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--- cluster:73 [2021/07/01 15:53]
hmeij07 [Galario CPU+GPU]
+++ cluster:73 [2024/02/16 11:17] (current)
hmeij07 [LAMMPS CPU/GPU]
@@ Line 3: / Line 3: @@
 ====== 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''
@@ Line 19: / Line 24: @@
 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
+.168.102.251 greentail52-eth0
+.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
+.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
+.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
+.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:
+.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
+-10-28 20:30:00 INFO:       ***** Start a BUSCO v5.5.0 analysis, current time: 10/28/2023 20:30:00 *****
+-10-28 20:30:00 INFO:       Configuring BUSCO with local environment
+-10-28 20:30:00 INFO:       Mode is genome
+-10-28 20:30:00 INFO:       'Force' option selected; overwriting previous results directory
+-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 ======
@@ Line 28: / Line 683: @@
       * 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>
@@ Line 102: / Line 763: @@
     * 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>
@@ Line 131: / Line 804: @@
 </code>
-For astronomy group added ('conda list' to see all packages installed)
+For astronomy group (amhughes and students) added ('conda list' to see all packages installed)
 <code>
@@ Line 141: / Line 814: @@
 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 ======
@@ Line 153: / Line 1024: @@
   * git clone https://github.com/Amber-MD/pytraj; cd pytra
   * python ./setup.py install
-  * requires CentOS7 so queues mwgpu, amber128 and exx96
+  * requires CentOS7 so queues mwgpu, <del>amber128</del> and exx96
   * or for debugging use greentail52
   * /share/apps/CENTOS7/amber/pytraj
@@ Line 193: / Line 1064: @@
 ====== OpenHPC ======
-So I remember where I put the repos ''/share/apps/src/greentail52/openhpc''
+So I remember where I put the tar repo file
-  * whitetail tar ball for centos7/warewulf (no slurm)
+  * OpenHPC v2.4
-  * http://repos.openhpc.community/OpenHPC/2.0RC1/CentOS_8/x86_64/
+  * Rocky 8.5
-  * http://repos.openhpc.community/ohpc-1.3/1.3.9/base/CentOS_7/x86_64/
+  * Slurm 20.11.8
-  * https://github.com/warewulf/warewulf3 (master git zip file)
+  * 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/CENTOS/intel/oneapi/setvars.sh
+  * source /share/apps/CENTOS7/intel/oneapi/setvars.sh
 <code>
@@ Line 227: / Line 1130: @@
 </code>
-  * Test version is installed on local disk on host **greentail52**
+  * __Test__ version is installed on local disk on host **greentail52**
   * source /opt/intel/oneapi/setvars.sh
   * Read [[cluster:203|ICC vs ICX]]
@@ Line 244: / Line 1147: @@
   * centos7 R v 3.6.0
   * use your HPC username and credentials
+<code>
+# native OS installation for rstudio
+/bin/R
+</code>
 ====== DMTCP =====
@@ Line 367: / Line 1277: @@
 </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
+.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 688: / Line 1725: @@
   * location: /share/apps/FastQC/0.11.8
   * 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 698: / Line 1738: @@
 <code>
+# env
 export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
 export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
@@ Line 711: / Line 1752: @@
   hdf5               conda-forge/linux-64::hdf5-1.10.3-hba1933b_1001
   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>
 **Trinity** assembles transcript sequences from Illumina RNA-Seq data.
@@ Line 1348: / Line 2406: @@
 [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]]
+  * program v13,2.1 installed
+  * program v13.2 installed
   * program: mcc, math, mathematica (v 12.2)
@@ Line 1545: / Line 2607: @@
 ====== 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 **
@@ Line 2446: / Line 3569: @@
   * https://edwards.sdsu.edu/research/c11-on-centos-6/
     * 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>
@@ Line 2602: / Line 3725: @@
 ====== 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 **
@@ Line 3029: / Line 4158: @@
 <code>
+# update
+[hmeij@greentail52 ~]$ java --version
+java 20.0.2 2023-07-18
 export JAVAHOME=/home/apps/j2sdk1.4.2_17/bin:$PATH
 export CLASSPATH=$JAVAHOME/lib:$CLASSPATH
@@ Line 3383: / Line 4518: @@
 ====== Matlab ======
+  * installed R2023a
+  * installed R2022a
+  * installed R2021a
   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''
@@ Line 3403: / Line 4542: @@
 ====== Stata ======
+  * program stata[-mp|-se] in your $PATH, version 18
+  * 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

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