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 [2019/10/02 17:42] hmeij07 [R & R/parallel] |
cluster:73 [2020/06/18 19:03] hmeij07 [Sequencing Tools] |
||
---|---|---|---|
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 / | ||
+ | |||
+ | ====== Sequencing Tools ====== | ||
+ | |||
+ | * macs python package (macs2 see below) | ||
+ | * http:// | ||
+ | * https:// | ||
+ | * https:// | ||
+ | * https:// | ||
+ | |||
+ | < | ||
+ | |||
+ | 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: | ||
+ | |||
+ | ====== Paleogenomics Tools ====== | ||
+ | |||
+ | Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: | ||
+ | |||
+ | * http:// | ||
+ | * Samtools: Reading/ | ||
+ | * BCFtools: | ||
+ | * HTSlib: A C library for reading/ | ||
+ | |||
+ | < | ||
+ | |||
+ | # add to environment | ||
+ | export PATH=/ | ||
+ | export PATH=/ | ||
+ | export PATH=/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | * 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 ====== | ||
Line 89: | Line 185: | ||
====== 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 1088: | Line 1199: | ||
====== 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 1832: | Line 1974: | ||
====== 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 1972: | Line 2133: | ||
====== 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 1986: | Line 2185: | ||
* 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 2377: | Line 2576: | ||
* Python 2.7.15 | * Python 2.7.15 | ||
* compile with enable-share | * compile with enable-share | ||
- | * numpy and scipy packages | + | * numpy and scipy packages, and |
+ | * Successfully installed Send2Trash-1.5.0 backports-abc-0.5 futures-3.3.0 ipaddress-1.0.22 | ||
+ | * ipykernel-4.10.1 jupyter-client-5.3.4 jupyterlab-0.33.12 jupyterlab-launcher-0.11.2 | ||
+ | * notebook-5.7.8 prometheus-client-0.7.1 python-dateutil-2.8.0 singledispatch-3.4.0.3 | ||
+ | * subprocess32-3.5.4 terminado-0.8.2 tornado-5.1.1 | ||
< | < | ||
Line 2561: | Line 2765: | ||
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 | ||
Line 2675: | Line 2896: | ||
* 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 2688: | Line 2909: | ||
* http:// | * http:// | ||
- | Details about the Matlab configuration/ | + | |
====== Stata ====== | ====== Stata ====== |