Table of Contents
Software
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
— 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).
Please note that what you find in /usr/local/bin is local to the head node and /home/apps/bin is available cluster wide (which is in your default PATH)
Most of the compilations have been performed by Intel's icc/ifort compilers.
Old compilations, mostly located in /share/apps, are RHEL 5.5
Newer compilations are done with CentOS 6.10 (since summer 2013)
on either cottontail2 or node n33 located at /share/apps/CENTOS6
Some compilations require 7.x and are in /share/apps/CENTOS7
Julia
- /share/apps/julia/julia-1/10.4
- link in /share/apps/bin
- runs on centos7 and rocky8
Miniconda3-py311
- Starting a new branch, the other Miniconda3 section listed on this is quite loaded
- Python 3.11
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:$LD_LIBRARY_PATH
- conda install (same as what is listed on openhpc miniconda3-py311) page
- cudatoolkit=10.2 cudnn=7 for exx96 queue
- same error, module cudatoolkit not found, but I found Cupy and it does load
- thayerlab
# pollacklab [hmeij@greentail52 ~]$ 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 ~]$
- mdtraj, matplotlib, pandas
[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
>>>
- seaborn
- also in miniconda3/py311 on rock8 module (used pip3)
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
- joblib (thayerlab)
joblib conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0
Masurca
- module: masurca/4.1.0
- supports openmp (maybe)
- queues mwgpu, exx96 (centos 7)
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
Trimmomatic
- binary download and stage
- java -jar trimmomatic-0.39.jar …
/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
HPC SDK
- 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.
- 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 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
- contains package mpi4py, multithreading
- import erfa (needs to be loaded too), added later (pycuda, h5py for helios)
- to find
libcuda.so.1set export path below
- emcee/2.2.1-foss-2019a
- 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)
# 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:\
$LD_LIBRARY_PATH
# discover all modules
module use /sanscratch/CENTOS7/easybuild/4.4.2/modules/all
# view availability
module avail
# load
module load module_name
# list modules loaded
module list
# check, start app, import package (by full module name)
# note that these modules use different python versions
which python
python
>>>help('modules')
# unload all modules (better to exit shell and start new one,
# purge will also unload system modules...
module purge
Hoomd
HOOMD-blue is a Python package that runs simulations of particle systems on CPUs and GPUs.
- requires both minconda3 (centos7) and cuda-10.2 (so queue exx96 only)
- python3.x included
- starrlab
Set up env for miniconda and cuda
export CUDAHOME=/usr/local/cuda-10.2 export PATH=/usr/local/cuda-10.2/bin:$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
- installed/updated were…
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
- and
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
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
# 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"
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,
amber128, exx96- debug server greentail52
- PREFIX=/share/apps/CENTOS7/miniconda3
- python 3.9
- gcc 9.2
- cmake 3.8.5
- chernofflab
# 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
Guppy Server
- https://github.com/nanoporetech/megalodon, find community page
- standalone build
- Local accelerated basecalling for Nanopore data
- v5.0.11
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)
Guppy Client
- miniconda3 python3.9
- Python client library for Guppy.
- Full Python client library for communicating with guppy_basecall_server.
- v0.1.0
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
Medaka
- miniconda3
- Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data.
- v1.4.3
# 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
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
/share/apps/CENTOS7/flye/2.9.2/bin/flye --version 2.9.2-b1794
- v2.9.1 (October 2022)
- python bin/flye
- change the PATHs accordingly
/share/apps/CENTOS7/flye/2.9.1/bin/flye --version 2.9.1-b1780
- v2.9 (August 2021)
- python bin/flye
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
Filtlong
- binary
- Filtlong is a tool for filtering long reads by quality.
- v0.2.1
# 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:$PATH ldd `which filtlong`
Bamtools
- standalone build
- C++ API & command-line toolkit for working with BAM data
- v2.5.2
export PATH=/share/apps/CENTOS7/bamtools/2.5.2/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS7/bamtools/2.5.2/lib:$LD_LIBRARY_PATH ldd `which bamtools`
BBmap
- location: /share/apps/CENTOS7/bbmap/39.01
- java programs
Pilon
- location: /share/apps/CENTOS7/pilon/
- just one big jar file
- latest java is in $PATH
[hmeij@greentail52 pilon]$ 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>
haslr
- miniconda3 env
- conda install -c bioconda haslr
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
Compiled from source, do not source miniconda3, we are using standalone pyhton3
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
stLFR
- same centos 7 environment
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
BUSCO
- conda package fails on glib 2.17, weird
[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 ...
picard
- Warning: using Java 20 but only Java 17 has been tested.
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]$
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
— Henk 2021/07/07 15:38
# sample scripts in /zfshomes/hmeij/amhughes # read README, it's complicated
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.
- 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
-
- 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
# 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:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
Successfully installed absl-py-0.12.0 astunparse-1.6.3 cachetools-4.2.2 flatbuffers-1.12 gast-0.4.0 google-auth-1.30.2 google-auth-oauthlib-0.4.4 google-pasta-0.2.0 grpcio-1.34.1 h5py-3.1.0 keras-nightly-2.5.0.dev2021032900 keras-preprocessing-1.1.2 markdown-3.3.4 numpy-1.19.5 oauthlib-3.1.1 opt-einsum-3.3.0 protobuf-3.17.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 requests-oauthlib-1.3.0 rsa-4.7.2 tensorboard-2.5.0 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.0 tensorflow-2.5.0 tensorflow-estimator-2.5.0 termcolor-1.1.0 typing-extensions-3.7.4.3 werkzeug-2.0.1 wrapt-1.12.1
Miniconda3
- add to ~/.bashrc and log back in, then check: 'which python pip conda'
- the conda initialization code block is list under DeepChem section above
- likely will only run on centos7, so
- queues: mwgpu, amber128, exx96
- for debug host use greentail52
Due to technical limitations, the conda package does not support GPUs according to web site. You must build manual libraries for GPU, see “gallario CPU+GPU” section above
source /share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh export PATH=/share/apps/CENTOS7/amber/miniconda3/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/lib:$LD_LIBRARY_PATH which mpirun python conda
# 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
For astronomy group (amhughes and students) added ('conda list' to see all packages installed)
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
For nwells/smithlab added
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
Then — Henk 2021/11/24 13:16
# 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
Added
— Henk 2022/01/03 14:35
# https://github.com/merenlab/anvio/issues/1479
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.
- iqtree fcohanlab/jwang06
[hmeij@greentail52 ~]$ iqtree --version IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020
- calterlab, annika (used pip to install)
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
For Lammps (starrlab) 23April2023, consult install file
- /share/apps/CENTOS7/lammps/25Apr2023.install
- make yes-ml-pace
- make yes-gpu
# 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)
pytraj
Pytraj is a wrapper for cpptraj
- 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,
amber128and exx96 - or for debugging use greentail52
- /share/apps/CENTOS7/amber/pytraj
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
Ovito
- /usr/local/bin/ovito → /usr/local/ovito-basic-3.5.0-x86_64/bin/ovito
- on nodes
cottontailandgreentail52 - 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
[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
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
# 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
- Test version is installed on local disk on host greentail52
- source /opt/intel/oneapi/setvars.sh
- Read ICC vs ICX
StringTie2
- Requires CentOS 7 so queues mwgpu, amber128, exx96
- /share/apps/CENTOS7/stringtie2/stringtie2 binarie
Rstudio
- centos7 R v 3.6.0
- use your HPC username and credentials
# native OS installation for rstudio /bin/R
DMTCP
- /share/apps/CENTOS7/dmtcp/3.0.0
- this came from the CRAC source, trying to install gpu checkpoint tool
- 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)
- jfabry/kthayer
Sequencing Tools #2
- macs python package (macs2 see below)
- padillalab
export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH" export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH" Successfully installed macs-1.4.3 # note: macs2 Python version must >= 3.6! # or change python version to # ls /share/apps/CENTOS6/python/2.7.9/bin/macs2 /share/apps/CENTOS6/python/2.7.9/bin/macs2 # or change python version to which python: /share/apps/CENTOS7/python/3.8.3/bin/python pip list: Package Version --------------- ------- bowtie 0.11.0 MACS2 2.2.7.1 numpy 1.18.5 picard 2.3.2 scipy 1.4.1 export PATH="/share/apps/CENTOS6/sequencingtools/bowtie2-2.4.1-linux-x86_64:$PATH" export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib64:/share/apps/CENTOS6/gcc/4.8.4/lib:$LD_LIBRARY_PATH which gcc: /share/apps/CENTOS6/gcc/4.8.4/bin/gcc which python: /share/apps/CENTOS6/miniconda2/bin/python which perl: /share/apps/CENTOS6/miniconda2/bin/perl export PATH=/share/apps/CENTOS6/R/3.6.1b/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/3.6.1b/lib64:$LD_LIBRARY_PATH export PATH=/home/apps/CENTOS6/R/packages/bin:$PATH export LD_LIBRARY_PATH=/home/apps/CENTOS6/R/packages/lib:$LD_LIBRARY_PATH which R: /share/apps/CENTOS6/R/3.6.1b/bin/R ldd /home/apps/CENTOS6/R/3.6.1b/lib64/R/bin/exec/R java --version: java 12.0.2 2019-07-16 # /share/apps/java/latest -> jdk-12.0.2 java -jar /share/apps/CENTOS6/sequencingtools/picard-2.23.0/picard.jar -h USAGE: PicardCommandLine <program name> [-h] export PATH=/share/apps/CENTOS6/sequencingtools/bedtools-2.29.2/bin:$PATH bedtools --version: bedtools v2.29.2
Deep Learning Software Stack
- queue
exx96provides access to docker containers and- digits, tensorflow, pytorch, caffe, rapidsai
- cuda (several versions)
- jupyterlab
- portainer
- consult Docker Containers Usage
- QAC
Paleogenomics Tools
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
- Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
- BCFtools:Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
- HTSlib: A C library for reading/writing high-throughput sequencing data
- Archeology (kbrunson)
# add to environment export PATH=/share/apps/CENTOS6/samtools/1.10/bin:$PATH export PATH=/share/apps/CENTOS6/bcftools/1.10.2/bin:$PATH export PATH=/share/apps/CENTOS6/htslib/1.10.2/bin:$PATH
- Program for analysing NGS data
# does not seem to work against htslib version above... export HTSSRC=/share/apps/CENTOS6/ANGSD/htslib export PATH=/share/apps/CENTOS6/ANGSD/angsd:$PATH
- BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
# with local java jre1.8.0_212 export PATH=/share/apps/CENTOS6/beast/2.6.0/bin:$PATH
- sratools https://github.com/ncbi/sra-tools/
- The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
- requires centos7 (glibc) so queues mwgpu, amber128, exx96
export PATH=/share/apps/CENTOS7/sratools/sratoolkit.2.11.0-centos_linux64/bin:$PATH
- adapterremoval https://github.com/MikkelSchubert/adapterremoval
These are all part of Miniconda3 (centos7), to setup the environment consult
-
- queues: mwgpu, amber128, exx96, debug server greentail52
They are also available via Miniconda2 (centos6), consult
-
- queues: hp12, mw256fd, tinymem, debug server swallowtail
[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
- mapDamage2
- docker container is broke
- requires centos6 so queues hp12, mw128 .. may run elsewhere?
- conda install -c 'bioconda' mapdamage2
# 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
- PCAngsd, requires miniconda3's python
- apparently the repo is needed
/share/apps/CENTOS7/pcangsd/1.1.0
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
- angsd, requires miniconda3, same environment as pcangsd
- add location of angsd to PATH env
$ 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)
- Standard RAxML version
# 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
- qualimap
- java & R app, probably will work in centos7 and rocky8
- /share/apps/CENTOS7/qualimap/2.3
- 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
CD-HIT
CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses.
- /share/apps/CENTOS6/cd-hit-v4.8.1-2019-0228/
OpenStructure
Open-Source Computational Structural Biology Framework
- v 1.9
- recipe at /share/apps/CENTOS6/openstructure/1.9-install.txt
- Starrlab
OpenStructure relies on these applications and Python 2.7.15 (see python2 section).
-- Boost version: 1.68.0
-- Found the following Boost libraries:
-- python
-- unit_test_framework
-- filesystem
-- system
-- iostreams
-- program_options
-- regex
-- thread
-- Found ZLIB: /share/apps/CENTOS6/zlib/1.2.11/lib/libz.so (found version "1.2.11")
-- Found PNG: /share/apps/CENTOS6/lpng/1.6.37/lib/libpng.so (found version "1.2.49")
-- Found EIGEN: /share/apps/CENTOS6/eigen/3.2.10
-- Numpy headers found
-- Found FFTW: /share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so
-- Found TIFF: /share/apps/CENTOS6/tiff/4.0.9/lib/libtiff.so (found version "4.0.9")
# setup the environment
egrep ^export /share/apps/CENTOS6/openstructure/1.9-install.txt
ost --help
Usage:
ost [ost options] [script to execute] [script parameters]
or
ost [action name] [action options]
Remarkably complex compilations.
PyCharm EDU
An Easy and Professional Tool to Learn & Teach Programming with Python
- /share/apps/pycharm/2018.03/bin
Paml
Phylogenetic Analysis by Maximum Likelihood (PAML)…programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
- /share/apps/paml/paml4.9i
- add the bin/ directory to your PATH (see examples on this page)
- fcolanlab (wmei, ndelgaudio)
Spyder
- Spyder: The Scientific Python Development Environment
- See Python 3.5.2 for more details
Python3
- Python 3.8.3
- /share/apps/CENTOS7/python/3.8.3 (so queues mwgpu, exx96)
- most packages found on this page
- picked up mpirun from miniconda2 apps (that may be a problem)
- Added to 3.8.3 “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.
“
— Henk 2021/02/18 14:41
# needed for _ctypes to compile properly for https retrievals yum install openssl openssl-devel yum install yum install libffi-devel libffi tar -xvf ../Python-3.8.3.tgz cd Python-3.8.3/ ./configure --prefix=/share/apps/CENTOS7/python/3.8.3 --enable-optimizations make make install pip3 install --upgrade pip # make symbolic links python3->pyhton, pip3->pip # drop all the packages in from previous versions https://dokuwiki.wesleyan.edu/doku.php?id=cluster:73#python3 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 which pip3 python3 /share/apps/CENTOS7/python/3.8.3/bin/pip3 /share/apps/CENTOS7/python/3.8.3/bin/python3
Added to both 3.5.2 versions
pycuda
— Henk 2020/02/18 08:45
Added to both 3.5.2 versions
Successfully installed
boto-2.49.0 boto3-1.12.0 botocore-1.15.0 gensim-3.8.1 jmespath-0.9.4 s3transfer-0.3.3 smart-open-1.9.0
joblib, scikit-learn, sklearn
Requirement already satisfied:
keras keras-preprocessing keras-applications
tensorflow (requires centos7)
— Henk 2020/02/17 13:02
Added to both 3.5.2 versions
jupyter-notebook only runs in 3.5.2 (non-mpi)
— Henk 2019/07/23 09:04
Successfully installed Send2Trash-1.5.0 ipywidgets-7.5.0 jupyter-1.0.0 jupyter-client-5.3.1 jupyter-console-6.0.0 notebook-6.0.0 prometheus-client-0.7.1 terminado-0.8.2 widgetsnbextension-3.5.0 json5-0.8.5 jupyterlab-1.0.2 jupyterlab-server-1.0.0 tornado-6.0.3
Added to both python versions 3.5.2 and 3.5.2-mpi the following modules all needed for Spyder.
— Henk 2019/04/25 09:21
Successfully installed PyQT5-5.12.1 PyQt5-sip-4.19.15 Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 alabaster-0.7.12 asn1crypto-0.24.0 astroid-2.2.5 attrs-19.1.0 babel-2.6.0 backcall-0.1.0 bleach-3.1.0 certifi-2019.3.9 cffi-1.12.3 chardet-3.0.4 cloudpickle-0.8.1 cryptography-2.6.1 decorator-4.4.0 defusedxml-0.6.0 docutils-0.14 entrypoints-0.3 idna-2.8 imagesize-1.1.0 ipykernel-5.1.0 ipython-7.4.0 ipython-genutils-0.2.0 isort-4.3.17 jedi-0.13.3 jeepney-0.4 jsonschema-3.0.1 jupyter-client-5.2.4 jupyter-core-4.4.0 keyring-19.0.1 lazy-object-proxy-1.3.1 mccabe-0.6.1 mistune-0.8.4 nbconvert-5.4.1 nbformat-4.4.0 numpydoc-0.9.1 packaging-19.0 pandocfilters-1.4.2 parso-0.4.0 pexpect-4.7.0 pickleshare-0.7.5 prompt-toolkit-2.0.9 psutil-5.6.1 ptyprocess-0.6.0 pycodestyle-2.5.0 pycparser-2.19 pyflakes-2.1.1 pygments-2.3.1 pylint-2.3.1 pyqtwebengine-5.12.1 pyrsistent-0.14.11 pyzmq-18.0.1 qtawesome-0.5.7 qtconsole-4.4.3 qtpy-1.7.0 requests-2.21.0 rope-0.14.0 secretstorage-3.1.1 snowballstemmer-1.2.1 sphinx-2.0.1 sphinxcontrib-applehelp-1.0.1 sphinxcontrib-devhelp-1.0.1 sphinxcontrib-htmlhelp-1.0.2 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.2 sphinxcontrib-serializinghtml-1.1.3 spyder-3.3.4 spyder-kernels-0.4.4 testpath-0.4.2 tornado-6.0.2 traitlets-4.3.2 typed-ast-1.3.4 urllib3-1.24.2 wcwidth-0.1.7 webencodings-0.5.1 wrapt-1.11.1 wurlitzer-1.0.2
- program: python v 3.5.2 mpi enabled
- /share/apps/CENTOS6/python/3.5.2-mpi (used in astronomy with emcee and mpi4py)
Environment
export PATH=/share/apps/CENTOS6/openmpi/3.1.3/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/openmpi/3.1.3/lib:$LD_LIBRARY_PATH which mpicc /share/apps/CENTOS6/openmpi/3.1.3/bin/mpicc CC=mpicc LDSHARED="mpicc -shared" ./configure --prefix=/share/apps/CENTOS6/python/3.5.2-mpi export PATH=/share/apps/CENTOS6/python/3.5.2-mpi/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/3.5.2-mpi/lib:$LD_LIBRARY_PATH <code> Packages <code> Successfully installed nltk-3.4 Successfully installed numpy-1.16.2 Successfully installed scipy-1.2.1 Successfully installed Cython-0.29.6 Successfully installed jenkspy-0.1.5 Successfully installed pandas-0.24.2 python-dateutil-2.8.0 pytz-2018.9 Successfully installed argparse-1.4.0 Installing collected packages: readline Successfully installed mpi4py-3.0.1 Successfully installed emcee-2.2.1 Installed /home/apps/CENTOS6/python/3.5.2-mpi/lib/python3.5/site-packages/pandas2-0.0.0-py3.5.egg Successfully installed cycler-0.10.0 Successfully installed kiwisolver-1.0.1 Successfully installed matplotlib-3.0.3 pyparsing-2.3.1 Successfully installed seaborn-0.9.0 Successfully installed subprocess32-3.5.3 Successfully installed astropy-3.1.2 Successfully installed pathlib2-2.3.3 Successfully installed scandir-1.10.0 Successfully installed os0-0.2.14 Successfully installed pickle-utils-0.1
- program: python v 3.5.2 not mpi enabled
- /share/apps/CENTOS6/python/3.5.2 (heavily used in DNA sequencing tools)
- python3, pip3, nltk v3.2.1, numpy v1.11.2
- Cython-0.27.3, jenkspy-0.1.4
- Pandas-0.21.0
- OpenPyXL
- and also …
Successfully installed emcee-2.2.1 Requirement already satisfied: mpi4py in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (2.0.0) Successfully installed argparse-1.4.0 Successfully installed readline-6.2.4.1 Requirement already satisfied: pandas in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (0.21.0) Requirement already satisfied: python-dateutil>=2 in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from pandas) (2.6.1) Requirement already satisfied: pytz>=2011k in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from pandas) (2017.3) Requirement already satisfied: numpy>=1.9.0 in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from pandas) (1.15.4) Requirement already satisfied: six>=1.5 in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from python-dateutil>=2->pandas) (1.11.0) Installed /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages/pandas2-0.0.0-py3.5.egg Successfully installed cycler-0.10.0 kiwisolver-1.0.1 matplotlib-3.0.3 pyparsing-2.3.1 seaborn-0.9.0 Installed /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages/subprocess32-3.5.3-py3.5.egg Successfully installed astropy-3.1.2 Successfully installed pathlib2-2.3.3 Requirement already satisfied: matplotlib in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (3.0.3) Requirement already satisfied: cycler>=0.10 in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from matplotlib) (0.10.0) Requirement already satisfied: numpy>=1.10.0 in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from matplotlib) (1.15.4) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from matplotlib) (2.3.1) Requirement already satisfied: python-dateutil>=2.1 in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from matplotlib) (2.6.1) Requirement already satisfied: kiwisolver>=1.0.1 in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from matplotlib) (1.0.1) Requirement already satisfied: six in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from cycler>=0.10->matplotlib) (1.11.0) Requirement already satisfied: setuptools in /home/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib) (20.10.1)
- install dir: /share/apps/CENTOS6/python/3.5.2
export PATH=/share/apps/CENTOS6/python/3.5.2/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/3.5.2/lib:$LD_LIBRARY_PATH
— Henk 2017/02/06 10:45 Added to 3.5
Copying mpi4py.egg-info to /share/apps/CENTOS6/python/3.5.2/lib/python3.5/site-packages/mpi4py-2.0.0-py3.5.egg-info but I had to change the code and I do not know what the impact might be src/mpi4py.MPI.c /* __pyx_v_rd = MPI_CONVERSION_FN_NULL; */ __pyx_v_rd = 0; Use this env pointing to old MPI versions export MPI_DIR=/share/apps/openmpi/1.2+intel-10 export PATH=/share/apps/CENTOS6/python/3.5.2/bin:$PATH export PATH=/share/apps/openmpi/1.2+intel-10/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/3.5.2/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/share/apps/openmpi/1.2+intel-10/lib:$LD_LIBRARY_PATH
These versions of python can be set with your PYTHONPATH and PYTHONHOME env variables. For syntax, see the Autodock section.
- program: python v 3.0.1
- install dir: /share/apps/python/3.0.1
Kallisto & Trinity & FastQC
FastQC A quality control tool for high throughput sequence data.
java -versionlatest JDK installed, in default PATHwhich java- location: /share/apps/FastQC/0.11.8
- requires centos6, may not run on centos7
- queues: hp12, tinymem, mw256fd mw128
- debug server swallowtail
- biolab (coolonlab, tearley)
kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
- also installed using miniconda2 packages (see below, set the PATH variable)
# env export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH" export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH" bwa: 0.7.17-h84994c4_5 bioconda perl: 5.26.2-h14c3975_1002 conda-forge bowtie bioconda/linux-64::bowtie-1.2.2-py27h2d50403_1 tbb conda-forge/linux-64::tbb-2019.4-h6bb024c_0 star bioconda/linux-64::star-2.7.0d-0 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
Trinity assembles transcript sequences from Illumina RNA-Seq data.
- also installed using miniconda2 packages (see above, set the PATH variable)
Trinity seems to need makeblastdb. BLAST finds regions of similarity between biological sequences.
- add to PATH /share/apps/CENTOS6/ncbi-blast-2.9.0+/bin
- add '/share/apps/CENTOS6/glibc-2.14/lib' to LD_LIBRARY_PATH
export TRINITY_HOME=/share/apps/CENTOS6/trinityrnaseq-Trinity-v2.8.4
export PATH=$TRINITY_HOME:$PATH
python 2.7 modules (these do not work with Trinity...bowtie2, jellyfish, salmon?)
bowtie2-2.3.4.3 | py27he860b03_1 11.9 MB bioconda
jellyfish conda-forge/linux-64::jellyfish-0.6.1-py27h14c3975_1000
bzip2-1.0.6 | h14c3975_1002 415 KB conda-forge
icu-58.2 | hf484d3e_1000 22.6 MB conda-forge
jemalloc-5.1.0 | hf484d3e_1000 10.2 MB conda-forge
libboost-1.67.0 | h46d08c1_4 20.9 MB
salmon-0.13.1 | h86b0361_0 4.2 MB bioconda
xz-5.2.4 | h14c3975_1001 366 KB conda-forge
trinity modules
Inchworm: has been Installed Properly
Chrysalis: has been Installed Properly
QuantifyGraph: has been Installed Properly
GraphFromFasta: has been Installed Properly
ReadsToTranscripts: has been Installed Properly
parafly: has been Installed Properly
slclust: has been Installed Properly
collectl: has been Installed Properly
Apparently bowtie, jellyfish, and salmon are not found as python modules. Install binaries from
and put them in the miniconda2 directory as that is the python used.
- Sample Run (must run on mw256fd using local scratch 5TB)
#!/bin/bash
# submit via 'bsub < run_trinity'
#BSUB -n 24
#BSUB -R "span[hosts=1]"
#BSUB -q mw256fd
#BSUB -J trinity
#BSUB -o trinity_assembly
#BSUB -e trinity_stderr
export TRINITY_HOME=/share/apps/CENTOS6/trinityrnaseq-Trinity-v2.8.4
export PATH=$TRINITY_HOME:$PATH
export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
export PATH="/share/apps/CENTOS6/python/3.5.2/samtools-1.9/bin:$PATH"
export PATH="/share/apps/CENTOS6/miniconda2/bowtie2-2.3.5-linux-x86_64:$PATH"
export PATH="/share/apps/CENTOS6/miniconda2/jellyfish-2.2.10:$PATH"
export PATH="/share/apps/CENTOS6/miniconda2/salmon-0.13.1_linux_x86_64/bin:$PATH"
export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/salmon-0.13.1_linux_x86_64/lib:$LD_LIBRARY_PATH"
# unique job scratch dirs
MYSANSCRATCH=/sanscratch/$LSB_JOBID
MYLOCALSCRATCH=/localscratch/$LSB_JOBID
MYLOCALSCRATCH5TB=/localscratch5tb/$LSB_JOBID
export MYSANSCRATCH MYLOCALSCRATCH MYLOCALSCRATCH5TB
# cd to remote working directory, only exists on mw256fd nodes
cd $MYLOCALSCRATCH5TB
pwd
Trinity --seqType fq --max_memory 240G \
--left /sanscratch/tearley/seqs/illumina/fwd.fastq.gz \
--right /sanscratch/tearley/seqs/illumina/rev.fastq.gz --CPU 24 \
--long_reads /sanscratch/tearley/seqs/pacbio/ccs.fasta
# copy results to home (fix this brute force, keep results only...)
scp -r ./trinity_out_dir ~/trinity_out_dir_$LSB_JOBID
Sequencing Tools #1
All of these are located in /share/apps/CENTOS6/python/3.5.2/
Deepbinner: a deep convolutional neural network barcode demultiplexer for Oxford Nanopore reads
- set up environment, read Deepbinner.install
- deepbinner –help
- fcohanlab (ndelgaudio)
Canu: a single molecule sequence assembler for genomes large and small.
- set up environment, read Deepbinner.install
- canu –help
Eigen: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
- required for nanopolish which had a lot of problems
- read nanopolish.install
Nanopolish : Software package for signal-level analysis of Oxford Nanopore sequencing data.
- this build had a lot of problems
- remove all reference to openmp in this package
- Nicole reports it works; probably use on command line on cottontail2 only
BioPython : Aset of freely available tools for biological computation
- Also needs Gnu parallel
Samtools: is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
- Samtools Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
- BCFtools Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
- HTSlib A C library for reading/writing high-throughput sequencing data
- read samtools.install
Minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
- read minimap2.install
ZENO
- A software tool based on Monte Carlo methods, ZENO computes material properties at nanoscale
- /share/apps/CENTOS6/zeno5
Caution Consult file /share/apps/src/cottontail2/ZENO_configure regarding the fix that was applied to SphereCenterModel/NanoFLANNSort.cc which is not a fix at all. Your mileage may vary.
# zeno-mpi was compiled with this MPI flavor /share/apps/CENTOS6/miniconda2/bin/mpicc /share/apps/CENTOS6/miniconda2/bin/mpicxx # also setup these export NANOFLANN_DIR=/share/apps/CENTOS6/nanoflann export SPRNG_DIR=/share/apps/CENTOS6/sprng5
nanoflann
- Nearest Neighbor library (header only)
- does not need compiling except for test suite (requires c++11 and gcc 4.8.2 devtools)
- test suite in build/bin directory
- /share/apps/CentOS6/nanoflann
SPRNG
- The Scalable Parallel Random Number Generators Library (SPRNG)
- /share/apps/CENTOS6/sprng5/
- no mpi (fails)
Galario
Newer CPU+GPU standalone library version (top of page)
— Henk 2021/06/29 14:38
Newer CPU only version installed in Miniconda3 (top of page)
Miniconda3 is using python 3.8
— Henk 2021/06/22 15:41
Accelerated Library for Analysing Radio Interferometer Observations (CPU only)
- /share/apps/CENTOS6/miniconda2
- contains python 2.7.15
- packages galario, numpy, scipy, matplotlib, argparse, corner, time and others ('conda list' for full listing)
- packages mpi4py, emcee, astropy
[hmeij@cottontail ~]$ conda --version
conda 4.5.4
$HOME/.bashrc for galario
# added by Miniconda2 installer
export PATH="/share/apps/CENTOS6/miniconda2/bin:$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
FreeSurfer
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies
- /share/apps/CENTOS6/freesurfer/6.0.0
- gpu version local to n78
- sample programs /home/hmeij/freesurfer
- mindlab (ploui et al)
FSL
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
- /share/apps/CENTOS6/fls/5.0.10/bin
- gpu version local on n78
- sample programs /home/hmeij/fsl
- mindlab (ploui et al)
Campari
Molecular Modeling Software
- /share/apps/CENTOS6/campari/3
- serial and threads version
- no mpi version
- Uses FFTW 3.3.6 (see section to set env)
NOTE: Lots of errors in compiling serial mode.
NOTE2: When compiling campari_threads ewaldo.f90 fails terribly
FastTree
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
- www: http://www.microbesonline.org/fasttree v2.1
- /share/apps/bin/
SageMath
Mathematics software, a viable free open source alternative to Magma, Maple, Mathematica and Matlab.
- /share/apps/sage/7.6
- executables: sage (linked in via /share/apps/bin/sage)
# compiled against CentOS 6.4 (sharptail6) using this python version export PATH=/share/apps/CENTOS6/python/2.7.9/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.9/lib:$LD_LIBRARY_PATH
Blast
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
- /share/apps/ncbi-blast-2.5.0+/bin
- executables: blastn, blastp, etc
JAGS
Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation that can be controlled from R.
- v4.2.0 libs and startup script at /share/apps/CENTOS6/jags/4.2.0
- Probably need to set PATH and LD_LIBRARY_PATH, examples on this page
BLCR
Compiled for every queue, for usage consult BLCR Checkpoint in OL3 and BLCR Checkpoint in OL3 for serial and parallel approaches.
- program: cr_run, cr_restart and cr_checkpoint
- install dir: /share/apps/blcr/0.8.5/queue
PyTransit
Astronomy package for exoplanet searches.
- astrolab
Installed into Python 2.7.10 on CentOS6.x, making sure CentOS gcc and gfortran are first in path.
# select vanilla python to use for centos6.x 64 bit # also installed easy_install and pulled down new Numpy export PATH=/share/apps/CENTOS6/python/2.7.10/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.10/lib:$LD_LIBRARY_PATH # notes: had to change --opt flag # had to use the MAC line for compilation to avoid the invalid ELF header error python setup.py config_fc --fcompiler=gnu95 --opt="-03" \ --f90flags="-cpp -fopenmp -march=native -mno-avx" build python setup.py install Writing /share/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/PyTransit-1.0-py2.7.egg-info # later added Using /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/numpy-1.10.1-py2.7-linux-x86_64.egg Finished processing dependencies for emcee==2.1.0 Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/astropy-1.1rc2-py2.7-linux-x86_64.egg Writing /share/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/scipy-0.16.1-py2.7.egg-info # make sure correct mpi tools env MPICC=/path/to/mpicc pip install mpi4py
For MPI4py had to force MPI-2
export PATH=/home/apps/openmpi/1.2+intel-10/bin:$PATH export LD_LIBRARY_PATH=/home/apps/openmpi/1.2+intel-10/lib:$LD_LIBRARY_PATH python setup.py build --configure python setup.py install
And added on 09Aug2017 https://github.com/lkreidberg/batman Writing /share/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/batman_package-2.4.5-py2.7.egg-info
There is also a version in /share/apps/CENTOS6/blcr_soft with PyTransit and Emcee
OpenMP
Intel compiler library for parallel jobs.
- www: http://openmp.org
- /share/apps/CENTOS6/libomp/
Add to your LD_LIBRARY_PATH
LigPlus
Automatically generates schematic diagrams of protein-ligand interactions for a given PDB file.
- /share/apps/LigPlus/lib/exe_linux
MACS
Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. .
- /share/apps/CENTOS6/python/lib/python2.7/site-packages/
Should use Python 2.7.9 (see python section on setting up environment) on CentOS6 nodes.
Modeller
MODELLER is used for homology or comparative modeling of protein three-dimensional structures.
- program: mod9.13 (either invoked directly or with python, see below)
- install dir: /home/apps/modeller/9.13
- examples, demos and guides also posted
Please read the license at https://salilab.org/modeller/registration.html
How to use modeller: read /share/apps/modeller/9.13/INFO.TXT or visit web site.
Miriad
Miriad, a package of highly-specialized radio astronomy software.
- program: see below, binary download, no requirement checks.
- astrolab (kflaherty)
# Define your Miriad environment by invoking the initialization scripts
% . MIRRC.sh
# in sh-like shells, or
% source MIRRC
Astropy
Compiled with /share/apps/python/2.6.1/bin/python …
- program: see below
Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/astropy-0.3.1-py2.6-linux-x86_64.egg Processing dependencies for astropy==0.3.1 Searching for numpy==1.6.2 Best match: numpy 1.6.2 Processing numpy-1.6.2-py2.6-linux-x86_64.egg numpy 1.6.2 is already the active version in easy-install.pth Installing f2py script to /share/apps/python/2.6.1/bin Using /home/apps/python/2.6.1/lib/python2.6/site-packages/numpy-1.6.2-py2.6-linux-x86_64.egg Finished processing dependencies for astropy==0.3.1
Emcee + MPI4py
For the latest version of emcee+mpi4py (03/15/2019) see the section of python 3.5.2 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:73#python
Which is also used by the biology group for https://dokuwiki.wesleyan.edu/doku.php?id=cluster:73#sequencing_tools
Compiled with /share/apps/python/2.6.1/bin/python …
- program: see below
- astrolab (kflaherty)
Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/emcee-2.1.0-py2.6.egg Processing dependencies for emcee==2.1.0 Searching for numpy==1.6.2 Best match: numpy 1.6.2 Processing numpy-1.6.2-py2.6-linux-x86_64.egg numpy 1.6.2 is already the active version in easy-install.pth Installing f2py script to /share/apps/python/2.6.1/bin Using /home/apps/python/2.6.1/lib/python2.6/site-packages/numpy-1.6.2-py2.6-linux-x86_64.egg Finished processing dependencies for emcee==2.1.0 Writing /share/apps/python/2.6.1/lib/python2.6/site-packages/mpi4py-1.3.1-py2.6.egg-info # it found /home/apps/openmpi/1.2+intel-10/bin/mpicc so be sure to use mpirun from there too export PATH=/home/apps/openmpi/1.2+intel-10/bin:$PATH
Also added emcee to python 2.7.10, see the section on pyTransit
Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/argparse-1.4.0-py2.6.egg Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/pandas2-0.0.0-py2.6.egg Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/subprocess32-3.5.3-py2.6-linux-x86_64.egg
PyRosetta
(Rosetta 2.2, 3.0 and 3.5 also are installed)
Compiled with /share/apps/python/2.6.1/bin/python …
- program: PyRosetta Bundle 2014wk05 in bin suddirectory
- install dir: /home/apps/pyrosetta/2014wk05
- doxygen in html dir, user guide also posted
- demos and tools also posted
Please read the license at /share/apps/pyrosetta/2014wk05/License.2014wk05
Note: although it probably does not matter, the python compile was performed under CentOS6 because latest phenix version requires that. So target queues mw256 and mw256fd.
Gromacs
Gromacs-2020.3 for GPU (RTX2080S)
exx96queue- see /share/apps/CENTOS7/gromacs/2020.3.install for env
- change env in script below
Gromacs-2018 for GPU (RTX2080S)
exx96queue- /zfshomes/hmeij/k20redo/run.rtx sample script
Gromacs-2018 for GPU (K20/GTX1080
Gromacs 5.1.4: there is only one version
- cpu plus mvapich2 mpi
- uses the gpu env as below but do not request a gpu resource
- can run on both mwgpu and mw256fd in cpu/mpi mode
- sample /home/hmeij/jobs/gpu/gromacs2016.cpu.mpi
Gromacs 5.1.2: there are four versions
- cpu only (thread_mpi), cpu-mpi (openmpi), cpu-gpu (thread_mpi), mpi-gpu (openmpi)
- compilations are done a bit differently switching to mpicc/mpiCC for mpi versions
- consult the file /share/apps/CENTOS6/gromacs/build-5.1.2.txt to set up your environment
- There is a template script at /home/hmeij/jobs/gpu/gromacs2016.sub
- it gets as far as launching gromacs at least
- no more
mdrunreplaced bygmx
- and use the correct wrapper program, read Submitting GPU Jobs
For the latest version there are 6 compilations. Gromacs developers are pretty verbal in terms of “compile on a host where you are goig to run it”. For v5.0.1, the nomeclature is like this:
- /path/to/gromacs/5.0.1-[cpu only “icc”|mpi|destination queue(s)]
- you will need to setup the proper environment, see below
- /share/apps/gromacs/5.0.1-icc-hp12
- /share/apps/gromacs/5.0.1-mpi-hp12
- /share/apps/gromacs/5.0.1-icc-mw256 [all queues starting with this string]
- /share/apps/gromacs/5.0.1-mpi-mw256 [all queues starting with this string]
- /share/apps/gromacs/5.0.1-icc-mwgpu
- /share/apps/gromacs/5.0.1-mpi-mwgpu
The file /share/apps/gromacs/build-5.0.1.sh will show you notes on compiling. Update: The GPU versions failed to compile with icc/icpc but did compile with gcc. will investigate later on this strange behavior. — Meij, Henk 2014/10/01 15:33
# for all versions . /share/apps/intel/composerxe/bin/iccvars.sh intel64 . /share/apps/gromacs/5.0.1 [-icc or -mpi] [-hp12 or -mw256 or -mwgpu] /bin/GMXRC.sh # for all "icc versions" you are done # for all "mpi versions" add this export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$LD_LIBRARY_PATH # for all "gpu versions" add this export PATH=\ /cm/shared/apps/gcc/4.7.0/bin:/cm/shared/apps/cuda50/sdk/5.0.35/bin/linux/release:\ /cm/shared/apps/lammps/cuda/2013-01-27/:/cm/shared/apps/amber/amber12/bin:\ /cm/shared/apps/namd/ibverbs-smp-cuda/2013-06-02/:/usr/lib64/qt-3.3/bin:\ /usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/sbin:/usr/sbin:\ /cm/shared/apps/cuda50/toolkit/5.0.35/bin:/cm/shared/apps/cuda50/sdk/5.0.35/bin/linux/release:\ /cm/shared/apps/cuda50/libs/current/bin:/cm/shared/apps/cuda50/toolkit/5.0.35/open64/bin:\ /cm/shared/apps/mvapich2/gcc/64/1.6/bin:/cm/shared/apps/mvapich2/gcc/64/1.6/sbin export LD_LIBRARY_PATH=\ /cm/shared/apps/gcc/4.7.0/lib:/cm/shared/apps/gcc/4.7.0/lib64:\ /cm/shared/apps/cuda50/toolkit/5.0.35/lib64:/cm/shared/apps/amber/amber12/lib:\ /cm/shared/apps/amber/amber12/lib64:\ /cm/shared/apps/namd/ibverbs-smp-cuda/2013-06-02/:/cm/shared/apps/cuda50/toolkit/5.0.35/lib64:\ /cm/shared/apps/cuda50/libs/current/lib64:/cm/shared/apps/cuda50/toolkit/5.0.35/open64/lib:\ /cm/shared/apps/cuda50/toolkit/5.0.35/extras/CUPTI/lib:/cm/shared/apps/mvapich2/gcc/64/1.6/lib
- program: mdrun (v4.6)
- install dir: /share/apps/gromacs/4.6-icc
- docs: on the web
- Compiled with ICC, you'll need this line (replace dot with source in csh)
- Can run native ThreadMPI for parallel jobs but confined to a single node.
# source for Intel compiler setup . /share/apps/intel/composerxe/bin/iccvars.sh intel64 # and source the GMXRC for your shell . /share/apps/gromacs/4.6-icc[or -mpi]/bin/GMXRC.[bash|zsh|csh]
- program: mdrun_mpi (v4.6)
- install dir: /share/apps/gromacs/4.6-mpi
- docs: on the web
- Compiled against OpenMPI, you'll need these lines in addition to lines above
- Can run parallel jobs across multiple nodes (use the lava wrapper program as usual)
export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$LD_LIBRARY_PATH
Mathematica
- program v13,2.1 installed
- program v13.2 installed
- program: mcc, math, mathematica (v 12.2)
- install dir: /share/apps/CENTOS7/mathematica/12.2
- docs: on the web
- Centos7, use queues mwgpu, amber128 or exx96
- For GUI launch on greentail52
- Parallel kernels
- Parallel Computing
Eigen
- program: headers files in /share/apps/eigen/3.0.5 or with cmake in /share/apps/eigen/3.0.5/build
- install dir: see above
- docs: on the web
Found Intel fortran compiler, so may have to source (albeit it should be platform independent)
. /share/apps/intel/composerxe/bin/iccvars.sh intel64 . /share/apps/intel/composerxe/bin/ifortvars.sh intel64
EON
- program: eonclient (client) and python (version 2.6.1, see PyPAL section, requires Numpy)
- install dir: client and server, see above
- docs: on the web
SERVER export PATH=/home/apps/python/2.6.1/bin/:$PATH Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/eon-0.0.0-py2.6.egg CLIENT eonclient -h Usage: eonclient [options] inputConfile [outputConfile] Job Type: -m Minimization of inputConfile saves to outputConfile -s Single point energy of inputConfile -o Optimization method [default: qm] Required Options: -p The potential (e.g. qsc, lj, eam_al)
SAS
SAS (v9.2 64 bits) is now available on the compute clusters. This software is an enormous statistical package and lots more, see http://www.sas.com It should be invoked in batch mode on the compute nodes just like all other software (ie command like “sas filename.sas” in job submission scripts). Some pointers, code, manual and an online tutor can be found at
The QAC has well trained tutors in SAS, for more info http://qac.wesleyan.edu
Wordom
- program: wordom v0.22 32 bit
- install dir: /usr/local/bin/ on greentail only
- docs: /usr/local/docs/wordom_ug.pdf
Note: Lapack and Blas packages are needed and were installed on host greentail only. Hence the program will only work on this host. If it needs to be available on compute nodes, please let me know.
unixODBC
- program: API with which to access Data Sources
- install dir: installed with
yum install unixODBC - docs:
This package works together with mysql-connector-odbc-5.1.8.-1.rhel5.x86_64.rpm (from http://dev.mysql.com/downloads/connector/odbc/ installed in OS) and pyodbc (from http://code.google.com/p/pyodbc/downloads/list installed into python 2.7.2).
OMSSA
- program: Open Mass Spectrometry Search Algorithm (OMSSA), from NCBI.
- install dir: /home/apps/omssa
- docs:
go language
- program: g6
- install dir: /home/apps/go
- docs: doc/ in install_dir
- www: http://golang.org/
export PATH=/share/apps/go/bin:$PATH
Correlation Analysis
- program: several, consult the README file
- install dir: /share/apps/mmdevel
- docs: browse install dir
Notes: “coulomb” did not compile with OpenMPI, MVApich1 or 2, but finally compiled against MVApich 0.99 (upgrade to 1.2)… the rest was compiled with gcc an 6g (from go language). In order to run the MPI binary, do not use a our lsf/lava wrappers but build up the command line with -np and -machinefile parameters.
export GOROOT=/share/apps/go export PATH=/share/apps/go/bin:/share/apps/mvapich/1.2+gnu-4.1.2+gen2/bin:$PATH export LD_LIBRARY_PATH=/share/apps/mvapich/1.2+gnu-4.1.2+gen2/lib:$LD_LIBRARY_PATH
FFTW MPI
- 3.3.6 compiled with icc/ifort
- /configure –prefix=/share/apps/fftw/3.3.6 \
- CC=icc CXX=icpc F77=ifort FC=ifort CFLAGS=-O3\
- –enable-openmp –enable-threads
- NOTE: –enable-mpi did not work
export PATH=/share/apps/fftw/3.3.6/bin:$PATH export LD_LIBRARY_PATH=/share/apps/fftw/3.3.6/lib:$LD_LIBRARY_PATH
- program: libfftw_mpi.a
- install dir: /home/apps/fftw/2.1.5_mpi
- docs: also consult the lammps section for FFTW
- www: see below
Note: Relies on v2 of FFTW (a C subroutine library for computing the discrete Fourier transform), view http://www.fftw.org/
Compiled as follows, you may have to set up your environment similarly:
export PATH=/share/apps/intel/cce/10.0.025/bin:\ /share/apps/openmpi/1.2+intel-10/bin:\ $PATH export LD_LIBRARY_PATH=/share/apps/intel/cce/10.0.025/lib:\ /share/apps/openmpi/1.2+intel-10/lib:\ /share/apps/intel/cmkl/10.0.011/lib/em64t:\ $LD_LIBRARY_PATH ./configure --prefix=/share/apps/fftw/2.1.5_mpi \ --enable-mpi CC=icc CXX=icpc F77=ifort FC=ifort
Plumed
- v2.3
- on node n78:/usr/local/plumed-2.3
- compiled with mpich3 mpicxx
- v 1.x
- program: a portable plug-in for free energy calculations with molecular dynamics
- install dir: /home/apps/amber/9serial+ifort+plumed
- docs: inside install dir
You may to have set the following:
export MKL_HOME=/share/apps/intel/cmkl/9.1.021 export AMBERHOME=/share/apps/amber/9serial+ifort+plumed export LD_LIBRARY_PATH=/share/apps/intel/cmkl/9.1.021/lib/64:$LD_LIBRARY_PATH
SDA
- program: Simulation of Diffusional Association, programs in bin/ directory
- install dir: /home/apps/sda/5.01
- docs: inside install dir
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
# 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 >>>
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
# 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:$LD_LIBRARY_PATH # the "make" versions of lmp with quip do not work, deleted them # did find on nvdia dev forum reference problem disappears when using cmake (vs make) # these lmp binaries do work /share/apps/CENTOS7/lammps/29Oct2020/single_single/bin/lmp /share/apps/CENTOS7/lammps/29Oct2020/single_double/bin/lmp /share/apps/CENTOS7/lammps/29Oct2020/double_double/bin/lmp # however I had to load non-mpi version of libquid.a into lmp # witch seems ok given parallel work is driven by -suffix gpu # sample script: ~hmeij/k20redo/run.rtx.lammps2
CPU only -Centos6
- /share/apps/CENTOS6/lammps/29Oct20.install
- read for env and compilation env: lmp_mpi
CPU only OR CPU+GPU for exx96 queue - CentOS7
- 3Mar2020 added USER-REAXC
- For KOKKOS MPI aware version /share/apps/CENTOS7/openmpi/4.0.4-ucx with UCX
- git download of latest did not work (lots of fortran errors?)
- latest tarball is still 3Mar2020 (?)
- added user-eaxc (but had to remove package python)
- “kokkos” version includes GPU accelerator
- please read /share/apps/CENTOS7/lammps/3Mar2020.install
# CPU /share/apps/CENTOS7/lammps/3Mar2020/lmp_serial+user-omp+user-reaxc /share/apps/CENTOS7/lammps/3Mar2020/lmp_mpi+user-omp+user-reaxc # CPU+GPU /share/apps/CENTOS7/lammps/3Mar2020/lmp_mpi-single-single_kokkos_cuda_mpi+user-omp+user-reaxc # env export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$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
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
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
CPU ONLY
- /share/apps/CENTOS6/lammps/3Mar2020
- lmp_mpi, lmp_serial
- consult this file for packages installed and compilations
- /share/apps/CENTOS6/lammps/03Mar2020.install
- should work on all queues
- sample script in ~hmeij/k20redo/run.cpu.lammps
CPU or GPU
- added lmp_mpi-single-single+user-omp
- /share/apps/CENTOS7/lammps/3Mar2020
- lmp_mpi-[double-double|single-double|single-single]
- consult this file for packages installed and compilations
- /share/apps/CENTOS7/lammps/03Mar2020.install
- CUDA_ARCH = sm_75 (probably only works on queue exx96)
- sample script in ~hmeij/k20redo/run.rtx.lammps
# simple colloid example CPU run -n1 Performance: 493311 tau/day, 1141 timesteps/s GPU run gpu4=1 double-double: 1.1x Performance: 571354 tau/day, 1322 timesteps/s GPU run gpu4=1 single-double: 1.2x Performance: 608498 tau/day, 1408 timesteps/s GPU run gpu4=1 single-single: 1.3x Performance: 623405 tau/day, 1443 timesteps/s
- /share/apps/CENTOS6/lammps/22Aug18
- consult lammps-11Aug17 page
- /share/apps/CENTOS6/lammps/31MAR17
- lmp_serial_icc, lmp_mpi (with Kiss FFT)
- lmp_gpu_single, lmp_gpu_double and lmp_gpu_mixed with the accelerator library (arch=35) consult http://lammps.sandia.gov/doc/Section_accelerate.html
- Please read the lammps-install.txt file, it did not all go according to docs.
- Sample job: /home/hmeij/lammps/colloid-gpu/run.gpu2
- lmp_gnu, lmp_gpu done the “malaysian” way, consutl the lammps-install-usm.txt file
- this serial and gpu version will have more packages
- /share/apps/CENTOS6/blcr_soft/lammps/16Feb16
- can be checkpointed
- /share/apps/CENTOS6/lammps/10AUG15
- lmp_serial_icc, lmp_mpi, lpm_mpi-with-fft
- lmp_cuda_single, lmp_cuda_double with the USER-CUDA accelerator library (arch=35) consult http://lammps.sandia.gov/doc/accelerate_cuda.html
- lmp_mpi.[1,2,3,4] correspond to the precision levels below
precision=N to set the precision level N = 1 for single precision (default) N = 2 for double precision N = 3 for positions in double precision N = 4 for positions and velocities in double precision
To use any of these you will need to setup the environment, like detailed below (PATH, LD_LIBRARY_PATH). Here is the environment showing you the version of the software used in compilation of lmp_cuda_double. The other versions used the same compiler (ICC) and MPI version (OpenMPI 1.8.4).
Note: According to the docs with USER-CUDA you must have 1 cpu MPI process for 1 GPU, so 1:1, 2:2 …
### USER-CUDA sample script /home/hmeij/sharptail/run_user-cuda.gpu export PATH=/home/apps/bin:\ /bin:\ /usr/bin:\ /usr/local/sbin:\ /usr/sbin:\ /sbin:\ /usr/sbin:\ /usr/lib64/qt-3.3/bin:\ /cm/local/apps/cuda50/libs/304.54/bin:\ /cm/shared/apps/cuda50/toolkit/5.0.35/bin:\ /cm/shared/apps/cuda50/sdk/5.0.35/bin/linux/release:\ /cm/shared/apps/cuda50/libs/current/bin:\ /cm/shared/apps/cuda50/toolkit/5.0.35/open64/bin:\ /cm/shared/apps/mvapich2/gcc/64/1.6/bin:\ /cm/shared/apps/mvapich2/gcc/64/1.6/sbin:\ /cm/shared/apps/lammps/cuda/2013-01-27/:\ /share/apps/CENTOS6/openmpi/1.8.4/bin:\ /share/apps/CENTOS6/python/2.7.9/bin:\ /share/apps/CENTOS6/lammps/10Aug15:\ /home/hmeij/bin:\ $PATH export LD_LIBRARY_PATH=/cm/local/apps/cuda50/libs/304.54/lib64:\ /cm/shared/apps/cuda50/toolkit/5.0.35/lib64:\ /cm/shared/apps/cuda50/toolkit/5.0.35/lib:\ /cm/shared/apps/cuda50/libs/current/lib64:\ /cm/shared/apps/cuda50/toolkit/5.0.35/open64/lib:\ /cm/shared/apps/cuda50/toolkit/5.0.35/extras/CUPTI/lib:\ /share/apps/CENTOS6/openmpi/1.8.4/lib/:\ /share/apps/CENTOS6/python/2.7.9/lib:\ /cm/local/apps/cuda50/libs/304.54/lib64:\ /cm/local/apps/cuda50/libs/304.54/lib/:\ $LD_LIBRARY_PATH
go to How to submit GPU jobs with Lammps
- program: (compiled with mpicxx, different than presious versions
- install dir: /home/apps/CENTOS6/lammps/9Dec14 … consult the README file to set up environment
Note: all versions have package yes-colloid installed.
- lmp_serial_icc, lmp_mpi, lmp_mpi-with-fft (compiled with icc v12 and mpicxx v1.4.4)
. /share/apps/intel/composerxe/bin/iccvars.sh intel64 . /share/apps/intel/composerxe/bin/ifortvars.sh intel64 export MKL_HOME=/share/apps/intel/composerxe/mkl export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$LD_LIBRARY_PATH export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH
- lmp_serial, lmp_openmpi (compiled with gcc 4.8.4 and mpicxx 1.8.4)
export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib64:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/openmpi/1.8.4/lib:$LD_LIBRARY_PATH export PATH=/share/apps/CENTOS6/openmpi/1.4.4/bin:$PATH
- program: lmp_serialwes, lmp_linuxwes, lmp_tbirdwes (linux and tbird compiled with openmpi 1.4.4)
- install dir: /home/apps/lammps/01Feb14 … consult the README file to set up environment
- program: lmp_serialwes, lmp_linuxwes, lmp_tbirdwes (linux and tbird compiled with openmpi 1.4.4)
- install dir: /home/apps/lammps/06Feb12 … consult the README file
- program: lmp_something_wes
- install dir: /home/apps/lammps/22Jun11
- docs: online at web site
Please consult the README file to set up your environment properly. The '22Jun11' LAMMPS version was compiled with Intel compilers v12 and the OpenMPI mpicc compiler of v1.4.3
- program: lmp_something_wes
- install dir: /home/apps/lammps/30Mar10
- docs: online at web site
Note: Relies on v2 of FFTW (a C subroutine library for computing the discrete Fourier transform), view http://www.fftw.org/
Compiled with a variety of compilers and MPI flavors. Your mileage may vary as serious warnings were generated at compile time. However, lmp_serial_wes and lmp_tbird_wes compiled without any errors.
You may have redefine your PATH and LD_LIBRARY_PATH, please consult /share/apps/lammps/30Mar10/README
- program: pizza.py
- install dir: /home/apps/lammps/pizza-9Oct15
- docs: inside install dir
- program: pizza.py
- install dir: /home/apps/lammps/pizza-24Nov10
- docs: inside install dir
Pizza.py is a loosely integrated collection of tools, many of which provide pre- and post-processing capability for the LAMMPS molecular dynamics, ChemCell cell modeling, and SPPARKS kinetic Monte Carlo packages. (yea, “loosely” is right). In order for this to work a new python flavor was installed. Please read the section about python/2.6.1.tcltk in the python section here
Libraries
- fortran functions of all kind
- install dir: /home/apps/libraries/libs (links to all)
- docs: on the web
Please note the appropriate citation and reference guides for each library (found on web site).
- fft, fast fourier transforms
- libfftpack.a
- lapack 3.2.1
- …/lapack/3.2.1/ [blas_intel.a, lapack_intel.a, tmglib_intel.a]
- minpack (version less)
- …/minpack/libminpack_intel.a
- quadpack (version less)
- …/quadpack/libquadpack_intel.a
- ranlib.f 1.1
- …/ranlib.f/librandpack_intel.a
Note: compiled with ifort
GSL
- program: GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
- install dir: /home/apps/gsl/1.9
- docs: in man/ directory of install dir
Note: compiled with gcc
Newbend
- program: see the demo_ouput.txt files
- install dir: /home/apps/newbend
- docs: none
- www: none
Note: Contact David Beveridge for more information (dbeveridge@wes)
Please note, there is an 'Aborted' event in one of the demos. glibc throws an error documented in the demo_output.txt file. Seems to still generate output though.
Curves+
- program: cur+, canal, cdif, sumr
- install dir: /home/apps/amber/Curves
- docs: on web site
Note: compiled with ifort
Naccess
- program: naccess
- install dir: /home/apps/naccess/2.1.1
- docs: on web site
Note: compiled with ifort
Phenix
Note: For internal, non-commercial, research and development purposes only. Consult the LICENSE file and Citing information. Users need to set their environment, examples shown.
Version below only works on queues mw256 and mw256fd
- program: phenix linux 2.6, x86_64, FC12
- install dir: /home/apps/phenix/phenix-1.8.4
- docs: in documentation/ directory of install dir
# csh users:
source /share/apps/phenix/1.8.4/phenix-1.8.4-1496/phenix_env
# bash users:
source /share/apps/phenix/1.8.4/phenix-1.8.4-1496/phenix_env.sh
Version below only works on queue hp12
- program: phenix, linux kernel 2.6, x86_64
- install dir: /home/apps/phenix/phenix-1.5-2
- docs: in documentation/ directory of install dir
# bash users: source /share/apps/phenix/phenix-1.5-2/phenix_env.sh
Expokit
- program: sample_? located in fortran subdirectory
- install dir: /home/apps/expokit
- docs: on the web
Note: our hardware/platform not supported, compiled with ifort (minor warnings)
WHAM
- program: wham (Weighted Histogram Analysis Method)
- install dir: /home/apps/wham/2.0.2
- docs: /home/apps/wham/2.0.2/docs
Note: wham compiled with warnings using icc. wham-2d failed to compile.
Emacs
- on head node only in /usr/bin
- version 21.4.1
Autodock Vina
- we also have the autoduck4 program - check below (search for autodock4)
- update with 1.1.2 in /share/apps/autodock
- moved the beta version out of the way and linked to 1.1.2 version
* program: vina v 1.0 beta 03 (for molecular docking and virtual screening)
- install dir: /home/apps/bin
- docs:
export PATH=/share/apps/autodock:$PATH # or export PATH=/share/apps/autodock/autodock_vina_1_1_2_linux_x86/bin:$PATH
Also linked in via /home/apps/bin which is in default PATH.
NetBeans
- program: several, v 6.0.1
- install dir: /usr/local/netbeans/6.0.1
- install dir: /usr/local/glassfish/v2ur1 http (28080), https (28181), admin (24848)
- install dir: /usr/local/apache-tomcat/6.0.14
- docs:
- www: http://netbeans.org
BaseMap
- program: Geometry Entry - Open Source (GEOS)
- install dir: /usr/local/lib v 2.2.3
- docs:
- program: Basemap (plot on map projections (with coastlines and political boundaries) using matplotlib.
- egg info: /home/apps/python/2.6.1/lib/python2.6/site-packages/basemap-0.99.3-py2.6.egg-info
- docs:
PyPat
- program: python egg, version 1.0)
- egg info: /home/apps/python/2.6.1/lib/python2.6/site-packages/PyPat-1.0-py2.6.egg-info
- docs: /home/apps/docs/pypat-1.0
The dependencies for PyPat … drummroll … incredible!
In order to run some PyPat programs or invoke some of the underlying programs you may have to set some of the published environment variables listed below.
Python
- Installed 2.6.1 (see notes below)
- Must be compiled with zlib module (unsure)
- Must have Python-PMW (PyMol requirement, unsure)
export PYTHONHOME=/home/apps/python/2.6.1
ImageMagick
- Latest default version, see below.
NumPy & Scipy
- program: (python egg, version 1.2.1)
- egg info: /home/apps/python/2.6.1/lib/python2.6/site-packages/numpy-1.2.1-py2.6.egg-info
- docs: guide posted on web site
NumPy was configured against the CMKL BLAS and LAPACK by uncommenting the lines for [cmkl] in site.cfg
export LD_LIBRARY_PATH=/home/apps/intel/cmkl/10.0.011/lib/em64t:$LD_LIBRARY_PATH export PYTHONHOME=/home/apps/python/2.6.1
It appears you also need to set your PATH to find the appropriate binary:
export PATH=/home/apps/python/2.6.1/bin:$PATH
Also upgrade and installed installed
Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/numpy-1.6.2-py2.6-linux-x86_64.egg
Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/scipy-0.11.0-py2.6-linux-x86_64.egg
NumPy require the installation of Nose.
Nose
- program: (python egg, version 0.10.4)
- egg info: /home/apps/python/2.6.1/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg-info
- docs: guide posted on web site
MatPlotLib
- program: (python egg, version 0.98.5.2)
- egg info: /home/apps/python/2.6.1/lib/python2.6/site-packages/matplotlib-0.98.5.2.egg-info
- docs:
Note: needed to add the location of the numpy python egg to the basedir array so that setup.py could find the egg.
export LD_LIBRARY_PATH=/home/apps/intel/cmkl/10.0.011/lib/em64t:$LD_LIBRARY_PATH export PYTHONHOME=/home/apps/python-2.6.1
PyMOL
- program: (python egg, versionless)
- egg info: /home/apps/python/2.6.1/lib/python2.6/site-packages/pymol-1.1.0-py2.6.egg-info
- docs:
export LD_LIBRARY_PATH=/home/apps/intel/cmkl/10.0.011/lib/em64t:$LD_LIBRARY_PATH export PYTHONHOME=/home/apps/python-2.6.1 export PYMOL_PATH=/home/apps/python-2.6.1/lib/python-2.6.1/site-packages/pymol
PyMOL required the presence of libglut. Installed rpm -ivh freeglut-devel-2.2.0-14.x86_64.rpm package.
PyMOL libraries have also been installed in the following location:
export LD_LIBRARY_PATH=/home/apps/pymol/1.1:$LD_LIBRARY_PATH
The following was not required by PyPat, but was requested for installation from http://sitemaker.umich.edu/carlsonlab/resources.html
Automated Flooding and Clustering source code
- program: (python egg build from source code)
- egg: /home/apps/python/2.6.1/lib/python2.6/site-packages/AutoClustering-1.0-py2.6.egg-info
- www: carlson web site
Global wRMSD Fit source code
- program: (python source code)
- file: /home/apps/python/scripts/global_wrmsd_v8.3.py
- www: carlson web site
- required: /home/apps/python/2.6.1/lib/python2.6/site-packages/biopython-1.54b-py2.6.egg-info
- required: Numpy (set PATH, PYTHONPATH and LD_LIBRARY_PATH)
Local wRMSD Fit source code
- program: (python source code)
- file: /home/apps/python/scripts/local_wrmsd_v07.py
- www: carlson web site
- required: same as Global
wRMSD input preparation
- program: (python source code)
- file: /home/apps/python/scripts/prep_for wrmsd.py
- www: calson web site
PyMOL Rendering plug-in
- program: (python source code)
- file: /home/apps/python/scripts/rendering.[py|pyc]
- www: calson web site
Mesa
- program: open source implementation of OpenGL specification, a system for rendering #D graphics; v 6.5.1.-7.7
- install dir: (rpm based,
rpm -ql package_name)- mesa-GL
- mesa-libGL
- mesa-libGl-devel
- mesa-libGLU
- mesa-libGLU-devel
MGLTools
centos6
- program: MGLTools v 1.5.7 (
pmv,adt,vision,pythonsh) - install dir: /home/apps/CENTOS6/mgltools/1.5.7
below is rhel5
- program: MGLTools v 1.5.2 (
pmv,adt,vision,pythonsh) - install dir: /home/apps/mgltools/1.5.2
This package works with Autodock. This is a 64 bit installation against glibc 2.5+. You will need to adjust your PYTHONHOME and PYTHONPATH variables.
.cshrc: set path = (/home/apps/mgltools/1.5.2/bin $path) .bashrc export PATH=/home/apps/mgltools/1.5.2/bin:$PATH
VMD
Please try to run these on host
- 1.8.6 on
greentail(centos 5.x) for interactive use - 1.9.2 on
cotontail2(centos6.x) for interactive use - set your PATH and LD_LIBRARY_PATH accordingly
- program: Visual Molecular Dynamics v1.8.6 or v1.9.2
- install dir: /home/apps/CENTOS/vmd/[1.8.6|1.9.2]
- plugins dir: /home/apps/CENTOS/vmd/[1.8.6|1.9.2]/plugins
- ImageMagick (latest default version)
- NetPBM v10.47.05-11
- install dir: (RPM based: netpbm netpbm-devel netpbm-progs)
- docs: rpm -ql netpbm
MPlayer
- program: MPlayer Media Player (mplayer, mencoder)
- executable location: /home/apps/mplayer/2009-03-24 (SVN based)
Linked in via /home/apps/bin
PCASuite
- program: PCAsuite - Molecular Modeling and Bioinformatics Group
- executable location: /home/apps/bin/[pcazip, pcaunzip, pczdump]
- www: http://mmb.pcb.ub.es
Note: Compiled against v10 intel compilers, 64 bit. Program clearly configured for 32 bit operation.
Perl
- /usr/bin/perl, version 5.8.8
- Additional modules installed:
- Bundle::CPAN
- IO::Compress::Bzip2
- Archive::Zip
- PAR
- PAR::Dist
- PAR::Packer
- PDL (Scientific computing using Perl Dta Language)
Chem Tools
- programs: gcmc.exe, mmc.exe , micm.exe
- install dir: /home/apps/bin
- no documentation, contact the Beveridge research group
Note: compiled with ifort -f77rtl -o name.exe name.f
Warning: when compiling micm, ifort warns of 2-digit year.
Mead
- programs: consult the bin/ directory
- install dir: /home/apps/mead/2.2.8a
Note: configured with option –with-python which installed into /usr/lib/python2.4 (also copied to /home/apps/python/2.6.1/site_packages
Mopac
- program: mopac.exe (run via command ./runmopac “jobname”, expects a “jobname.dat” file)
- install dir: /home/apps/mopac/7
- example, docs: inside install_dir
NAMD
Version 2.7b1 was compiled from source against OpenMPI (1.2+intel-10). You may have to add the OpenMPI lib/ directory to your LD_LIBARY_PATH.
- program:
namd2(as well as some others) - install dir: /home/apps/namd/NAMD_2.7b1_Source/Linux-86_64-icc/
- docs: on web site
Following two install are binary distros:
- program:
namd2(as well as some others) - install dir: /home/apps/namd/NAMD_2.7b1_Linux-x86_64
- docs: on web site
- program:
namd2(as well as some others) - install dir: /home/apps/namd/NAMD_2.7b1_Linux-x86-TCP
- docs: on web site
Note: version 2.6 is swallowtail's version compiled against Topspin MPI.
- program:
namd2(as well as some others) - install dir: /home/apps/namd/NAMD_2.6_Source/Linux-amd64-MPI/
- docs: on web site
eport LD_LIBRARY_PATH=/usr/local/topspin/mpi/mpich/lib64
There is a sample page here: LINK
NAB
Note: this is the compiled copy of swallowtail and seems to find the libraries properly. NAB is now part of AmberTools so the newest nab program can be found in the /home/apps/amber/10+openmpi-1.2+intel-10/bin location.
- program: several programs in bin/ directories; main compiler
nab - install dir: /home/apps/nab/5.1.2
- docs:doc and examples directories in install dir
Users should set the NABHOME environment variable. Programs were compiled with icc with the -mpi flag.
If using csh/tcsh add to ~/.cshrc
- source /home/apps/nab/5.1.2/env.csh
or if using sh/bash add to ~/.bashrc
- . /home/apps/nab/5.1.2/env.sh
libsndfile
- program: C library for reading and writing files containing sampled sound.
- install dir: /home/apps/libsndfile/1.0.19
- docs: see below
Lame
- program: lame (high quality MPEG audio layer III (MP3) encoder)
- install dir: /home/apps/lame/398.2
- docs: see below
twoLame
- program: twolame (optimized MPEG audio layer II (MP2) encoder)
- install dir: /home/apps/twolame/0.3.10
- docs: see below
ImageMagick
- program: ImageMagick (montage, animate, and more)
- install dir: /home/apps/imagemagick/[6.4.8-5 and 6.5.0.2]/bin
- docs: inside install_dir/share
In order to make this the default in your PATH, for example …
export PATH=/home/apps/imagemagick/6.4.8-5/bin:$PATH
in your shell or add it to ~/.bashrc. The latest version is linked in via /home/apps/bin
gdb
- program: Gnu Debugger v 6.8
- install dir: /usr/local/gdb/6.8 (linked via /usr/local/bin)
- docs: see below
ddd
- program: Data Display Debugger v 3.3.12
- install dir: /usr/local/ddd/3.3.12
- docs: see below
- program: Data Display Debugger v 3.3.9
- install dir: /usr/local/ddd/3.3.9
- docs: see below
Delphi
- program: delphi v4 release 1.1 (precompiled binaries)
- install dir: /home/apps/delphi/DELPHI_2004_LINUX
- docs: examples and data dirs inside install_dir
Note: Please read the license agreement.
Grace
- program: Grace v 5.1.22 (with X11, EPS, MIF, JPEG, PNG support)
- install dir: /usr/local/grace/5.1.22/grace … default, linked via /usr/local/bin
- docs: user guide is located in doc/ inside install dir
- program: Grace v 5.1.20 (with X11, EPS, MIF, JPEG, PNG support)
- install dir: /usr/local/grace/5.1.20/grace
- docs: user guide is located in doc/ inside install dir
Mutt
- program: Mutt Mail User Agent v 1.5.18 (for those reading email locally)
- install dir: /usr/local
- docs:
man mutt - www: http://www.mutt.org
Gnuplot
- program: Gnuplot v 4.2.2
- install dir: /home/apps/gnuplot/4.2.4 (linked in via /share/apps/bin)
- docs:
man gnuplot
Qt
- program: Qt v 4.5.0
- install dir: /home/apps/qt/4.5.0
- docs: doc/html inside install_dir
- www: http://trolltech.com
- program: Qt v 4.3.0
- install dir: /home/apps/qt/4.3.0
- docs: doc/html inside install_dir
- www: http://trolltech.com
Make the programs available like so:
export PATH=/home/apps/qt/4.5.0/bin:$PATH
R & R/parallel
-
- C11++ on CentOS6, two version of gcc
- read the R-3.6.1_configure file in
/share/apps/CENTOS6/R/R-3.6.1_configure
install.packages('lme4', dependencies = TRUE)
install.packages('tidyverse', dependencies = TRUE)
install.packages('mice', dependencies = TRUE)
install.packages('rpart', dependencies = TRUE)
install.packages('party', dependencies = TRUE)
install.packages('caret', dependencies = TRUE)
install.packages('nnet', dependencies = TRUE)
install.packages('e1071', dependencies = TRUE)
install.packages('xgboost', dependencies = TRUE)
install.packages('kernlab', dependencies = TRUE)
install.packages('randomForest', dependencies = TRUE)
- R 3.6.1 (running against “packages”, had to comment out libcurl version check)
- New java jdk-12.0.2 (by default in your path)
- packages lme4 and tidyverse installed (dependencies=TRUE)
- packages: mice, rpart, party, caret, randomforest, nnet, e1071, kernLab, xgboost
- note: had to make a link to omp.h from gcc 4.8.4 to OS native gcc…works?
export PATH=/share/apps/CENTOS6/R/packages/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/packages/lib:$LD_LIBRARY_PATH export PATH=/share/apps/CENTOS6/R/3.6.1b/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/3.6.1b/lib64:$LD_LIBRARY_PATH export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib64:/share/apps/CENTOS6/gcc/4.8.4/lib:$LD_LIBRARY_PATH #export PATH=/share/apps/java/jdk-12.0.2/bin:$PATH #export LD_LIBRARY_PATH=/share/apps/java/jdk-12.0.2/lib:$LD_LIBRARY_PATH
- R 3.5.1 (new libcurl package)
- Uses same old java home 1.7.0_21 (jdk or jre?), should remember to update
- package lme4 installed
export PATH=/home/apps/CENTOS6/R/packages/bin:$PATH export LD_LIBRARY_PATH=/home/apps/CENTOS6/R/packages/lib:$LD_LIBRARY_PATH export PATH=/home/apps/CENTOS6/R/3.5.1/bin:$PATH export LD_LIBRARY_PATH=/home/apps/CENTOS6/R/3.5.1/lib64:$LD_LIBRARY_PATH export PATH=/share/apps/java/jdk1.7.0_21/bin:$PATH export LD_LIBRARY_PATH=/share/apps/java/jdk1.7.0_21/lib:$LD_LIBRARY_PATH
- R 3.4.3 (major pain with small packages ahead of distro versions, consult)
- Uses JAVA_HOME: /home/apps/java/java (points to jdk1.7.0_21, should update that)
export PATH=/home/apps/CENTOS6/R/3.4.3/bin:$PATH export LD_LIBRARY_PATH=/home/apps/CENTOS6/R/3.4.3/lib64:$LD_LIBRARY_PATH export PATH=/home/apps/CENTOS6/R/packages/bin:$PATH export LD_LIBRARY_PATH=/home/apps/CENTOS6/R/packages/lib:$LD_LIBRARY_PATH export MKL_HOME=/share/apps/intel/composerxe/mkl
Native CentOS R is most up to date on node swallowtail for interactive use. It also has a bunch of packages installed.
Note: All versions were compiled with Blas and Lapack libraries found in the Cluster Math Kernel Libraries.
- program: R v3.1.0 (default)
- install dir: /home/apps/R/3.1.0
- docs:
Set your environment as follows for 3.1.0
. /share/apps/intel/composerxe/bin/iccvars.sh intel64
. /share/apps/intel/composerxe/bin/ifortvars.sh intel64
export MKL_HOME=/share/apps/intel/composerxe/mkl
export PATH=/share/apps/R/3.1.0/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/R/3.1.0/lib64/R/lib:$LD_LIBRARY_PATH
Set your environment as follows for 2.14.1
- contains modules: Igraph and Multicore
. /share/apps/intel/composerxe/bin/iccvars.sh intel64
. /share/apps/intel/composerxe/bin/ifortvars.sh intel64
export MKL_HOME=/share/apps/intel/composerxe/mkl
export PATH=/share/apps/R/2.14.1/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/R/2.14.1/lib64/R/lib:$LD_LIBRARY_PATH
- program: R v2.8.1
- install dir: /home/apps/R/2.8.1
- docs:
Set your environment as follows for 2.8.1
. /share/apps/intel/cce/10.0.025/bin/iccvars.sh
. /share/apps/intel/fce/10.0.025/bin/ifortvars.sh
export PATH=/share/apps/R/2.8.1/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/intel/cmkl/10.0.011/lib/em64t:$LD_LIBRARY_PATH
- program: Rparallel v 0.61
- install dir: /home/apps/RParallel
- docs:
Please consult the README file in install dir to set your environment.
Galaxsee
- program: Galaxsee
- install dir: /home/apps/Gal
Small program to show the concept of parallel programmning using n-body physics problem. Compiled against old Topspin MPI.
export LD_LIBRARY_PATH=/usr/local/topspin/mpi/mpich/lib64:$LD_LIBRARY_PATH
Dowser
- program: several programs in bin/ and bin/linux/ directories
- install dir: /home/apps/dowser
- docs: DOCS/ directory in install dir
Note: users of dowser should add one of the following lines …
if using csh/tcsh add to ~/.cshrc
- source /home/apps/dowser/dowserinit.csh
or if using sh/bash add to ~/.bashrc
- . /home/apps/dowser/dowserinit.sh
Amber
Amber 22
Details on how to run on CentOS7 can be found at
Amber 20
- Two versions compiled,
- one for cuda 8.0/mpich3 for queue amber128
- one for queues mwgpu and exx96 (cuda 9.2/openmpi).
- Consult the run.amber20 script to set up environment
- /share/apps/CENTOS7/amber/amber20/run.amber20
- Both are installed in /usr/local/amber20
AMBER 18
- /share/apps/CENTOS7/amber/amber18
- compiled on
n33with a/usr/local/n37-cuda-9.2soft link - view compile steps at /share/apps/CENTOS7/amber/amber18.install
- when submitting on
exx96we're mixing- 10.2 cuda drivers
- 9.2 toolkits
- some speed results below K20 vs RTX2080s, Amber 16 vs 18
- sample jobs at ~hmeij/k20redo/run.amber[16|18]
# compiled on n33 [hmeij@n33 amber18]$ ls -l bin/pmemd* -rwxr-xr-x 1 hmeij its 3549803 Mar 30 10:19 bin/pmemd lrwxrwxrwx 1 hmeij its 15 Mar 30 11:57 bin/pmemd.cuda -> pmemd.cuda_SPFP -rwxr-xr-x 1 hmeij its 93895208 Mar 30 12:11 bin/pmemd.cuda_DPFP -rwxr-xr-x 1 hmeij its 94734272 Mar 30 13:07 bin/pmemd.cuda_DPFP.MPI lrwxrwxrwx 1 hmeij its 19 Mar 30 12:51 bin/pmemd.cuda.MPI -> pmemd.cuda_SPFP.MPI -rwxr-xr-x 1 hmeij its 75579744 Mar 30 11:57 bin/pmemd.cuda_SPFP -rwxr-xr-x 1 hmeij its 76418760 Mar 30 12:51 bin/pmemd.cuda_SPFP.MPI -rwxr-xr-x 1 hmeij its 4304392 Mar 30 11:23 bin/pmemd.MPI # some quick results | Average timings for all steps: ~hmeij/k20redo/run.amber18 - mwgpu - K20 | ns/day = 2.84 seconds/ns = 30385.24 ~hmeij/k20redo/run.amber18 - exx96 - RTX2080S | ns/day = 11.66 seconds/ns = 7408.08 ~hmeij/k20redo/run.amber16 - exx96 - RTX2080S | ns/day = 7.09 seconds/ns = 12185.91
AMBER 16
- on node n78 in /usr/local
- cuda 8 for GTX1080Ti GPUs
- plumed2.3
AMBER 16
- program: v 16 sander.MPI, sander.LES.MPI, pmemd, pmemd.MPI (compilation details in path)
- install dir: /home/apps/CENTOS6/amber/amber16
- includes AmberTools 17, python miniconda
- docs: doc dir inside install_dir, please read Amber17.pdf
- sample script: ~hmeij/amber/cd/run.cpu
- no gpu capabilitities, requires cuda 7.5+
# next line important for Amber python modules, miniconda source /share/apps/CENTOS6/amber/amber16/amber.sh export AMBERHOME=/share/apps/CENTOS6/amber/amber16 export PATH=$AMBERHOME/bin:$PATH export PATH=/share/apps/CENTOS6/python/2.7.9/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.9/lib:$LD_LIBRARY_PATH export PATH=/share/apps/CENTOS6/openmpi/1.8.4/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/openmpi/1.8.4/lib/:$LD_LIBRARY_PATH
AMBER 12
- program: v12 sander.MPI, sander.LES.MPI, pmemd, pmemd.MPI (compilation details in path)
- install dir: /home/apps/amber/12cpuonly
- includes AmberTools 1.3
- docs: doc dir inside install_dir, please read Amber12.pdf
Has been compiled using Intel v12 compilers and Openmpi 1.4.4, hence you need the code below to setup your environment. This v12 version of Amber is for serial and parallel runs for CPUs only (not GPUs). The appropriate wrapper is the lava.openmpi.wrapper script. Script runiing v9 and v10 version of Amber are identical to this v12 version once paths have been adjusted.
export AMBERHOME=/share/apps/amber/12cpu-only export PATH=$AMBERHOME/bin:$PATH . /share/apps/intel/composerxe/bin/iccvars.sh intel64 . /share/apps/intel/composerxe/bin/ifortvars.sh intel64 export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$LD_LIBRARY_PATH
AMBER 9
- program: version 9 of sander.MPI, pmemd (compilation details in path)
- install dir: /home/apps/amber/9+openmpi-1.2+intel9
- docs: doc dir inside install_dir
Please invoke with appropriate wrapper script.
Some related details about the Amber installation(s) and how to run Amber jobs on the cluster can be found at this Link. This is old information but may help you along.
For sander.MPI and pmemd please add the following line to your ~/.bashrc file
export LD_LIBRARY_PATH=/home/apps/intel/cmkl/9.1.021/lib/em64t:$LD_LIBRARY_PATH
AMBER 10
- program: v 10 sander.MPI, sander.LES.MPI, pmemd, pmemd.MPI (compilation details in path)
- install dir: /home/apps/amber/10+openmpi-1.2+intel-10
- includes AmberTools 1.2
- docs: doc dir inside install_dir, please read Amber10.pdf
Please invoke with appropriate wrapper script.
Some related details about the Amber installation(s) and how to run Amber jobs on the cluster can be found at this Link. This is old information but may help you along.
For sander.MPI and pmemd please add the following line to your ~/.bashrc file (I compiled 9 and 10 against same CMKL version to avoid confusion).
export LD_LIBRARY_PATH=/home/apps/intel/cmkl/9.1.021/lib/em64t:$LD_LIBRARY_PATH
AmberTools 1.2 has been installed.
RIP Scripts has been installed, consult http://boscoh.com/rip Location: /home/apps/amber/rip-scripts In order to use, you will need to point to Phyton 2.6.1 which contains the Numpy egg.
Rosetta
(PyRosetta v2.011 is also installed)
Both below compiled with /share/apps/python/2.6.1/bin/python …
- program: Rosetta 3.5 (see compiler note below)
- install dir: /home/apps/rosetta/3.5
- others: database, biotools, demos, bin (add latter to $PATH)
Please read the license at /share/apps/rosetta/LICENSE-3.0
- program: Rosetta 3.0 (see compiler note below)
- install dir: /home/apps/rosetta/3.0
- others: database, biotools, demos, bin (add latter to $PATH)
Please read the license at /share/apps/rosetta/LICENSE-3.0
Note: this is a 64-bit compilation using python 2.6.1 and therefore is an “unsupported” configuration.
- program: Rosetta++ 2.2.0 (see compiler note below)
- install dir: /home/apps/rosetta/2.2.0
- scripts, database & docs: inside install_dir
Please read the license at /share/apps/rosetta/LICENSE-2.2.0
Note: this is a 64-bit compilation (done on swallowtail) using target gcc64 and therefore is an “unsupported” configuration.
Gaussian
EMT64 x86_64 version (for mw256[fd], mw128, tinymem)
- program: Gaussian 16 (
g16) - install dir: /home/apps/gaussian/g16root
EMT64 x86_64 version (for hp12)
- program: Gaussian GDV H11.1
- install dir: /share/apps/gaussian/gdvh11
export gdvroot="/share/apps/gaussian/gdvh11" . $gdvroot/gdv/bsd/gdv.profile
EMT64 x86_64 version (for swallowtail/petaltail)
- program: Gaussian 09 Revision (
g09) - install dir: /home/apps/gaussian/g09root
AMD64 x86_64 version (for sharptail)
- program: Gaussian 09 Revision (
g09) - install dir: /home/apps/gaussian/g09root_amd64
AMD64 x86_64 version (for sharptail)
- program: Linda 8.2 (
g09) - install dir: /home/apps/gaussian/g09root_amd64_linda
AMD64 & EMT64 x86_64 version (for both swallowtail/petaltail and sharptail clusters)
- program: GaussView v5
- install dir: 'gv' in all g09root directories listed above
Please note that if run from sharptail, you must explictedly enable x-forwarding when connecting to this host, like so
ssh -X sharptail
ENVIRONMENT
Users will want to add the following to their .login file:
setenv g09root "dir" setenv GAUSS_SCRDIR "scr-dir" source $g09root/g09/bsd/g09.login # sets up G09 run environment.
The <dir> in the first command is the location of the g09 directory. For example, if the path to this directory is /usr/local/g09, then set g09root to /usr/local. The <scr-dir> in the second command is a directory to be used by default for Gaussian 09 scratch files. There should be plenty of disk space available at this location.
Bourne-type shell users would use these commands instead of the ones above:
g09root="dir" GAUSS_SCRDIR="scr-dir" export g09root GAUSS_SCRDIR . $g09root/g09/bsd/g09.profile
DOCUMENTATION
- Gaussian 09 User's Reference:
- G09 IOPs Reference:
- G09 Linda:
- GaussView 5 Reference:
Note: in order to use this application you must be a member of group gaussian. Please send request to the administrator.
Details about the Gaussian installation and how to run Gaussian jobs on the cluster can be found at this Link. Please read that page.
Openbabel
You will need to add the bin/ and lib/ directories to your PATH and LD_LIBRABY_PATH env parameters (example son this page)
For CentOS6.x (mw256[fd] queues), compiled with cmake/gcc
- program Openbabel (v 2.3.2)
- install dir: /share/apps/CENTOS6/openbabel/2.3.2
- docs: check web site
For RHEL5.x and CentOS5.x (hp12 queue), compiled with ICC/ifort
- program Openbabel (v 2.2.1)
- install dir: /share/apps/openbabel/2.2.1
- docs: check web site
- program Openbabel (v 2.1.1)
- install dir: /share/apps/openbabel/2.1.1
- docs: check web site
AutoDock
- program: AutoDock 4.0.1 and AutoGrid 4.0.0 (
autodock4, autogrid4) - install dir: /home/apps/autodock
- docs: unknown, check web site
Note. Requires Openbabel. You need to add the following lines to your ~/.bashrc file or program.
export PATH=/home/apps/autodock:/home/apps/openbabel/2.1.1/bin:$PATH export PYTHONPATH=/home/apps/openbabel/2.1.1/site-packages:$PYTHONPATH export PERL5LIB=/home/apps/openbabel/2.1.1/lib/perl:$PERL5LIB export LD_LIBRARY_PATH=/home/apps/openbabel/2.1.1/lib:$LD_LIBRARY_PATH
Note. The perl plugin will not compile. Have a message to the list.
— Meij, Henk 2008/01/25 15:39
MPI
OpenMPI
- program: OpenMPI v 3.1.3
- install dir: /share/apps/CENTOS6/openmpi/3.1.3
- program: OpenMPI v 1.10.2
- install dir: /share/apps/CENTOS6/openmpi/1.10.2
- CHECKPOINTING SUPPORT (be sure in combination with BLCR, consultBLCR Checkpoint in OL3
- program: OpenMPI 1.6.5
- install dir: /share/apps/CENTOS6/openmpi-1.6.5.cr
- program: OpenMPI v 1.8.4 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /home/apps/CENTOS6/openmpi/1.8.4/bin/ (compiled with gcc 4.8.4 !!!)
- docs: inside install dir in dirs man & share
export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib64:$LD_LIBRARY_PATH
- program: OpenMPI v 1.4.4 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /home/apps/openmpi/1.4.4+intel-12/bin/ (compiled with icc/ifort intel v12)
- docs: inside install dir in dirs man & share
- program: OpenMPI v 1.4.3 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /home/apps/openmpi/1.4.3+intel-12/bin/ (compiled with icc/ifort intel v12)
- docs: inside install dir in dirs man & share
For v1.4.3/v1.4.4 you will have to set:
. /share/apps/intel/composerxe/bin/iccvars.sh intel64 . /share/apps/intel/composerxe/bin/ifortvars.sh intel64 #also change (not sure it matters), LD_LIBRARY_PATH is modified by above scripts export MKL_HOME=/share/apps/intel/composerxe/mkl
- program: OpenMPI v 1.3.1 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /home/apps/openmpi/1.3.1+intel-10/bin/ (compiled with icc/ifort intel v10)
- docs: inside install dir in dirs man & share
- program: OpenMPI v 1.2 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …) DEFAULT
- install dir: /home/apps/openmpi/1.2+intel-9/bin/ (compiled with icc/ifort intel v9)
- docs: inside install dir in dirs man & share
- program: OpenMPI v 1.2 (default)(programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /home/apps/openmpi/1.2+intel-10/bin/ (compiled with icc/ifort intel v10)
- docs: inside install dir in dirs man & share
- program: OpenMPI v 1.2 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /opt/openmpi/gnu/bin/ (compiled with default gcc 4.1.2)
- docs: inside install dir in dirs man & share
MVAMPICH
- program: Mvapich v 0.9.9 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /home/apps/mvampich/0.9.9 (compiled with intel v 10)
- docs: inside install dir in dirs man & doc
LAM
Warning end-of-life, please use OpenMPI
- program: LAM v 7.1.3 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /home/apps/lam/7.1.3 (includes xmpi, compiled with intel v 10)
- docs: inside install dir in dirs man & doc
Other Gnu MPI Flavors
- program: Mpich1 v 1.2.7 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /opt/mpich1/gnu/bin/ (compiled with default gcc 4.1.2)
- program: Mpich2 v 1.0.6 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /opt/mpich1/gnu/bin/ (compiled with default gcc 4.1.2)
- program: Mvapich1 v 1.2.7 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /opt/mvapich1/gnu/bin/ (compiled with default gcc 4.1.2)
- program: Mvapich2 v 2.1.0 (programs like mpicc, mpiCC, mpif77, mpif90, mpirun …)
- install dir: /opt/mvapich1/gnu/bin/ (compiled with default gcc 4.1.2)
Those are pretty old i suggest you do not use them.
OFED
- program: OFED v 1.0.0
- install dir: /opt/ofed/gnu/bin/mpi-selector (compiled with default gcc 4.1.2)
TopSpin
- program: mpicc, mpirun etc
- install dir: /usr/local/topspin
Note: the is the mpich MPI suite of libraries that came with OCS 4.1.1 (swallowtail). In case users compiled programs against these libraries. Not supported anymore in OCS 5.1. Suggest using the latest OpenMPI flavor.
Java
- program: java, javac etc
- install dir: /home/apps/java/<version> where version 4.2.17 or 1.5.0_15 or 1.6.0_05
- docs: install install_dir
- www: http://java.sun.com/
Versions are installed with the most recent linked into users' environments via /share/apps/bin. JAVAHOME points to /home/apps/java/java which is the latest version. To set another flavor as your default java, here is an example:
# 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:$CLASSPATH
drwxrwxr-x 9 root root 4096 Aug 20 2007 j2sdk1.4.2_07 drwxr-xr-x 9 root root 4096 Oct 5 06:05 jdk1.5.0_14 drwxr-xr-x 9 root root 4096 Jun 14 2007 jdk1.6.0_02 drwxr-xr-x 7 root root 4096 Nov 10 2005 jre1.5.0_06 drwxr-xr-x 20 root root 4096 Feb 20 11:20 netbeans-6.0.1
- program: NetBeans IDE 6.0 (netbeans)
- install dir: /share/apps/java/
- docs:
Python2
Note 2.7 branch is end of life 01/01/2020
Note: since the latest update to CentOS 6.10 the native python in the OS is /usr/bin/python v2.6.6
- Python 2.7.15
- compile with enable-share
- numpy and scipy packages, and
- Successfully installed Send2Trash-1.5.0 backports-abc-0.5 futures-3.3.0 ipaddress-1.0.22
- ipykernel-4.10.1 jupyter-client-5.3.4 jupyterlab-0.33.12 jupyterlab-launcher-0.11.2
- notebook-5.7.8 prometheus-client-0.7.1 python-dateutil-2.8.0 singledispatch-3.4.0.3
- subprocess32-3.5.4 terminado-0.8.2 tornado-5.1.1
export PATH=/share/apps/CENTOS6/python/2.7.15/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.15/lib:$LD_LIBRARY_PATH
- 2.7.15 embedded in miniconda2 installation, see Galario software entry.
- 2.7.10 two versions, the one in
blcr_softcan be checkpointed- /share/apps/CentOS6/python/2.7.10
- /share/apps/CENTOS6/blcr_soft/python/2.7.10
— Henk 2017/02/06 10:47 Added to /share/apps/CENTOS6/blcr/pyton/2.7.10 …
export PATH=/share/apps/CENTOS6/python/2.7.10/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.10/lib:$LD_LIBRARY_PATH ...or... export PYTHONHOME=/share/apps/CENTOS6/blcr_soft/python/2.7.10 export PYTHONPATH=/home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages export PATH=$PYTHONHOME/bin:$PATH REBOUND: https://github.com/hannorein/rebound ; http://rebound.readthedocs.io/en/latest/ REBOUNDx: https://github.com/dtamayo/reboundx Installing collected packages: pandas Successfully installed pandas-0.19.2
Added to /share/apps/CENTOS6/python/2.7.10 — Henk 2019/03/15 11:14
Using /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/numpy-1.10.1-py2.7-linux-x86_64.egg Adding scipy 0.16.1 to easy-install.pth file Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/argparse-1.4.0-py2.7.egg Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/readline-6.2.4.1-py2.7-linux-x86_64.egg Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/pandas2-0.0.0-py2.7.egg Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/emcee-3.0rc2-py2.7.egg Adding mpi4py 2.0.0 to easy-install.pth file Using /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg Using /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/astropy-1.1rc2-py2.7-linux-x86_64.egg Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/scandir-1.10.0-py2.7-linux-x86_64.egg Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/subprocess32-3.5.3-py2.7-linux-x86_64.egg Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/pandas-0.24.2-py2.7-linux-x86_64.egg Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/seaborn-0.9.0-py2.7.egg Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/numpy-1.16.2-py2.7-linux-x86_64.egg Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/os0-0.2.14-py2.7.egg Installed /home/apps/CENTOS6/python/2.7.10/lib/python2.7/site-packages/pickle_utils-0.1-py2.7.egg
Added to /share/apps/CENTOS6/blcr_soft/python/2.7.10 — Henk 2019/03/16 08:40
Successfully installed argparse-1.4.0 Successfully installed readline-6.2.4.1 Successfully installed numpy-1.16.2 Successfully installed scipy-1.2.1 emcee in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/emcee-2.1.0-py2.7.egg (2.1.0) mpi4py in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages (2.0.0) pandas in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages (0.19.2) pytz>=2011k in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/pytz-2016.3-py2.7.egg (from pandas) (2016.3) numpy>=1.7.0 in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages (from pandas) (1.16.2) python-dateutil in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/python_dateutil-2.5.2-py2.7.egg (from pandas) (2.5.2) six>=1.5 in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/six-1.10.0-py2.7.egg (from python-dateutil->pandas) (1.10.0) Installed /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/pandas2-0.0.0-py2.7.egg matplotlib in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg (1.5.1) numpy>=1.6 in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages (from matplotlib) (1.16.2) python-dateutil in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/python_dateutil-2.5.2-py2.7.egg (from matplotlib) (2.5.2) pytz in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/pytz-2016.3-py2.7.egg (from matplotlib) (2016.3) cycler in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/cycler-0.10.0-py2.7.egg (from matplotlib) (0.10.0) pyparsing!=2.0.0,!=2.0.4,>=1.5.6 in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/pyparsing-2.1.1-py2.7.egg (from matplotlib) (2.1.1) six>=1.5 in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/six-1.10.0-py2.7.egg (from python-dateutil->matplotlib) (1.10.0) Installing collected packages: seaborn Successfully installed subprocess32-3.5.3 astropy in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages/astropy-1.1.2-py2.7-linux-x86_64.egg (1.1.2) numpy>=1.6.0 in /home/apps/CENTOS6/blcr_soft/python/2.7.10/lib/python2.7/site-packages (from astropy) (1.16.2) Successfully installed pathlib2-2.3.3 scandir-1.10.0 Successfully installed os0-0.2.14 Successfully installed pickle-utils-0.1
- program: python v 2.7.9
- install dir: /home/apps/CentOS6/python/2.7.9
Note: v 2.7.9 also contains Numpy 1.9.2 and Cython 0.22 and MACS2 2.1.0 Note: Should not be used on queue hp12 Note: Successfully installed insane-1.0rc1 simopt-0.1
export PYTHONHOME=/home/apps/CentOS6/python/2.7.9 export PYTHONPATH=/home/apps/CentOS6/python/2.7.9/site-packages:$PYTHONPATH export PATH=$PYTHONHOME/bin:$PATH
- program: python v 2.7.2
- install dir: /home/apps/python/2.7.2
v 2.7.2 also contains pyodbc which relies on unixODBC and a mysql connector, consult section unixODBC.
v. 2.7.2 also contains
- PythoScale: http://www.rbvi.ucsf.edu/trac/Pythoscape
export PYTHONHOME=/home/apps/python/2.7.2 export PYTHONPATH=/home/apps/python/2.7.2/site-packages export PATH=$PYTHONHOME/bin:$PATH
- program: python v 2.6.1
- install dir: /home/apps/python/2.6.1
- setuptools egg (pknots)
- MySQl-python egg (pknots)
- Pmw egg (PyMol)
- program: python v 2.6.1 with Tcl/Tk and Togl required for PyOpenGL (see lammps section)
- install dir: /home/apps/python/2.6.1.tcltk
- Although older version of Tcl/Tk and Togl exist in redhat OS, newer versions are also installed in /usr/local
- python 2.6.1 was recompiled against the above and staged in install dir
- next setuptools was installed in site-packages
- setup.py then installed the PyOpenGL package
- program: python v 2.5.4
- install dir: /home/apps/python/2.5.4
- program: default python v 2.4.3
- install dir: /usr/bin
Note: there is another version of Python (2.5) hiding inside MGLtools at /home/apps/mgltools/1.5.2/bin/python. Read the section on MGLtools for more information.
Compilers
G95 Compiler
- program: G95 v 0.9.1 compiler (g95) compiled with GCC v 4.1.2 (core)
- install dir: /home/apps/g95/0.9.1
- docs: G95Manual.pdf inside install_dir
- www: http://www.g95.org
GNU Compilers
For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, look for samples on this page …
- program: GCC v 9.2.0
- /share/apps/CENTOS6/9.2.0
- note: libgomp disabled for nanopolish compile attempt
wget ftp://ftp.nluug.nl/mirror/languages/gcc/releases/gcc-9.2.0/gcc-9.2.0.tar.gz tar zxvf gcc-9.2.0.tar.gz cd gcc-9.2.0 ./contrib/download_prerequisites ./configure --prefix=/share/apps/CENTOS6/gcc/9.2.0 --disable-libgomp --disable-multilib make make install
- program: GCC v 4.8.4
- install dir: /home/apps/CENTOS6/gcc/4.8.4
- docs: man inside install_dir
- www: http://gcc.gnu.org
Note: GMP, MPFR and MPC build into GCC. There are also standalone packges.
[hmeij@petaltail gcc]$ export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH [hmeij@petaltail gcc]$ export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib64:$LD_LIBRARY_PATH [hmeij@petaltail gcc]$ which gcc /share/apps/CENTOS6/gcc/4.8.4/bin/gcc [hmeij@petaltail gcc]$ gcc test.c [hmeij@petaltail gcc]$ ./a.out Hello world
For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, look for samples on this page …
- program: GCC v 4.8.0
- install dir: /home/apps/gcc/4.8.0
- docs: man inside install_dir
- www: http://gcc.gnu.org
Note: Used the gcc-build approach so you will not need references to GMP, MPFR and MPC using GCC.
- program: GCC v 4.7.2
- also needs /share/apps/gcc/gmp/4.3.2
- and /share/apps/gcc/mpfr/2.4.2
- or /share/apps/gcc/mpc/0.8.1
- install dir: /home/apps/gcc/4.7.2
- docs: man inside install_dir
- www: http://gcc.gnu.org
Note: Used the gcc-build approach so you will not need references to GMP, MPFR and MPC using GCC.
- program: GCC v 4.3.3
- install dir: /home/apps/gcc/4.3.3
- docs: man inside install_dir
- www: http://gcc.gnu.org
- program: GCC v 4.2.0
- install dir: /home/apps/gcc/4.2.0
- docs: man inside install_dir
- www: http://gcc.gnu.org
- program: default GCC v 4.1.2 compilers (gcc, g++, no fortran)
- docs: rpm -ql gcc
- program: GCC v 4.0.3
- install dir: /home/apps/gcc/4.0.3 (core only)
- docs: man inside install_dir
- www: http://gcc.gnu.org
Intel
UPDATE 2021 latest version of icc/icx and ifort/ifx are inside OneAPI, search this page
UPDATE 2016 parallel studio cluster edition installed
- 2 ifort and 2 icc float licenses
- icc/ifort are in your path
- for location do something like 'env | grep ^INTEL'
UPDATE, 3 years later, we bought a new version, things change
- ifort and icc are all together now with MKL and other stuff …
- consult the README file in /share/apps/intel/composerxe/
- you will need to source the environment as explained in the README files
- the default icc/ifort will remain the old version for now
- …
- can be used on all login nodes as well …
- install dir: /home/apps/intel/[cc|cce|fc|fce|idbe]/version/bin
- cc|fc 32 bit compilers
- cce|fce 64 bit compilers
- v 09.1.043 was our evaluation copy and will remain
- v 09.1.047 was our first installed version
- v 10.0.25 is the default in your $PATH
- docs: man 'compiler_name' and 'compiler_name -help'
- also in install_dir/compiler_name/version/doc
Cluster Math Kernel Libraries
- latest version in OneAPI, search this page
- see Intel parallel studio
- /home/apps/intel/cmkl
- 9.1.021 … [old]
- 9.1.023 …
- 10.0.011 … default, set in $MKL_HOME
Intel Threading Building Blocks
- latest version is in OneAPI, search this pages
- see Intel parallel studio
- tied to our Intel C compiler license … v 2.0
- relevant files sourced at login (setting up LIBRARY_PATH and DYLD_LIBRARY_PATH)
- install_dir: /home/apps/intel/tbb/2.0
- docs: docs/ directory inside install_dir
- web: TBB
Matlab
- installed R2023a
- installed R2022a
- installed R2021a
- program: Matlab, link to binary is 'matlab' in
/share/apps/bin- R2020b, campus wide license so no more restrictions on licenses
- No Distributed Computing Engine or Matlab Parallel (for now)
- install dir: /share/apps/CENTOS7/matlab/R2020bISO
- docs & www: http://mathworks.com
- CentOS7 required use on queues mwgpu, amber128 and exx96
- For GUI launch on greentail52
Note:
- Matlab can do GPU computations
- Matlab can do Hadoop computations
Stata
- program stata[-mp|-se] in your $PATH, version 18
- v17 will still run so add '17' to the command like 'stata-mp17'
- so that makes for 12 licenses
- program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se
- install dir: /share/apps/stata/
- docs: at web site
export PATH=/share/apps/stata/17:$PATH