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cluster:73 [2021/06/10 14:48] hmeij07 [pytraj] |
cluster:73 [2021/06/22 19:24] hmeij07 [Miniconda3] |
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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 / | ||
+ | |||
+ | ====== VSEARCH ====== | ||
+ | |||
+ | VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization ... an alternative to USEARCH; offers search and clustering algorithms that are often orders of magnitude faster than BLAST. | ||
+ | |||
+ | * https:// | ||
+ | * requires centos7 | ||
+ | * centos7 queues; mwgpu, amber128, exx96 | ||
+ | * debug host greentail52 | ||
+ | * / | ||
+ | |||
====== DeepChem ====== | ====== DeepChem ====== | ||
+ | |||
+ | | ||
* First installed latest Miniconda | * First installed latest Miniconda | ||
- | * / | + | * / |
* put the code block below in ~/.bashrc and log back in | * put the code block below in ~/.bashrc and log back in | ||
* https:// | * https:// | ||
- | * install | + | * installed |
+ | * pip installed tensorflow-2.5 | ||
+ | * Note: miniconda contains (Your python: python=3.8) | ||
+ | * "conda install -c ambermd pytraj" | ||
+ | * CentOS7 so queues mwgpu, amber128, exx96 | ||
+ | * or for debugging use greentail52 | ||
< | < | ||
- | # add to ~/.bashrc and log back in, then check: 'which conda' | + | # add to ~/.bashrc and log back in, then check: ' |
# >>> | # >>> | ||
# !! Contents within this block are managed by 'conda init' !! | # !! Contents within this block are managed by 'conda init' !! | ||
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tensorboard-plugin-wit-1.8.0 tensorflow-2.5.0 tensorflow-estimator-2.5.0 | tensorboard-plugin-wit-1.8.0 tensorflow-2.5.0 tensorflow-estimator-2.5.0 | ||
termcolor-1.1.0 typing-extensions-3.7.4.3 werkzeug-2.0.1 wrapt-1.12.1 | termcolor-1.1.0 typing-extensions-3.7.4.3 werkzeug-2.0.1 wrapt-1.12.1 | ||
+ | </ | ||
+ | |||
+ | ====== Miniconda3 ====== | ||
+ | |||
+ | * add to ~/.bashrc and log back in, then check: 'which python pip conda' | ||
+ | * the code block is list under DeepChem section above | ||
+ | |||
+ | < | ||
+ | # https:// | ||
+ | conda install -c conda-forge galario | ||
+ | |||
+ | fftw | ||
+ | galario | ||
+ | libblas | ||
+ | libcblas | ||
+ | libgfortran-ng | ||
+ | libgfortran4 | ||
+ | liblapack | ||
+ | libopenblas | ||
+ | numpy conda-forge/ | ||
+ | python_abi | ||
+ | scipy conda-forge/ | ||
+ | | ||
</ | </ | ||
====== pytraj ====== | ====== pytraj ====== | ||
+ | |||
+ | | ||
* https:// | * https:// | ||
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* python ./setup.py install | * python ./setup.py install | ||
* requires CentOS7 so queues mwgpu, amber128 and exx96 | * requires CentOS7 so queues mwgpu, amber128 and exx96 | ||
+ | * or for debugging use greentail52 | ||
* / | * / | ||
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* 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 "acpipe" | + | * Added to 3.8.3 "acpype" |
* https:// | * https:// | ||
+ | From website:\\ | ||
+ | " | ||
+ | We now have an up to date webservice at http:// | ||
+ | (but it does not have the amb2gmx funcionality). | ||
+ | |||
+ | To run acpype, locally, with its all functionalities, | ||
+ | |||
+ | However, if one wants acpype just to emulate amb2gmx.pl, one needs nothing at all but Python. | ||
+ | "\\ | ||
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