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cluster:215 [2024/02/14 21:17] hmeij07 [Lammps] |
cluster:215 [2024/05/10 16:24] hmeij07 [Miniconda3-py312] |
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https:// | https:// | ||
https:// | https:// | ||
+ | |||
+ | |||
+ | ===== FLAG ===== | ||
+ | |||
+ | < | ||
+ | |||
+ | # needs to be on local disk, NFS compile location fails | ||
+ | # needs to run as root (?) and needs internet access | ||
+ | # used n101 | ||
+ | |||
+ | module load singularity | ||
+ | singularity config fakeroot --add root | ||
+ | |||
+ | cd /home | ||
+ | unzip FLAG-main.zip | ||
+ | mv FLAG-main FLAG-20240425 | ||
+ | date > build.log | ||
+ | ./ | ||
+ | |||
+ | |||
+ | INFO: Build complete: singularity_flag.image | ||
+ | Entering the examples directory | ||
+ | Moving the singularity_flag singularity image to the examples directory | ||
+ | Creating initial files/ | ||
+ | |||
+ | Singularity FLAG image built and initial files setup in the examples directory. | ||
+ | |||
+ | # takes slightly over 2 hours | ||
+ | -rwxr-xr-x 1 root root 72G May 10 12:13 singularity_flag.image | ||
+ | |||
+ | </ | ||
+ | |||
+ | ===== Miniconda3-py312 ===== | ||
+ | |||
+ | |||
+ | * module: miniconda3/ | ||
+ | * Miniconda framework with python 3.12.1 | ||
+ | * module show miniconda3/ | ||
+ | * https:// | ||
+ | * weirlab (sakkas) | ||
+ | |||
+ | < | ||
+ | |||
+ | module load miniconda3/ | ||
+ | conda list | grep pymol | ||
+ | |||
+ | pymol | ||
+ | pymol-bundle | ||
+ | pymol-web-examples | ||
+ | |||
+ | </ | ||
+ | |||
===== Crest/XTB ===== | ===== Crest/XTB ===== | ||
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* hoomd v4.3.0 with cuda toolkit 11.6 | * hoomd v4.3.0 with cuda toolkit 11.6 | ||
* https:// | * https:// | ||
+ | * multi-gpu | ||
+ | * https:// | ||
+ | * FAQ: My simulation does not run significantly faster on exactly two GPUs compared to one GPU. | ||
+ | * This is expected. HOOMD uses special optimizations for single-GPU runs | ||
< | < | ||
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>>> | >>> | ||
>>> | >>> | ||
- | >>> | + | >>> |
- | >>> | + | True |
+ | >>> | ||
</ | </ |