ASPECT INSTALLATION - UBUNTU 14.04 v3.0
Phil Heron, Durham University
Oct 2017
email: philip.j.heron@durham.ac.uk
This is the setup guide for installing ASPECT on the Ubuntu 14.04.
There are some prerequisites for this endeavour, one of them being a basic knowledge of linux commands and VI editor commands.
Below are a few links to these as a refresher or to get you up to speed.
Linux commands: https://diyhacking.com/linux-commands-for-beginners/
VI Editor commands: https://www.cs.colostate.edu/helpdocs/vi.html
For this guide, lines that start with > indicate a terminal window. Anything after the > is what is needed to type in the terminal window.
e.g.,
>
> pwd
/ddn/home/
In order to install ASPECT you need to install the numerical code deal.ii. To do this, we need to use the installer package, Candi.
Therefore, we need to install deal.ii (and it’s components trilinos and p4est) via Candi first.
STEP 1 - setting up modules
sudo apt-get install build-essential wget automake \
autoconf gfortran \
openmpi-bin openmpi-common \
libopenmpi-dev cmake subversion \
git libblas-dev liblapack-dev \
libblas3gf liblapack3gf \
libsuitesparse-dev libtool \
libboost-all-dev splint tcl \
tcl-dev environment-modules qt4-dev-tools
STEP 2 - downloading Candi
To download Candi we should set up a new folder for the installation.
> pwd
/home/
> mkdir install
> cd install
To download Candi, we can use a git command which will download the whole package into your folder.
> git clone https://github.com/dealii/candi
> cd candi
> ls
AUTHORS LICENSE README.md candi.cfg candi.sh deal.II-toolchain
STEP 3 - editing Candi setup
As candi can download a great number of packages that deal.ii can work with, we only need to download the ones that are directly relevant to ASPECT. As a result, we can can comment out the packages that we do not need (which are open cascade, PETSC, SLEPC).
In the candi folder:
> ls
AUTHORS LICENSE README.md candi.cfg candi.sh deal.II-toolchain
> vi candi.cfg
line 19 needs to be edited to:
INSTALL_PATH=/home/install/candi (or wherever the candi folder is located)
We need to edit the following from line 48, by putting a # in the first column (therefore commenting out that line).
The packages open cascade, parmetis, superlu_dist, petsc, and slepc need to be commented out:
#PACKAGES="${PACKAGES} once:opencascade"
#PACKAGES="${PACKAGES} once:parmetis"
#PACKAGES="${PACKAGES} once:superlu_dist"
PACKAGES="${PACKAGES} once:hdf5"
PACKAGES="${PACKAGES} once:p4est"
PACKAGES="${PACKAGES} once:trilinos"
#PACKAGES="${PACKAGES} once:petsc"
#PACKAGES="${PACKAGES} once:slepc"
PACKAGES="${PACKAGES} dealii"
From here we need to exit the candi.cfg file and edit the candi.sh file.
> vi candi.sh
We need to edit the path to the build directories, to point to the ddn/data folder:
PREFIX=/home/install/deal.ii-candi *or wherever you would like the code to build*
STEP 4 - running Candi
From here we can run candi.
> ./candi.sh -j<N>
(where <N> is the number of processors you have available to run the configuration and installation of deal.ii and it’s dependencies). I would recommend running -j8.
Therefore it would be:
> ./candi.sh -j8
You are asked to review the set up of candi once the installation begins. Press enter for these parts unless you notice an error. The program will make sure you have the relevant external libraries installed and then make sure the compilers are correct: c++ etc.
When using -j8 it took 40 minutes.
Build finished in 2386 seconds.
Summary of timings:
dealii-prepare: 0 s
hdf5: 161 s
p4est: 101 s
trilinos: 988 s
dealii: 1112 s
Head to the dealii build directory to test:
> cd /home/install//deal.ii-candi/tmp/build/deal.II-v8.5.1
> make test
This should run 10 tests, they all should pass
Start 1: step.debug
1/10 Test #1: step.debug ....................... Passed 30.08 sec
Start 2: step.release
2/10 Test #2: step.release ..................... Passed 27.75 sec
Start 3: affinity.debug
3/10 Test #3: affinity.debug ................... Passed 20.79 sec
Start 4: mpi.debug
4/10 Test #4: mpi.debug ........................ Passed 23.10 sec
Start 5: tbb.debug
5/10 Test #5: tbb.debug ........................ Passed 19.57 sec
Start 6: p4est.debug
6/10 Test #6: p4est.debug ...................... Passed 24.46 sec
Start 7: step-trilinos.debug
7/10 Test #7: step-trilinos.debug .............. Passed 27.25 sec
Start 8: lapack.debug
8/10 Test #8: lapack.debug ..................... Passed 19.17 sec
Start 9: umfpack.debug
9/10 Test #9: umfpack.debug .................... Passed 25.24 sec
Start 10: gsl.debug
10/10 Test #10: gsl.debug ........................ Passed 20.01 sec
100% tests passed, 0 tests failed out of 10
Total Test time (real) = 237.45 sec
Built target test
STEP 5 - building ASPECT
Wherever you would like ASPECT to be downloaded, go into the directory and acquire the development package of ASPECT by:
> git clone --recursive https://github.com/geodynamics/aspect.git
Once downloaded, we can begin to build and then configure. For the build we need to let ASPECT know where deal.ii is, and from there deal.ii is configured and linked to trilinos and p4est.
> cd aspect
> ls
AUTHORS CTestConfig.cmake VERSION cookbooks docker tests
CMakeLists.txt LICENSE benchmarks data include
CONTRIBUTING.md README.md cmake doc source
> cmake -DDEAL_II_DIR=/home/install/deal.ii-candi/tmp/build/deal.II-v8.5.1 .
Once the cmake is complete, you need to make the executable:
> make -j<N>
Again, I would recommend using a number of processors for this make, as it can take a while.
I used j8 and it took 5 minutes.
STEP 6 - testing ASPECT
Once complete, run a make test to check to see if the executable is working correct:
> cd tests
> make test
Running tests...
Test project /home/aspect/tests
Start 1: quick_mpi
1/1 Test #1: quick_mpi ........................ Passed 14.66 sec
100% tests passed, 0 tests failed out of 1
Total Test time (real) = 14.73 sec
For the whole setup, you will need the module loaded as specified at the start. If you stop this process half way through and being again, you will need to reload the modules.
STEP 7 - making the release version of ASPECT (and not debug)
> cd ../
> pwd
/home/aspect
> make release
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Phil Heron 