cluster:73
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cluster:73 [2020/03/06 12:51] hmeij07 [Software] |
cluster:73 [2020/06/19 17:30] hmeij07 [Python3] |
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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 / | ||
| Line 15: | Line 15: | ||
| Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
| - | ===== Deep Learning Stack ===== | + | ====== Sequencing Tools #2 ====== |
| + | |||
| + | * macs python package (macs2 see below) | ||
| + | * http:// | ||
| + | * https:// | ||
| + | * https:// | ||
| + | * https:// | ||
| + | * padillalab | ||
| + | |||
| + | < | ||
| + | |||
| + | export PATH="/ | ||
| + | export LD_LIBRARY_PATH="/ | ||
| + | Successfully installed macs-1.4.3 | ||
| + | |||
| + | # or change python version to | ||
| + | # ls / | ||
| + | / | ||
| + | |||
| + | # or change python version to | ||
| + | which python: / | ||
| + | pip list: Package | ||
| + | --------------- ------- | ||
| + | bowtie | ||
| + | MACS2 | ||
| + | numpy | ||
| + | picard | ||
| + | scipy | ||
| + | |||
| + | |||
| + | export PATH="/ | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | |||
| + | which gcc: / | ||
| + | which python: / | ||
| + | which perl: / | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | which R: / | ||
| + | ldd / | ||
| + | |||
| + | java --version: java 12.0.2 2019-07-16 # / | ||
| + | java -jar / | ||
| + | USAGE: PicardCommandLine <program name> [-h] | ||
| + | |||
| + | export PATH=/ | ||
| + | bedtools --version: bedtools v2.29.2 | ||
| + | |||
| + | </ | ||
| + | |||
| + | ====== Deep Learning | ||
| * queue '' | * queue '' | ||
| - | * digits, tensorflow, pytorch, caffe, rapidsai | + | |
| * cuda (several versions) | * cuda (several versions) | ||
| * jupyterlab | * jupyterlab | ||
| * portainer | * portainer | ||
| * consult [[cluster: | * consult [[cluster: | ||
| + | * QAC | ||
| ====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
| Line 32: | Line 88: | ||
| * BCFtools: | * BCFtools: | ||
| * HTSlib: A C library for reading/ | * HTSlib: A C library for reading/ | ||
| + | * Archeology (kbrunson) | ||
| < | < | ||
| Line 79: | Line 136: | ||
| * https:// | * https:// | ||
| * recipe at / | * recipe at / | ||
| + | * Starrlab | ||
| OpenStructure relies on these applications and Python 2.7.15 (see python2 section). | OpenStructure relies on these applications and Python 2.7.15 (see python2 section). | ||
| Line 133: | Line 191: | ||
| * add the bin/ directory to your PATH (see examples on this page) | * add the bin/ directory to your PATH (see examples on this page) | ||
| * http:// | * http:// | ||
| + | * fcolanlab (wmei, ndelgaudio) | ||
| ====== Spyder ====== | ====== Spyder ====== | ||
| Line 141: | Line 200: | ||
| ====== Python3 ====== | ====== Python3 ====== | ||
| + | |||
| + | * Python 3.8.3 | ||
| + | * / | ||
| + | * most packages found on this page | ||
| + | * picked up mpirun from miniconda2 apps (that may be a problem) | ||
| Added to both versions\\ | Added to both versions\\ | ||
| Line 343: | Line 407: | ||
| * location: / | * location: / | ||
| * https:// | * https:// | ||
| + | * biolab (jcoolon, tearley) | ||
| Line 463: | Line 528: | ||
| - | ====== Sequencing Tools ====== | + | ====== Sequencing Tools #1 ====== |
| All of these are located in / | All of these are located in / | ||
| Line 472: | Line 537: | ||
| * deepbinner --help | * deepbinner --help | ||
| * https:// | * https:// | ||
| + | * fcohanlab (ndelgaudio) | ||
| **Canu**: a single molecule sequence assembler for genomes large and small. | **Canu**: a single molecule sequence assembler for genomes large and small. | ||
| Line 580: | Line 646: | ||
| * gpu version local to n78 | * gpu version local to n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== FSL ====== | ====== FSL ====== | ||
| Line 589: | Line 656: | ||
| * gpu version local on n78 | * gpu version local on n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== Campari ====== | ====== Campari ====== | ||
| Line 658: | Line 726: | ||
| * www: https:// | * www: https:// | ||
| + | * astrolab | ||
| Line 762: | Line 831: | ||
| * program: see below, binary download, no requirement checks. | * program: see below, binary download, no requirement checks. | ||
| * www: http:// | * www: http:// | ||
| + | * astrolab (kflaherty) | ||
| < | < | ||
| Line 808: | Line 878: | ||
| * program: see below | * program: see below | ||
| * www: http:// | * www: http:// | ||
| + | * astrolab (kflaherty) | ||
| < | < | ||
| Line 1155: | Line 1226: | ||
| ====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
| + | ** CPU ONLY ** | ||
| + | * / | ||
| + | * lmp_mpi, lmp_serial | ||
| + | * consult this file for packages installed and compilations | ||
| + | * / | ||
| + | * should work on all queues | ||
| + | * sample script in ~hmeij/ | ||
| + | |||
| + | |||
| + | ** CPU or 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: | ||
| Line 2058: | Line 2160: | ||
| ====== 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** | ||
| Line 2072: | Line 2212: | ||
| * 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, | ||
| Line 2783: | Line 2923: | ||
| * program: Matlab, link to binary is ' | * program: Matlab, link to binary is ' | ||
| - | * R2018a, campus wide license so no more restrictions on licenses | + | * R2020a, campus wide license so no more restrictions on licenses |
| - | * No Distributed Computing Engine (for now) | + | * No Distributed Computing Engine |
| - | * install dir: / | + | * install dir: / |
| * docs & www: http:// | * docs & www: http:// | ||
| Line 2796: | Line 2936: | ||
| * http:// | * http:// | ||
| - | Details about the Matlab configuration/ | + | |
| ====== Stata ====== | ====== Stata ====== | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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