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 [2020/06/18 18:26] hmeij07 [Sequencing Tools] |
cluster:73 [2021/02/18 19:42] hmeij07 [Python3] |
||
---|---|---|---|
Line 3: | Line 3: | ||
====== 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 / | ||
Line 15: | Line 19: | ||
Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
- | ====== Sequencing Tools ====== | + | ====== DMTCP ===== |
+ | |||
+ | * / | ||
+ | * this came from the CRAC source, trying to install gpu checkpoint tool | ||
+ | * [[cluster: | ||
+ | * but plugin will not compile, checking with developers 12 Dec 2020 | ||
+ | |||
+ | * 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 | ||
< | < | ||
Line 22: | Line 51: | ||
export LD_LIBRARY_PATH="/ | export LD_LIBRARY_PATH="/ | ||
Successfully installed macs-1.4.3 | 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="/ | ||
Line 43: | Line 87: | ||
USAGE: PicardCommandLine <program name> [-h] | USAGE: PicardCommandLine <program name> [-h] | ||
+ | export PATH=/ | ||
+ | bedtools --version: bedtools v2.29.2 | ||
</ | </ | ||
Line 54: | Line 100: | ||
* portainer | * portainer | ||
* consult [[cluster: | * consult [[cluster: | ||
+ | * QAC | ||
====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
Line 63: | Line 110: | ||
* BCFtools: | * BCFtools: | ||
* HTSlib: A C library for reading/ | * HTSlib: A C library for reading/ | ||
+ | * Archeology (kbrunson) | ||
< | < | ||
Line 110: | Line 158: | ||
* 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 164: | Line 213: | ||
* 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 173: | Line 223: | ||
====== 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) | ||
+ | |||
+ | * Added to 3.8.3 " | ||
+ | * https:// | ||
+ | |||
+ | --- // | ||
+ | |||
+ | < | ||
+ | |||
+ | # 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\\ | ||
--- // | --- // | ||
Line 374: | Line 453: | ||
* location: / | * location: / | ||
* https:// | * https:// | ||
+ | * biolab (jcoolon, tearley) | ||
Line 494: | Line 574: | ||
- | ====== Sequencing Tools ====== | + | ====== Sequencing Tools #1 ====== |
All of these are located in / | All of these are located in / | ||
Line 503: | Line 583: | ||
* 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 611: | Line 692: | ||
* gpu version local to n78 | * gpu version local to n78 | ||
* sample programs / | * sample programs / | ||
+ | * mindlab (ploui et al) | ||
====== FSL ====== | ====== FSL ====== | ||
Line 620: | Line 702: | ||
* gpu version local on n78 | * gpu version local on n78 | ||
* sample programs / | * sample programs / | ||
+ | * mindlab (ploui et al) | ||
====== Campari ====== | ====== Campari ====== | ||
Line 689: | Line 772: | ||
* www: https:// | * www: https:// | ||
+ | * astrolab | ||
Line 793: | Line 877: | ||
* program: see below, binary download, no requirement checks. | * program: see below, binary download, no requirement checks. | ||
* www: http:// | * www: http:// | ||
+ | * astrolab (kflaherty) | ||
< | < | ||
Line 839: | Line 924: | ||
* program: see below | * program: see below | ||
* www: http:// | * www: http:// | ||
+ | * astrolab (kflaherty) | ||
< | < | ||
Line 884: | Line 970: | ||
====== Gromacs ===== | ====== Gromacs ===== | ||
+ | |||
+ | Gromacs-2020.3 for GPU (RTX2080S) | ||
+ | * '' | ||
+ | * see / | ||
+ | * change env in script below | ||
+ | |||
+ | Gromacs-2018 for GPU (RTX2080S) | ||
+ | * '' | ||
+ | * **/ | ||
Line 991: | Line 1086: | ||
[[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 | ||
Line 1001: | Line 1097: | ||
* http:// | * http:// | ||
- | Job submissions should go to queue // | + | |
====== Eigen ===== | ====== Eigen ===== | ||
Line 1185: | Line 1281: | ||
====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
+ | |||
+ | ** CPU only ** -Centos6 | ||
+ | |||
+ | * / | ||
+ | * read for env and compilation env: 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 ** | ** CPU ONLY ** | ||
Line 1197: | Line 1346: | ||
** CPU or GPU ** | ** CPU or GPU ** | ||
+ | |||
+ | * added lmp_mpi-single-single+user-omp | ||
* / | * / | ||
Line 1203: | Line 1354: | ||
* / | * / | ||
* CUDA_ARCH = sm_75 (probably only works on queue exx96) | * CUDA_ARCH = sm_75 (probably only works on queue exx96) | ||
- | * sample script in ~hmeij/ | + | |
< | < | ||
Line 2120: | Line 2271: | ||
====== Amber ====== | ====== Amber ====== | ||
+ | |||
+ | ** Amber 20 ** | ||
+ | |||
+ | * Two versions compiled, | ||
+ | * one for cuda 8.0/mpich3 for queue amber128 | ||
+ | * one for queues mwgpu and exx96 (cuda 9.2/ | ||
+ | |||
+ | * Consult the run.amber20 script to set up environment | ||
+ | * / | ||
+ | |||
+ | * Both are installed in / | ||
+ | |||
+ | |||
** AMBER 18 ** | ** AMBER 18 ** |