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cluster:73 [2020/01/31 12:59] hmeij07 [GNU Compilers] |
cluster:73 [2020/04/06 17:03] hmeij07 [Amber] |
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**[[cluster: | **[[cluster: | ||
- | ===== Software ===== | + | ====== 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 / | ||
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on either cottontail2 or node n33 located at / | on either cottontail2 or node n33 located at / | ||
Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
+ | |||
+ | ====== Deep Learning Software Stack ====== | ||
+ | |||
+ | * queue '' | ||
+ | * **digits, tensorflow, pytorch, caffe, rapidsai** | ||
+ | * cuda (several versions) | ||
+ | * jupyterlab | ||
+ | * portainer | ||
+ | * consult [[cluster: | ||
====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
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====== 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\\ | ||
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====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
+ | * / | ||
+ | * lmp_mpi-[double-double|single-double|single-single] | ||
+ | * consult this file for packages installed and compilations | ||
+ | * / | ||
+ | * CUDA_ARCH = sm_75 (probably only works on queue exx96) | ||
+ | * sample script in ~hmeij/ | ||
+ | < | ||
+ | |||
+ | # simple colloid example | ||
+ | CPU run -n1 | ||
+ | Performance: | ||
+ | GPU run gpu4=1 double-double: | ||
+ | Performance: | ||
+ | GPU run gpu4=1 single-double: | ||
+ | Performance: | ||
+ | GPU run gpu4=1 single-single: | ||
+ | Performance: | ||
+ | |||
+ | </ | ||
* / | * / | ||
* consult [[cluster: | * consult [[cluster: | ||
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====== 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 " | ||
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====== Amber ====== | ====== Amber ====== | ||
+ | |||
+ | ** AMBER 18 ** | ||
+ | |||
+ | * **/ | ||
+ | * compiled on '' | ||
+ | * view compile steps at / | ||
+ | * when submitting on '' | ||
+ | * 10.2 cuda drivers | ||
+ | * 9.2 toolkits | ||
+ | * some speed results below K20 vs RTX2080s, Amber 16 vs 18 | ||
+ | * sample jobs at ~hmeij/ | ||
+ | |||
+ | |||
+ | < | ||
+ | |||
+ | # compiled on n33 | ||
+ | [hmeij@n33 amber18]$ ls -l bin/pmemd* | ||
+ | -rwxr-xr-x 1 hmeij its 3549803 Mar 30 10:19 bin/pmemd | ||
+ | lrwxrwxrwx 1 hmeij its 15 Mar 30 11:57 bin/ | ||
+ | -rwxr-xr-x 1 hmeij its 93895208 Mar 30 12:11 bin/ | ||
+ | -rwxr-xr-x 1 hmeij its 94734272 Mar 30 13:07 bin/ | ||
+ | lrwxrwxrwx 1 hmeij its 19 Mar 30 12:51 bin/ | ||
+ | -rwxr-xr-x 1 hmeij its 75579744 Mar 30 11:57 bin/ | ||
+ | -rwxr-xr-x 1 hmeij its 76418760 Mar 30 12:51 bin/ | ||
+ | -rwxr-xr-x 1 hmeij its 4304392 Mar 30 11:23 bin/ | ||
+ | |||
+ | # some quick results | ||
+ | | | ||
+ | |||
+ | ~hmeij/ | ||
+ | | | ||
+ | ~hmeij/ | ||
+ | | | ||
+ | ~hmeij/ | ||
+ | | | ||
+ | |||
+ | |||
+ | </ | ||
**AMBER 16** | **AMBER 16** | ||
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* docs: doc dir inside install_dir, | * docs: doc dir inside install_dir, | ||
* www: http:// | * www: http:// | ||
- | * sample script: | + | * sample script: |
* no gpu capabilitities, | * no gpu capabilitities, | ||