cluster:73
Differences
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| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
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cluster:73 [2020/06/19 16:08] hmeij07 [Sequencing Tools #2] |
cluster:73 [2020/07/31 19:10] hmeij07 |
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| ====== Software ====== | ====== Software ====== | ||
| + | ** | ||
| + | IMPORTANT NOTE: Since moving to the TrueNAS/ZFS appliance all references to ''/ | ||
| + | |||
| + | --- // | ||
| The listings below will be updated as software is installed, location is / | The listings below will be updated as software is installed, location is / | ||
| Line 14: | Line 18: | ||
| on either cottontail2 or node n33 located at / | on either cottontail2 or node n33 located at / | ||
| Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
| + | |||
| + | ====== EMBOSS ====== | ||
| + | |||
| + | * / | ||
| + | * / | ||
| + | * https:// | ||
| + | * jfabry/ | ||
| ====== Sequencing Tools #2 ====== | ====== Sequencing Tools #2 ====== | ||
| Line 201: | Line 212: | ||
| ====== 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\\ | ||
| --- // | --- // | ||
| Line 919: | Line 954: | ||
| ====== Gromacs ===== | ====== Gromacs ===== | ||
| + | |||
| + | Gromacs-2020.3 for GPU (RTX2080S) | ||
| + | * '' | ||
| + | * see / | ||
| + | * change env in script below | ||
| + | |||
| + | Gromacs-2018 for GPU (RTX2080S) | ||
| + | * '' | ||
| + | * **/ | ||
| Line 1026: | Line 1070: | ||
| [[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 | ||
| Line 1036: | Line 1081: | ||
| * http:// | * http:// | ||
| - | Job submissions should go to queue // | + | |
| ====== Eigen ===== | ====== Eigen ===== | ||
| Line 1220: | Line 1265: | ||
| ====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
| + | |||
| + | ** CPU ONLY v2 CentOS7 ** | ||
| + | |||
| + | * add user-opm on next compile ... done ... binaries with string +user-omp | ||
| + | * / | ||
| + | * lmp_serial, lmp_mpi | ||
| + | * //latest// openmpi version as of today v4.0.4 | ||
| + | * consult this file for packages installed and compilations | ||
| + | * / | ||
| + | * should work only on exx96 and mwgpu queues | ||
| + | |||
| + | < | ||
| + | | ||
| + | | ||
| + | </ | ||
| ** CPU ONLY ** | ** CPU ONLY ** | ||
| Line 1232: | Line 1292: | ||
| ** CPU or GPU ** | ** CPU or GPU ** | ||
| + | |||
| + | * added lmp_mpi-single-single+user-omp | ||
| * / | * / | ||
| Line 1238: | Line 1300: | ||
| * / | * / | ||
| * CUDA_ARCH = sm_75 (probably only works on queue exx96) | * CUDA_ARCH = sm_75 (probably only works on queue exx96) | ||
| - | * sample script in ~hmeij/ | + | |
| < | < | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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