% setenv DVHOST bh0.phas.ubc.caFirst ensure that the CVSROOT and CVS_RSH environment variables have been set as follows
setenv CVSROOT ':ext:email@example.com:/home/cvs'(it is recommended that you insert the above in ~/.cshrc or ~/.cshrc.user).
setenv CVS_RSH '/usr/bin/ssh'
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/waveOnce the check-out is complete, change to the pamr directory and build the distribution: note that the source command sets some environment variables needed for proper compilation of the software.
% cd pamr
% source ~matt/scripts/soINTEL-mpi-orc
CC = /global/software/openmpi-1.4.3/intel//bin/mpicc
LDFLAGS = -O3 ...
% configure --prefix=`pwd`
checking for gcc... /global/software/openmpi-1.4.3/intel//bin/mpicc
checking for C compiler default output file name... a.out
. . config.status: creating w/examples/wave/Makefile
config.status: creating w/examples/nbs/Makefile
config.status: creating w/doc/Makefile
for f in src amrd doc test examples/wave examples/nbs w; do \
(cd $f; make install) \
sdftodv *sdf done
Made all ... no installation
make: Leaving directory `/global/home/matt/tmp/pamr/w/examples/nbs'
make: Leaving directory `/global/home/matt/tmp/pamr/w'
Now change to the examples/wave directory---it should contain an executable, wave
% cd examples/wave % ls -l wave
-rwxr-xr-x 1 matt matt 858605 Jun 13 10:40 wave*
Change to the run_2d subdirectory
% cd run_2dCopy an appropriate PBS batch submission file for the example, and submit the job---which uses 8 processors---to the batch queue using qsub
% cp ~matt/templates/pamr-wave.pbs . % qsub pamr-wave.pbsWait for the batch job to finish: you can use qstat -u $LOGNAME command to monitor the status of your job, but you can tell when the job has completed by the appearance of the standard output and standard error files associated with the run. These will have names of the form pamr-wave.o[Job id] and pamr-wave.e[Job id] where [Job id] is the numeric part of the Job id which is returned by the qsub command.
% cd run_2d % ls *sdf
wave_2d_L0_phi_tl2_0.sdf wave_2d_L0_phi_tl2_3.sdf wave_2d_L0_phi_tl2_6.sdf
wave_2d_L0_phi_tl2_1.sdf wave_2d_L0_phi_tl2_4.sdf wave_2d_L0_phi_tl2_7.sdf
Send all of these to DV using sdftodv:
% sdftodv *sdfThen select Merge -> All Registers in DV, enable AMR in the Options panel, and visualize the results.