Installation suggestions for Cactus WaveToy and required software
contributed by
Wm. Robert Johnston, Jose D. Zamora and Jorge A. Ramos Oliveira
with the exceptional guidance of
Dr. Carlos Lousto, Dr. Manuela Campanelli, Dr. Thomas Radke
Note: These directions are not authoritative
by any means--consult the original sources!
Cactus is a software package designed for scientific computing on
parallel platforms. The package includes individual modular "thorn"
programs for specific applications (computation, output, etc.) run
through a generic core "flesh" program. WaveToy is a demonstration of
Cactus written by the Cactus team. It implements a simple simulation
of wave equations. These installation steps deal with this program.
1. Learn about Cactus
2. Install the Intel C++ and FORTRAN compilers:
The Intel C++ and FORTRAN compilers are required
for most Cactus applications, so these must be installed if not on the platform
already. Both are available in unsupported free versions for LINUX platforms
from the Intel website (
http://www.intel.com
). The license agreement and limitations are found there also. Links
for downloading both compilers are at this page:
with the non-commercial unsupported software for
Linux being the desired choice. In each case, you must complete a registration
form including an e-mail address before downloading. An e-mail will be sent
to this address with an attached license file. Save these attached files.
Put the downloaded files, which are tarred (*.tar) each in a separate directory
and untar them:
tar -xvf (filename).tar
Get into root for the installation:
su
(and enter password at prompt) After untarring there
will be an install file in the directory; execute this:
./install
select install the compiler and use the default answers
to the questions. As directed by the e-mail, the license files must be
moved to the license directory:
mv (licensefile) /opt/intel/licenses/
after which you can exit root
exit
You will need to alter a configuration file to specify
the path to the compilers. The following should be added to the .bash_profile
file (this file is probably in your home directory; there may be additional
files with this name that do not need to be changed):
######## Intel compilers ########
export IA32ROOT=/opt/intel/compiler60/ia32
export PATH=${PATH}:${IA32ROOT}/bin
export LD_LIBRARY_PATH=${IA32ROOT}/lib
export INTEL_FLEXLM_LICENSE=/opt/intel/licenses
export PATH=${PATH}:/opt/intel/compiler60/ia32/bin/
###LAM ssh protocol 1 ###
export LAMRSH="ssh -1"export
You may test each compiler with a simple "hello world" program. For those not familiar with one or another of these languages, an example for C++ is:
#include <stdio.h>
main()
{
printf("hello world");
return 0;
}
and an example for FORTRAN is:
PROGRAM hello
WRITE (*,*) 'hello world'
STOP
END
Note that each line must begin with six blank spaces for some FORTRAN versions. Consult a textbook or reference source for details on these languages. To compile these test programs, the following commands will work if you have successfully specified the paths:
ifc fortest.f
icc ctest.c
where fortest.f and ctest.c are the files for the FORTRAN and C++ test programs, respectively. Each command will generate a compiled version a.out (which will overwrite any existing a.out file!) To run this, enter:
./a.out
which should in each case display
hello world
An error message on compile complaining that ifc or icc is unknown may indicate that the path is not specified. The commands
/opt/intel/compiler60/ia32/ifc fortest.f
/opt/intel/compiler60/ia32/icc ctest.c
modified for the appropriate location will override
the default location (from the .bash_profile file) and compile each test
program.
3. Install HDF5
If HDF5 is not on your platform, various versions
exist. These instructions are based on starting from a tarred gzipped copy
of hdf5-1.4.0 which can be found
here
. (Alternately, you can go to the HDF Group of the National Center for
Supercomputing Applications and download the current version, hdf5-1.4.3,
from
http://hdf.ncsa.uiuc.edu/register5.html
although it is not guaranteed Cactus will function at compile time.)
Once you have the file, the process requires you to be in root (as above).
Move the file to the /usr/local/ directory:
mv hdf5-1.4.0-stream.tar.gz /usr/local/
To untar and unzip this file:
tar -xzf hdf5-1.4.0-stream.tar.gz
This will create hdf5-1.4.0 plus various directories.
Create a link to hdf5-1.4.0:
ln -s hdf5-1.4.0/ hdf5
cd /usr/local/bin/
ln -s
/usr/local/hdf5/bin/* .
Note that the last command has a point at its end.
This means link everything in the directory /usr/local/hdf5/bin to the
actual directory, namely /usr/local/bin.
4. Check other required programs
Cactus also requires Perl and LAM, both standard
on Linux installations. The standard C and FORTRAN compilers may also be
used by some thorn arrangements. If needed, Perl can be obtained from
http://www.perl.org/
.
5. Download Cactus
perl GetCactus WaveDemo.th
and use the default answers. This creates a Cactus
directory and downloads the thorns specified in the above thornlist. Move
the files WaveDemo.par and WaveDemo.th to the Cactus main directory:
mv WaveDemo.par Cactus/
mv WaveDemo.th Cactus/
cd Cactus/
6. Configure and Compile
The easiest way to specify configurations for the
compilation is to use a configuration file. Here is an example:
#WDoptions.config file--configuration options for WaveDemo
#using the Intel compilers
MPI=LAM
CPP=<path>/Cactus/lib/sbin/cpp.pl #needed to compile FORTRAN code
CC=icc
CXX=icc
F77=ifc
F90=ifc
F77_OPTIMISE_FLAGS=-O0
F90_OPTIMISE_FLAGS=-O0
HDF5=yes
HDF5_DIR=/usr/local/hdf5
PTHREADS=yes
SILENT=no
LDFLAGS=-W1,-rpath,/usr/local/lib
#LDFLAGS=-static
LAM_DIR=/etc/
Where <path> is the path needed to specify the location
of the cpp.pl file. This line may be optional. It specifies to use the cactus preprocessor. This
setting is useful when you need to compile Fortran source code.
Some aspects will be specific to your system. In
particular, the HDF5_DIR and LAM_DIR must be the directory locations for
HDF5 and LAM in your computer. Note that the second LDFLAGS statement is
commented out; these are two alternate settings suggested by the Cactus team.
If you get errors regarding MPI/LAM when running, experiment with interchanging
these. The arguments "icc" and "ifc" specify the Intel C and FORTRAN compilers,
respectively; these can be set to respective system compilers for debugging.
To create the configuration for compiling, enter in Cactus main directory
this:
gmake WaveDemo-config THORNLIST=WaveDemo.th options=*.config
where *.config is the configuration file name you
are using, in this example,WDoptions.config. The command gmake has to be
executed in the directory containing the Makefile file of Cactus, for this
is why you have to be in the Cactus main directory. If this step is successful,
the end of the output will tell you to use the following command to compile:
gmake WaveDemo
This should result in an executable file,
exe/cactus_WaveDemo.
If any errors occur, try executing:
gmake checkout
and manually download the required thorns. LAM must
be implemented, which can be done with the command
lamboot -v (lam_machines)
where lam_machines is a file simply containing the
name of the machine(s) being used. Ask your system administrator for these
names. Short of attempting to run WaveDemo, two means of checking your
results are
gmake checkout
gmake WaveDemo-testsuite
which will perform some checks of the thorns,
arrangements,
etc., you have installed. Some common problems encountered during compiling
are discussed on the Cactus FAQs list and in the Cactus users mail group.
Some I have encountered:
- C and/or FORTRAN compiler can?t produce executables: the path for
the icc and/or ifc compilers is incorrectly specified. Check the path in
the .bash_profile file discussed in step 1.
- hdf5 libraries can?t be located: One or another of the LDFLAGS
settings in the above configuration file should address this. If not, see
Cactus FAQs #27 and 28 for additional information.
- "It seems that [at least] one of processes that was started with
mpirun did not invoke MPI_INIT before quitting": Check that LAM is enabled
using the lamboot -v command referred to above or see the Cactus FAQs.
7. Run Cactus WaveToy Demo
To run on a single platform, enter
./exe/cactus_WaveDemo WaveDemo.par
or to simulate running in parallel, enter
mpirun -np X ./exe/cactus_WaveDemo WaveDemo.par
where X is an integer number representing the number
of machines you want to simulate. You want X to be 2, for a number greater
than 3 induces a very large overhead and a waist of CPU cycles, which means
your application will run very slow. An example of the expected screen
output is on the Cactus WaveToy page. Additional output files are generated
and placed in the WaveDemo subdirectory.
8. Installing IsoView, OpenDx, XGraph
These visualization tools are here for some reason.
IsoView, for example, is used to view a stream of isosurfaces created by
the thorn CactusPUGHIO/IsoSurfacer. This can even be done from a remote
machine. OpenDX is a nice tool for viewing 3-D surfaces from all angles
possible, just play with it so you can see what can it do. XGraph converts
data files with different formats to create 1-D plots with animation, zooming
and more.
8.1 Installing OpenMotif
Motif is required by OpenDx and other programs. To
download it go to:
http://www.opengroup.org/openmotif/downloads.html
The page is going to ask you to fill a registration form, and then continue
to download. Click on "Mainsite" (other mirrors will work just fine), then
click on the folder "R2.1.30" and then on "Tars". Create a directory called
Viztools on your home directory and another directory called MotifMasterdir
in it. Download the file openmotif.2.1.30.tar.gz in this final directory.
Untar the file as root:
tar -xzf openmotif.2.1.30.tar.gz
Create a directory in Viztools:
mkdir MotifBuilddir
Create a symbolic link between MotifMasterdir and
MotifBuilddir:
lndir ../MotifMasterdir ../MotifBuilddir
note that you have to put the absolute path to the
file. Add the following to the .bash_profile file:
PATH=$PATH:$HOME/Viztools/MotifBuilddir.
Construct the necessary links for construction as follows:
cd MotifBuilddir/motif
mkdir -p imports/x11
cd imports/x11
ln -s <abs_path_to_X11_bin_dir> bin
ln -s <abs_path_to_X11_includes_dir> include
ln -s <abs_path_to_X11_libs_dir> libs
Set your current directory as follows:
cd MotifBuilddir/motif
type and execute:
make World >& world.log
make install >&
install .log
Wait for a few minutes... and exit root.
8.2 Installing IsoView
tar -xzf IsoView_linux.tar.gz
Add to your path the following:
PATH=$PATH:HOME/Viztools.
Reboot and re-enter.
8.3 Installing OpenDx
Go to OpenDx's homepage:
http://www.opendx.org/dlBinary.html
. Fill out the form. Store the desired rpm (*.rpm) belonging to your
Operating system in the subdirectory Viztools. In this case we worked on
linux RedHat 7.1 so we downloaded opendx-4.2.0-1.i386.rpm. Enter as root:
rpm -i opendx-4.2.0-1.i386.rpm
Exit root.
OpenDX needs an extra module in order to be able to read the files (in HDF5 format) generated by Cactus. You can download this module from Cactus web site
.
NOTE:
There is a bug in OpenDX 4.2 that does not allow to build the ImportHDF5 modules. Edit $DX_DIR/lib_linux/arch.mak, replacing '@DX_RTL_LDFLAGS@' by '--shared', and things should work smoothly.
8.4 Installing XGraph
tar -xzf xgraph_linus_binary.tar.gz
Add to your path:
PATH=$PATH:$HOME/Viztools/xgraph.
Log out and re-enter.
