Installing Overture on a Freshly Installed Ubuntu


Overture is part of Advance CompuTational Software (ACTS) collections, a set of tools mainly funded by Department of Energy (DOE) to make it easier for the end users to write high-performance scientific applications. If you haven’t visited their website; perhaps it is time now to do it (click here).

http://acts.nersc.gov/

Overture focuses on providing a set of object-oriented tools that are particularly useful in Computational Fluid Dynamics (CFD) and combustion problems. Particularly if you are interested to solve these problems in complex domains and perhaps moving geometry, Overture can be quite handy. (click here).

http://acts.nersc.gov/overture/#Introduction

There exists an instruction on how to install Overture on linux and Mac systems. However, depending on your system configuration, you might miss a few prerequisite packages that are necessary to compile Overture or Overture prerequisites.

This post explains how to install Overture on a newly installed Ubuntu 10.04 (fresh out of the box). I personally tested the procedure twice (so it should work). I’ve tried to document all the steps that I took to successfully install Overture and CG. So, I am hoping that I have not missed any steps here in this post. The start point is that you have just finished installing Ubuntu 10.04 LTS and you want to proceed with Overture installations. here are the steps.

Upgrade: First, upgrade everything, Ubuntu will suggest that automatically on the first boot.

Prepare the compilers: Now, you need to prepare your system to compile different packages. A fresh install of Ubuntu contains gcc but not other required compilers. (well, it has some other compilers too). So, the first step is to  prepare your system to configure, make and build packages. Here are the packages that you need.

  • build-essential
  • manpages-dev
  • gfortran
  • autoconf
  • automake
  • mpich2 (for parallel processing, this gives you mpiXXX compilers)

You can either install them on a command line by issueing

sudo apt-get install PackageName

or use the Ubuntu GUI Synaptic Package Manager to install them. Either case is fine. If you are asked to install some extra packages as the prerequisite, well, just allow the installer to do it. I am not listing those packages here.

CSH and/or TCSH: There are some scripts in Overture that requires csh or tcsh. If you want to use those scripts you also need to install these two shell too (using apt-get or the GUI one).

OpenMOTIF: Overture requires MOTIF. You can either follow the instruction on overture website, or even simpler than that you can just use apt-get to install:

  • libmotif3
  • libmotif3-dev

That will take care of OpenMotif pretty much.

OpenGL and other required packages: Now you have to take care of OpenGL. Ubuntu apparently comes with OpenGL already installed; however, what’s available is not enough to compile packages that depend on OpenGL. Also, Overture make use of some X11 packages that you need to install. Well, for various part of the code (overture or overture prerequisites) you need all of the following packages installed:

  • libgl1-mesa-dev
  • libglu1-xorg
  • libglu1-xorg-dev
  • libglut3
  • libglut3-dev
  • x11proto-gl-dev
  • x11proto-print-dev
  • libjpeg62-dev
  • libzip-dev
  • libperl-dev
  • libXpm-dev
  • libXp-dev
  • libxmu-dev
  • libxi-dev

That was a long list. I know. But they are all needed. (and the packages that they are depending, I am not listing them).

Installing HDF5

Before installing HDF5 you need to make a symbolic link to “make”, calling it “gmake”. The easiest way is to just type “which make” and wherever the make is (most possibly in /usr/bin) make a symbolic link to make called gmake by issueing:

sudo ln -s make gmake

Now you are ready to install HDF5. The latest version of HDF5 as of this writing is 1.8.8 and you can obtain it on:

http://www.hdfgroup.org/HDF5/

The link on overture installation instruction didn’t work for me. So, obtained the source codes for HDF5 from the above link. Just follow the instruction that comes with HDF5 and you should be good to go. Here are the steps:

  • unzip the downloaded HDF5 package
  • type ./configure –prefix=$INSTALLDIR
  • make
  • make check (optional but I recommend it)
  • make install
  • make check-install (optional but I recommend it)

INSTALLDIR tells the configure where to install HDF5. I chose to install HDF5 in /usr/local/hdf5. When you are installing a package in a directory where needs a root access, instead of using sudo I have found it quite easier to first make the folder by issueing “sudo mkdir dirname” and then using “sudo chown username:usergroup dirname” give myself the permission to write in the folder. Once I am done with the installation I just revert back the ownership by issuing “sudo chown root:root dirname”. Well, you might find this approach easier like me.

Installing A++:

Now it is time to install A++. Just follow the instruction given on Overture website (click here). It should work. I didn’t installed P++. So, I can’t give you any instruction on that.

Installing LAPACK:

Now you need to install BLAS and LAPACK. The latest version of LAPACK as if this writing is 3.4.0, that can be downloaded from:

http://www.netlib.org/lapack/#_lapack_version_3_4_0_2

Unpack lapack package and change your folder. Inside unpacked lapack package folder type:

cp make.inc.example make.inc

and then

make blaslib lapacklib tmglib

Then copy “liblapack.a”, “librefblas.a”, and “libtmglib.a” to a location that you want them to be. I chosed to put them in /usr/local/lapack/lib. I also dubplicated “librefblas.a” to a file called “libblas.a”. Apparently that’s what most packages look for.

Installing PETSC:

Now it is time to install PETSC. PETSC is optional, but I decided to install it. Download PETSC here. The version I downloaded was petsc-2.3.2-p10. Here is how to install petsc

  • Unpack the package
  • cd to the petsc unpacked package
  • export PETSC_DIR=`pwd`
  • ./config/configure.py -with-debugging=0 -with-fortran=0 -with-matlab=0 -with-mpi=0 –with-shared=1 -with-dynamic=1 –prefix=$PETSCINSTALLDIR –download-c-blas-lapack=1
  • export PETSC_ARCH=”The architecture suggested at the end of configure”
  • make all
  • make install
  • make test (optional but I recommend it)

Make sure you have a write permission on PETSCINSTALLDIR. You can also tell petsc configuration where your blas and lapack libraries are; instead of letting PETSC to download it again.

Installing Overture:

Now you must be ready to install Overture. Just follow the instruction on overture website (click here). The installation instruction should work.

Some note on defenv: If you have followed the same instruction as here you should set XLIBS, MOTIF and OpenGL to /usr. HDF and APlusPlus, LAPACK, Overture, CG, and CGBUILDERPREFIX depends on where you have installed those packages or you want to install Overture and CG. You don’t need to touch anything else in defenv. However, I decided to make everything into bash, so I duplicated defenv to defenv_bash and changed the file accordingly.

After compiling Overture, if you run check.p it will fail. But don’t panic. All you need to do is to issue:

export PATH=./:$PATH

Your installation is fine, but check.p requires ./ to be in the path.

Now it is time to install CG. Before compiling CG you need to edit one of its file. Edit CGDIR/sm/src/getRayleighSpeed.C and change the printf to cout and make the necessary changes for that. Otherwise it will fail to compile. Now just follow the instruction on overture website to compile CG (click here).

Now you can enjoy Overture and CG.

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4 Responses to Installing Overture on a Freshly Installed Ubuntu

  1. djps says:

    Any idea how to install this on ubuntu 11.10? The files listed for the installation of OpenGL aren’t all available for my version. Was this on a 32 or 64bit machine? thanks

  2. Chris says:

    Do you recall the versions used? (compilers, HDF5, etc)

    Thanks

    • mabouali says:

      Very good question. And I am afraid that I do not recall the version for all of the packages. The version for HDF5 was 1.8.8. LAPACK was 3.4.0. PETSC was petsc-2.3.2-p10. Well, these were on the document already and I don’t recall the version for other packages.

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