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Installation notes for Ubuntu 18.04 LTS

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madscatt edited this page Oct 22, 2018 · 12 revisions

Installation notes for Ubuntu 18.04 LTS

This example used a new installation on a machine without running any system updates. This starts from a minimal ubuntu installation using the ubuntu-18.04.1-desktop-amd64.iso file. System / software updates were carried out before following the steps listed below.

Versions of installed software are listed below. Using other versions of the required software is not guaranteed to work.

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

> sudo apt-get install tcsh

> sudo apt-get install build-essential gfortran

> tcsh

Need to edit build/gnu/Makefile_gnu in order to compile correctly. Change the file by commenting out this line

$(error AVX-compatible CPU requires gcc version >= 4.6.0 for CHARMM compilation)

and copying this line to avoid the error

CCPP := g++ -Dgnu -DLINUX64 $(I8DUM2)$

so that the if/else condition is

17 ifeq "$(GCC_GTEQ_460)" "1"$ 18 CCPP := g++ -Dgnu -DLINUX64 $(I8DUM2) -fabi-version=0$ 19 else $ 20 FIND_AVX := $(shell fgrep avx /proc/cpuinfo 2>/dev/null | wc -l)$ 21 ifeq "$(FIND_AVX)" "0"$ 22 CCPP := g++ -Dgnu -DLINUX64 $(I8DUM2)$ 23 else$ 24 CCPP := g++ -Dgnu -DLINUX64 $(I8DUM2)$ 25 # $(error AVX-compatible CPU requires gcc version >= 4.6.0 for CHARMM compilation)$ 26 endif$ 27 endif$

`>

Setup a build

> 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

Now, exit out of the tcsh and return to the original bash shell

> exit

  1. Download Anaconda Python. Version 5.X Python 2.7 64-bit.

    https://www.anaconda.com/download

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

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 compilers and other required packages

> sudo apt-get install swig git

  1. Install CUDA Toolkit for your hardware

https://developer.nvidia.com/cuda-downloads

In this example, the Linux Ubuntu 14.04 x86_64 run file (local) was used so that the installation location could easily be provided. See the NVIDIA website for instructions regarding the drivers and testing your installation prior to proceeding to the next step.

> sudo sh cuda_10.0.130_410.48_linux.run

Install location: /share/apps/local/cuda-10.0

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

  1. Install sasmol.

> cd /share/apps/local/bin

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. 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=$PATH:/share/apps/local/cuda-10.0/lib64

  1. Install pandoc and create symbolic link

> sudo apt-get install pandoc

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

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

> cd /share/apps/local/bin

> 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

The following is based on general installation instructions found at http://genapp.rocks/wiki/wiki/install

> sudo apt-get update && sudo apt-get -y install subversion build-essential && sudo mkdir /src && sudo chmod a+rwx /src && cd /src && svn co svn://svn.genapp.rocks/svn/base/genappalpha genapp

> /src/genapp/sbin/install

This will result in the following information.

/src/genapp/etc/config.json contains global system information.
this is used to setup individual applications values.
to build a default config.json file
/src/genapp/sbin/setconfig.pl -pj
and verify the information is correct.
NB: if the machine is not publically exposed, you probably want to change the hostip and hostname, as it will 
likely report the public ip of your firewall.
You can get a full set of options listed by running /src/genapp/sbin/setconfig.pl -h
If you know the ethernet interface to run on, /src/genapp/sbin/setconfig.pl -if network-interface-id can be helpful
The -f option will force the changes to a previously set /src/genapp/etc/config.json file
The full options are listed by /src/genapp/sbin/setconfig.pl -h
You can also manually edit /src/genapp/etc/config.json

Once you are satisified that the setting are correct 
you can rerun /src/genapp/sbin/install

In our particular case running

> /src/genapp/sbin/setconfig.pl -pj

resulted in

{"os_release" : "14.04",
"https" : 0,
"hostname" : "ubuntu",
"hostip" : "10.211.55.13",
"os" : "ubuntu",
"webroot" : "/var/www/html",
"messaging" : {
"udphostip" : "127.0.0.1",
"tcphostip" : "127.0.0.1",
"wsport" : 37777,
"udpport" : 37779,
"tcpport" : 37780,
"zmqhostip" : "127.0.0.1",
"wssport" : 80,
  "zmqport" : 37778
}
}

Note that you need to make sure that these settings are appropriate for your environment.
So to continue the installation

> /src/genapp/sbin/install

This completes the general GenApp installation. 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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