cluster:73
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cluster:73 [2020/06/18 18:57] hmeij07 [Sequencing Tools] |
cluster:73 [2021/02/18 19:42] hmeij07 [Python3] |
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| ====== 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 | + | * macs python package |
| * http:// | * http:// | ||
| * https:// | * https:// | ||
| * https:// | * https:// | ||
| * https:// | * https:// | ||
| + | * padillalab | ||
| < | < | ||
| Line 28: | 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 62: | Line 100: | ||
| * portainer | * portainer | ||
| * consult [[cluster: | * consult [[cluster: | ||
| + | * QAC | ||
| ====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
| Line 71: | Line 110: | ||
| * BCFtools: | * BCFtools: | ||
| * HTSlib: A C library for reading/ | * HTSlib: A C library for reading/ | ||
| + | * Archeology (kbrunson) | ||
| < | < | ||
| Line 118: | 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 172: | 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 181: | 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 382: | Line 453: | ||
| * location: / | * location: / | ||
| * https:// | * https:// | ||
| + | * biolab (jcoolon, tearley) | ||
| Line 502: | Line 574: | ||
| - | ====== Sequencing Tools ====== | + | ====== Sequencing Tools #1 ====== |
| All of these are located in / | All of these are located in / | ||
| Line 511: | 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 619: | Line 692: | ||
| * gpu version local to n78 | * gpu version local to n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== FSL ====== | ====== FSL ====== | ||
| Line 628: | Line 702: | ||
| * gpu version local on n78 | * gpu version local on n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== Campari ====== | ====== Campari ====== | ||
| Line 697: | Line 772: | ||
| * www: https:// | * www: https:// | ||
| + | * astrolab | ||
| Line 801: | 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 847: | Line 924: | ||
| * program: see below | * program: see below | ||
| * www: http:// | * www: http:// | ||
| + | * astrolab (kflaherty) | ||
| < | < | ||
| Line 892: | Line 970: | ||
| ====== Gromacs ===== | ====== Gromacs ===== | ||
| + | |||
| + | Gromacs-2020.3 for GPU (RTX2080S) | ||
| + | * '' | ||
| + | * see / | ||
| + | * change env in script below | ||
| + | |||
| + | Gromacs-2018 for GPU (RTX2080S) | ||
| + | * '' | ||
| + | * **/ | ||
| Line 999: | 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 1009: | Line 1097: | ||
| * http:// | * http:// | ||
| - | Job submissions should go to queue // | + | |
| ====== Eigen ===== | ====== Eigen ===== | ||
| Line 1193: | 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 1205: | Line 1346: | ||
| ** CPU or GPU ** | ** CPU or GPU ** | ||
| + | |||
| + | * added lmp_mpi-single-single+user-omp | ||
| * / | * / | ||
| Line 1211: | 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 2128: | 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 ** | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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