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cluster:73 [2020/06/19 16:08] hmeij07 [Sequencing Tools #2] |
cluster:73 [2020/07/15 18:48] hmeij07 [LAMMPS CPU/GPU] |
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* https:// | * https:// | ||
* https:// | * https:// | ||
- | * padillalab | + | * padillalab |
< | < | ||
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====== Python3 ====== | ====== Python3 ====== | ||
- | Added to both versions\\ | + | * Python 3.8.3 |
+ | * / | ||
+ | * most packages found on this page | ||
+ | * picked up mpirun from miniconda2 apps (that may be a problem) | ||
+ | |||
+ | < | ||
+ | |||
+ | # needed for _ctypes to compile properly for https retrievals | ||
+ | yum install openssl openssl-devel | ||
+ | yum install yum install libffi-devel libffi | ||
+ | |||
+ | tar -xvf ../ | ||
+ | cd Python-3.8.3/ | ||
+ | ./configure --prefix=/ | ||
+ | make | ||
+ | make install | ||
+ | pip3 install --upgrade pip | ||
+ | # make symbolic links python3-> | ||
+ | # drop all the packages in from previous versions | ||
+ | https:// | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | Added to both 3.5.2 versions\\ | ||
pycuda\\ | pycuda\\ | ||
--- // | --- // | ||
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====== Gromacs ===== | ====== Gromacs ===== | ||
+ | |||
+ | Gromacs-2018 for GPU (RTX2080) | ||
+ | * '' | ||
+ | * **/ | ||
Line 1026: | Line 1054: | ||
[[https:// | [[https:// | ||
- | * program: mcc, math, mathematica (v 11.0.1) | + | * program: mcc, math, mathematica (v 12.1) |
- | * install dir: / | + | * install dir: / |
* docs: on the web | * docs: on the web | ||
* www: http:// | * www: http:// | ||
+ | * Campus wide license, use any queue. | ||
* Parallel kernels | * Parallel kernels | ||
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* http:// | * http:// | ||
- | Job submissions should go to queue // | + | |
====== Eigen ===== | ====== Eigen ===== | ||
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====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
+ | |||
+ | ** CPU ONLY v2 CentOS7 ** | ||
+ | |||
+ | * / | ||
+ | * lmp_serial, lmp_mpi | ||
+ | * latest openmpi version | ||
+ | * consult this file for packages installed and compilations | ||
+ | * / | ||
+ | * should work only on exx96 and mwgpu queues | ||
+ | |||
+ | < | ||
+ | | ||
+ | | ||
+ | </ | ||
** CPU ONLY ** | ** CPU ONLY ** | ||
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* / | * / | ||
* CUDA_ARCH = sm_75 (probably only works on queue exx96) | * CUDA_ARCH = sm_75 (probably only works on queue exx96) | ||
- | * sample script in ~hmeij/ | + | |
< | < |