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Installation Notes for RHEL 7.6 Server

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madscatt edited this page Mar 22, 2019 · 11 revisions

Installation notes for RHEL 7.6 Server

This example used a new installation on a machine without running any system updates. Versions of installed software are listed below. Using other versions of the required software is not guaranteed to work.

Note that this example begins from a RHEL 7.6 Server with many RPMS already installed as listed on this file initial_installed_rpms.txt

The installation directory for the dependencies in this installation example will be

/share/apps/local

The installation directory can be changed by replacing /share/apps/local with your desired location. Note that one must also edit the trunk/sassie/util/sasconfig.py file prior to running the final sassie installation script as discussed in the sassie configuration page.

Commands to be typed at the command line are shown in "code blocks" with the ">" symbol as shown below:

>

  1. Download NAMD http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD

    Version 2.12 (2016-12-22) Platforms: Linux-x86_64-multicore (64-bit Intel/AMD single node)

  1. Make a directory to install dependencies and components:

> sudo mkdir -p /share/apps/local/bin

  1. Move the compressed NAMD archive to /share/apps/local/bin

> sudo mv ~/Downloads/NAMD_2.12_Linux-x86_64-multicore.tar.gz /share/apps/local/bin

  1. Change to the /share/apps/local/bin/ directory and compress the NAMD archive and create a soft-link

> cd /share/apps/local/bin

> sudo tar -xvzf NAMD_2.12_Linux-x86_64-multicore.tar.gz

> sudo ln -s NAMD_2.12_Linux-x86_64-multicore namd

Thus, in our example, to run NAMD from within SASSIE one will have to enter the installation path (/share/apps/local/bin) into the trunk/sassie/util/sasconfig.py file as discussed in the sassie configuration page.

  1. Download CHARMM lite, uncompress and change to the directory

    CHARMM install scripts require csh/tcsh

> tool/NewCharmmTree c40b1_gnu

Compile CHARMM

> ./install.com gnu gfortran

Copy and rename the compiled binary to your installation bin directory

> sudo cp exec/gnu/charmm /share/apps/local/bin/charmm.exe

  1. Download Anaconda Python. Version 5.3.0 Python 2.7 64-bit.

    https://repo.anaconda.com/archive/

> sudo bash Anaconda2-5.3.0-Linux-x86_64.sh

NOTE: there has been a report that Anaconda2-5.3.1 has a problem compiling fortran extensions with the fortran in RHEL 7.5

Accept the legal terms and then change the default installation location to

>>> /share/apps/local/anaconda2

  1. Install additional Python modules

> sudo /share/apps/local/anaconda2/bin/conda install -c auto mocker=1.1.1

> sudo /share/apps/local/anaconda2/bin/conda install -c conda-forge weave

  1. Install sasmol.

git clone https://github.com/madscatt/sasmol.git

edit sasmol/src/python/sasconfig.py to point at your installation path

(in our case we are installing in /share/apps/local ...)

installation_path = '/share/apps/local' installation_bin_path = '/share/apps/local/bin'

> cd sasmol

> sudo /share/apps/local/anaconda2/bin/python setup.py install

  1. Follow pre-installation instructions from NVIDIA

See the NVIDIA website for instructions regarding the drivers and testing your installation prior to proceeding to the next step ([https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html] (https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html). The following worked in our case.

Make sure your copy of RHEL is registered to grant you access to RPMS etc.

> sudo subscription-manager repos --enable rhel-server-rhscl-7-rpms

> sudo yum install devtoolset-7

(note that using the "run" installer did not work)

To use the Nvidia RPM one must first enable EPEL repo and install liba-vdapu and dkms

> wget http://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm

> sudo rpm -ivh epel-release-latest-7.noarch.rpml

> sudo yum install libva-vdpau-driver dkms

Download the following RPM from Nvidia and install (via CUDA Toolkit 10.0 Archive)

> sudo rpm -iv cuda-repo-rhel7-10-0-local-10.0.130-410.48-1.0-1.x86_64.rpm

> sudo yum install cuda

(note that this method of installation places the cuda tree into /usr/local/cuda-10.0)

> sudo ln -s /usr/local/cuda-10.0 /share/apps/local/cuda

  1. Create a file at /etc/modprobe.d/blacklist-nouveau.conf with the following contents:

blacklist nouveau

options nouveau modeset=0

Regenerate the kernel initramfs:

> sudo dracut --force

  1. Add environment labels to .bashrc

export PATH=/share/apps/local/anaconda2/bin:$PATH

export PATH=/share/apps/local/cuda-10.0/bin:$PATH

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/local/cuda-10.0/lib64

Note that these additions to .bashrc are done both to the user and root $HOME directories

NOTE: if you use a different CUDA version then the cuda-10.0 in the commands above should be edited to point to the version you installed. We have used cuda-8.0 successfully on other installations.

  1. Install pandoc and create symbolic link

https://pandoc.org/installing.html

sudo yum install pandoc

> sudo ln -s /share/apps/local/anaconda2/bin/pandoc /share/apps/local/bin/pandoc

  1. Download ZAZZIE_1.5 from GitHub (this repository)

> git clone https://github.com/madscatt/zazzie_1.5.git

  1. Edit sasconfig.py file for installation parameters

The details of this procedure is discussed on the following sassie configuration page

  1. Run sassie installer

> cd zazzie_1.5/trunk

> sudo /share/apps/local/anaconda2/bin/python installer.py

  1. Install GenApp

General installation instructions are found at http://genapp.rocks/wiki/wiki/install

Once completed one should go through the "after install" steps to verify that all the necessary web- and application services are running correctly.

  1. Install sassie_1_5 web-application

This section goes over the steps to enable the GenApp side of sassie-web and is based on information on the following web-page : http://genapp.rocks/wiki/wiki/install_app

NOTE, sassie_1_5 is used here instead of sassie_1.5 due to requirements of GenApp naming.

> export GENAPP=/src/genapp ; export PATH=$GENAPP/bin:$PATH

> /src/genapp/sbin/getapp.pl -gen svn sassie_1_5

With the python that is going to run sassie-web, run the following script

> cd /opt/genapp/sassie_1_5

> python prepend_python_she_bang.py

again, where "python" in the above line is the full path and python executable that sassie is installed.

Now, recompile the sassie-web application with the modified python path

> genapp.pl

to complete the installation of sassie-web.

Verify that sassie-web is running by opening a browser and

http://__HOST_IP__/sassie_1_5

(where the HOST_IP is replaced with the hostip discussed above, for instance:

http://10.211.55.13/sassie_1_5

will work for our example. Note that http://127.0.0.1/sassie_1_5 will also work but only on the machine running the server.

At this point one should go through the "quick-start" guide using the files and example inputs provided to thoroughly test your installation.

https://sassie-web.chem.utk.edu/sassie2/docs/sassie-web-quick-start/quick-start.html

Further GenApp configuration (Feedback, Messaging, Administration etc.) information is found on the GenApp page: http://genapp.rocks/wiki/wiki/install

Note:

(sassie DOCS are not yet enabled in the installation)

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