Install instructions for LIGGGHTS (OS: Red Hat 6.*)

Submitted by neven.marticnevic on Fri, 06/23/2017 - 10:17

Hi all,

Please can somebody give me instructions for successfully installation LIGGGHTS on Red Hat 6.* OS.
Currently I am working my master degree and for final simulation I need more cores. Until now I install LIGGGHTS on Ubuntu which is on VirtualBox on my PC. This was enough for learning LIGGGHTS and make simulations (1-2 seconds) with 200 000 particles. But for final simulation I will have 2 million to 6 million particles. So I contact my professor and he offered me cluster which is on my college (240 cores - http://hpc-core.um.si/wiki/index.php/Glavna_stran).

So the main problem is that I have not got any experience with installation and compiling on Red Hat, neither professors have experience with installation of LIGGGHTS until now.

So professors said that if I can get some instructions how to do that, they will help me. This will be very useful for next simulations with LIGGGHTS and next generation of students.

Thank You on any help!!!
Best regards, Neven Martinčević.
contact mail: nemartincevic@gmail.com

mschramm | Fri, 06/23/2017 - 16:41

My workstation is on RedHat 6.9
You will want to check to make sure the cluster has the needed software to compile liggghts. These should be the same for your ubuntu version (make, gzip, openmpi, ect...)
On my machine, I have modules that can load and unload different items. You may need to "load" some needed modules to compile liggghts.
As an example, when I need to recompile liggghts I have to load openmpi, and dev-toolset-4 (I dont need to load the toolset, I just like to...).
module load openmpi-1.10-x86_64 devtoolset/4

From here, you can go to src and make fedora. This is where you may want to contact the people who maintain the cluster and ask if you need anything special in the makefile.

neven.marticnevic | Sat, 06/24/2017 - 12:15

Hi mschramm,

About: "You will want to check to make sure the cluster has the needed software to compile liggghts. These should be the same for your ubuntu version (make, gzip, openmpi, ect...)"
So when I was installing LIGGGHTS on Ubuntu on my PC I follow these steps:
sudo apt-get install libvtk5-dev libeigen2-dev libopenmpi-dev g++ git-core
sudo apt-get install build-essential git
sudo apt-get install openmpi-common openmpi-bin libopenmpi-dev

##Checking installations
which mpirun
/usr/bin/mpirun comes up?
which mpic++
/usr/bin/mpic++ comes up?
mpic++ -v
gcc-Version 4.7.3 (Ubuntu/Linaro 4.7.3-1ubuntu1) comes up at the last line?

sudo apt-get install cmake
sudo apt-get install cmake-curses-gui

Then i downloaded LIGGGHTS: $ git clone git://github.com/CFDEMproject/LIGGGHTS-PUBLIC.git liggghts
And then I compiled with $ make fedora in /src directory.

So this steps will work or not?

Here is what listed in hpc core when I type commands:
which mpirun
/opt/openmpi/bin/mpirun
which mpic++
/opt/openmpi/bin/mpic++
which mpic++ -v comes up
[martincevic@hpc-core nas]$ mpic++ -v
"Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/u sr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstr ap --enable-shared --enable-threads=posix --enable-checking=release --with-syste m-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique- object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt= gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --en able-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/ja va/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tun e=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC)"

So this libraries will be enough to successfully compile program?
And how to compiled? With make fedora? Or something else...

Best regards ...Neven

mschramm | Mon, 06/26/2017 - 16:04

This should work. Make sure gzip is installed on the server as well.
Make fedora should work just fine, but you may want to contact the hpc department and describe the program to them and give them the make fedora makefile.
They may suggest some changes so the program works better on their hpc.

arnom's picture

arnom | Tue, 06/27/2017 - 15:50

Hi,

I strongly suggest that you get in touch with your HPC administrators as an installation on a cluster is usually not trivial (particularly if you have no experience yourself). We will be rewriting the installation guides rather soon (1 - 2 weeks) as they are currently a bit out of date.

What is important for your cluster is that VKT and its development files are available. I also suggest that you first try to use "make auto" instead of "make fedora" as it tries to find some stuff automatically. Please use the following guide at for compilation with "make auto": https://www.cfdem.com/media/DEM/docu/Section_start.html#making-liggghts-...

If I can help you with the installation do not hesitate to ask for further information.

Best,
Arno

DCS team member & LIGGGHTS(R) core developer

neven.marticnevic | Thu, 06/29/2017 - 17:56

Hi,

First of all many thanks to both of You!

I passed contex of these forum theme to my professors, and they will try to install it on cluster with 20 cores for now.
If this will work then they will install it on hpc cluster, as I mentioned above.

Best regards, Neven.

P.S. Arnom can You upload newest installation guides after You finished them?

arnom's picture

arnom | Wed, 07/05/2017 - 14:47

Yes those guides will be uploaded to the website with the next release (possibly Friday or early next week)

DCS team member & LIGGGHTS(R) core developer

shivagoud's picture

shivagoud | Fri, 09/15/2017 - 12:25

Sir, please provide me the link for installation procedure of LIGGGHTS on red hat 6.
I have to send the procedure to H.P.C. provider.