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cluster:73 [2021/08/19 13:01] hmeij07 [Kallisto & Trinity & FastQC] |
cluster:73 [2021/10/27 19:18] hmeij07 [OneAPI] |
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Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
- | ====== Miniconda2 ===== | + | ====== EasyBuild ====== |
+ | |||
+ | | ||
+ | * maybe use alongside OpenHPC modules? | ||
+ | * replacement for miniconda? | ||
+ | |||
+ | EasyBuild 4.4.2 supports 2469 different software packages (incl. toolchains, bundles) | ||
+ | * [[cluster: | ||
+ | |||
+ | ====== 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) | ||
+ | * python3.x included | ||
+ | * 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 | ||
Line 341: | Line 400: | ||
numpy | numpy | ||
time 1.8 h516909a_0 | time 1.8 h516909a_0 | ||
+ | astropy | ||
+ | attrs conda-forge/ | ||
+ | click conda-forge/ | ||
+ | coverage | ||
+ | hypothesis | ||
+ | iniconfig | ||
+ | more-itertools | ||
+ | packaging | ||
+ | pluggy | ||
+ | psutil | ||
+ | py | ||
+ | pyparsing | ||
+ | pytest | ||
+ | pytest-arraydiff | ||
+ | pytest-astropy | ||
+ | pytest-astropy-he~ conda-forge/ | ||
+ | pytest-cov | ||
+ | pytest-doctestplus conda-forge/ | ||
+ | pytest-filter-sub~ conda-forge/ | ||
+ | pytest-mock | ||
+ | pytest-openfiles | ||
+ | pytest-remotedata | ||
+ | sortedcontainers | ||
+ | toml | ||
+ | |||
</ | </ | ||
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* Production version is installed in / | * Production version is installed in / | ||
- | * source / | + | * source / |
< | < | ||
Line 493: | Line 577: | ||
</ | </ | ||
- | * Test version is installed on local disk on host **greentail52** | + | * __Test__ |
* source / | * source / | ||
* Read [[cluster: | * Read [[cluster: | ||
Line 510: | Line 594: | ||
* centos7 R v 3.6.0 | * centos7 R v 3.6.0 | ||
* use your HPC username and credentials | * use your HPC username and credentials | ||
+ | |||
+ | < | ||
+ | |||
+ | # native OS installation for rstudio | ||
+ | /bin/R | ||
+ | |||
+ | </ | ||
====== DMTCP ===== | ====== DMTCP ===== | ||
Line 634: | Line 725: | ||
</ | </ | ||
- | * 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 | ||
Line 643: | Line 734: | ||
</ | </ | ||
+ | |||
+ | * **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 | ||
+ | |||
+ | </ | ||
+ | |||
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* location: / | * location: / | ||
* https:// | * https:// | ||
- | * biolab (jcoolon, tearley) | + | |
+ | * queues: hp12, tinymem, mw256fd mw128 | ||
+ | * debug server swallowtail | ||
+ | | ||