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cluster:73 [2021/03/01 17:09] hmeij07 [Rstudio] |
cluster:73 [2021/06/15 12:33] hmeij07 [VirtualFlow] |
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Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
- | ===== Rstudio ===== | + | ====== 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 ====== | ||
+ | |||
+ | | ||
+ | |||
+ | * 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 ====== | ||
+ | |||
+ | * https:// | ||
+ | * / | ||
+ | * on nodes '' | ||
+ | * uses freeglut/ | ||
+ | |||
+ | ====== OpenHPC ====== | ||
+ | |||
+ | So I remember where I put the repos ''/ | ||
+ | |||
+ | * whitetail tar ball for centos7/ | ||
+ | * http:// | ||
+ | * http:// | ||
+ | * https:// | ||
+ | |||
+ | ====== OneAPI ====== | ||
+ | |||
+ | * Requires CentOS 7 so queues mwgpu, amber128, exx96 | ||
+ | |||
+ | * Production version is installed in / | ||
+ | * source / | ||
+ | |||
+ | < | ||
+ | # which icc icx icpc icpx dpcpp ifort ifx mpirun mpicc python clang clang++ | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | # in addition these were installed | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | </ | ||
+ | |||
+ | * Test version is installed on local disk on host **greentail52** | ||
+ | * source / | ||
+ | * Read [[cluster: | ||
+ | |||
+ | |||
+ | ====== StringTie2 ====== | ||
+ | |||
+ | * Requires CentOS 7 so queues mwgpu, amber128, exx96 | ||
+ | * / | ||
+ | * https:// | ||
+ | |||
+ | ====== Rstudio | ||
* http:// | * http:// | ||
Line 1093: | Line 1249: | ||
[[https:// | [[https:// | ||
- | * program: mcc, math, mathematica (v 12.1) | + | * program: mcc, math, mathematica (v 12.2) |
- | * install dir: / | + | * install dir: / |
* docs: on the web | * docs: on the web | ||
* www: http:// | * www: http:// | ||
- | * Campus wide license, use any queue. | + | * Centos7, use queues mwgpu, amber128 or exx96 |
+ | * For GUI launch on greentail52 | ||
* Parallel kernels | * Parallel kernels | ||
Line 1288: | Line 1445: | ||
====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
+ | |||
+ | ** USER_QUIP ** | ||
+ | |||
+ | This is a version of lammps (29Oct20, last stable) that contains all packages with user-quip. | ||
+ | |||
+ | It does compile with MPI (mpif90), not ifort, in CentOS7 ... was tricky, solution for MPI was the '' | ||
+ | |||
+ | * Requires CentOS 7 so queues: mwgpu, amber128, exx96 for cpu-only binaries | ||
+ | * Rwequires CentOS7 plus Cuda 10.2 so queue: exx96 for cpu+gpu binaries | ||
+ | |||
+ | Read, if you wish | ||
+ | |||
+ | * / | ||
+ | * / | ||
+ | |||
+ | **Environments** | ||
+ | |||
+ | < | ||
+ | |||
+ | # serial - cpu only (although quippy compiled, it refused to install) | ||
+ | # MPI STUBS is compiled in | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | / | ||
+ | |||
+ | # mpi - cpu only | ||
+ | # gfortran_openmpi | ||
+ | |||
+ | export QUIP_LIBRARY=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | / | ||
+ | |||
+ | |||
+ | # mpi - cpu+gpu | ||
+ | # gfortran_openmpi arch | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export QUIP_LIBRARY=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export CUDA_HOME=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | # the " | ||
+ | # did find on nvdia dev forum reference problem disappears when using cmake (vs make) | ||
+ | # these lmp binaries do work | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
+ | # however I had to load non-mpi version of libquid.a into lmp | ||
+ | # witch seems ok given parallel work is driven by -suffix gpu | ||
+ | |||
+ | # sample script: ~hmeij/ | ||
+ | |||
+ | </ | ||
** CPU only ** -Centos6 | ** CPU only ** -Centos6 | ||
Line 3003: | Line 3227: | ||
===== Intel ===== | ===== Intel ===== | ||
- | UPDATE, 2016 parallel studio cluster edition installed | + | UPDATE |
+ | latest version of icc/icx and ifort/ifx are inside OneAPI, search this page | ||
+ | |||
+ | UPDATE | ||
+ | parallel studio cluster edition installed | ||
* 2 ifort and 2 icc float licenses | * 2 ifort and 2 icc float licenses | ||
Line 3031: | Line 3259: | ||
====== Cluster Math Kernel Libraries ====== | ====== Cluster Math Kernel Libraries ====== | ||
+ | |||
+ | * latest version in OneAPI, search this page | ||
* see Intel parallel studio | * see Intel parallel studio | ||
Line 3040: | Line 3270: | ||
====== Intel Threading Building Blocks ====== | ====== Intel Threading Building Blocks ====== | ||
+ | |||
+ | * latest version is in OneAPI, search this pages | ||
* see Intel parallel studio | * see Intel parallel studio | ||
Line 3054: | Line 3286: | ||
* program: Matlab, link to binary is ' | * program: Matlab, link to binary is ' | ||
- | * R2020a, campus wide license so no more restrictions on licenses | + | * R2020b, campus wide license so no more restrictions on licenses |
* No Distributed Computing Engine or Matlab Parallel (for now) | * No Distributed Computing Engine or Matlab Parallel (for now) | ||
- | * install dir: / | + | * install dir: / |
* docs & www: http:// | * docs & www: http:// | ||
+ | * CentOS7 required use on queues mwgpu, amber128 and exx96 | ||
+ | * For GUI launch on greentail52 | ||
Note: | Note: | ||
Line 3071: | Line 3304: | ||
====== 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=/ |
</ | </ | ||