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cluster:73 [2021/09/28 18:27]
hmeij07 [Paleogenomics Tools] 		cluster:73 [2021/10/15 14:13]
hmeij07 [Hoomd]
Line 19: Line 19:
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\ Some compilations require 7.x and are in /share/apps/CENTOS7 \\
  
-====== Miniconda2 =====+====== Hoomd ====== 
 + 
 +HOOMD-blue is a Python package that runs simulations of particle systems on CPUs and GPUs. 
 + 
 +  * https://hoomd-blue.readthedocs.io/en/latest/index.html 
 +  * requires both minconda3 (centos7) **and** cuda-10.2 (so queue exx96 only) 
 +  * python3.x included 
 +  * starrlab 
 + 
 +Set up env for miniconda and cuda 
 + 
 +<code> 
 + 
 + export CUDAHOME=/usr/local/cuda-10.2 
 + export PATH=/usr/local/cuda-10.2/bin:$PATH 
 + export LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib:$LD_LIBRARY_PATH 
 + export LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib64:$LD_LIBRARY_PATH 
 + 
 + source /share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh 
 + export PATH=/share/apps/CENTOS7/amber/miniconda3/bin:$PATH 
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/lib:$LD_LIBRARY_PATH 
 + 
 + which mpirun python conda 
 + which nvcc 
 + 
 +# installation (not sure how this works, does the * not get expanded in shell?) 
 +# seems to have worked forcing gpu package install on greentail52 
 + conda install -c conda-forge hoomd=*=*gpu* 
 + 
 + 
 +$ conda list | egrep -i "cuda|hoomd" 
 +cudatoolkit               11.0.221             h6bb024c_0   
 +hoomd                     2.9.4           gpu_py38h02d30ca_1    conda-forge 
 + 
 +</code> 
 + 
 +   * installed/updated were... 
 + 
 +<code> 
 + 
 +    ca-certificates-2021.10.8  |       ha878542_0         139 KB  conda-forge 
 +    certifi-2021.10.8          |   py38h578d9bd_0         145 KB  conda-forge 
 +    conda-4.10.3               |   py38h578d9bd_2         3.0 MB  conda-forge 
 +    cudatoolkit-11.0.221       |       h6bb024c_0       622.9 MB 
 +    hoomd-2.9.4                |gpu_py38h02d30ca_1        46.2 MB  conda-forge 
 +    openssl-1.1.1h             |       h516909a_0         2.1 MB  conda-forge 
 +    tbb-2020.2                 |       hc9558a2_0         1.4 MB  conda-forge 
 + 
 +</code>  
 + 
 +====== Miniconda2 ======
  
   * miniconda2 (python 2.7) is hiding in section   * miniconda2 (python 2.7) is hiding in section
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07

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