This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
cluster:73 [2020/01/14 15:07] hmeij07 [Paleogenomics Tools] |
cluster:73 [2020/03/06 12:52] hmeij07 |
||
---|---|---|---|
Line 2: | Line 2: | ||
**[[cluster: | **[[cluster: | ||
+ | ====== Software ====== | ||
The listings below will be updated as software is installed, location is / | The listings below will be updated as software is installed, location is / | ||
Line 10: | Line 10: | ||
Most of the compilations have been performed by Intel' | Most of the compilations have been performed by Intel' | ||
- | The list of software was primarily compiled under RHEL5.1 but more recent compilation | + | Old compilations, |
+ | Newer compilations are done with CentOS 6.10 (since summer 2013) \\ | ||
+ | on either | ||
+ | Some compilations require 7.x and are in / | ||
+ | |||
+ | ====== Deep Learning Stack ====== | ||
+ | |||
+ | * queue '' | ||
+ | * digits, tensorflow, pytorch, caffe, rapidsai | ||
+ | * cuda (several versions) | ||
+ | * jupyterlab | ||
+ | * portainer | ||
+ | * consult [[cluster: | ||
====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
Line 129: | Line 141: | ||
====== Python3 ====== | ====== Python3 ====== | ||
+ | |||
+ | Added to both versions\\ | ||
+ | pycuda\\ | ||
+ | --- // | ||
+ | |||
+ | 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, | ||
+ | \\ | ||
+ | Requirement already satisfied: | ||
+ | keras keras-preprocessing keras-applications\\ | ||
+ | tensorflow (requires centos7)\\ | ||
+ | --- // | ||
+ | |||
Added to both 3.5.2 versions\\ | Added to both 3.5.2 versions\\ | ||
Line 1872: | Line 1899: | ||
====== R & R/parallel ====== | ====== R & R/parallel ====== | ||
+ | |||
+ | * https:// | ||
+ | * C11++ on CentOS6, two version of gcc | ||
+ | * read the R-3.6.1_configure file in ''/ | ||
+ | |||
+ | < | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | </ | ||
+ | |||
* R 3.6.1 (running against " | * R 3.6.1 (running against " | ||
Line 2606: | Line 2652: | ||
For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, | For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, | ||
+ | |||
+ | * program: GCC v 9.2.0 | ||
+ | * / | ||
+ | * note: libgomp disabled for nanopolish compile attempt | ||
+ | |||
+ | < | ||
+ | |||
+ | wget ftp:// | ||
+ | tar zxvf gcc-9.2.0.tar.gz | ||
+ | cd gcc-9.2.0 | ||
+ | ./ | ||
+ | ./configure --prefix=/ | ||
+ | make | ||
+ | make install | ||
+ | |||
+ | |||
+ | </ | ||
* program: GCC v 4.8.4 | * program: GCC v 4.8.4 |