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cluster:73 [2021/04/13 14:15] hmeij07 [LAMMPS CPU/GPU] |
cluster:73 [2021/06/22 19:49] hmeij07 [Galario] |
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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 ====== | ||
+ | |||
+ | | ||
+ | |||
+ | * 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 | ||
+ | * or for debugging use greentail52 | ||
+ | |||
+ | < | ||
+ | # 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 | ||
+ | </ | ||
+ | |||
+ | ====== Miniconda3 ====== | ||
+ | |||
+ | * add to ~/.bashrc and log back in, then check: 'which python pip conda' | ||
+ | * the conda initialization code block is list under DeepChem section above | ||
+ | * likely will only run on centos7, so | ||
+ | * queues: mwgpu, amber128, exx96 | ||
+ | * for debug host use greentail52 | ||
+ | |||
+ | < | ||
+ | # https:// | ||
+ | conda install -c conda-forge galario | ||
+ | |||
+ | fftw | ||
+ | galario | ||
+ | libblas | ||
+ | libcblas | ||
+ | libgfortran-ng | ||
+ | libgfortran4 | ||
+ | liblapack | ||
+ | libopenblas | ||
+ | numpy conda-forge/ | ||
+ | python_abi | ||
+ | scipy conda-forge/ | ||
+ | | ||
+ | mpi conda-forge/ | ||
+ | mpi4py | ||
+ | openmpi | ||
+ | | ||
+ | </ | ||
+ | |||
+ | For astronomy group added (' | ||
+ | |||
+ | < | ||
+ | argparse | ||
+ | corner | ||
+ | emcee | ||
+ | galario | ||
+ | matplotlib | ||
+ | numpy | ||
+ | time 1.8 h516909a_0 | ||
+ | </ | ||
+ | |||
+ | ====== 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 | ||
+ | * or for debugging use greentail52 | ||
+ | * / | ||
+ | |||
+ | |||
+ | |||
+ | < | ||
+ | |||
+ | | ||
+ | | ||
+ | |||
+ | # 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 ====== | ====== OpenHPC ====== | ||
Line 282: | Line 430: | ||
* 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. | ||
+ | "\\ | ||
--- // | --- // | ||
Line 721: | Line 878: | ||
====== Galario ====== | ====== Galario ====== | ||
+ | |||
+ | Newer GPU enabled version installed in Miniconda3 (top of page)\\ | ||
+ | --- // | ||
+ | |||
Accelerated Library for Analysing Radio Interferometer Observations | Accelerated Library for Analysing Radio Interferometer Observations | ||
Line 1341: | Line 1502: | ||
This is a version of lammps (29Oct20, last stable) that contains all packages with 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 '' | + | 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 | + | * 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 | Read, if you wish | ||
Line 1350: | Line 1512: | ||
* / | * / | ||
- | Environments | + | **Environments** |
< | < | ||
Line 1363: | Line 1525: | ||
# mpi - cpu only | # mpi - cpu only | ||
- | # OpenMPI | + | # gfortran_openmpi |
export QUIP_LIBRARY=/ | export QUIP_LIBRARY=/ | ||
Line 1374: | Line 1536: | ||
- | # serial | + | # 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 | ||
- | (to come, hopefully) | + | # sample script: ~hmeij/ |
</ | </ | ||
Line 3171: | Line 3356: | ||
====== 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=/ |
</ | </ | ||