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cluster:73 [2020/02/25 15:42] hmeij07 [R & R/parallel] |
cluster:73 [2020/12/14 14:38] hmeij07 [LAMMPS CPU/GPU] |
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**[[cluster: | **[[cluster: | ||
- | ===== Software ===== | + | ====== Software ====== |
+ | |||
+ | IMPORTANT NOTE: **Since moving to the TrueNAS/ZFS appliance all references to** ''/ | ||
+ | |||
+ | --- // | ||
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 / | ||
+ | |||
+ | ====== DMTCP ===== | ||
+ | |||
+ | * Installed as package ins OS on all nodes | ||
+ | * v2.5.2 | ||
+ | * dmctp_launch ... etc | ||
+ | |||
+ | ====== EMBOSS ====== | ||
+ | |||
+ | * / | ||
+ | * / | ||
+ | * https:// | ||
+ | * jfabry/ | ||
+ | |||
+ | ====== 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 1.4.1 | ||
+ | |||
+ | |||
+ | 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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* BCFtools: | * BCFtools: | ||
* HTSlib: A C library for reading/ | * HTSlib: A C library for reading/ | ||
+ | * Archeology (kbrunson) | ||
< | < | ||
Line 70: | Line 153: | ||
* 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\\ | + | * Python 3.8.3 |
+ | * / | ||
+ | * most packages found on this page | ||
+ | * picked up mpirun from miniconda2 apps (that may be a problem) | ||
+ | |||
+ | < | ||
+ | |||
+ | # needed for _ctypes to compile properly for https retrievals | ||
+ | yum install openssl openssl-devel | ||
+ | yum install yum install libffi-devel libffi | ||
+ | |||
+ | tar -xvf ../ | ||
+ | cd Python-3.8.3/ | ||
+ | ./configure --prefix=/ | ||
+ | make | ||
+ | make install | ||
+ | pip3 install --upgrade pip | ||
+ | # make symbolic links python3-> | ||
+ | # drop all the packages in from previous versions | ||
+ | https:// | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | Added to both 3.5.2 versions\\ | ||
pycuda\\ | pycuda\\ | ||
--- // | --- // | ||
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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) | ||
< | < | ||
Line 799: | Line 914: | ||
* program: see below | * program: see below | ||
* www: http:// | * www: http:// | ||
+ | * astrolab (kflaherty) | ||
< | < | ||
Line 844: | Line 960: | ||
====== Gromacs ===== | ====== Gromacs ===== | ||
+ | |||
+ | Gromacs-2020.3 for GPU (RTX2080S) | ||
+ | * '' | ||
+ | * see / | ||
+ | * change env in script below | ||
+ | |||
+ | Gromacs-2018 for GPU (RTX2080S) | ||
+ | * '' | ||
+ | * **/ | ||
Line 951: | Line 1076: | ||
[[https:// | [[https:// | ||
- | * program: mcc, math, mathematica (v 11.0.1) | + | * program: mcc, math, mathematica (v 12.1) |
- | * install dir: / | + | * install dir: / |
* docs: on the web | * docs: on the web | ||
* www: http:// | * www: http:// | ||
+ | * Campus wide license, use any queue. | ||
* Parallel kernels | * Parallel kernels | ||
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* http:// | * http:// | ||
- | Job submissions should go to queue // | + | |
====== Eigen ===== | ====== Eigen ===== | ||
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====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
+ | *** CPU only - CentOS6 | ||
+ | * / | ||
+ | * read for compilation env and packages installed: lmp_mpi | ||
+ | |||
+ | ** CPU only OR CPU+GPU** | ||
+ | |||
+ | * 3Mar2020 added USER-REAXC | ||
+ | * For KOKKOS MPI aware version | ||
+ | * git download of latest did not work (lots of fortran errors?) | ||
+ | * latest tarball is still 3Mar2020 (?) | ||
+ | * added user-eaxc (but had to remove package python) | ||
+ | * " | ||
+ | * please read **/ | ||
+ | |||
+ | < | ||
+ | |||
+ | # CPU | ||
+ | / | ||
+ | / | ||
+ | |||
+ | # CPU+GPU | ||
+ | / | ||
+ | |||
+ | # env | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | </ | ||
+ | |||
+ | ** CPU ONLY v2 CentOS7 ** | ||
+ | |||
+ | * add user-opm on next compile ... done ... binaries with string +user-omp | ||
+ | * / | ||
+ | * lmp_serial, lmp_mpi | ||
+ | * //latest// openmpi version as of today v4.0.4 | ||
+ | * consult this file for packages installed and compilations | ||
+ | * / | ||
+ | * should work only on exx96 and mwgpu queues | ||
+ | |||
+ | < | ||
+ | | ||
+ | | ||
+ | </ | ||
+ | |||
+ | ** 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 ** | ||
+ | |||
+ | * added lmp_mpi-single-single+user-omp | ||
+ | |||
+ | * / | ||
+ | * 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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====== 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 2774: | Line 3024: | ||
* 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 2787: | Line 3037: | ||
* http:// | * http:// | ||
- | Details about the Matlab configuration/ | + | |
====== Stata ====== | ====== Stata ====== |