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cluster:73 [2021/04/12 19:17] hmeij07 [LAMMPS CPU/GPU] |
cluster:73 [2021/06/10 12:55] hmeij07 [Ovito] |
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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 / | ||
+ | |||
+ | ====== 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 ====== | ====== OpenHPC ====== | ||
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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 not compile with MPI, nor ifort in CentOS7, so there is only a " | + | 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 | ||
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* / | * / | ||
- | Environments | + | **Environments** |
< | < | ||
# serial - cpu only (although quippy compiled, it refused to install) | # serial - cpu only (although quippy compiled, it refused to install) | ||
+ | # MPI STUBS is compiled in | ||
export PATH=/ | export PATH=/ | ||
export LD_LIBRARY_PATH=/ | export LD_LIBRARY_PATH=/ | ||
- | # serial | + | / |
+ | |||
+ | # 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 | ||
- | (to come, hopefully) | + | # sample script: ~hmeij/ |
</ | </ | ||
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====== 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=/ |
</ | </ | ||