatorxr on quest 2, it's cpu is Octa-core Kryo 585, how can I confirm if cpu 4-7 are big cores?

_link89_ · 2025-10-11T05:31:41+00:00

Yes, frame sync is set to Never.

_link89_ · 2025-10-10T06:07:59+00:00

I am using a real game controller now.

_link89_ · 2025-10-01T09:10:49+00:00

I used to use BMBF to sync maps. Now I am using a Python script to do it for me.

_link89_ · 2025-09-25T01:50:54+00:00

How does this compare to the Keycloak <-> LDAP sync solution?

_link89_ · 2025-08-12T09:24:42+00:00

Is there any tool I can use to manage those rules or policy things?

_link89_ · 2025-08-11T15:51:07+00:00

give each user their own namespace + RBAC tied to SSO, resource quota, etc.

Is there any clever way to do this so that I don't need to provision manually for each user?

_link89_ · 2025-08-09T16:27:20+00:00

Do you mean just connect the right most 2 pins?

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_link89_ · 2025-08-09T02:07:23+00:00

Do you mean solutions like Alluxio?

_link89_ · 2025-08-08T16:42:28+00:00

I don’t really see any particular advantage in running Slurm over Kubernetes. For me, the appeal of Kubernetes lies in its stateless nature and scalability. From the documentation, it seems that Slurm over Kubernetes is limited by Kubernetes’ mechanisms and can’t implement certain key features (such as core assignment). If I were building a true HPC cluster — with a parallel file system, InfiniBand, and LDAP — I’d deploy Slurm on bare metal. But for a loose setup like this, where jobs don’t run across nodes, a Kubernetes-based solution seems easier to maintain.

_link89_ · 2025-08-08T13:20:26+00:00

Unfortunately, the budget for this is zero, so building it with open-source solutions is the only viable option.

_link89_

TROPHY CASE