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cluster:73 [2023/10/31 10:16]
hmeij07 [Miniconda3-py311] 		cluster:73 [2024/02/16 11:17] (current)
hmeij07 [LAMMPS CPU/GPU]
Line 70: Line 70:
 │ Using Python 3.11.4. Type "help()" for help.                       │ │ Using Python 3.11.4. Type "help()" for help.                       │
 └────────────────────────────────────────────────────────────────────┘ └────────────────────────────────────────────────────────────────────┘
 +
 +sage: exit
 +(sage) [hmeij@greentail52 ~]$ conda deactivate
 +[hmeij@greentail52 ~]$ 
 +
 +</code>
 +
 +  * **mdtraj, matplotlib, pandas**
 +
 +<code>
 +
 +[hmeij@greentail52 ~]$ which python                                                                                      
 +/share/apps/CENTOS7/miniconda3-py311/bin/python
 +                                                                          
 +[hmeij@greentail52 ~]$ python
 +Python 3.11.4 (main, Jul  5 2023, 13:45:01) [GCC 11.2.0] on linux
 +Type "help", "copyright", "credits" or "license" for more information.
 +>>> import mdtraj as mt
 +>>> 
 +
 +</code>
 +
 +  * ** seaborn**
 +  * https://seaborn.pydata.org/index.html
 +  * also in miniconda3/py311 on rock8 module (used pip3)
 +
 +<code>
 +
 +  patsy              conda-forge/noarch::patsy-0.5.4-pyhd8ed1ab_0
 +  seaborn            conda-forge/noarch::seaborn-0.13.0-hd8ed1ab_0
 +  seaborn-base       conda-forge/noarch::seaborn-base-0.13.0-pyhd8ed1ab_0
 +  statsmodels        conda-forge/linux-64::statsmodels-0.14.0-py311h1f0f07a_3
  
 </code> </code>
Line 618: Line 650:
 </code> </code>
  
 +** picard **
 +
 +  * https://github.com/broadinstitute/picard
 +  * Warning: using Java 20 but only Java 17 has been tested.
 +
 +<code>
 +
 +picard centos7, weird
 +> Failed to load native library 'libnative-platform.so' for Linux amd64.
 +
 +picard centos8
 +
 +[hmeij@cottontail2 20231108]$ pwd
 +/share/apps/CENTOS8/picard/20231108
 +
 +[hmeij@cottontail2 20231108]$ ls -l build/libs/
 +total 119872
 +-rw-r--r-- 1 hmeij its 62520451 Nov  8 11:46 picard-3.1.0-3-ga9194bd97-SNAPSHOT-all.jar
 +-rw-r--r-- 1 hmeij its  1856980 Nov  8 11:01 picard-3.1.0-3-ga9194bd97-SNAPSHOT.jar
 +-rw-r--r-- 1 hmeij its 62520451 Nov  8 11:46 picard.jar
 +[hmeij@cottontail2 20231108]$ 
 +
 +
 +</code>
 ====== Galario CPU+GPU ====== ====== Galario CPU+GPU ======
  
Line 1328: Line 1384:
  
 </code> </code>
 +
 +
 +  * **qualimap **
 +  * http://qualimap.conesalab.org/
 +  * java & R app, probably will work in centos7 and rocky8
 +  * /share/apps/CENTOS7/qualimap/2.3
 +
 +  * **gatk**
 +  * https://github.com/broadinstitute/gatk
 +  * java & R app. probably will work in centos7 and rocky8
 +  *  /share/apps/CENTOS7/gatk/4.4.0.0
 +
 +For both apps above java is v20, developers want and tested v17
 +
 +For both apps you may find R local in operating system or a recent versions at
 +
 +  * (rocky 8) module load R/4.1.2
 +
 +
 +
  
  
Line 2531: Line 2607:
  
 ====== LAMMPS CPU/GPU ====== ====== LAMMPS CPU/GPU ======
 +
 +** 7Feb2024 **
 +
 +
 +  * /share/apps/CENTOS7/lammps/7Feb2024 (feature version vs latest stable)
 +  * lmp_serial and lmp_mpi
 +  * 3 cuda versions with 3 different precision settings 
 +  * compiled against cuda 10.2 on exx96, may work in mwgpu cuda-11.2
 +  * notes: /share/apps/CENTOS7/lammps/7Feb2024.install (setup env, look for export statements)
 +  * does **not** support openmp, look for the OpenHPC version for that
  
 ** 25Apr2023** ** 25Apr2023**
cluster/73.1698761779.txt.gz · Last modified: 2023/10/31 10:16 by hmeij07

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