cluster:73
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| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
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cluster:73 [2021/06/10 12:55] hmeij07 [Ovito] |
cluster:73 [2021/06/15 19:22] hmeij07 [pytraj] |
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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:// | ||
| + | * Two flavors: centos6/ | ||
| + | * centos7 queues; mwgpu, amber128, exx96 | ||
| + | * / | ||
| + | * / | ||
| + | |||
| + | ====== VirtualFlow ====== | ||
| + | |||
| + | | ||
| + | https:// | ||
| + | |||
| + | TBD | ||
| + | ====== DeepChem ====== | ||
| + | |||
| + | | ||
| + | |||
| + | * First installed latest Miniconda | ||
| + | * / | ||
| + | * put the code block below in ~/.bashrc and log back in | ||
| + | * https:// | ||
| + | * installed stable/ | ||
| + | * pip installed tensorflow-2.5 | ||
| + | * Note: miniconda contains (Your python: python=3.8) | ||
| + | * "conda install -c ambermd pytraj" | ||
| + | * CentOS7 so queues mwgpu, amber128, exx96 | ||
| + | |||
| + | < | ||
| + | # add to ~/.bashrc and log back in, then check: 'which python pip conda' | ||
| + | # >>> | ||
| + | # !! Contents within this block are managed by 'conda init' !! | ||
| + | __conda_setup=" | ||
| + | if [ $? -eq 0 ]; then | ||
| + | eval " | ||
| + | else | ||
| + | if [ -f "/ | ||
| + | . "/ | ||
| + | else | ||
| + | export PATH="/ | ||
| + | fi | ||
| + | fi | ||
| + | unset __conda_setup | ||
| + | # <<< | ||
| + | |||
| + | </ | ||
| + | |||
| + | |||
| + | < | ||
| + | Successfully installed absl-py-0.12.0 astunparse-1.6.3 | ||
| + | cachetools-4.2.2 flatbuffers-1.12 gast-0.4.0 google-auth-1.30.2 | ||
| + | google-auth-oauthlib-0.4.4 google-pasta-0.2.0 grpcio-1.34.1 | ||
| + | h5py-3.1.0 keras-nightly-2.5.0.dev2021032900 keras-preprocessing-1.1.2 | ||
| + | markdown-3.3.4 numpy-1.19.5 oauthlib-3.1.1 opt-einsum-3.3.0 | ||
| + | protobuf-3.17.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 requests-oauthlib-1.3.0 | ||
| + | rsa-4.7.2 tensorboard-2.5.0 tensorboard-data-server-0.6.1 | ||
| + | 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 | ||
| + | </ | ||
| ====== pytraj ====== | ====== pytraj ====== | ||
| + | |||
| + | | ||
| * https:// | * https:// | ||
| Line 28: | Line 92: | ||
| * 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 | ||
| + | * / | ||
cluster/73.txt ยท Last modified: 2024/05/15 12:58 by hmeij07
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