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cluster:73 [2023/02/10 14:52]
hmeij07 [OpenHPC] 		cluster:73 [2023/07/04 12:24]
hmeij07 [Sequencing Tools #3]
Line 346: Line 346:
 ** Flye ** ** Flye **
  
-Somewhat annoying, no miniconda3 package, so local install, use minconda3 environment as listed top of this section (python 3.9, gcc 9.2)+Somewhat annoying, no miniconda3 package, (python 3.9, gcc 9.2). Local building (without installation) on centos7 greentail52. 
 + 
 +  * v2.9.2 (June 2023) 
 +  * python bin/flye 
 +    * chnage the PATHS accordingly 
 + 
 +<code> 
 + 
 +/share/apps/CENTOS7/flye/2.9.2/bin/flye --version 
 +2.9.2-b1794 
 + 
 +</code>
  
   * v2.9.1 (October 2022)   * v2.9.1 (October 2022)
Line 373: Line 384:
 </code> </code>
  
-  * https://github.com/fenderglass/Flye  
-  * miniconda3  
-  * De novo assembler for single molecule sequencing reads using repeat graphs  
-  * v2.8.3 
  
-<code> 
- 
-# To activate this environment, use 
-#     $ conda activate flye 
-# To deactivate an active environment, use 
-#     $ conda deactivate 
- 
-</code> 
  
 ** Filtlong ** ** Filtlong **
Line 719: Line 718:
 fasteners-0.18 mmtf-python-1.1.3  fasteners-0.18 mmtf-python-1.1.3 
 mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4 mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4
 +
 +</code>
 +
 +For **Lammps** (starrlab) 23April2023, consult install file
 +
 +  *  /share/apps/CENTOS7/lammps/25Apr2023.install
 +  * make yes-ml-pace
 +  * make yes-gpu
 +  * https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
 +
 +<code>
 +
 +# Note: you must add this line to you env
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/pkgs/cudatoolkit-11.0.221-h6bb024c_0/lib:$LD_LIBRARY_PATH
 +
 +# Note2: had to install 'conda install cudnn' and make two links 
 +to higher level libraries (a must not do) 
 +for libcudnn.so.8 and libcusolver.so.11
 +
 +[hmeij@greentail52 ~]$ which python
 +/share/apps/CENTOS7/amber/miniconda3/bin/python
 +[hmeij@greentail52 ~]$ pip list | grep tensorflow
 +mesh-tensorflow              0.1.19
 +tensorflow                   2.8.0
 +tensorflow-addons            0.15.0
 +tensorflow-datasets          4.4.0
 +tensorflow-estimator         2.7.0
 +tensorflow-gan               2.1.0
 +tensorflow-hub               0.12.0
 +tensorflow-io-gcs-filesystem 0.32.0
 +tensorflow-metadata          1.4.0
 +tensorflow-probability       0.15.0
 +[hmeij@greentail52 ~]$ which pacemaker
 +/usr/bin/which: no pacemaker in (...failed to install
  
 </code> </code>
Line 2078: Line 2111:
  
 [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]] [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]]
 +
 +  * program v13,2.1 installed
 +
 +  * program v13.2 installed
  
   * program: mcc, math, mathematica (v 12.2)   * program: mcc, math, mathematica (v 12.2)
Line 2275: Line 2312:
  
 ====== LAMMPS CPU/GPU ====== ====== LAMMPS CPU/GPU ======
 +
 +** 25Apr2023**
 +
 +  * /share/apps/CENTOS7/lammps/25Arp2023
 +  * lmp_serial and lmp_mpi
 +  * 3 cuda versions with 3 different precision settings
 +  * notes: /share/apps/CENTOS7/lammps/25Apr2023.install
 +  * does **not** support openmp, look for the OpenHPC version for that
 +  * 05/24/2023 remade with package CREATION added
 +  * also read miniconda3 section for tensorflow/pacemaker info
 +
 +<code>
 +
 +# CPU
 +
 + export PATH=/share/apps/CENTOS7/gcc/6.5.0/bin/:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/6.5.0/lib64:$LD_LIBRARY_PATH
 + export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 + export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 + which mpirun mpicc python gcc
 +
 +
 +# CPU + GPU (exx96 queue, may run on test and amber128 queues)
 +
 + export CUDA_HOME=/usr/local/cuda
 + export PATH=/usr/local/cuda/bin:$PATH
 + export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
 + export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
 + which nvcc
 +
 +# related for starrlab
 +# https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
 +
 +[hmeij@cottontail2 ~]$ module load miniconda3/py39
 +[hmeij@cottontail2 ~]$ which pacemaker
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/pacemaker
 +[hmeij@cottontail2 ~]$ pacemaker --version
 +pacemaker/pyace version: 0.2.7+77.g8b40c11
 +ace_evaluator   version: 2022.6.27
 +
 +[hmeij@cottontail2 ~]$ python
 +Python 3.9.10 | packaged by conda-forge | (main, Feb  1 2022, 21:24:11) 
 +[GCC 9.4.0] on linux
 +Type "help", "copyright", "credits" or "license" for more information.
 +>>> import pyace as py
 +>>> 
 +
 +
 +</code>
  
 ** USER_QUIP ** ** USER_QUIP **
Line 4119: Line 4207:
 ====== Matlab ====== ====== Matlab ======
  
 +  * installed R2023a
  
 +  * installed R2022a
 +
 +  * installed R2021a
  
   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''
Line 4139: Line 4231:
  
 ====== Stata ====== ====== Stata ======
 +
 +  * program stata[-mp|-se] in your $PATH, version 18
 +  * v17 will still run so add '17' to the command like 'stata-mp17'
 +  * so that makes for 12 licenses 8-)
  
   * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se    * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se 
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07

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