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cluster:73 [2020/12/14 14:45] hmeij07 [DMTCP] |
cluster:73 [2021/04/13 19:34] hmeij07 [LAMMPS CPU/GPU] |
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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 / | ||
+ | |||
+ | ====== 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 ===== | ||
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* this came from the CRAC source, trying to install gpu checkpoint tool | * this came from the CRAC source, trying to install gpu checkpoint tool | ||
* [[cluster: | * [[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 226: | 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 1080: | 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 | ||
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====== 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 compile with MPI (mpif90), not ifort, in CentOS7 ... was tricky, solution for MPI was the '' | ||
+ | |||
+ | * Requires CentOS 7 so queues: mwgpu, amber128, exx96 for cpu-only binaries | ||
+ | * Rwequires CentOS7 plus Cuda 10.2 so queue: exx96 for cpu+gpu binaries | ||
+ | |||
+ | Read, if you wish | ||
+ | |||
+ | * / | ||
+ | * / | ||
+ | |||
+ | **Environments** | ||
+ | |||
+ | < | ||
+ | |||
+ | # serial - cpu only (although quippy compiled, it refused to install) | ||
+ | # MPI STUBS is compiled in | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | / | ||
+ | |||
+ | # mpi - cpu only | ||
+ | # gfortran_openmpi | ||
+ | |||
+ | export QUIP_LIBRARY=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | / | ||
+ | |||
+ | |||
+ | # mpi - cpu+gpu | ||
+ | # gfortran_openmpi arch | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export QUIP_LIBRARY=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export CUDA_HOME=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
+ | </ | ||
** CPU only ** -Centos6 | ** CPU only ** -Centos6 | ||
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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 ** | ||
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===== 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 | ||
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====== Cluster Math Kernel Libraries ====== | ====== Cluster Math Kernel Libraries ====== | ||
+ | |||
+ | * latest version in OneAPI, search this page | ||
* see Intel parallel studio | * see Intel parallel studio | ||
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====== Intel Threading Building Blocks ====== | ====== Intel Threading Building Blocks ====== | ||
+ | |||
+ | * latest version is in OneAPI, search this pages | ||
* see Intel parallel studio | * see Intel parallel studio | ||
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* 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: |