Compiling and running the PAMR wave example on vnfe4

NOTE: This build uses the Intel compilers, and the Myrinet OpenMPI/GM MPI library, which is the recommended practice at the current time (this is a change from pre-August 2008, when use of the PGI compilers and MPICH was recommended).

It is also assumed that you have DV running on your local workstation, and that, in your vnfe4 shell, you have set DVHOST to the name of said workstation.

First ensure that the CVSROOT and CVS_RSH environment variables have been set 

setenv CVSROOT ':ext:cvs@vnfe4.physics.ubc.ca:/home2/cvs'
setenv CVS_RSH '/usr/bin/ssh'
(it is recommended that you insert the above in your ~/.cshrc).

Now cd to some convenient working directory and check out the pamr distribution 

% cvs co pamr
cvs server: Updating pamr
U pamr/.laliases
U pamr/KNOWN_ISSUES
       .
       .
       .
U pamr/test/Makefile.in
U pamr/test/test1.c
cvs server: Updating pamr/wave

Once the check-out is complete, change to the pamr directory, and build the distribution.  

Note that parts of the package are still under development, so you can currently expect 
to see a lot of error messages which you can safely ignore.

% cd pamr
% source ~matt/scripts/soINTEL-myr-ompi
% configure --prefix=`pwd`
creating cache ./config.cache
checking for Unix flavour... LINUX
checking for gcc... 
       .
       .
creating amrd/Makefile
creating examples/wave/Makefile
creating doc/Makefile
% make
echo; echo "Making in src test amrd examples/wave doc"

Making in src test amrd examples/wave doc
for f in src test amrd examples/wave doc; do \
       .
       .
       .
ls -lt Wiley_chapter.ps
-rw-r--r--    1 matt     choptuik    11844 Aug 15 14:51 Wiley_chapter.ps
make[1]: Leaving directory ...
% cd examples/wave
% cp ~matt/templates/pamr-wave-myr-openmpi.pbs .
% qsub pamr-wave-myr-openmpi.pbs
Wait for batch job to finish. 
% cd run_2d
% ls *sdf
wave_2d_L0_phi_tl2_0.sdf  wave_2d_L0_phi_tl2_2.sdf
wave_2d_L0_phi_tl2_1.sdf  wave_2d_L0_phi_tl2_3.sdf
% sdftodv *sdf
Then select Merge All Registers in DV, enable AMR in the Options panel, and visualize the results.
Maintained by choptuik@physics.ubc.ca. Supported by CIAR, CFI and NSERC