cluster:215
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cluster:215 [2025/01/15 20:30] hmeij07 [Magma] |
cluster:215 [2025/06/24 19:01] (current) hmeij07 [Python] |
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| https:// | https:// | ||
| + | |||
| + | ===== ChimeraX ===== | ||
| + | |||
| + | * https:// | ||
| + | * installed on sharptail2 | ||
| ===== Magma ===== | ===== Magma ===== | ||
| Line 19: | Line 24: | ||
| * Magma is a large, well-supported software package designed for computations in algebra, number theory, algebraic geometry, and algebraic combinatorics. | * Magma is a large, well-supported software package designed for computations in algebra, number theory, algebraic geometry, and algebraic combinatorics. | ||
| * The binary is linked into $PATH via ''/ | * The binary is linked into $PATH via ''/ | ||
| - | * sharptail2 and cottontail2 for debugging | + | * <del>sharptail2 and cottontail2 for debugging</ |
| * tinymem (n46-n59) | * tinymem (n46-n59) | ||
| * mw128 (n60-n77) | * mw128 (n60-n77) | ||
| * amber128 (n78) | * amber128 (n78) | ||
| - | * test (n100-n101) | + | * test (n100-n101) |
| * mw256 (n102-n107) | * mw256 (n102-n107) | ||
| * mwgpu256 (n108-n117) | * mwgpu256 (n108-n117) | ||
| Line 36: | Line 41: | ||
| export MAGMAPASSFILE=/ | export MAGMAPASSFILE=/ | ||
| + | export MAGMA_SYSTEM_SPEC=/ | ||
| [root@n103 ~]# magma | [root@n103 ~]# magma | ||
| Line 57: | Line 63: | ||
| ===== AutoDock-GPU ===== | ===== AutoDock-GPU ===== | ||
| + | |||
| + | * cuda-12.6 only added | ||
| + | * mwgpu256 queue | ||
| + | * gcc 9 needed for openmp | ||
| + | * module load autodock/ | ||
| + | * / | ||
| * https:// | * https:// | ||
| Line 351: | Line 363: | ||
| >>> | >>> | ||
| [hmeij@cottontail2 ~]$ | [hmeij@cottontail2 ~]$ | ||
| + | |||
| + | </ | ||
| + | |||
| + | * **g_mmpba** | ||
| + | * https:// | ||
| + | * calterlab (Kayla) | ||
| + | |||
| + | < | ||
| + | |||
| + | $ module load python/ | ||
| + | $ python3 -m pip install g_mmpbsa | ||
| + | Collecting g_mmpbsa | ||
| + | Downloading g_mmpbsa-3.0.9-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (3.0 kB) | ||
| + | ... | ||
| + | Installing collected packages: g_mmpbsa | ||
| + | Successfully installed g_mmpbsa-3.0.9 | ||
| + | |||
| </ | </ | ||
cluster/215.1736973004.txt.gz ยท Last modified: 2025/01/15 20:30 by hmeij07
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