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cluster:73 [2021/08/25 12:49] hmeij07 [Rstudio] |
cluster:73 [2021/10/15 14:09] hmeij07 [Hoomd] |
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Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
- | ====== Miniconda2 ===== | + | ====== Hoomd ====== |
+ | |||
+ | HOOMD-blue is a Python package that runs simulations of particle systems on CPUs and GPUs. | ||
+ | |||
+ | * https:// | ||
+ | * requires both minconda3 (centos7) **and** cuda-10.2 (so queue exx96 only) | ||
+ | * starrlab | ||
+ | |||
+ | Set up env for miniconda and cuda | ||
+ | |||
+ | < | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | which mpirun python conda | ||
+ | which nvcc | ||
+ | |||
+ | # installation (not sure how this works, does the * not get expanded in shell?) | ||
+ | # seems to have worked forcing gpu package install on greentail52 | ||
+ | conda install -c conda-forge hoomd=*=*gpu* | ||
+ | |||
+ | |||
+ | $ conda list | egrep -i " | ||
+ | cudatoolkit | ||
+ | hoomd | ||
+ | |||
+ | </ | ||
+ | |||
+ | * installed/ | ||
+ | |||
+ | < | ||
+ | |||
+ | ca-certificates-2021.10.8 | ||
+ | certifi-2021.10.8 | ||
+ | conda-4.10.3 | ||
+ | cudatoolkit-11.0.221 | ||
+ | hoomd-2.9.4 | ||
+ | openssl-1.1.1h | ||
+ | tbb-2020.2 | ||
+ | |||
+ | </ | ||
+ | |||
+ | ===== Miniconda2 ===== | ||
* miniconda2 (python 2.7) is hiding in section | * miniconda2 (python 2.7) is hiding in section | ||
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</ | </ | ||
- | * https:// | + | |
* The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | * The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | ||
* requires centos7 (glibc) so queues mwgpu, amber128, exx96 | * requires centos7 (glibc) so queues mwgpu, amber128, exx96 | ||
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</ | </ | ||
+ | |||
+ | * **adapterremoval** https:// | ||
+ | * **bwa** https:// | ||
+ | * **bowtie2** http:// | ||
+ | |||
+ | These are all part of Miniconda3 (centos7), to setup the environment consult | ||
+ | |||
+ | * https:// | ||
+ | * queues: mwgpu, amber128, exx96, debug server greentail52 | ||
+ | |||
+ | They are also available via Miniconda2 (centos6), consult | ||
+ | |||
+ | * https:// | ||
+ | * queues: hp12, mw256fd, tinymem, debug server swallowtail | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@greentail52 ~]$ conda list | egrep " | ||
+ | adapterremoval | ||
+ | bowtie2 | ||
+ | bwa | ||
+ | |||
+ | </ | ||
+ | |||