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cluster:73 [2021/05/10 19:45] hmeij07 [OpenHPC] |
cluster:73 [2021/06/11 12:52] hmeij07 [VirtualFlow] |
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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 ====== | ||
+ | |||
+ | | ||
+ | |||
+ | ====== 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 ====== | ||
+ | |||
+ | | ||
+ | |||
+ | * https:// | ||
+ | * From AMBER distribution (Linux, OSX) | ||
+ | * pytraj is included in AMBER (version >= 16): ambermd.org | ||
+ | * so below I opted for source code installation with python 3.8.3 | ||
+ | * git clone https:// | ||
+ | * python ./setup.py install | ||
+ | * requires CentOS7 so queues mwgpu, amber128 and exx96 | ||
+ | * / | ||
+ | |||
+ | |||
+ | |||
+ | < | ||
+ | |||
+ | | ||
+ | | ||
+ | |||
+ | # An environment resource file for CPPTRAJ has been created: | ||
+ | / | ||
+ | # You may ' | ||
+ | |||
+ | |||
+ | |||
+ | Installed / | ||
+ | Processing dependencies for pytraj==2.0.6.dev0 | ||
+ | Searching for numpy==1.20.3 | ||
+ | Best match: numpy 1.20.3 | ||
+ | Adding numpy 1.20.3 to easy-install.pth file | ||
+ | Installing f2py script to / | ||
+ | Installing f2py3 script to / | ||
+ | Installing f2py3.8 script to / | ||
+ | |||
+ | Using / | ||
+ | Finished processing dependencies for pytraj==2.0.6.dev0 | ||
+ | |||
+ | </ | ||
====== Ovito ====== | ====== Ovito ====== | ||
Line 3202: | Line 3302: | ||
====== Stata ====== | ====== Stata ====== | ||
- | * program: Stata v 15, 6-user network license, includes stata, stata-mp, stata-se | + | * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se |
- | * install dir: / | + | * install dir: / |
* docs: at web site | * docs: at web site | ||
* http:// | * http:// | ||
< | < | ||
- | export PATH=/ | + | export PATH=/ |
</ | </ | ||