cluster:73
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cluster:73 [2020/12/02 18:54] hmeij07 [EMBOSS] |
cluster:73 [2021/04/12 19:23] hmeij07 [LAMMPS CPU/GPU] |
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| Line 18: | 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 / | ||
| + | |||
| + | ====== OpenHPC ====== | ||
| + | |||
| + | So I remember where I put the repos ''/ | ||
| + | |||
| + | * whitetail tar ball for centos7/ | ||
| + | * http:// | ||
| + | * http:// | ||
| + | * https:// | ||
| + | |||
| + | ====== OneAPI ====== | ||
| + | |||
| + | * Requires CentOS 7 so queues mwgpu, amber128, exx96 | ||
| + | |||
| + | * Production version is installed in / | ||
| + | * source / | ||
| + | |||
| + | < | ||
| + | # which icc icx icpc icpx dpcpp ifort ifx mpirun mpicc python clang clang++ | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | # in addition these were installed | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | </ | ||
| + | |||
| + | * Test version is installed on local disk on host **greentail52** | ||
| + | * source / | ||
| + | * Read [[cluster: | ||
| + | |||
| + | |||
| + | ====== StringTie2 ====== | ||
| + | |||
| + | * Requires CentOS 7 so queues mwgpu, amber128, exx96 | ||
| + | * / | ||
| + | * https:// | ||
| + | |||
| + | ====== Rstudio ====== | ||
| + | |||
| + | * http:// | ||
| + | * https:// | ||
| + | * centos7 R v 3.6.0 | ||
| + | * use your HPC username and credentials | ||
| ====== DMTCP ===== | ====== 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 | * Installed as package ins OS on all nodes | ||
| Line 222: | Line 281: | ||
| * 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 1076: | Line 1140: | ||
| [[https:// | [[https:// | ||
| - | * program: mcc, math, mathematica (v 12.1) | + | * program: mcc, math, mathematica (v 12.2) |
| - | * install dir: / | + | * install dir: / |
| * docs: on the web | * docs: on the web | ||
| * www: http:// | * www: http:// | ||
| - | * Campus wide license, use any queue. | + | * Centos7, use queues mwgpu, amber128 or exx96 |
| + | * For GUI launch on greentail52 | ||
| * Parallel kernels | * Parallel kernels | ||
| Line 1271: | Line 1336: | ||
| ====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
| + | |||
| + | ** USER_QUIP ** | ||
| + | |||
| + | This is a version of lammps (29Oct20, last stable) that contains all packages with user-quip. | ||
| + | |||
| + | It does not compile with MPI, nor ifort in CentOS7, so there is only a " | ||
| + | |||
| + | * Requires CentOS 7 so queues: mwgpu, amber128, exx96 | ||
| + | |||
| + | Read, if you wish | ||
| + | |||
| + | * / | ||
| + | * / | ||
| + | |||
| + | Environments | ||
| + | |||
| + | < | ||
| + | |||
| + | # serial - cpu only (although quippy compiled, it refused to install) | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | / | ||
| + | |||
| + | # serial - cpu+gpu | ||
| + | |||
| + | (to come, hopefully) | ||
| + | |||
| + | </ | ||
| + | |||
| + | ** CPU only ** -Centos6 | ||
| + | |||
| + | * / | ||
| + | * read for env and compilation env: lmp_mpi | ||
| ** CPU only OR CPU+GPU** | ** CPU only OR CPU+GPU** | ||
| Line 2256: | Line 2355: | ||
| ====== 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 ** | ||
| Line 2968: | Line 3080: | ||
| ===== Intel ===== | ===== Intel ===== | ||
| - | UPDATE, 2016 parallel studio cluster edition installed | + | UPDATE |
| + | latest version of icc/icx and ifort/ifx are inside OneAPI, search this page | ||
| + | |||
| + | UPDATE | ||
| + | parallel studio cluster edition installed | ||
| * 2 ifort and 2 icc float licenses | * 2 ifort and 2 icc float licenses | ||
| Line 2996: | Line 3112: | ||
| ====== Cluster Math Kernel Libraries ====== | ====== Cluster Math Kernel Libraries ====== | ||
| + | |||
| + | * latest version in OneAPI, search this page | ||
| * see Intel parallel studio | * see Intel parallel studio | ||
| Line 3005: | Line 3123: | ||
| ====== Intel Threading Building Blocks ====== | ====== Intel Threading Building Blocks ====== | ||
| + | |||
| + | * latest version is in OneAPI, search this pages | ||
| * see Intel parallel studio | * see Intel parallel studio | ||
| Line 3019: | Line 3139: | ||
| * program: Matlab, link to binary is ' | * program: Matlab, link to binary is ' | ||
| - | * R2020a, campus wide license so no more restrictions on licenses | + | * R2020b, campus wide license so no more restrictions on licenses |
| * No Distributed Computing Engine or Matlab Parallel (for now) | * No Distributed Computing Engine or Matlab Parallel (for now) | ||
| - | * install dir: / | + | * install dir: / |
| * docs & www: http:// | * docs & www: http:// | ||
| + | * CentOS7 required use on queues mwgpu, amber128 and exx96 | ||
| + | * For GUI launch on greentail52 | ||
| Note: | Note: | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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