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cluster:73 [2020/07/13 18:58] hmeij07 [Mathematica] |
cluster:73 [2021/02/12 16:18] hmeij07 [Amber] |
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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 / | ||
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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 / | ||
+ | |||
+ | ====== 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 ====== | ||
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====== Gromacs ===== | ====== Gromacs ===== | ||
- | Gromacs-2018 for GPU (RTX2080) | + | Gromacs-2020.3 for GPU (RTX2080S) |
+ | * '' | ||
+ | * see / | ||
+ | * change env in script below | ||
+ | |||
+ | Gromacs-2018 for GPU (RTX2080S) | ||
* '' | * '' | ||
* **/ | * **/ | ||
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====== 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 ** | ||
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** CPU or GPU ** | ** CPU or GPU ** | ||
+ | |||
+ | * added lmp_mpi-single-single+user-omp | ||
* / | * / | ||
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====== 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 ** |