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cluster:73 [2023/11/08 11:51] hmeij07 [Sequencing Tools #3] |
cluster:73 [2024/02/16 11:17] (current) hmeij07 [LAMMPS CPU/GPU] |
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(sage) [hmeij@greentail52 ~]$ conda deactivate | (sage) [hmeij@greentail52 ~]$ conda deactivate | ||
[hmeij@greentail52 ~]$ | [hmeij@greentail52 ~]$ | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **mdtraj, matplotlib, pandas** | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@greentail52 ~]$ which python | ||
+ | / | ||
+ | | ||
+ | [hmeij@greentail52 ~]$ python | ||
+ | Python 3.11.4 (main, Jul 5 2023, 13:45:01) [GCC 11.2.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | </ | ||
+ | |||
+ | * ** seaborn** | ||
+ | * https:// | ||
+ | * also in miniconda3/ | ||
+ | |||
+ | < | ||
+ | |||
+ | patsy conda-forge/ | ||
+ | seaborn | ||
+ | seaborn-base | ||
+ | statsmodels | ||
</ | </ | ||
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</ | </ | ||
+ | |||
+ | |||
+ | * **qualimap ** | ||
+ | * http:// | ||
+ | * java & R app, probably will work in centos7 and rocky8 | ||
+ | * / | ||
+ | |||
+ | * **gatk** | ||
+ | * https:// | ||
+ | * java & R app. probably will work in centos7 and rocky8 | ||
+ | * / | ||
+ | |||
+ | For both apps above java is v20, developers want and tested v17 | ||
+ | |||
+ | For both apps you may find R local in operating system or a recent versions at | ||
+ | |||
+ | * (rocky 8) module load R/4.1.2 | ||
+ | |||
+ | |||
+ | |||
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====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
+ | |||
+ | ** 7Feb2024 ** | ||
+ | |||
+ | |||
+ | * / | ||
+ | * lmp_serial and lmp_mpi | ||
+ | * 3 cuda versions with 3 different precision settings | ||
+ | * compiled against cuda 10.2 on exx96, may work in mwgpu cuda-11.2 | ||
+ | * notes: / | ||
+ | * does **not** support openmp, look for the OpenHPC version for that | ||
** 25Apr2023** | ** 25Apr2023** |