This is an old revision of the document!
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
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
# 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:$PATH
# does not seem to work against htslib version above... export HTSSRC=/share/apps/CENTOS6/ANGSD/htslib export PATH=/share/apps/CENTOS6/ANGSD/angsd:$PATH
# with local java jre1.8.0_212 export PATH=/share/apps/CENTOS6/beast/2.6.0/bin:$PATH
CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses.
Open-Source Computational Structural Biology Framework
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.
An Easy and Professional Tool to Learn & Teach Programming with Python
Phylogenetic Analysis by Maximum Likelihood (PAML)…programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
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
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
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)
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:$LD_LIBRARY_PATH
These versions of python can be set with your PYTHONPATH and PYTHONHOME env variables. For syntax, see the Autodock section.
FastQC A quality control tool for high throughput sequence data.
java -version
latest JDK installed, in default PATH which java
kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH" export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH" bwa: 0.7.17-h84994c4_5 bioconda perl: 5.26.2-h14c3975_1002 conda-forge bowtie bioconda/linux-64::bowtie-1.2.2-py27h2d50403_1 tbb conda-forge/linux-64::tbb-2019.4-h6bb024c_0 star bioconda/linux-64::star-2.7.0d-0 hdf5 conda-forge/linux-64::hdf5-1.10.3-hba1933b_1001 kallisto bioconda/linux-64::kallisto-0.45.0-hdcc98e5_0
Trinity assembles transcript sequences from Illumina RNA-Seq data.
Trinity seems to need makeblastdb. BLAST finds regions of similarity between biological sequences.
export TRINITY_HOME=/share/apps/CENTOS6/trinityrnaseq-Trinity-v2.8.4 export PATH=$TRINITY_HOME:$PATH python 2.7 modules (these do not work with Trinity...bowtie2, jellyfish, salmon?) bowtie2-2.3.4.3 | py27he860b03_1 11.9 MB bioconda jellyfish conda-forge/linux-64::jellyfish-0.6.1-py27h14c3975_1000 bzip2-1.0.6 | h14c3975_1002 415 KB conda-forge icu-58.2 | hf484d3e_1000 22.6 MB conda-forge jemalloc-5.1.0 | hf484d3e_1000 10.2 MB conda-forge libboost-1.67.0 | h46d08c1_4 20.9 MB salmon-0.13.1 | h86b0361_0 4.2 MB bioconda xz-5.2.4 | h14c3975_1001 366 KB conda-forge trinity modules Inchworm: has been Installed Properly Chrysalis: has been Installed Properly QuantifyGraph: has been Installed Properly GraphFromFasta: has been Installed Properly ReadsToTranscripts: has been Installed Properly parafly: has been Installed Properly slclust: has been Installed Properly collectl: has been Installed Properly
Apparently bowtie, jellyfish, and salmon are not found as python modules. Install binaries from
and put them in the miniconda2 directory as that is the python used.
#!/bin/bash # submit via 'bsub < run_trinity' #BSUB -n 24 #BSUB -R "span[hosts=1]" #BSUB -q mw256fd #BSUB -J trinity #BSUB -o trinity_assembly #BSUB -e trinity_stderr export TRINITY_HOME=/share/apps/CENTOS6/trinityrnaseq-Trinity-v2.8.4 export PATH=$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
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
Canu: a single molecule sequence assembler for genomes large and small.
Eigen: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
Nanopolish : Software package for signal-level analysis of Oxford Nanopore sequencing data.
BioPython : Aset of freely available tools for biological computation
Samtools: is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
Minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
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
Accelerated Library for Analysing Radio Interferometer Observations
[hmeij@cottontail ~]$ conda --version conda 4.5.4 $HOME/.bashrc for galario # added by Miniconda2 installer export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
Molecular Modeling Software
NOTE: Lots of errors in compiling serial mode.
NOTE2: When compiling campari_threads ewaldo.f90 fails terribly
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
Mathematics software, a viable free open source alternative to Magma, Maple, Mathematica and Matlab.
# 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
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation that can be controlled from R.
Compiled for every queue, for usage consult BLCR Checkpoint in OL3 and BLCR Checkpoint in OL3 for serial and parallel approaches.
Astronomy package for exoplanet searches.
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
Intel compiler library for parallel jobs.
Add to your LD_LIBRARY_PATH
Automatically generates schematic diagrams of protein-ligand interactions for a given PDB file.
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. .
Should use Python 2.7.9 (see python section on setting up environment) on CentOS6 nodes.
MODELLER is used for homology or comparative modeling of protein three-dimensional structures.
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, a package of highly-specialized radio astronomy software.
# Define your Miriad environment by invoking the initialization scripts % . MIRRC.sh # in sh-like shells, or % source MIRRC
Compiled with /share/apps/python/2.6.1/bin/python …
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
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 …
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:$PATH
Also added emcee to python 2.7.10, see the section on pyTransit
Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/argparse-1.4.0-py2.6.egg Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/pandas2-0.0.0-py2.6.egg Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/subprocess32-3.5.3-py2.6-linux-x86_64.egg
(Rosetta 2.2, 3.0 and 3.5 also are installed)
Compiled with /share/apps/python/2.6.1/bin/python …
Please read the license at /share/apps/pyrosetta/2014wk05/License.2014wk05
Note: although it probably does not matter, the python compile was performed under CentOS6 because latest phenix version requires that. So target queues mw256
and mw256fd
.
Gromacs-2018 for GPU (K20/GTX1080
Gromacs 5.1.4: there is only one version
Gromacs 5.1.2: there are four versions
mdrun
replaced by gmx
For the latest version there are 6 compilations. Gromacs developers are pretty verbal in terms of “compile on a host where you are goig to run it”. For v5.0.1, the nomeclature is like this:
The file /share/apps/gromacs/build-5.0.1.sh will show you notes on compiling. Update: The GPU versions failed to compile with icc/icpc but did compile with gcc. will investigate later on this strange behavior. — Meij, Henk 2014/10/01 15:33
# for all versions . /share/apps/intel/composerxe/bin/iccvars.sh intel64 . /share/apps/gromacs/5.0.1 [-icc or -mpi] [-hp12 or -mw256 or -mwgpu] /bin/GMXRC.sh # for all "icc versions" you are done # for all "mpi versions" add this export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$LD_LIBRARY_PATH # for all "gpu versions" add this export PATH=\ /cm/shared/apps/gcc/4.7.0/bin:/cm/shared/apps/cuda50/sdk/5.0.35/bin/linux/release:\ /cm/shared/apps/lammps/cuda/2013-01-27/:/cm/shared/apps/amber/amber12/bin:\ /cm/shared/apps/namd/ibverbs-smp-cuda/2013-06-02/:/usr/lib64/qt-3.3/bin:\ /usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/sbin:/usr/sbin:\ /cm/shared/apps/cuda50/toolkit/5.0.35/bin:/cm/shared/apps/cuda50/sdk/5.0.35/bin/linux/release:\ /cm/shared/apps/cuda50/libs/current/bin:/cm/shared/apps/cuda50/toolkit/5.0.35/open64/bin:\ /cm/shared/apps/mvapich2/gcc/64/1.6/bin:/cm/shared/apps/mvapich2/gcc/64/1.6/sbin export LD_LIBRARY_PATH=\ /cm/shared/apps/gcc/4.7.0/lib:/cm/shared/apps/gcc/4.7.0/lib64:\ /cm/shared/apps/cuda50/toolkit/5.0.35/lib64:/cm/shared/apps/amber/amber12/lib:\ /cm/shared/apps/amber/amber12/lib64:\ /cm/shared/apps/namd/ibverbs-smp-cuda/2013-06-02/:/cm/shared/apps/cuda50/toolkit/5.0.35/lib64:\ /cm/shared/apps/cuda50/libs/current/lib64:/cm/shared/apps/cuda50/toolkit/5.0.35/open64/lib:\ /cm/shared/apps/cuda50/toolkit/5.0.35/extras/CUPTI/lib:/cm/shared/apps/mvapich2/gcc/64/1.6/lib
# source for Intel compiler setup . /share/apps/intel/composerxe/bin/iccvars.sh intel64 # and source the GMXRC for your shell . /share/apps/gromacs/4.6-icc[or -mpi]/bin/GMXRC.[bash|zsh|csh]
export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$LD_LIBRARY_PATH
Job submissions should go to queue mathematica which containes licensed nodes (all the hp12 nodes for now).
Found Intel fortran compiler, so may have to source (albeit it should be platform independent)
. /share/apps/intel/composerxe/bin/iccvars.sh intel64 . /share/apps/intel/composerxe/bin/ifortvars.sh intel64
SERVER export PATH=/home/apps/python/2.6.1/bin/:$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 (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
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.
yum install unixODBC
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).
export PATH=/share/apps/go/bin:$PATH
Notes: “coulomb” did not compile with OpenMPI, MVApich1 or 2, but finally compiled against MVApich 0.99 (upgrade to 1.2)… the rest was compiled with gcc an 6g (from go language). In order to run the MPI binary, do not use a our lsf/lava wrappers but build up the command line with -np and -machinefile parameters.
export GOROOT=/share/apps/go export PATH=/share/apps/go/bin:/share/apps/mvapich/1.2+gnu-4.1.2+gen2/bin:$PATH export LD_LIBRARY_PATH=/share/apps/mvapich/1.2+gnu-4.1.2+gen2/lib:$LD_LIBRARY_PATH
export PATH=/share/apps/fftw/3.3.6/bin:$PATH export LD_LIBRARY_PATH=/share/apps/fftw/3.3.6/lib:$LD_LIBRARY_PATH
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:\ $LD_LIBRARY_PATH ./configure --prefix=/share/apps/fftw/2.1.5_mpi \ --enable-mpi CC=icc CXX=icpc F77=ifort FC=ifort
You may to have set the following:
export MKL_HOME=/share/apps/intel/cmkl/9.1.021 export AMBERHOME=/share/apps/amber/9serial+ifort+plumed export LD_LIBRARY_PATH=/share/apps/intel/cmkl/9.1.021/lib/64:$LD_LIBRARY_PATH
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/:\ $LD_LIBRARY_PATH
go to How to submit GPU jobs with Lammps
Note: all versions have package yes-colloid installed.
. /share/apps/intel/composerxe/bin/iccvars.sh intel64 . /share/apps/intel/composerxe/bin/ifortvars.sh intel64 export MKL_HOME=/share/apps/intel/composerxe/mkl export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$LD_LIBRARY_PATH export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH
export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$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
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
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
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
Please note the appropriate citation and reference guides for each library (found on web site).
Note: compiled with ifort
Note: compiled with gcc
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.
Note: compiled with ifort
Note: compiled with ifort
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
# 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
# bash users: source /share/apps/phenix/phenix-1.5-2/phenix_env.sh
Note: our hardware/platform not supported, compiled with ifort (minor warnings)
Note: wham
compiled with warnings using icc. wham-2d
failed to compile.
* program: vina v 1.0 beta 03 (for molecular docking and virtual screening)
export PATH=/share/apps/autodock:$PATH # or export PATH=/share/apps/autodock/autodock_vina_1_1_2_linux_x86/bin:$PATH
Also linked in via /home/apps/bin which is in default PATH.
The dependencies for PyPat … drummroll … incredible!
In order to run some PyPat programs or invoke some of the underlying programs you may have to set some of the published environment variables listed below.
Python
export PYTHONHOME=/home/apps/python/2.6.1
ImageMagick
NumPy & Scipy
NumPy was configured against the CMKL BLAS and LAPACK by uncommenting the lines for [cmkl] in site.cfg
export LD_LIBRARY_PATH=/home/apps/intel/cmkl/10.0.011/lib/em64t:$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:$PATH
Also upgrade and installed installed
Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/numpy-1.6.2-py2.6-linux-x86_64.egg
Installed /home/apps/python/2.6.1/lib/python2.6/site-packages/scipy-0.11.0-py2.6-linux-x86_64.egg
NumPy require the installation of Nose.
Nose
MatPlotLib
Note: needed to add the location of the numpy python egg to the basedir
array so that setup.py could find the egg.
export LD_LIBRARY_PATH=/home/apps/intel/cmkl/10.0.011/lib/em64t:$LD_LIBRARY_PATH export PYTHONHOME=/home/apps/python-2.6.1
PyMOL
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
Global wRMSD Fit source code
Local wRMSD Fit source code
wRMSD input preparation
PyMOL Rendering plug-in
rpm -ql package_name
)centos6
pmv
,adt
,vision
,pythonsh
)below is rhel5
pmv
,adt
,vision
,pythonsh
)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
Please try to run these on host
greentail
(centos 5.x) for interactive usecotontail2
(centos6.x) for interactive useLinked in via /home/apps/bin
Note: Compiled against v10 intel compilers, 64 bit. Program clearly configured for 32 bit operation.
Note: compiled with ifort -f77rtl -o name.exe name.f
Warning: when compiling micm, ifort warns of 2-digit year.
Note: configured with option –with-python which installed into /usr/lib/python2.4 (also copied to /home/apps/python/2.6.1/site_packages
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.
namd2
(as well as some others) Following two install are binary distros:
namd2
(as well as some others) namd2
(as well as some others) Note: version 2.6 is swallowtail's version compiled against Topspin MPI.
namd2
(as well as some others) eport LD_LIBRARY_PATH=/usr/local/topspin/mpi/mpich/lib64
There is a sample page here: LINK
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.
nab
Users should set the NABHOME environment variable. Programs were compiled with icc
with the -mpi
flag.
If using csh/tcsh add to ~/.cshrc
or if using sh/bash add to ~/.bashrc
In order to make this the default in your PATH, for example …
export PATH=/home/apps/imagemagick/6.4.8-5/bin:$PATH
in your shell or add it to ~/.bashrc. The latest version is linked in via /home/apps/bin
Note: Please read the license agreement.
man mutt
man gnuplot
Make the programs available like so:
export PATH=/home/apps/qt/4.5.0/bin:$PATH
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
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
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.
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
. /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
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
Please consult the README file in install dir to set your environment.
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:$LD_LIBRARY_PATH
Note: users of dowser should add one of the following lines …
if using csh/tcsh add to ~/.cshrc
or if using sh/bash add to ~/.bashrc
AMBER 16
AMBER 16
# next line important for Amber python modules, miniconda source /share/apps/CENTOS6/amber/amber16/amber.sh export AMBERHOME=/share/apps/CENTOS6/amber/amber16 export PATH=$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/:$LD_LIBRARY_PATH
AMBER 12
Has been compiled using Intel v12 compilers and Openmpi 1.4.4, hence you need the code below to setup your environment. This v12 version of Amber is for serial and parallel runs for CPUs only (not GPUs). The appropriate wrapper is the lava.openmpi.wrapper script. Script runiing v9 and v10 version of Amber are identical to this v12 version once paths have been adjusted.
export AMBERHOME=/share/apps/amber/12cpu-only export PATH=$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:$LD_LIBRARY_PATH
AMBER 9
Please invoke with appropriate wrapper script.
Some related details about the Amber installation(s) and how to run Amber jobs on the cluster can be found at this Link. This is old information but may help you along.
For sander.MPI and pmemd
please add the following line to your ~/.bashrc file
export LD_LIBRARY_PATH=/home/apps/intel/cmkl/9.1.021/lib/em64t:$LD_LIBRARY_PATH
AMBER 10
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.
(PyRosetta v2.011 is also installed)
Both below compiled with /share/apps/python/2.6.1/bin/python …
Please read the license at /share/apps/rosetta/LICENSE-3.0
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.
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.
EMT64 x86_64 version (for mw256[fd], mw128, tinymem)
g16
)EMT64 x86_64 version (for hp12)
export gdvroot="/share/apps/gaussian/gdvh11" . $gdvroot/gdv/bsd/gdv.profile
EMT64 x86_64 version (for swallowtail/petaltail)
g09
)AMD64 x86_64 version (for sharptail)
g09
)AMD64 x86_64 version (for sharptail)
g09
)AMD64 & EMT64 x86_64 version (for both swallowtail/petaltail and sharptail clusters)
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 . $g09root/g09/bsd/g09.profile
DOCUMENTATION
Note: in order to use this application you must be a member of group gaussian
. Please send request to the administrator.
Details about the Gaussian installation and how to run Gaussian jobs on the cluster can be found at this Link. Please read that page.
You will need to add the bin/ and lib/ directories to your PATH and LD_LIBRABY_PATH env parameters (example son this page)
For CentOS6.x (mw256[fd] queues), compiled with cmake/gcc
For RHEL5.x and CentOS5.x (hp12 queue), compiled with ICC/ifort
autodock4, autogrid4
)Note. Requires Openbabel. You need to add the following lines to your ~/.bashrc file or program.
export PATH=/home/apps/autodock:/home/apps/openbabel/2.1.1/bin:$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:$LD_LIBRARY_PATH
Note. The perl plugin will not compile. Have a message to the list.
— Meij, Henk 2008/01/25 15:39
export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib64:$LD_LIBRARY_PATH
For v1.4.3/v1.4.4 you will have to set:
. /share/apps/intel/composerxe/bin/iccvars.sh intel64 . /share/apps/intel/composerxe/bin/ifortvars.sh intel64 #also change (not sure it matters), LD_LIBRARY_PATH is modified by above scripts export MKL_HOME=/share/apps/intel/composerxe/mkl
Warning end-of-life, please use OpenMPI
Those are pretty old i suggest you do not use them.
Note: the is the mpich MPI suite of libraries that came with OCS 4.1.1 (swallowtail). In case users compiled programs against these libraries. Not supported anymore in OCS 5.1. Suggest using the latest OpenMPI flavor.
Versions are installed with the most recent linked into users' environments via /share/apps/bin. JAVAHOME points to /home/apps/java/java
which is the latest version. To set another flavor as your default java, here is an example:
export JAVAHOME=/home/apps/j2sdk1.4.2_17/bin:$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
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
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
blcr_soft
can be checkpointed— 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
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:$PATH
v 2.7.2 also contains pyodbc which relies on unixODBC and a mysql connector, consult section unixODBC.
v. 2.7.2 also contains
export PYTHONHOME=/home/apps/python/2.7.2 export PYTHONPATH=/home/apps/python/2.7.2/site-packages export PATH=$PYTHONHOME/bin:$PATH
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.
For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, look for samples on this page …
wget ftp://ftp.nluug.nl/mirror/languages/gcc/releases/gcc-9.2.0/gcc-9.2.0.tar.gz tar zxvf gcc-9.2.0.tar.gz cd gcc-9.2.0 ./contrib/download_prerequisites ./configure --prefix=/share/apps/CENTOS6/gcc/9.2.0 --disable-libgomp --disable-multilib make make install
Note: GMP, MPFR and MPC build into GCC. There are also standalone packges.
[hmeij@petaltail gcc]$ 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 $LD_LIBRARY_PATH, look for samples on this page …
Note: Used the gcc-build approach so you will not need references to GMP, MPFR and MPC using GCC.
Note: Used the gcc-build approach so you will not need references to GMP, MPFR and MPC using GCC.
UPDATE, 2016 parallel studio cluster edition installed
UPDATE, 3 years later, we bought a new version, things change
/share/apps/bin
Note:
Details about the Matlab configuration/installation and how to run Matlab jobs on the cluster can be found at this Link. Please read that page, the distributed and parallel job submissions are quite different from what we are used to on our matlab host “rintintin”.
export PATH=/share/apps/stata/15:$PATH