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cluster:73 [2021/10/15 14:09] hmeij07 [Hoomd] |
cluster:73 [2021/11/22 17:15] hmeij07 [Hoomd] |
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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 / | ||
+ | |||
+ | ====== EasyBuild ====== | ||
+ | |||
+ | EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. | ||
+ | |||
+ | * supports 2469 different software packages (incl. toolchains, bundles) | ||
+ | * local page with lots of details | ||
+ | |||
+ | Easybuild uses '' | ||
+ | |||
+ | **Installed modules** and their dependencies | ||
+ | |||
+ | * astropy/ | ||
+ | * https:// | ||
+ | * contains package mpi4py, multithreading | ||
+ | * import erfa (needs to be loaded too), added later (pycuda, h5py for helios) | ||
+ | * to find '' | ||
+ | * emcee/ | ||
+ | * https:// | ||
+ | * contains package mpi4py, multithreading | ||
+ | * PyCUDA/ | ||
+ | * | ||
+ | |||
+ | To use module, discover the modules and load desired module. On '' | ||
+ | |||
+ | < | ||
+ | |||
+ | # cuda libs location | ||
+ | export LD_LIBRARY_PATH=\ | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | $LD_LIBRARY_PATH | ||
+ | |||
+ | |||
+ | # discover all modules | ||
+ | module use / | ||
+ | |||
+ | # view availability | ||
+ | module avail | ||
+ | |||
+ | # load | ||
+ | module load module_name | ||
+ | |||
+ | # list modules loaded | ||
+ | module list | ||
+ | |||
+ | # check, start app, import package (by full module name) | ||
+ | # note that these modules use different python versions | ||
+ | which python | ||
+ | python | ||
+ | >>> | ||
+ | |||
+ | # unload all modules (better to exit shell and start new one, | ||
+ | # purge will also unload system modules... | ||
+ | module purge | ||
+ | |||
+ | </ | ||
====== Hoomd ====== | ====== Hoomd ====== | ||
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* https:// | * https:// | ||
* requires both minconda3 (centos7) **and** cuda-10.2 (so queue exx96 only) | * requires both minconda3 (centos7) **and** cuda-10.2 (so queue exx96 only) | ||
+ | * python3.x included | ||
* starrlab | * starrlab | ||
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</ | </ | ||
- | ===== Miniconda2 ===== | + | * and |
+ | |||
+ | < | ||
+ | |||
+ | conda install -c conda-forge gsd | ||
+ | |||
+ | |||
+ | The following NEW packages will be INSTALLED: | ||
+ | |||
+ | _openmp_mutex | ||
+ | gsd conda-forge/ | ||
+ | libgomp | ||
+ | |||
+ | The following packages will be UPDATED: | ||
+ | |||
+ | certifi | ||
+ | conda | ||
+ | libgcc-ng | ||
+ | openssl | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | |||
+ | ====== Miniconda2 | ||
* miniconda2 (python 2.7) is hiding in section | * miniconda2 (python 2.7) is hiding in section | ||
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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 / |
< | < | ||
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</ | </ | ||
- | * Test version is installed on local disk on host **greentail52** | + | * __Test__ |
* source / | * source / | ||
* Read [[cluster: | * Read [[cluster: |