Comments (3)
- For two nodes, we recommend putting two processes on the first node and one process on the second one.
- Running speed depends on so much environment parameters, such as memory, GPUs, CPUs, network bandwidth, disk bandwidth. I am sorry that I can not give you an estimation. However, it is some benchmark tests in https://www.nature.com/articles/s41592-018-0223-8. Moreover, you can use https://github.com/thuem/THUNDER-demo-datasets as benchmarks. Download failure is due to lack of Github LFS service, https://git-lfs.github.com.
- Sorry, currently, there is no local scratch support in THUNDER.
- Currently, THUNDER will read all particles in physical memory. We are working the memory buffer system which will load particles into physical memory when needed. We hope to release this feature soon. A present solution to his "out of memory" issue is to use SWAP. By configuring SWAP to a larger partition, it will get this issue solved.
Best regards,
Mingxu
from thunder.
Thanks. Besides, could thunder support LFS cluster?
from thunder.
Sure.
In Tsinghua, we use LFS and SLURM as job manager.
If you have any problem with running THUNDER using LFS job manager, please contact us.
from thunder.
Related Issues (20)
- Compiling error HOT 6
- Sample data HOT 9
- THUNDER runs on cpu cluster HOT 1
- a runtime crash reported by Professor Jiang, USTC HOT 1
- Weired behavior when start running HOT 1
- make fails HOT 2
- Integration in Scipion? HOT 2
- Make fail in CPU/GPU mode - CUDA 10.1 - THUNDERconfig.h not found? HOT 12
- Job stuck in CTF estimation step HOT 4
- Questions about THUNDER running
- Kernel CTF calculation error HOT 1
- about RELION_2_THU.py HOT 2
- GPU version dies but CPU version complete a 2D job HOT 1
- make problem HOT 8
- Crash during 1st iteration of GPU refinement HOT 2
- make problem - ubuntu 17.10 HOT 1
- make problem Debian 4.9 HOT 1
- How to continue a crashed run HOT 1
- E-mail notification test HOT 17
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from thunder.