User Tools

Site Tools


cluster:73

Warning: Undefined array key -1 in /usr/share/dokuwiki/inc/html.php on line 1458

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
cluster:73 [2020/06/29 13:15]
hmeij07 [Python3]
cluster:73 [2024/02/16 11:17] (current)
hmeij07 [LAMMPS CPU/GPU]
Line 3: Line 3:
  
 ====== Software ====== ====== Software ======
 +
 +[[cluster:215|OpenHPC Software]] for **Rocky 8**
 +
 +Below is all centos 6 and/or 7, which may or may not run in 8.
 +
 +
 +IMPORTANT NOTE: **Since moving to the TrueNAS/ZFS appliance all references to** ''/home/apps'' **should be replaced with** ''/share/apps'' **which points to** ''/zfshomes/apps''
 +
 + --- //[[hmeij@wesleyan.edu|Henk]] 2020/07/31 15:08//  
  
 The listings below will be updated as software is installed, location is /share/apps/ or /home/apps/ (same thing). The listings below will be updated as software is installed, location is /share/apps/ or /home/apps/ (same thing).
Line 14: Line 23:
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\ on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\ Some compilations require 7.x and are in /share/apps/CENTOS7 \\
 +
 +
 +
 +====== Miniconda3-py311 ======
 +
 +  * Starting a new branch, the other Miniconda3 section listed on this is quite loaded
 +  * Python 3.11
 +
 +<code>
 +
 +source /share/apps/CENTOS7/miniconda3-py311/etc/profile.d/conda.sh
 +or
 +export PATH=/share/apps/CENTOS7/miniconda3-py311/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/miniconda3-py311/lib:$LD_LIBRARY_PATH
 +which mpirun python conda
 +conda list
 +
 +export CUDA_HOME=/usr/local/cuda
 +export PATH=/usr/local/cuda/bin:$PATH
 +export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
 +export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
 +
 +
 +</code>
 +
 +  * conda install (same as what is listed on openhpc [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:215#miniconda3-py311|miniconda3-py311]]) page
 +  * cudatoolkit=10.2 cudnn=7 for exx96 queue
 +  * same error, module cudatoolkit not found, but I found Cupy and it does load
 +  * https://docs.cupy.dev/en/stable/overview.html
 +  * thayerlab
 +
 +<code>
 +
 +# pollacklab
 +
 +[hmeij@greentail52 ~]$ source /share/apps/CENTOS7/miniconda3-py311/etc/profile.d/conda.sh
 +
 +[hmeij@greentail52 ~]$ conda activate sage
 +
 +(sage) [hmeij@greentail52 ~]$ sage --version
 +SageMath version 10.0, Release Date: 2023-05-20
 +
 +(sage) [hmeij@greentail52 ~]$ sage
 +┌────────────────────────────────────────────────────────────────────┐
 +│ SageMath version 10.0, Release Date: 2023-05-20                    │
 +│ Using Python 3.11.4. Type "help()" for help.                       │
 +└────────────────────────────────────────────────────────────────────┘
 +
 +sage: exit
 +(sage) [hmeij@greentail52 ~]$ conda deactivate
 +[hmeij@greentail52 ~]$ 
 +
 +</code>
 +
 +  * **mdtraj, matplotlib, pandas**
 +
 +<code>
 +
 +[hmeij@greentail52 ~]$ which python                                                                                      
 +/share/apps/CENTOS7/miniconda3-py311/bin/python
 +                                                                          
 +[hmeij@greentail52 ~]$ python
 +Python 3.11.4 (main, Jul  5 2023, 13:45:01) [GCC 11.2.0] on linux
 +Type "help", "copyright", "credits" or "license" for more information.
 +>>> import mdtraj as mt
 +>>> 
 +
 +</code>
 +
 +  * ** seaborn**
 +  * https://seaborn.pydata.org/index.html
 +  * also in miniconda3/py311 on rock8 module (used pip3)
 +
 +<code>
 +
 +  patsy              conda-forge/noarch::patsy-0.5.4-pyhd8ed1ab_0
 +  seaborn            conda-forge/noarch::seaborn-0.13.0-hd8ed1ab_0
 +  seaborn-base       conda-forge/noarch::seaborn-base-0.13.0-pyhd8ed1ab_0
 +  statsmodels        conda-forge/linux-64::statsmodels-0.14.0-py311h1f0f07a_3
 +
 +</code>
 +
 +
 +====== Masurca ======
 +
 +
 +  * module: masurca/4.1.0
 +  * https://github.com/alekseyzimin/masurca/releases
 +  * supports openmp (maybe)
 +  * queues mwgpu, exx96 (centos 7)
 +
 +
 +<code>
 +
 +export PATH=/share/apps/CENTOS7/masurca/4.1.0/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/masurca/4.1.0/lib:$LD_LIBRARY_PATH
 +
 +
 +[hmeij@cottontail2 ~]$ masurca --version
 +version 4.1.0
 +
 +
 +</code>
 +
 +====== Trimmomatic ======
 +
 +  * http://www.usadellab.org/cms/?page=trimmomatic
 +  * binary download and stage
 +  * java -jar trimmomatic-0.39.jar ...
 +
 +<code>
 +
 +/share/apps/CENTOS6/Trimmomatic-0.39/
 +[root@cottontail Trimmomatic-0.39]# ll
 +total 176
 +drwxr-xr-x 2 root root      8 Apr  8  2019 adapters
 +-rw-r--r-- 1 root root  35147 May 16  2018 LICENSE
 +-rw-r--r-- 1 root root 128502 Apr  8  2019 trimmomatic-0.39.jar
 +
 +</code>
 +
 +
 +====== HPC SDK ======
 +
 +    * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:212
 +    * Nvidia SDK v 22.2
 +
 +====== Magenta ======
 +
 +An open source research project exploring the role of machine learning as a tool in the creative process.  Magenta is distributed as an open source Python library, powered by TensorFlow. This library includes utilities for manipulating source data (primarily music and images), using this data to train machine learning models, and finally generating new content from these models.
 +
 +  * https://magenta.tensorflow.org/
 +  * installed in miniconda3's python3
 +  * queues: mwgpu, amber128, exx96
 +  * (MUSC/hgonzalez)
 +
 +====== EasyBuild ======
 +
 +EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
 +
 +  * supports 2469 different software packages (incl. toolchains, bundles)
 +  * local page with lots of details  **[[cluster:209|EasyBuild]]**
 +
 +Easybuild uses ''environment-modules'' to control the environment. Load the module of interest and all dependencies will be taken care of. See below.
 +
 +**Installed modules** and their dependencies
 +
 +  * astropy/4.2.1-fosscuda-2020b
 +    * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:209#astropy
 +    * contains package mpi4py, multithreading
 +    * import erfa (needs to be loaded too), added later (pycuda, h5py for helios)
 +    * to find ''libcuda.so.1'' set export path below
 +  * emcee/2.2.1-foss-2019a
 +    * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:209#emcee
 +    * contains package mpi4py, multithreading
 +  * PyCUDA/2020.1-fosscuda-2020b
 +    * 
 +
 +To use module, discover the modules and load desired module. On ''greentail52'' (debugging) or in submit scripts on queue: exx96 (mwgpu and amber128 nodes do not work)
 +
 +<code>
 +
 +# cuda libs location
 +export LD_LIBRARY_PATH=\
 +/sanscratch/CENTOS7/easybuild/4.4.2/software/CUDAcore/11.1.1/lib64:\
 +/sanscratch/CENTOS7/easybuild/4.4.2/software/CUDAcore/11.1.1/lib:\
 +/sanscratch/CENTOS7/easybuild/4.4.2/software/CUDAcore/11.1.1/targets/x86_64-linux/lib/stubs:\
 +$LD_LIBRARY_PATH
 +
 +
 +# discover all modules
 +module use /sanscratch/CENTOS7/easybuild/4.4.2/modules/all
 +
 +# view availability
 +module avail
 +
 +# load
 +module load module_name
 +
 +# list modules loaded
 +module list
 +
 +# check, start app, import package (by full module name)
 +# note that these modules use different python versions
 +which python
 +python
 +>>>help('modules')
 +
 +# unload all modules (better to exit shell and start new one,
 +# purge will also unload system modules...
 +module purge
 +
 +</code>
 +
 +====== Hoomd ======
 +
 +HOOMD-blue is a Python package that runs simulations of particle systems on CPUs and GPUs.
 +
 +  * https://hoomd-blue.readthedocs.io/en/latest/index.html
 +  * requires both minconda3 (centos7) **and** cuda-10.2 (so queue exx96 only)
 +  * python3.x included
 +  * starrlab
 +
 +Set up env for miniconda and cuda
 +
 +<code>
 +
 + export CUDAHOME=/usr/local/cuda-10.2
 + export PATH=/usr/local/cuda-10.2/bin:$PATH
 + export LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib:$LD_LIBRARY_PATH
 + export LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib64:$LD_LIBRARY_PATH
 +
 + source /share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh
 + export PATH=/share/apps/CENTOS7/amber/miniconda3/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/lib:$LD_LIBRARY_PATH
 +
 + which mpirun python conda
 + which nvcc
 +
 +# installation (not sure how this works, does the * not get expanded in shell?)
 +# seems to have worked forcing gpu package install on greentail52
 + conda install -c conda-forge hoomd=*=*gpu*
 +
 +
 +$ conda list | egrep -i "cuda|hoomd"
 +cudatoolkit               11.0.221             h6bb024c_0  
 +hoomd                     2.9.4           gpu_py38h02d30ca_1    conda-forge
 +
 +
 +# ahh, hamed found an error
 +conda install -c conda-forge cudatoolkit=10.2
 +
 +The following packages will be DOWNGRADED:
 +
 +  cudatoolkit                           11.0.221-h6bb024c_0 --> 10.2.89-hfd86e86_1
 +  hoomd                            2.9.4-gpu_py38h02d30ca_1 --> 2.9.4-gpu_py38h5bdc439_1
 +
 +
 +</code>
 +
 +   * installed/updated were...
 +
 +<code>
 +
 +    ca-certificates-2021.10.8  |       ha878542_0         139 KB  conda-forge
 +    certifi-2021.10.8          |   py38h578d9bd_0         145 KB  conda-forge
 +    conda-4.10.3                 py38h578d9bd_2         3.0 MB  conda-forge
 +    cudatoolkit-11.0.221             h6bb024c_0       622.9 MB
 +    hoomd-2.9.4                |gpu_py38h02d30ca_1        46.2 MB  conda-forge
 +    openssl-1.1.1h                   h516909a_0         2.1 MB  conda-forge
 +    tbb-2020.2                       hc9558a2_0         1.4 MB  conda-forge
 +
 +</code> 
 +
 +  * and
 +
 +<code>
 +
 +conda install -c conda-forge gsd
 +
 +
 +The following NEW packages will be INSTALLED:
 +
 +  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
 +  gsd                conda-forge/linux-64::gsd-2.5.1-py38h6c62de6_0
 +  libgomp            conda-forge/linux-64::libgomp-11.2.0-h1d223b6_11
 +
 +The following packages will be UPDATED:
 +
 +  certifi                          2021.10.8-py38h578d9bd_0 --> 2021.10.8-py38h578d9bd_1
 +  conda                               4.10.3-py38h578d9bd_2 --> 4.10.3-py38h578d9bd_4
 +  libgcc-ng           pkgs/main::libgcc-ng-9.1.0-hdf63c60_0 --> conda-forge::libgcc-ng-11.2.0-h1d223b6_11
 +  openssl                                 1.1.1h-h516909a_0 --> 1.1.1l-h7f98852_0
 +
 +</code>
 +
 +
 +
 +====== Miniconda2 ======
 +
 +  * miniconda2 (python 2.7) is hiding in section
 +  * "Kallisto & Trinity & FastQC"
 +    * some packages require centos 6 (like cufflinks)
 +  * many packages are also available in miniconda3 section
 +    * requires centos 7 (python 3.9)
 +
 +====== Sequencing Tools #4 ======
 +
 +Added to miniconda3, see section "Miniconda3"
 +
 +  * Requires centos7 so queues mwgpu, amber128, exx96
 +    * debug server greentail52
 +    * PREFIX=/share/apps/CENTOS7/miniconda3
 +    * python 3.9
 +  * jcoolon lab
 +    
 +
 +<code>
 +
 +# environment
 +source /share/apps/CENTOS7/miniconda3/etc/profile.d/conda.sh
 +export PATH=/share/apps/CENTOS7/miniconda3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/miniconda3/lib:$LD_LIBRARY_PATH
 +
 +
 +    libgcc-7.2.0                     h69d50b8_2         304 KB  conda-forge
 +    samtools-1.7                              1         1.0 MB  bioconda
 +    bowtie2-2.2.5              |   py38hed8969a_7        11.8 MB  bioconda
 +    perl-5.26.2                |    h36c2ea0_1008        15.4 MB  conda-forge
 +    bedtools-2.30.0            |       hc088bd4_0        14.0 MB  bioconda
 +
 +# cufflinks requires centos 6, weird, so also added to miniconda2, 
 +# see section "Kallisto & Trinity & FastQC"
 +
 +</code>
 +
 +====== Sequencing Tools #3 ======
 +
 +Suite of tools for high-accuracy basecaling, assembly, polishing, and alignment. Installed in a specific miniconda3 environment (see below).
 +
 +  * Requires centos7 so queues mwgpu, <del>amber128</del>, exx96
 +    * debug server greentail52
 +  * PREFIX=/share/apps/CENTOS7/miniconda3
 +    * python 3.9
 +    * gcc 9.2
 +    * cmake 3.8.5
 +  * chernofflab
 +
 +<code>
 +
 +# environment for all modules
 +source /share/apps/CENTOS7/miniconda3/etc/profile.d/conda.sh
 +export PATH=/share/apps/CENTOS7/miniconda3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/miniconda3/lib:$LD_LIBRARY_PATH
 +export PATH=/share/apps/CENTOS7/gcc/9.2.0/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/9.2.0/lib64:$LD_LIBRARY_PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/9.2.0/lib:$LD_LIBRARY_PATH
 +export PATH=/share/apps/CENTOS7/cmake/3.12.1/bin:$PATH
 +
 +which conda python pip mpirun gcc cmake
 +python --version
 +
 +/share/apps/CENTOS7/miniconda3/bin/conda
 +/share/apps/CENTOS7/miniconda3/bin/python
 +/share/apps/CENTOS7/miniconda3/bin/pip
 +/share/apps/CENTOS7/miniconda3/bin/mpirun
 +/share/apps/CENTOS7/gcc/9.2.0/bin/gcc
 +/share/apps/CENTOS7/cmake/3.12.1/bin/cmake
 +
 +
 +</code>
 +
 +** Guppy Server **
 +
 +  * https://github.com/nanoporetech/megalodon, find community page
 +  * standalone build
 +  * Local accelerated basecalling for Nanopore data
 +  * v5.0.11
 +
 +<code>
 +
 +export PATH=/share/apps/CENTOS7/guppy/5.0.11/ont-guppy-cpu/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/guppy/5.0.11/ont-guppy-cpu/lib:$LD_LIBRARY_PATH
 +ldd `which guppy_basecall_server`
 +
 +# cpu; note as user start server on scratch server greentail52
 +guppy_basecall_server --config dna_r9.4.1_450bps_fast.cfg -p 5555 -l /tmp/guppy &
 +
 +# check if running, use ''kill'' command to terminate
 +lsof -i:5555
 +COMMAND     PID      USER   FD   TYPE    DEVICE SIZE/OFF NODE NAME
 +guppy_bas 80002 bchernoff   12u  IPv4 959121280      0t0  TCP *:personal-agent (LISTEN)
 +
 +# nodes can reach this server at this IP or start their own on localhost:port
 +192.168.102.251 greentail52-eth0
 +10.10.102.251   greentail52-eth1 (preferred)
 +
 +</code>
 +
 +** Guppy Client **
 +
 +  * https://github.com/nanoporetech/pyguppyclient
 +  * miniconda3 python3.9
 +  * Python client library for Guppy.
 +  * Full Python client library for communicating with guppy_basecall_server.
 +  * v0.1.0
 +
 +<code>
 +
 +pip install cython PyUnicode timer
 +pip install pyguppyclient
 +Successfully installed flatbuffers-1.11 ont-fast5-api-3.3.0 pyguppyclient-0.0.6 pyzmq-17.1.2
 +
 +note: from pyguppyclient import GuppyBasecallerClient, yield_reads
 +success, but do not know how to execute the example
 +
 +</code>
 +
 +** Medaka **
 +
 +  * https://github.com/nanoporetech/medaka
 +  * miniconda3
 +  * Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data.
 +  * v1.4.3
 +
 +<code>
 +
 +# To activate this environment, use
 +#     $ conda activate medaka
 +# To deactivate an active environment, use
 +#     $ conda deactivate
 +
 +# requires
 +(medaka)$ conda list | egrep -i "samtools|minimap2|tabix|bgzip" 
 +minimap2                  2.21                 h5bf99c6_0    bioconda
 +pbgzip                    2016.08.04           h36cd882_2    bioconda
 +py-bgzip                  0.4.0            py38ha8cb210_0    conda-forge
 +samtools                  1.12                 h9aed4be_1    bioconda
 +tabix                     1.11                 hdfd78af_0    bioconda
 +
 +</code>
 +
 +** Flye **
 +
 +Somewhat annoying, no miniconda3 package, (python 3.9, gcc 9.2). Local building (without installation) on centos7 greentail52.
 +
 +  * setup env as for all packages in #3, see top of section
 +  * v2.9.2 (June 2023)
 +  * python bin/flye
 +    * change the PATHS accordingly
 +
 +<code>
 +
 +/share/apps/CENTOS7/flye/2.9.2/bin/flye --version
 +2.9.2-b1794
 +
 +</code>
 +
 +  * v2.9.1 (October 2022)
 +  * python bin/flye
 +    * change the PATHs accordingly
 +
 +<code>
 +
 +/share/apps/CENTOS7/flye/2.9.1/bin/flye --version
 +2.9.1-b1780
 +
 +</code>
 +
 +  * v2.9 (August 2021)
 +  * python bin/flye
 +
 +<code>
 +
 +export PATH=/share/apps/CENTOS7/flye/2.9/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/flye/2.9/lib:$LD_LIBRARY_PATH
 +which flye
 +/share/apps/CENTOS7/flye/2.9/bin/flye
 +flye --version
 +2.9-b1774
 +
 +</code>
 +
 +
 +
 +** Filtlong **
 +
 +  * https://github.com/rrwick/Filtlong
 +  * binary
 +  * Filtlong is a tool for filtering long reads by quality.
 +  * v0.2.1
 +
 +<code>
 +
 +# note: fails with gcc 9.2, native gcc ok 4.8.5, UNSET gcc92/miniconda3 env
 +export PATH=/share/apps/CENTOS7/Filtlong/0.2.1/bin:$PATH
 +ldd `which filtlong`
 +
 +</code>
 +
 +** Bamtools**
 +
 +  * https://github.com/pezmaster31/bamtools 
 +  * standalone build
 +  * C++ API & command-line toolkit for working with BAM data 
 +  * v2.5.2
 +
 +<code>
 +
 +export PATH=/share/apps/CENTOS7/bamtools/2.5.2/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/bamtools/2.5.2/lib:$LD_LIBRARY_PATH
 +ldd `which bamtools`
 +
 +</code>
 +
 +** BBmap **
 +
 +  * location: /share/apps/CENTOS7/bbmap/39.01
 +  * java programs
 +  * https://sourceforge.net/projects/bbmap/
 +
 +** Pilon **
 +
 +  * location: /share/apps/CENTOS7/pilon/
 +  * just one big jar file
 +  * latest java is in $PATH
 +
 +<code>
 +
 +[hmeij@greentail52 pilon]$ java -jar pilon-1.24.jar --help
 +Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500
 +
 +    Usage: pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam]
 +                 [...other options...]
 +           pilon --help for option details 
 +<snip>
 +
 +</code>
 +
 +** haslr **
 +
 +  * miniconda3 env
 +  * https://github.com/vpc-ccg/haslr
 +  * conda install -c bioconda haslr
 +
 +<code>
 +
 +The following NEW packages will be INSTALLED:
 +
 +  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
 +  fastutils          bioconda/linux-64::fastutils-0.3-hdcf5f25_4
 +  haslr              bioconda/linux-64::haslr-0.8a1-py39hd65a603_4
 +  k8                 bioconda/linux-64::k8-0.2.5-hdcf5f25_4
 +  libgomp            conda-forge/linux-64::libgomp-13.2.0-h807b86a_2
 +  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5
 +  minia              bioconda/linux-64::minia-3.2.6-hdcf5f25_3
 +  minimap2           bioconda/linux-64::minimap2-2.26-he4a0461_1
 +  pluggy             conda-forge/noarch::pluggy-1.3.0-pyhd8ed1ab_0
 +  ruamel.yaml        conda-forge/linux-64::ruamel.yaml-0.17.32-py39hd1e30aa_0
 +  ruamel.yaml.clib   conda-forge/linux-64::ruamel.yaml.clib-0.2.7-py39h72bdee0_1
 +  toolz              conda-forge/noarch::toolz-0.12.0-pyhd8ed1ab_0
 +
 +</code>
 +
 +Compiled from source, do **not** source miniconda3, we are using standalone pyhton3
 +
 +<code>
 +
 +export PATH=/share/apps/CENTOS7/gcc/9.2.0/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/9.2.0/lib64:$LD_LIBRARY_PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/9.2.0/lib:$LD_LIBRARY_PATH
 +export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +[hmeij@greentail52 20231006]$ which python
 +/share/apps/CENTOS7/python/3.8.3/bin/python
 +
 +[hmeij@greentail52 20231006]$ pwd
 +/share/apps/CENTOS7/haslr/20231006
 +
 +[hmeij@greentail52 20231006]$ ll bin
 +total 11448
 +-rwxr-xr-x 1 hmeij its   123448 Oct  6 15:01 fastutils
 +-rwxr-xr-x 1 hmeij its  3823032 Oct  6 15:04 haslr_assemble
 +-rwxr-xr-x 1 hmeij its    19949 Oct  6 14:48 haslr.py
 +-rwxr-xr-x 1 hmeij its 20969840 Oct  6 14:59 minia
 +-rwxr-xr-x 1 hmeij its    23856 Oct  6 15:01 minia_nooverlap
 +-rwxr-xr-x 1 hmeij its   951922 Oct  6 14:59 minimap2
 +
 +</code>
 +
 +
 +** stLFR **
 +
 +  * same centos 7 environment
 +  * https://github.com/BGI-Qingdao/stLFR_GapCloser
 +
 +<code>
 +
 +cd /share/apps/CENTOS7/stLFR/20230929
 +
 +[hmeij@greentail52 20230929]$ ./Release/stLFR_GapCloser -h
 +Version:
 + 1.00
 +
 +Contact:
 + dengli1@genomics.cn && guolidong@genomics.cn
 +
 +Usage:
 + stLFR_GapCloser [options]
 +...
 +
 +
 +# and another request by Luis
 +# https://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2
 +
 +[hmeij@greentail52 stLFR]$ pwd 
 +/share/apps/CENTOS7/stLFR
 +[hmeij@greentail52 stLFR]$ ll GapCloser-bin-v1.12-r6/
 +total 175
 +-rwxr-xr-x 1 hmeij its 184713 Jan 11  2013 GapCloser
 +-rw-r--r-- 1 hmeij its  44533 Jan 11  2013 GapCloser_Manual.pdf
 +
 +</code>
 +
 +** BUSCO **
 +
 +  * https://busco.ezlab.org/busco_userguide.html#docker-image
 +  * conda package fails on glib 2.17, weird
 +
 +<code>
 +
 +[hmeij@n79 ~]$ docker images
 +REPOSITORY                         TAG                            IMAGE ID            CREATED             SIZE
 +ezlabgva/busco                     v5.5.0_cv1                     30d3e831aba7        2 months ago        2.88GB
 +
 +
 +[hmeij@n79 busco_wd]$ docker run --rm -v $(pwd):/busco_wd -u $(id -u):$(id -g) ezlabgva/busco:v5.5.0_cv1 busco -i /busco_wd/assembly.fasta -l actinopterygii_odb10 -o Busco_Output -m geno -f
 +2023-10-28 20:30:00 INFO:       ***** Start a BUSCO v5.5.0 analysis, current time: 10/28/2023 20:30:00 *****
 +2023-10-28 20:30:00 INFO:       Configuring BUSCO with local environment
 +2023-10-28 20:30:00 INFO:       Mode is genome
 +2023-10-28 20:30:00 INFO:       'Force' option selected; overwriting previous results directory
 +2023-10-28 20:30:00 INFO:       Downloading information on latest versions of BUSCO data...
 +
 +that's a problem, trying to reach the internet ...
 +
 +</code>
 +
 +** picard **
 +
 +  * https://github.com/broadinstitute/picard
 +  * Warning: using Java 20 but only Java 17 has been tested.
 +
 +<code>
 +
 +picard centos7, weird
 +> Failed to load native library 'libnative-platform.so' for Linux amd64.
 +
 +picard centos8
 +
 +[hmeij@cottontail2 20231108]$ pwd
 +/share/apps/CENTOS8/picard/20231108
 +
 +[hmeij@cottontail2 20231108]$ ls -l build/libs/
 +total 119872
 +-rw-r--r-- 1 hmeij its 62520451 Nov  8 11:46 picard-3.1.0-3-ga9194bd97-SNAPSHOT-all.jar
 +-rw-r--r-- 1 hmeij its  1856980 Nov  8 11:01 picard-3.1.0-3-ga9194bd97-SNAPSHOT.jar
 +-rw-r--r-- 1 hmeij its 62520451 Nov  8 11:46 picard.jar
 +[hmeij@cottontail2 20231108]$ 
 +
 +
 +</code>
 +====== Galario CPU+GPU ======
 +
 +    * c/c++ compiled library with FFTW3
 +    * should be gpu and cpu able (not sure how to work it yet)
 +    * install notes at /share/apps/CENTOS7/galario/1.2.2-install
 +    * sample program at /zfshomes/hmeij/amhughes/run-gpu
 +    * requires centos7
 +      * queues: mwgpu, amber128, exx96
 +      * debug node greentail52
 +
 +**GPU is nonfunctional**
 +
 +Conversion of python code to C binaries was successful \\
 +read the history.txt file
 + --- //[[hmeij@wesleyan.edu|Henk]] 2021/07/07 15:38//
 +
 +<code>
 +
 +# sample scripts in /zfshomes/hmeij/amhughes
 +
 +# read README, it's complicated
 +
 +</code>
 +
 +====== VSEARCH ======
 +
 +VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization ... an alternative to USEARCH; offers search and clustering algorithms that are often orders of magnitude faster than BLAST. 
 +
 +  * https://github.com/torognes/vsearch
 +  * requires centos7
 +  * centos7 queues; mwgpu, amber128, exx96
 +    * debug host greentail52
 +  * /share/apps/CENTOS7/vsearch/2.17.0/bin/vsearch
 +
 +
 +====== DeepChem ======
 +
 + DeepChem is a deep learning tool built for bio/chem research
 +
 +  * First installed latest Miniconda
 +  * /share/apps/CENTOS7/amber/miniconda3, see below
 +    * put the code block below in ~/.bashrc and log back in
 +  * https://deepchem.io/ 
 +    * installed stable/conda/gpu=no
 +  * pip installed tensorflow-2.5  
 +  * Note: miniconda contains (Your python: python=3.8)
 +    * "conda install -c ambermd pytraj" fails to install
 +  * CentOS7 so queues mwgpu, amber128, exx96
 +    * or for debugging use greentail52
 +
 +<code>
 +# add to ~/.bashrc and log back in, then check: 'which python pip conda'
 +# >>> conda initialize >>>
 +# !! Contents within this block are managed by 'conda init' !!
 +__conda_setup="$('/share/apps/CENTOS7/amber/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
 +if [ $? -eq 0 ]; then
 +    eval "$__conda_setup"
 +else
 +    if [ -f "/share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh" ]; then
 +        . "/share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh"
 +    else
 +        export PATH="/share/apps/CENTOS7/amber/miniconda3/bin:$PATH"
 +    fi
 +fi
 +unset __conda_setup
 +# <<< conda initialize <<<
 +
 +</code>
 +
 +
 +<code>
 +Successfully installed absl-py-0.12.0 astunparse-1.6.3 
 +cachetools-4.2.2 flatbuffers-1.12 gast-0.4.0 google-auth-1.30.2 
 +google-auth-oauthlib-0.4.4 google-pasta-0.2.0 grpcio-1.34.1 
 +h5py-3.1.0 keras-nightly-2.5.0.dev2021032900 keras-preprocessing-1.1.2 
 +markdown-3.3.4 numpy-1.19.5 oauthlib-3.1.1 opt-einsum-3.3.0 
 +protobuf-3.17.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 requests-oauthlib-1.3.0 
 +rsa-4.7.2 tensorboard-2.5.0 tensorboard-data-server-0.6.1 
 +tensorboard-plugin-wit-1.8.0 tensorflow-2.5.0 tensorflow-estimator-2.5.0 
 +termcolor-1.1.0 typing-extensions-3.7.4.3 werkzeug-2.0.1 wrapt-1.12.1
 +</code>
 +
 +====== Miniconda3 ======
 +
 +  * add to ~/.bashrc and log back in, then check: 'which python pip conda'
 +    * the conda initialization code block is list under DeepChem section above
 +  * likely will only run on centos7, so
 +    * queues: mwgpu, amber128, exx96
 +    * for debug host use greentail52
 +
 +** Due to technical limitations, the conda package does not support GPUs ** according to web site. You must build manual libraries for GPU, see "gallario CPU+GPU" section above
 +
 +<code>
 +
 +source /share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh
 +export PATH=/share/apps/CENTOS7/amber/miniconda3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/lib:$LD_LIBRARY_PATH
 +which mpirun python conda
 +
 +</code>
 +
 +
 +<code>
 +# https://github.com/mtazzari/galario (CPU only apparently)
 +conda install -c conda-forge galario
 +
 +  fftw               conda-forge/linux-64::fftw-3.3.8-nompi_hfc0cae8_1114
 +  galario            conda-forge/linux-64::galario-1.2.2-py38h9d68f60_1002
 +  libblas            conda-forge/linux-64::libblas-3.9.0-8_openblas
 +  libcblas           conda-forge/linux-64::libcblas-3.9.0-8_openblas
 +  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-h14aa051_19
 +  libgfortran4       conda-forge/linux-64::libgfortran4-7.5.0-h14aa051_19
 +  liblapack          conda-forge/linux-64::liblapack-3.9.0-8_openblas
 +  libopenblas        conda-forge/linux-64::libopenblas-0.3.12-pthreads_hb3c22a3_1
 +  numpy              conda-forge/linux-64::numpy-1.19.4-py38hf0fd68c_1
 +  python_abi         conda-forge/linux-64::python_abi-3.8-1_cp38
 +  scipy              conda-forge/linux-64::scipy-1.5.3-py38h828c644_0
 +  
 +    mpi              conda-forge/linux-64::mpi-1.0-openmpi
 +  mpi4py             conda-forge/linux-64::mpi4py-3.0.3-py38h2e4b629_2
 +  openmpi            pkgs/main/linux-64::openmpi-4.0.2-hb1b8bf9_1
 +  
 +  pandas             conda-forge/linux-64::pandas-1.1.4-py38h0ef3d22_0
 +  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
 +  pytz               conda-forge/noarch::pytz-2021.1-pyhd8ed1ab_0
 +  schwimmbad         conda-forge/linux-64::schwimmbad-0.3.2-py38h578d9bd_0
 +
 +  
 +</code>
 +
 +For astronomy group (amhughes and students) added ('conda list' to see all packages installed)
 +
 +<code>
 +argparse                  1.4.0                    pypi_0    pypi
 +corner                    2.2.1                    pypi_0    pypi
 +emcee                     3.0.2                    pypi_0    pypi
 +galario                   1.2.2           py38h9d68f60_1002    conda-forge
 +matplotlib                3.4.2                    pypi_0    pypi
 +numpy                     1.19.5                   pypi_0    pypi
 +time                      1.8                  h516909a_0    conda-forge
 +  astropy            conda-forge/linux-64::astropy-3.2.3-py38h516909a_0
 +  attrs              conda-forge/noarch::attrs-21.2.0-pyhd8ed1ab_0
 +  click              conda-forge/linux-64::click-8.0.3-py38h578d9bd_0
 +  coverage           pkgs/main/linux-64::coverage-5.5-py38h27cfd23_2
 +  hypothesis         conda-forge/noarch::hypothesis-6.23.4-pyhd8ed1ab_0
 +  iniconfig          conda-forge/noarch::iniconfig-1.1.1-pyh9f0ad1d_0
 +  more-itertools     conda-forge/noarch::more-itertools-8.10.0-pyhd8ed1ab_0
 +  packaging          conda-forge/noarch::packaging-21.0-pyhd8ed1ab_0
 +  pluggy             conda-forge/linux-64::pluggy-1.0.0-py38h578d9bd_1
 +  psutil             pkgs/main/linux-64::psutil-5.8.0-py38h27cfd23_1
 +  py                 conda-forge/noarch::py-1.10.0-pyhd3deb0d_0
 +  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
 +  pytest             conda-forge/linux-64::pytest-6.2.5-py38h578d9bd_0
 +  pytest-arraydiff   conda-forge/noarch::pytest-arraydiff-0.3-py_0
 +  pytest-astropy     conda-forge/noarch::pytest-astropy-0.9.0-pyhd8ed1ab_0
 +  pytest-astropy-he~ conda-forge/noarch::pytest-astropy-header-0.1.2-py_0
 +  pytest-cov         conda-forge/noarch::pytest-cov-3.0.0-pyhd8ed1ab_0
 +  pytest-doctestplus conda-forge/noarch::pytest-doctestplus-0.11.0-pyhd8ed1ab_0
 +  pytest-filter-sub~ conda-forge/noarch::pytest-filter-subpackage-0.1.1-py_0
 +  pytest-mock        conda-forge/noarch::pytest-mock-3.6.1-pyhd8ed1ab_0
 +  pytest-openfiles   conda-forge/noarch::pytest-openfiles-0.5.0-py_0
 +  pytest-remotedata  conda-forge/noarch::pytest-remotedata-0.3.2-pyh9f0ad1d_0
 +  sortedcontainers   conda-forge/noarch::sortedcontainers-2.4.0-pyhd8ed1ab_0
 +  toml               conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0
 +
 +</code>
 +
 +For nwells/smithlab added
 +
 +<code>
 +
 +conda install -c schrodinger pymol-bundle
 +
 +    package                    |            build
 +    ---------------------------|-----------------
 +    apbs-1.5                         h14c3975_3         277 KB  schrodinger
 +    biopython-1.78               py38h7b6447c_0         2.1 MB
 +    bzip2-1.0.8                |       h516909a_3         398 KB  conda-forge
 +    collada2gltf-2.1.4               h6bb024c_0         3.2 MB  schrodinger
 +    conda-4.10.3                 py38h578d9bd_0         3.1 MB  conda-forge
 +    curl-7.71.1                |       hbc83047_1         140 KB
 +    dbus-1.13.18                     hb2f20db_0         504 KB
 +    expat-2.4.1                |       h2531618_2         168 KB
 +    fontconfig-2.13.1          |    he4413a7_1000         327 KB  conda-forge
 +    freemol-1.158              |             py_2           6 KB  schrodinger
 +    freetype-2.10.4            |       h7ca028e_0         912 KB  conda-forge
 +    glew-2.0.0                                0         660 KB  schrodinger
 +    glib-2.69.0                |       h5202010_0         1.7 MB
 +    gst-plugins-base-1.14.0    |       hbbd80ab_1         4.8 MB
 +    gstreamer-1.14.0                 h28cd5cc_2         3.2 MB
 +    h5py-2.10.0                |nompi_py38hafa665b_105         1.1 MB  conda-forge
 +    hdf4-4.2.13                |       h3ca952b_2         714 KB
 +    hdf5-1.10.6                |nompi_h7c3c948_1111         3.1 MB  conda-forge
 +    icu-58.2                      hf484d3e_1000        22.6 MB  conda-forge
 +    jpeg-9d                    |       h36c2ea0_0         264 KB  conda-forge
 +    krb5-1.18.2                |       h173b8e3_0         1.3 MB
 +    libcurl-7.71.1                   h20c2e04_1         305 KB
 +    libglu-9.0.0                  he1b5a44_1001         413 KB  conda-forge
 +    libholoplaycore-0.1.0_rc4  |                1         325 KB  schrodinger
 +    libnetcdf-4.7.4            |nompi_h56d31a8_107         1.3 MB  conda-forge
 +    libpng-1.6.37              |       h21135ba_2         306 KB  conda-forge
 +    libssh2-1.9.0              |       hab1572f_5         225 KB  conda-forge
 +    libtiff-4.0.10                hc3755c2_1005         602 KB  conda-forge
 +    libuuid-2.32.1                h14c3975_1000          26 KB  conda-forge
 +    libxcb-1.13                |    h14c3975_1002         396 KB  conda-forge
 +    libxml2-2.9.10                   hb55368b_3         1.2 MB
 +    lz4-c-1.9.2                |       he1b5a44_3         203 KB  conda-forge
 +    mengine-1                  |       h14c3975_1         676 KB  schrodinger
 +    mpeg_encode-1              |       h14c3975_1         106 KB  schrodinger
 +    mtz2ccp4_px-1.0            |       h9ac9557_3         547 KB  schrodinger
 +    olefile-0.46                   pyh9f0ad1d_1          32 KB  conda-forge
 +    pcre-8.45                  |       h295c915_0         207 KB
 +    pdb2pqr-2.1.2+pymol        |             py_0         236 KB  schrodinger
 +    pillow-6.2.1                 py38h6b7be26_0         637 KB  conda-forge
 +    pmw-2.0.1+3                |             py_3          60 KB  schrodinger
 +    pthread-stubs-0.4          |    h36c2ea0_1001           5 KB  conda-forge
 +    pycollada-0.7.1+bdf414c7               py_1          80 KB  schrodinger
 +    pykerberos-1.2.1             py38h27cfd23_2         259 KB
 +    pymol-2.4.1                |   py38h4463551_0         8.5 MB  schrodinger
 +    pymol-bundle-2.4.1                        0          16 KB  schrodinger
 +    pymol-web-examples-2.4                    1         1.9 MB  schrodinger
 +    pyqt-5.9.2                   py38h05f1152_4         4.5 MB
 +    qt-5.9.7                         h5867ecd_1        68.5 MB
 +    rigimol-1.3                |                2         489 KB  schrodinger
 +    sip-4.19.13                |   py38he6710b0_0         277 KB
 +    xorg-libxau-1.0.9          |       h14c3975_0          13 KB  conda-forge
 +    xorg-libxdmcp-1.1.3        |       h516909a_0          18 KB  conda-forge
 +    zstd-1.4.5                       h9ceee32_0         619 KB
 +
 +
 +</code>
 +
 +Then
 + --- //[[hmeij@wesleyan.edu|Henk]] 2021/11/24 13:16//
 +
 +<code>
 +
 +# using pip3
 +Successfully installed magenta-2.1.3 python-rtmidi-1.1.2
 +
 +Successfully installed keras-2.7.0 libclang-12.0.0 tensorboard-2.7.0 \
 +tensorflow-2.7.0 tensorflow-estimator-2.7.0 tensorflow-io-gcs-filesystem-0.22.0
 +
 +</code>
 +
 +Added\\
 + --- //[[hmeij@wesleyan.edu|Henk]] 2022/01/03 14:35//\\
 +# https://github.com/merenlab/anvio/issues/1479
 +
 +<code>
 +
 +conda install -c bioconda samtools=1.9 --force-reinstall
 +
 +
 +The following NEW packages will be INSTALLED:
 +
 +  gettext            conda-forge/linux-64::gettext-0.19.8.1-hf34092f_1004
 +  htslib             bioconda/linux-64::htslib-1.9-h4da6232_3
 +  libdeflate         bioconda/linux-64::libdeflate-1.2-h516909a_1
 +  libglib            conda-forge/linux-64::libglib-2.66.3-hbe7bbb4_0
 +  libiconv           conda-forge/linux-64::libiconv-1.16-h516909a_0
 +
 +The following packages will be UPDATED:
 +
 +  cffi                pkgs/main::cffi-1.14.3-py38h261ae71_2 --> conda-forge::cffi-1.14.4-py38ha312104_0
 +  libedit            pkgs/main::libedit-3.1.20191231-h14c3~ --> conda-forge::libedit-3.1.20191231-h46ee950_2
 +  samtools                                            1.7-1 --> 1.9-h10a08f8_12
 +
 +The following packages will be SUPERSEDED by a higher-priority channel:
 +
 +  glib                    pkgs/main::glib-2.69.0-h5202010_0 --> conda-forge::glib-2.66.3-h58526e2_0
 +  libffi                   pkgs/main::libffi-3.3-he6710b0_2 --> conda-forge::libffi-3.2.1-he1b5a44_1007
 +  ncurses                 pkgs/main::ncurses-6.2-he6710b0_1 --> conda-forge::ncurses-6.1-hf484d3e_1002
 +  python                 pkgs/main::python-3.8.5-h7579374_1 --> conda-forge::python-3.8.3-cpython_he5300dc_0
 +  sqlite                pkgs/main::sqlite-3.33.0-h62c20be_0 --> conda-forge::sqlite-3.32.3-hcee41ef_1
 +
 +$ samtools --version
 +samtools 1.9
 +Using htslib 1.9
 +Copyright (C) 2018 Genome Research Ltd.
 +
 +</code>
 +
 +  * **iqtree** fcohanlab/jwang06
 +
 +<code>
 +
 +[hmeij@greentail52 ~]$ iqtree --version
 +IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020
 +
 +
 +</code>
 +
 +  * https://userguide.mdanalysis.org/stable/installation.html
 +  * calterlab, annika (used pip to install)
 +
 +<code>
 +
 +Successfully installed 
 +GridDataFormats-1.0.1 MDAnalysis-2.3.0 
 +fasteners-0.18 mmtf-python-1.1.3 
 +mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4
 +
 +</code>
 +
 +For **Lammps** (starrlab) 23April2023, consult install file
 +
 +  *  /share/apps/CENTOS7/lammps/25Apr2023.install
 +  * make yes-ml-pace
 +  * make yes-gpu
 +  * https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
 +
 +<code>
 +
 +# Note: you must add this line to you env
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/pkgs/cudatoolkit-11.0.221-h6bb024c_0/lib:$LD_LIBRARY_PATH
 +
 +# Note2: had to install 'conda install cudnn' and make two links 
 +to higher level libraries (a must not do) 
 +for libcudnn.so.8 and libcusolver.so.11
 +
 +[hmeij@greentail52 ~]$ which python
 +/share/apps/CENTOS7/amber/miniconda3/bin/python
 +[hmeij@greentail52 ~]$ pip list | grep tensorflow
 +mesh-tensorflow              0.1.19
 +tensorflow                   2.8.0
 +tensorflow-addons            0.15.0
 +tensorflow-datasets          4.4.0
 +tensorflow-estimator         2.7.0
 +tensorflow-gan               2.1.0
 +tensorflow-hub               0.12.0
 +tensorflow-io-gcs-filesystem 0.32.0
 +tensorflow-metadata          1.4.0
 +tensorflow-probability       0.15.0
 +[hmeij@greentail52 ~]$ which pacemaker
 +/usr/bin/which: no pacemaker in (...failed to install at first, see readme install file)
 +
 +</code>
 +
 +
 +====== pytraj ======
 +
 + Pytraj is a wrapper for cpptraj
 +
 +  * https://amber-md.github.io/pytraj/latest/installation.html#installation
 +  * From AMBER distribution (Linux, OSX)
 +  * pytraj is included in AMBER (version >= 16): ambermd.org
 +  * so below I opted for source code installation with python 3.8.3
 +  * git clone https://github.com/Amber-MD/pytraj; cd pytra
 +  * python ./setup.py install
 +  * requires CentOS7 so queues mwgpu, <del>amber128</del> and exx96
 +  * or for debugging use greentail52
 +  * /share/apps/CENTOS7/amber/pytraj
 +
 +
 +
 +<code>
 +
 + export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +
 +# An environment resource file for CPPTRAJ has been created:
 +  /zfshomes/apps/CENTOS7/amber/pytraj/cpptraj/cpptraj.sh
 +# You may 'source' this file to set up your environment for CPPTRAJ.
 +
 +
 +
 +Installed /zfshomes/apps/CENTOS7/python/3.8.3/lib/python3.8/site-packages/pytraj-2.0.6.dev0-py3.8-linux-x86_64.egg
 +Processing dependencies for pytraj==2.0.6.dev0
 +Searching for numpy==1.20.3
 +Best match: numpy 1.20.3
 +Adding numpy 1.20.3 to easy-install.pth file
 +Installing f2py script to /share/apps/CENTOS7/python/3.8.3/bin
 +Installing f2py3 script to /share/apps/CENTOS7/python/3.8.3/bin
 +Installing f2py3.8 script to /share/apps/CENTOS7/python/3.8.3/bin
 +
 +Using /zfshomes/apps/CENTOS7/python/3.8.3/lib/python3.8/site-packages
 +Finished processing dependencies for pytraj==2.0.6.dev0
 +
 +</code>
 +
 +====== Ovito ======
 +
 +  * https://www.ovito.org
 +  * /usr/local/bin/ovito -> /usr/local/ovito-basic-3.5.0-x86_64/bin/ovito
 +  * on nodes ''cottontail'' and ''greentail52''
 +  * uses freeglut/freeglut-devel libraries for opengl
 +
 +====== OpenHPC ======
 +
 +So I remember where I put the tar repo file
 +
 +  * OpenHPC v2.4
 +  * Rocky 8.5
 +  * Slurm 20.11.8
 +  * Warewulf 3.9
 +  * x86_64
 +
 +<code>
 +
 +[root@cottontail2 ~]# ll /share/apps/src/cottontail2/openhpc/
 +total 8290421
 +-rw------- 1 root root     562276 Mar 17 09:34 Install_guide-Rocky8-Warewulf-SLURM-2.4-x86_64.pdf
 +-rw-r--r-- 1 root root      10720 Mar 17 09:35 ohpc-release-2-1.el8.x86_64.rpm
 +-rw-r--r-- 1 root root 8531681280 Mar 17 09:33 OpenHPC-2.4.EL_8.x86_64.tar
 +
 +
 +
 +# this is all that is needed for ohpc base compute client
 +# see the recipe for cct2 and follow compute node only ingredients
 +
 +[root@cottontail2 ~]# ll /share/apps/src/cottontail2/ohpc-compute/
 +total 95196
 +-rw-r--r-- 1 root root  2696360 Feb 10 09:21 hwloc-ohpc-2.7.0-3.9.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root   266252 Feb 10 09:22 lmod-ohpc-8.7.6-12.3.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root     7268 Feb 10 09:22 ohpc-base-compute-2.6.1-5.1.ohpc.2.6.1.x86_64.rpm
 +-rw-r--r-- 1 root root     8204 Feb 10 09:23 ohpc-filesystem-2.6-2.3.ohpc.2.6.noarch.rpm
 +-rw-r--r-- 1 root root    10720 Feb 10 09:23 ohpc-release-2-1.el8.x86_64.rpm
 +-rw-r--r-- 1 root root     7124 Feb 10 09:27 ohpc-slurm-client-2.6.1-5.1.ohpc.2.6.1.x86_64.rpm
 +-rw-r--r-- 1 root root 74326532 Feb 10 09:23 singularity-ohpc-3.7.1-5.1.ohpc.2.1.x86_64.rpm
 +-rw-r--r-- 1 root root    22168 Feb 10 09:24 slurm-contribs-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root   247392 Feb 10 09:24 slurm-example-configs-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root 18764472 Feb 10 09:24 slurm-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root   176480 Feb 10 09:28 slurm-pam_slurm-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root   785112 Feb 10 09:25 slurm-slurmd-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
 +
 +</code>
 +
 +====== OneAPI ======
 +
 +  * Requires CentOS 7 so queues mwgpu, amber128, exx96
 +    * debug node greentail52
 +
 +  * Production version is installed in /share/apps/CENTOS7/intel/openapi (via **n78**)
 +  * source /share/apps/CENTOS7/intel/oneapi/setvars.sh
 +
 +<code>
 +# which icc icx icpc icpx dpcpp ifort ifx mpirun mpicc python clang clang++
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/intel64/icc
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/icx
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/intel64/icpc
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/icpx
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/dpcpp
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/intel64/ifort
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/ifx
 +/share/apps/CENTOS7/intel/oneapi/intelpython/latest/bin/mpirun
 +/share/apps/CENTOS7/intel/oneapi/mpi/2021.1.1/bin/mpicc
 +/share/apps/CENTOS7/intel/oneapi/intelpython/latest/bin/python
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/clang
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/clang++
 +# in addition these were installed
 +/share/apps/CENTOS7/intel/oneapi/mkl/2021.1.1
 +/share/apps/CENTOS7/intel/oneapi/pytorch/1.5.0
 +/share/apps/CENTOS7/intel/oneapi/tensorflow/2.2.0
 +</code>
 +
 +  * __Test__ version is installed on local disk on host **greentail52**
 +  * source /opt/intel/oneapi/setvars.sh
 +  * Read [[cluster:203|ICC vs ICX]]
 +
 +
 +====== StringTie2 ======
 +
 +  * Requires CentOS 7 so queues mwgpu, amber128, exx96
 +  * /share/apps/CENTOS7/stringtie2/stringtie2 binarie
 +  * https://github.com/skovaka/stringtie2
 +
 +====== Rstudio ======
 +
 +  * http://our-sanscratch-server:8787/
 +  * https://support.rstudio.com/hc/en-us/articles/200552316-Configuring-the-Server
 +  * centos7 R v 3.6.0
 +  * use your HPC username and credentials
 +
 +<code>
 +
 +# native OS installation for rstudio
 +/bin/R
 +
 +</code>
 +
 +====== DMTCP =====
 +
 +  * /share/apps/CENTOS7/dmtcp/3.0.0
 +  * this came from the CRAC source, trying to install gpu checkpoint tool
 +  * [[cluster:198|GPU checkpoint/restart]]
 +  * 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 ======
 +
 +  * /share/apps/CENTOS6/EMBOSS
 +  * /share/apps/CENTOS6/EMBOSS/6.6.0.install (read to setup env)
 +  * https://www.ebi.ac.uk/services
 +  * jfabry/kthayer
  
 ====== Sequencing Tools #2 ====== ====== Sequencing Tools #2 ======
Line 119: Line 1277:
  
 </code> </code>
 +
 +  * **sratools** https://github.com/ncbi/sra-tools/
 +  * The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
 +  * requires centos7 (glibc) so queues mwgpu, amber128, exx96
 +
 +<code>
 +
 +export PATH=/share/apps/CENTOS7/sratools/sratoolkit.2.11.0-centos_linux64/bin:$PATH
 +
 +</code>
 +
 +  * **adapterremoval** https://github.com/MikkelSchubert/adapterremoval
 +  * **bwa** https://github.com/lh3/bwa
 +  * **bowtie2** http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
 +
 +These are all part of Miniconda3 (centos7), to setup the environment consult 
 +
 +  * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:73#miniconda3
 +    * queues: mwgpu, amber128, exx96, debug server greentail52
 +
 +They are also available via Miniconda2 (centos6), consult
 +
 +  * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:73#miniconda2
 +    * queues: hp12, mw256fd, tinymem, debug server swallowtail
 +
 +<code>
 +
 +[hmeij@greentail52 ~]$ conda list | egrep "adapterremoval|bwa|bowtie"
 +adapterremoval            2.3.2                hb7ba0dd_0    bioconda
 +bowtie2                   2.2.5            py38hed8969a_7    bioconda
 +bwa                       0.7.17               hed695b0_7    bioconda
 +
 +</code>
 +
 +  * **mapDamage2**
 +  * https://github.com/ginolhac/mapDamage/issues/25
 +  * docker container is broke
 +  * requires centos6 so queues hp12, mw128  .. may run elsewhere?
 +  * conda install -c 'bioconda' mapdamage2
 +
 +
 +<code>
 +
 +# env
 +export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
 +export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
 +
 +The following NEW packages will be INSTALLED:
 +
 +  mapdamage2         bioconda/linux-64::mapdamage2-2.0.6-1
 +  pysam              bioconda/linux-64::pysam-0.16.0.1-py27hc729bab_3
 +  seqtk              bioconda/linux-64::seqtk-1.3-h5bf99c6_3
 +
 +[hmeij@petaltail ~]$ mapDamage --version
 +2.0.6
 +
 +</code>
 +
 +  * **PCAngsd**, requires miniconda3's python
 +  * https://github.com/Rosemeis/pcangsd
 +  * apparently the repo is needed ''/share/apps/CENTOS7/pcangsd/1.1.0''
 +
 +<code>
 +
 +source /share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh
 +export PATH=/share/apps/CENTOS7/amber/miniconda3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/lib:$LD_LIBRARY_PATH
 +
 +which pcangsd
 +/share/apps/CENTOS7/amber/miniconda3/bin/pcangsd
 +pcangsd --version
 +pcangsd 1.10
 +
 +</code>
 +
 +  * **angsd**, requires miniconda3, same environment as pcangsd
 +  * http://www.popgen.dk/angsd/index.php/RealSFS
 +  * add location of angsd to PATH env 
 +
 +<code>
 +
 +$ pwd
 +/share/apps/CENTOS7/angsd/0.940/angsd
 +
 +$ ls -l angsd
 +-rwxr-xr-x 1 hmeij its 5517248 Jul  6 14:11 angsd
 +
 +$ ./angsd 
 + -> angsd version: 0.940-dirty (htslib: 1.16) build(Jul  6 2023 14:11:30)
 +
 +</code>
 +
 +  * **Standard RAxML version**
 +  * https://github.com/stamatak/standard-RAxML
 +
 +<code>
 +
 +# add path to $PATH
 +
 +[hmeij@greentail52 tmp]$ ll /share/apps/CENTOS7/raxml/8.2.12/
 +total 3202
 +-rwxr-xr-x 1 hmeij its 1177632 Apr 25 14:49 raxmlHPC-AVX
 +-rwxr-xr-x 1 hmeij its 1177632 Apr 25 14:49 raxmlHPC-AVX2
 +-rwxr-xr-x 1 hmeij its 1152040 Apr 25 14:49 raxmlHPC_serial
 +-rwxr-xr-x 1 hmeij its 1185704 Apr 25 14:49 raxmlHPC-SSE3
 +
 +</code>
 +
 +
 +  * **qualimap **
 +  * http://qualimap.conesalab.org/
 +  * java & R app, probably will work in centos7 and rocky8
 +  * /share/apps/CENTOS7/qualimap/2.3
 +
 +  * **gatk**
 +  * https://github.com/broadinstitute/gatk
 +  * java & R app. probably will work in centos7 and rocky8
 +  *  /share/apps/CENTOS7/gatk/4.4.0.0
 +
 +For both apps above java is v20, developers want and tested v17
 +
 +For both apps you may find R local in operating system or a recent versions at
 +
 +  * (rocky 8) module load R/4.1.2
 +
 +
 +
  
  
Line 205: Line 1490:
   * most packages found on this page   * most packages found on this page
   * picked up mpirun from miniconda2 apps (that may be a problem)   * picked up mpirun from miniconda2 apps (that may be a problem)
 +
 +  * Added to 3.8.3 "acpype"
 +  * https://github.com/alanwilter/acpype
 +
 +From website:\\
 +"
 +We now have an up to date webservice at http://bio2byte.be/acpype/ \\
 +(but it does not have the amb2gmx funcionality).
 +
 +To run acpype, locally, with its all functionalities, you need ANTECHAMBER from package AmberTools and Open Babel if your input files are of PDB format.
 +
 +However, if one wants acpype just to emulate amb2gmx.pl, one needs nothing at all but Python.
 +"\\
 + --- //[[hmeij@wesleyan.edu|Henk]] 2021/02/18 14:41//
  
 <code> <code>
Line 426: Line 1725:
   * location: /share/apps/FastQC/0.11.8   * location: /share/apps/FastQC/0.11.8
   * https://www.bioinformatics.babraham.ac.uk/projects/fastqc/   * https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-  * biolab (jcoolon, tearley)+  * requires centos6, may not run on centos7 
 +    * queues: hp12, tinymem, mw256fd mw128 
 +    * debug server swallowtail 
 +  * biolab (coolonlab, tearley)
  
  
Line 436: Line 1738:
 <code> <code>
  
 +# env
 export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH" export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
 export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH" export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
Line 449: Line 1752:
   hdf5               conda-forge/linux-64::hdf5-1.10.3-hba1933b_1001   hdf5               conda-forge/linux-64::hdf5-1.10.3-hba1933b_1001
   kallisto           bioconda/linux-64::kallisto-0.45.0-hdcc98e5_0   kallisto           bioconda/linux-64::kallisto-0.45.0-hdcc98e5_0
 +
 +
 +# --- //[[hmeij@wesleyan.edu|Henk]] 2021/08/19 08:55//
 +# Added packages below for Prof Coolon's lab (skalra)
 +
 +
 +conda list | egrep -i "samtools|bowtie2|bedtools|cufflinks"
 +bedtools                  2.30.0               h7d7f7ad_1    bioconda
 +bowtie2                   2.3.5.1          py27he513fc3_0    bioconda
 +cufflinks                 2.2.1                    py27_2    bioconda
 +samtools                  1.13                 h8c37831_0    
 +
 +# fcohan lab
 +[hmeij@petaltail ~]$ iqtree --version
 +IQ-TREE multicore version 2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021
  
 </code> </code>
 +
 +
  
 **Trinity** assembles transcript sequences from Illumina RNA-Seq data. **Trinity** assembles transcript sequences from Illumina RNA-Seq data.
Line 641: Line 1961:
 ====== Galario ======  ====== Galario ====== 
  
-Accelerated Library for Analysing Radio Interferometer Observations+Newer CPU+GPU standalone library version (top of page)\\ 
 + --- //[[hmeij@wesleyan.edu|Henk]] 2021/06/29 14:38// 
 + 
 +Newer CPU only version installed in Miniconda3 (top of page)\\ 
 +Miniconda3 is using python 3.8\\ 
 +--- //[[hmeij@wesleyan.edu|Henk]] 2021/06/22 15:41// 
 + 
 + 
 +Accelerated Library for Analysing Radio Interferometer Observations (CPU only)
  
   * /share/apps/CENTOS6/miniconda2   * /share/apps/CENTOS6/miniconda2
   * contains python 2.7.15   * contains python 2.7.15
-  * packages galario, numpy, scipy, others ('conda list' for full listing)+  * packages galario, numpy, scipy, matplotlib, argparse, corner, time and others ('conda list' for full listing)
   * packages mpi4py, emcee, astropy   * packages mpi4py, emcee, astropy
  
Line 655: Line 1983:
 # added by Miniconda2 installer # added by Miniconda2 installer
 export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH" export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
 +
 +    package                    |            build
 +    ---------------------------|-----------------
 +    certifi-2021.5.30          |   py37h89c1867_0         141 KB  conda-forge
 +    libblas-3.8.0              |      17_openblas          11 KB  conda-forge
 +    libcblas-3.8.0                  17_openblas          11 KB  conda-forge
 +    liblapack-3.8.0            |      17_openblas          11 KB  conda-forge
 +    libopenblas-0.3.10         |pthreads_hb3c22a3_4         7.8 MB  conda-forge
 +    libstdcxx-ng-9.3.0              h6de172a_19         4.0 MB  conda-forge
 +    numpy-1.21.0                 py37h038b26d_0         6.1 MB  conda-forge
 +    pandas-1.2.5                 py37h219a48f_0        11.8 MB  conda-forge
 +    pip-21.1.3                     pyhd8ed1ab_0         1.1 MB  conda-forge
 +    python-3.7.3                     h5b0a415_0        35.7 MB  conda-forge
 +    python-dateutil-2.8.1      |             py_0         220 KB  conda-forge
 +    python_abi-3.7                      2_cp37m           4 KB  conda-forge
 +    pytz-2021.1                |     pyhd8ed1ab_0         239 KB  conda-forge
 +    setuptools-49.6.0          |   py37h89c1867_3         947 KB  conda-forge
 +    six-1.16.0                     pyh6c4a22f_0          14 KB  conda-forge
 +    wheel-0.36.2                   pyhd3deb0d_0          31 KB  conda-forge
 +
 </code> </code>
  
Line 943: Line 2291:
  
 ====== Gromacs ===== ====== Gromacs =====
 +
 +Gromacs-2020.3 for GPU (RTX2080S)
 +  * ''exx96'' queue
 +  * see /share/apps/CENTOS7/gromacs/2020.3.install for env
 +  * change env in script below
 +
 +Gromacs-2018 for GPU (RTX2080S)
 +  * ''exx96'' queue
 +  * **/zfshomes/hmeij/k20redo/run.rtx sample script**
  
  
Line 1050: Line 2407:
 [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]] [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]]
  
-  * program: mcc, math, mathematica (v 11.0.1+  * program v13,2.1 installed 
-  * install dir: /share/apps/CENTOS6/mathematica/11.0.1+ 
 +  * program v13.2 installed 
 + 
 +  * program: mcc, math, mathematica (v 12.2
 +  * install dir: /share/apps/CENTOS7/mathematica/12.2
   * docs: on the web   * docs: on the web
   * www:  http://www.wolfram.com/mathematica/   * www:  http://www.wolfram.com/mathematica/
 +  * Centos7, use queues mwgpu, amber128 or exx96
 +  * For GUI launch on greentail52
  
   * Parallel kernels   * Parallel kernels
Line 1060: Line 2423:
     * http://reference.wolfram.com/mathematica/guide/ParallelComputing.html     * http://reference.wolfram.com/mathematica/guide/ParallelComputing.html
  
-Job submissions should go to queue //mathematica// which containes licensed nodes (all the hp12 nodes for now).+
  
 ====== Eigen ===== ====== Eigen =====
Line 1244: Line 2607:
  
 ====== LAMMPS CPU/GPU ====== ====== LAMMPS CPU/GPU ======
 +
 +** 7Feb2024 **
 +
 +
 +  * /share/apps/CENTOS7/lammps/7Feb2024 (feature version vs latest stable)
 +  * lmp_serial and lmp_mpi
 +  * 3 cuda versions with 3 different precision settings 
 +  * compiled against cuda 10.2 on exx96, may work in mwgpu cuda-11.2
 +  * notes: /share/apps/CENTOS7/lammps/7Feb2024.install (setup env, look for export statements)
 +  * does **not** support openmp, look for the OpenHPC version for that
 +
 +** 25Apr2023**
 +
 +  * /share/apps/CENTOS7/lammps/25Arp2023
 +  * lmp_serial and lmp_mpi
 +  * 3 cuda versions with 3 different precision settings
 +  * notes: /share/apps/CENTOS7/lammps/25Apr2023.install
 +  * does **not** support openmp, look for the OpenHPC version for that
 +  * 05/24/2023 remade with package CREATION added
 +  * also read miniconda3 section for tensorflow/pacemaker info
 +
 +<code>
 +
 +# CPU
 +
 + export PATH=/share/apps/CENTOS7/gcc/6.5.0/bin/:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/6.5.0/lib64:$LD_LIBRARY_PATH
 + export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 + export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 + which mpirun mpicc python gcc
 +
 +
 +# CPU + GPU (exx96 queue, may run on test and amber128 queues)
 +
 + export CUDA_HOME=/usr/local/cuda
 + export PATH=/usr/local/cuda/bin:$PATH
 + export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
 + export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
 + which nvcc
 +
 +# related for starrlab
 +# https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
 +
 +[hmeij@cottontail2 ~]$ module load miniconda3/py39
 +[hmeij@cottontail2 ~]$ which pacemaker
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/pacemaker
 +[hmeij@cottontail2 ~]$ pacemaker --version
 +pacemaker/pyace version: 0.2.7+77.g8b40c11
 +ace_evaluator   version: 2022.6.27
 +
 +[hmeij@cottontail2 ~]$ python
 +Python 3.9.10 | packaged by conda-forge | (main, Feb  1 2022, 21:24:11) 
 +[GCC 9.4.0] on linux
 +Type "help", "copyright", "credits" or "license" for more information.
 +>>> import pyace as py
 +>>> 
 +
 +
 +</code>
 +
 +** USER_QUIP **
 +
 +This is a version of lammps (29Oct20, last stable) that contains all packages with user-quip.
 +
 +It does compile with MPI (mpif90), not ifort, in CentOS7 ... was tricky, solution for MPI was the ''mpifort --showme:link'' answer
 +
 +  * Requires CentOS 7 so queues: mwgpu, amber128, exx96 for cpu-only binaries
 +  * Rwequires CentOS7 plus Cuda 10.2 so queue: exx96 for cpu+gpu binaries
 +
 +Read, if you wish  
 +
 +  * /share/apps/CENTOS7/lammps/QUIP-public.install 
 +  * /share/apps/CENTOS7/lammps/29Oct2020.install 
 +
 +**Environments**
 +
 +<code>
 +
 +# serial - cpu only (although quippy compiled, it refused to install)
 +# MPI STUBS is compiled in
 +
 +export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +
 +/share/apps/CENTOS7/lammps/29Oct2020/lmp_serial-with-quip.cpu -h
 +
 +# mpi - cpu only
 +# gfortran_openmpi
 +
 +export QUIP_LIBRARY=/share/apps/CENTOS7/lammps/QUIP-public/9Apr2021/linux_x86_64_gfortran_openmpi
 +export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 +
 +/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu -h
 +
 +
 +# mpi - cpu+gpu
 +# gfortran_openmpi arch
 +
 +export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +export QUIP_LIBRARY=/share/apps/CENTOS7/lammps/QUIP-public/9Apr2021/linux_x86_64_gfortran_openmpi
 +export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 +export CUDA_HOME=/usr/local/cuda
 +export PATH=/usr/local/cuda/bin:$PATH
 +export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
 +export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
 +
 +# the "make" versions of lmp with quip do not work, deleted them
 +# did find on nvdia dev forum reference problem disappears when using cmake (vs make)
 +# these lmp binaries do work
 +/share/apps/CENTOS7/lammps/29Oct2020/single_single/bin/lmp
 +/share/apps/CENTOS7/lammps/29Oct2020/single_double/bin/lmp
 +/share/apps/CENTOS7/lammps/29Oct2020/double_double/bin/lmp
 +
 +# however I had to load non-mpi version of libquid.a into lmp
 +# witch seems ok given parallel work is driven by -suffix gpu
 +
 +# sample script: ~hmeij/k20redo/run.rtx.lammps2
 +
 +</code>
 +
 +** CPU only ** -Centos6
 +
 +  *  /share/apps/CENTOS6/lammps/29Oct20.install
 +  * read for env and compilation env: lmp_mpi
 +
 +** CPU only OR CPU+GPU**  for ''exx96'' queue - CentOS7
 +
 +  * 3Mar2020 added USER-REAXC
 +  * For KOKKOS MPI aware version  /share/apps/CENTOS7/openmpi/4.0.4-ucx with UCX
 +  * git download of latest did not work (lots of fortran errors?)
 +  * latest tarball is still 3Mar2020 (?)
 +  * added user-eaxc (but had to remove package python)
 +  * "kokkos" version includes GPU accelerator
 +  * please read **/share/apps/CENTOS7/lammps/3Mar2020.install **
 +
 +<code>
 +
 +# CPU
 +/share/apps/CENTOS7/lammps/3Mar2020/lmp_serial+user-omp+user-reaxc
 +/share/apps/CENTOS7/lammps/3Mar2020/lmp_mpi+user-omp+user-reaxc
 +
 +# CPU+GPU
 +/share/apps/CENTOS7/lammps/3Mar2020/lmp_mpi-single-single_kokkos_cuda_mpi+user-omp+user-reaxc
 +
 +# env
 +
 + export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 + export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +
 + export CUDA_HOME=/usr/local/cuda
 + export PATH=/usr/local/cuda/bin:$PATH
 + export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
 + export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
 +
 +</code>
 +
 +** CPU ONLY v2 CentOS7 **
 +
 +  * add user-opm on next compile ... done ... binaries with string +user-omp
 +  * /share/apps/CENTOS7/lammps/3Mar2020
 +    * lmp_serial, lmp_mpi
 +  * //latest// openmpi version as of today v4.0.4
 +  * consult this file for packages installed and compilations
 +    * /share/apps/CENTOS7/lammps/03Mar2020.install
 +    * should work only on exx96 and mwgpu queues
 +
 +<code>
 + export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 +</code>
  
 ** CPU ONLY ** ** CPU ONLY **
Line 1256: Line 2800:
  
 ** CPU or GPU ** ** CPU or GPU **
 +
 +  * added lmp_mpi-single-single+user-omp
  
   * /share/apps/CENTOS7/lammps/3Mar2020   * /share/apps/CENTOS7/lammps/3Mar2020
Line 1262: Line 2808:
     * /share/apps/CENTOS7/lammps/03Mar2020.install     * /share/apps/CENTOS7/lammps/03Mar2020.install
     * CUDA_ARCH = sm_75 (probably only works on queue exx96)     * CUDA_ARCH = sm_75 (probably only works on queue exx96)
-  * sample script in ~hmeij/k20redo/run.rtx.lammps+  * **sample script in ~hmeij/k20redo/run.rtx.lammps**
  
 <code> <code>
Line 2023: Line 3569:
   * https://edwards.sdsu.edu/research/c11-on-centos-6/   * https://edwards.sdsu.edu/research/c11-on-centos-6/
     * C11++ on CentOS6, two version of gcc     * C11++ on CentOS6, two version of gcc
-    * read the R-3.6.1_configure file in ''/share/apps/src/cottontail2''+    * read the R-3.6.1_configure file in ''/share/apps/CENTOS6/R/R-3.6.1_configure''
  
 <code> <code>
Line 2179: Line 3725:
  
 ====== Amber ======  ====== Amber ====== 
 +
 +** Amber 22 **
 +
 +Details on how to run on CentOS7 can be found at
 +
 +  * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#amber22
 +
 +** Amber 20 **
 +
 +  * Two versions compiled, 
 +    * one for cuda 8.0/mpich3 for queue amber128
 +    * one for queues mwgpu and exx96 (cuda 9.2/openmpi).
 +
 +  * Consult the run.amber20 script to set up environment
 +    * /share/apps/CENTOS7/amber/amber20/run.amber20
 +
 +  * Both are installed in /usr/local/amber20
 +
 +
  
 ** AMBER 18 ** ** AMBER 18 **
Line 2593: Line 4158:
  
 <code> <code>
 +
 +# update
 +[hmeij@greentail52 ~]$ java --version
 +java 20.0.2 2023-07-18
 +
 +
 export JAVAHOME=/home/apps/j2sdk1.4.2_17/bin:$PATH export JAVAHOME=/home/apps/j2sdk1.4.2_17/bin:$PATH
 export CLASSPATH=$JAVAHOME/lib:$CLASSPATH export CLASSPATH=$JAVAHOME/lib:$CLASSPATH
Line 2891: Line 4462:
 ===== Intel  ===== ===== Intel  =====
  
-UPDATE, 2016 parallel studio cluster edition installed+UPDATE 2021 
 +latest version of icc/icx and ifort/ifx are inside OneAPIsearch this page 
 + 
 +UPDATE 2016  
 +parallel studio cluster edition installed
  
   * 2 ifort and 2 icc float licenses   * 2 ifort and 2 icc float licenses
Line 2919: Line 4494:
  
 ====== Cluster Math Kernel Libraries ====== ====== Cluster Math Kernel Libraries ======
 +
 +  * latest version in OneAPI, search this page
  
   * see Intel parallel studio   * see Intel parallel studio
Line 2928: Line 4505:
  
 ====== Intel Threading Building Blocks ====== ====== Intel Threading Building Blocks ======
 +
 +  * latest version is in OneAPI, search this pages
  
   * see Intel parallel studio   * see Intel parallel studio
Line 2939: Line 4518:
 ====== Matlab ====== ====== Matlab ======
  
 +  * installed R2023a
  
 +  * installed R2022a
 +
 +  * installed R2021a
  
   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''
-    * R2020a, campus wide license so no more restrictions on licenses +    * R2020b, campus wide license so no more restrictions on licenses 
     * No Distributed Computing Engine or Matlab Parallel (for now)     * No Distributed Computing Engine or Matlab Parallel (for now)
-  * install dir: /share/apps/CENTOS7/matlab/R2020a+  * install dir: /share/apps/CENTOS7/matlab/R2020bISO
   * docs & www: http://mathworks.com   * docs & www: http://mathworks.com
 +  * CentOS7 required use on queues mwgpu, amber128 and exx96 
 +  * For GUI launch on greentail52
  
 Note: Note:
Line 2959: Line 4543:
 ====== Stata ====== ====== Stata ======
  
-  * program: Stata v 15, 6-user network license, includes stata, stata-mp, stata-se  +  * program stata[-mp|-se] in your $PATH, version 18 
-  * install dir: /share/apps/stata/15+  * v17 will still run so add '17' to the command like 'stata-mp17' 
 +  * so that makes for 12 licenses 8-) 
 + 
 +  * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se  
 +  * install dir: /share/apps/stata/
   * docs: at web site   * docs: at web site
   * http://stata.com   * http://stata.com
  
 <code> <code>
-export PATH=/share/apps/stata/15:$PATH+export PATH=/share/apps/stata/17:$PATH
 </code> </code>
  
cluster/73.1593450912.txt.gz · Last modified: 2020/06/29 13:15 by hmeij07