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cluster:73 [2020/01/14 14:40] hmeij07 [Paleogenomics Tools] |
cluster:73 [2020/06/18 19:26] hmeij07 [Sequencing Tools #2] |
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**[[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 / | ||
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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 / | ||
+ | |||
+ | ====== Sequencing Tools #2 ====== | ||
+ | |||
+ | * macs python package (macs2 see below) | ||
+ | * http:// | ||
+ | * https:// | ||
+ | * https:// | ||
+ | * https:// | ||
+ | * padillalab (tpadillabena) | ||
+ | |||
+ | < | ||
+ | |||
+ | export PATH="/ | ||
+ | export LD_LIBRARY_PATH="/ | ||
+ | Successfully installed macs-1.4.3 | ||
+ | |||
+ | # or change python version to | ||
+ | # ls / | ||
+ | / | ||
+ | |||
+ | |||
+ | 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 Software Stack ====== | ||
+ | |||
+ | * queue '' | ||
+ | * **digits, tensorflow, pytorch, caffe, rapidsai** | ||
+ | * cuda (several versions) | ||
+ | * jupyterlab | ||
+ | * portainer | ||
+ | * consult [[cluster: | ||
+ | * QAC | ||
====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
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Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: | Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: | ||
+ | * http:// | ||
* Samtools: Reading/ | * Samtools: Reading/ | ||
* BCFtools: | * BCFtools: | ||
* HTSlib: A C library for reading/ | * HTSlib: A C library for reading/ | ||
+ | * Archeology (kbrunson) | ||
< | < | ||
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</ | </ | ||
+ | |||
+ | * https:// | ||
+ | * Program for analysing NGS data | ||
+ | |||
+ | < | ||
+ | |||
+ | # does not seem to work against htslib version above... | ||
+ | export | ||
+ | export PATH=/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | * https:// | ||
+ | * BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. | ||
+ | |||
+ | < | ||
+ | |||
+ | # with local java jre1.8.0_212 | ||
+ | export PATH=/ | ||
+ | |||
+ | </ | ||
+ | |||
====== CD-HIT ====== | ====== CD-HIT ====== | ||
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* 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). | ||
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* 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 ====== | ||
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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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* location: / | * location: / | ||
* https:// | * https:// | ||
+ | * biolab (jcoolon, tearley) | ||
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- | ====== Sequencing Tools ====== | + | ====== Sequencing Tools #1 ====== |
All of these are located in / | All of these are located in / | ||
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* 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. | ||
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* gpu version local to n78 | * gpu version local to n78 | ||
* sample programs / | * sample programs / | ||
+ | * mindlab (ploui et al) | ||
====== FSL ====== | ====== FSL ====== | ||
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* gpu version local on n78 | * gpu version local on n78 | ||
* sample programs / | * sample programs / | ||
+ | * mindlab (ploui et al) | ||
====== Campari ====== | ====== Campari ====== | ||
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* www: https:// | * www: https:// | ||
+ | * astrolab | ||
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* program: see below, binary download, no requirement checks. | * program: see below, binary download, no requirement checks. | ||
* www: http:// | * www: http:// | ||
+ | * astrolab (kflaherty) | ||
< | < | ||
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* program: see below | * program: see below | ||
* www: http:// | * www: http:// | ||
+ | * astrolab (kflaherty) | ||
< | < | ||
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====== 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: | ||
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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, | ||
Line 2583: | Line 2777: | ||
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 | ||
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* 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:// | ||
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* http:// | * http:// | ||
- | Details about the Matlab configuration/ | + | |
====== Stata ====== | ====== Stata ====== |