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cluster:73 [2020/01/30 13:06]
hmeij07 		cluster:73 [2020/03/06 12:51]
hmeij07 [Software]
Line 14: Line 14:
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\ on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\ Some compilations require 7.x and are in /share/apps/CENTOS7 \\
 +
 +===== Deep Learning Stack =====
 +
 +  * queue ''exx96'' provides access to docker containers and
 +    * digits, tensorflow, pytorch, caffe, rapidsai
 +    * cuda (several versions)
 +    * jupyterlab
 +    * portainer
 +  * consult [[cluster:193|Docker Containers Usage]]
  
 ====== Paleogenomics Tools ====== ====== Paleogenomics Tools ======
Line 132: Line 141:
  
 ====== Python3 ====== ====== Python3 ======
 +
 +Added to both versions\\
 +pycuda\\
 + --- //[[hmeij@wesleyan.edu|Henk]] 2020/02/18 08:45//
 +
 +Added to both 3.5.2 versions\\
 +Successfully installed\\
 +boto-2.49.0 boto3-1.12.0 botocore-1.15.0 gensim-3.8.1 jmespath-0.9.4 s3transfer-0.3.3 smart-open-1.9.0\\
 +joblib, scikit-learn, sklearn\\
 +\\
 +Requirement already satisfied:\\
 +keras keras-preprocessing keras-applications\\
 +tensorflow (requires centos7)\\
 + --- //[[hmeij@wesleyan.edu|Henk]] 2020/02/17 13:02//
 +
  
 Added to both 3.5.2 versions\\ Added to both 3.5.2 versions\\
Line 1875: Line 1899:
  
 ====== R & R/parallel ====== ====== R & R/parallel ======
 +
 +  * https://edwards.sdsu.edu/research/c11-on-centos-6/
 +    * C11++ on CentOS6, two version of gcc
 +    * read the R-3.6.1_configure file in ''/share/apps/src/cottontail2''
 +
 +<code>
 +install.packages('lme4', dependencies = TRUE)
 +install.packages('tidyverse', dependencies = TRUE)
 +install.packages('mice', dependencies = TRUE)
 +install.packages('rpart', dependencies = TRUE)
 +install.packages('party', dependencies = TRUE)
 +install.packages('caret', dependencies = TRUE)
 +install.packages('nnet', dependencies = TRUE)
 +install.packages('e1071', dependencies = TRUE)
 +install.packages('xgboost', dependencies = TRUE)
 +install.packages('kernlab', dependencies = TRUE)
 +install.packages('randomForest', dependencies = TRUE)
 +</code>
 +
  
   * R 3.6.1 (running against "packages", had to comment out libcurl version check)   * R 3.6.1 (running against "packages", had to comment out libcurl version check)
Line 2609: Line 2652:
  
 For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, look for samples on this page ... For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, look for samples on this page ...
 +
 +  * program: GCC v 9.2.0
 +  * /share/apps/CENTOS6/9.2.0
 +  * note: libgomp disabled for nanopolish compile attempt
 +
 +<code>
 +
 +  wget ftp://ftp.nluug.nl/mirror/languages/gcc/releases/gcc-9.2.0/gcc-9.2.0.tar.gz
 +  tar zxvf gcc-9.2.0.tar.gz
 +  cd gcc-9.2.0
 +  ./contrib/download_prerequisites
 +  ./configure --prefix=/share/apps/CENTOS6/gcc/9.2.0 --disable-libgomp --disable-multilib
 +  make
 +  make install
 +
 +
 +</code>
  
   * program: GCC v 4.8.4   * program: GCC v 4.8.4
cluster/73.txt ยท Last modified: 2024/05/15 12:58 by hmeij07

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