cluster:73
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cluster:73 [2020/06/29 17:15] hmeij07 [Python3] |
cluster:73 [2021/03/03 18:19] hmeij07 [Mathematica] |
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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 / | ||
| + | |||
| + | ====== Rstudio ====== | ||
| + | |||
| + | * http:// | ||
| + | * https:// | ||
| + | * centos7 R v 3.6.0 | ||
| + | * use your HPC username and credentials | ||
| + | |||
| + | ====== DMTCP ===== | ||
| + | |||
| + | * / | ||
| + | * this came from the CRAC source, trying to install gpu checkpoint tool | ||
| + | * [[cluster: | ||
| + | * but plugin will not compile, checking with developers 12 Dec 2020 | ||
| + | |||
| + | * Installed as package ins OS on all nodes | ||
| + | * v2.5.2 | ||
| + | * dmctp_launch ... etc | ||
| + | |||
| + | ====== EMBOSS ====== | ||
| + | |||
| + | * / | ||
| + | * / | ||
| + | * https:// | ||
| + | * jfabry/ | ||
| ====== Sequencing Tools #2 ====== | ====== Sequencing Tools #2 ====== | ||
| Line 205: | Line 234: | ||
| * most packages found on this page | * most packages found on this page | ||
| * picked up mpirun from miniconda2 apps (that may be a problem) | * picked up mpirun from miniconda2 apps (that may be a problem) | ||
| + | |||
| + | * Added to 3.8.3 " | ||
| + | * https:// | ||
| + | |||
| + | --- // | ||
| < | < | ||
| Line 943: | Line 977: | ||
| ====== Gromacs ===== | ====== Gromacs ===== | ||
| + | |||
| + | Gromacs-2020.3 for GPU (RTX2080S) | ||
| + | * '' | ||
| + | * see / | ||
| + | * change env in script below | ||
| + | |||
| + | Gromacs-2018 for GPU (RTX2080S) | ||
| + | * '' | ||
| + | * **/ | ||
| Line 1050: | Line 1093: | ||
| [[https:// | [[https:// | ||
| - | * program: mcc, math, mathematica (v 11.0.1) | + | * program: mcc, math, mathematica (v 12.2) |
| - | * install dir: / | + | * install dir: / |
| * docs: on the web | * docs: on the web | ||
| * www: http:// | * www: http:// | ||
| + | * Centos7, use queues mwgpu, amber128 or exx96 | ||
| + | * For GUI launch on greentail52 | ||
| * Parallel kernels | * Parallel kernels | ||
| Line 1060: | Line 1105: | ||
| * http:// | * http:// | ||
| - | Job submissions should go to queue // | + | |
| ====== Eigen ===== | ====== Eigen ===== | ||
| Line 1244: | Line 1289: | ||
| ====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
| + | |||
| + | ** CPU only ** -Centos6 | ||
| + | |||
| + | * / | ||
| + | * read for env and compilation env: lmp_mpi | ||
| + | |||
| + | ** CPU only OR CPU+GPU** | ||
| + | |||
| + | * 3Mar2020 added USER-REAXC | ||
| + | * For KOKKOS MPI aware version | ||
| + | * git download of latest did not work (lots of fortran errors?) | ||
| + | * latest tarball is still 3Mar2020 (?) | ||
| + | * added user-eaxc (but had to remove package python) | ||
| + | * " | ||
| + | * please read **/ | ||
| + | |||
| + | < | ||
| + | |||
| + | # CPU | ||
| + | / | ||
| + | / | ||
| + | |||
| + | # CPU+GPU | ||
| + | / | ||
| + | |||
| + | # env | ||
| + | |||
| + | | ||
| + | | ||
| + | | ||
| + | | ||
| + | |||
| + | | ||
| + | | ||
| + | | ||
| + | | ||
| + | |||
| + | </ | ||
| + | |||
| + | ** 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 1256: | Line 1354: | ||
| ** CPU or GPU ** | ** CPU or GPU ** | ||
| + | |||
| + | * added lmp_mpi-single-single+user-omp | ||
| * / | * / | ||
| Line 1262: | Line 1362: | ||
| * / | * / | ||
| * CUDA_ARCH = sm_75 (probably only works on queue exx96) | * CUDA_ARCH = sm_75 (probably only works on queue exx96) | ||
| - | * sample script in ~hmeij/ | + | |
| < | < | ||
| Line 2179: | Line 2279: | ||
| ====== Amber ====== | ====== Amber ====== | ||
| + | |||
| + | ** Amber 20 ** | ||
| + | |||
| + | * Two versions compiled, | ||
| + | * one for cuda 8.0/mpich3 for queue amber128 | ||
| + | * one for queues mwgpu and exx96 (cuda 9.2/ | ||
| + | |||
| + | * Consult the run.amber20 script to set up environment | ||
| + | * / | ||
| + | |||
| + | * Both are installed in / | ||
| + | |||
| + | |||
| ** AMBER 18 ** | ** AMBER 18 ** | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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