22July08; 07May08; 26Apr08 (Ed Bueler)

EXPLANATION OF THIS NOTE:  

I just updated a couple of computers to ubuntu 8.04.  
Partly this was to see how it worked, I rebuilt PISM from scratch, trying 
to do it just with Debian packages and without building PETSc from source. 

This time it worked, with a few minor hiccups.  

Below is what I did.  These comments should all apply to the stable0.1
source code branch as well; see https://gna.org/projects/pism.


***************** DEBIAN PACKAGES USED *******************

USING synaptic I FOUND AND INSTALLED THESE DEBIAN PACKAGES:

petsc-dev  (WHICH DEPENDS ON libpetsc2.3.3-dev; THIS PACKAGE 
            DEPENDS ON libpetsc2.3.3, libopenmpi-dev, libx11-dev,
            libblas-dev, liblapack-dev, gfortran, AND OTHERS; 
            NOTE libopenmpi-dev DEPENDS ON libopenmpi1 AND
            REPLACES openmpi-bin)

libgsl0-dev

libfftw3-dev

netcdf-bin  (I ALSO GRABBED nco AT THE SAME TIME)
 
libnetcdf-dev

g++    (WITHOUT THIS I SAW A COMPILE ERROR "gcc: error trying to exec 'cc1plus'")

subversion


***************** PISM *******************

THEN I GRABBED THE PISM DEVELOPMENT VERSION:

  svn co http://svn.gna.org/svn/pism/trunk pism-dev

(FOR stable0.1:  svn co http://svn.gna.org/svn/pism/branches/stable0.1 pism0.1 )

THEN, BASED ON THE "Installed Files" REPORTED FOR libpetsc2.3.3-dev USING
synaptic, I ADDED THE LINES

  export PETSC_DIR=/usr/lib/petscdir/2.3.3/
  export PETSC_ARCH=linux-gnu-c-opt
  export PATH=/home/bueler/pism-dev/bin/:/home/bueler/pism-dev/util/:$PATH

TO MY .bashrc.

(FOR stable0.1 it would be:
  export PATH=/home/bueler/pism0.1/bin/:/home/bueler/pism0.1/test/:$PATH
)

THEN I ENTERED pism-dev AND BUILT PISM WITHOUT ERRORS

  make

  make install


***************** RUNTIME ERROR MESSAGES FROM OPENMPI *****************

I RAN PISM AND IT WORKED BUT I GOT WARNING MESSAGES:

$ mpiexec -n 2 pismv -y 1
libibverbs: Fatal: couldn't read uverbs ABI version.
--------------------------------------------------------------------------
[0,1,0]: OpenIB on host bueler-laptop was unable to find any HCAs.
Another transport will be used instead, although this may result in 
lower performance.
--------------------------------------------------------------------------
. . .
PISMV (verification mode)
initializing Test A ...
. . .

THE USUAL TECHNIQUE, NAMELY GOOGLING THE ERROR MESSAGE, FOUND THIS COMMENT
(http://lists.alioth.debian.org/pipermail/pkg-openmpi-commits/2007-August/000044.html):

  "To get rid of the warning, you can either disable the use of the "openib" btl
   in /etc/openmpi/openmpi-mca-params.conf or pass "--mca btl ^openib" to mpirun
   or mpiexec. The configuration file contains a line to disable InfiniBand, you
   just have to comment it out."

THE WARNING MESSAGE COMES FROM THE (ASTONISHING ...  ;-) ) FACT THAT MY LAPTOP DOES
NOT HAVE AN InfiniBand CONNECTING ITS PROCESSORS TOGETHER!  IN FACT,

  mpiexec -n 2 --mca btl ^openib pismv -y 1

PRODUCES NO ERRORS.  FURTHERMORE, UNCOMMENTING THE LINE "#   btl = ^openib"
IN /etc/openmpi/openmpi-mca-params.conf PERMANENTLY REMOVED THE ERRORS SO THAT

  mpiexec -n 2 pismv -y 1

WORKED WITHOUT COMPLAINT


******************* CONCLUSION **********************

EVERYTHING IN PISM WORKS FINE NOW.  THIS WAS THE QUICKEST BUILD-FROM-SCRATCH FOR PISM 
SO FAR.


** PS **
A FINAL NOTE, INDIRECTLY CONNECTED.  THERE SEEMS TO BE NO ncview DEBIAN PACKAGE
YET.  BUT THIS SEQUENCE WORKED WITH MINIMAL PAIN: GRAB LATEST SOURCE

  ftp://cirrus.ucsd.edu/pub/ncview/ncview-1.93c.tar.gz

BASICALLY FOLLOW INSTALL INSTRUCTIONS IN TOP-LEVEL "README".  BUT ERROR ABOUT
MISSING x HEADERS ETC IS RESOLVED BY TWO THINGS, FIRST TO GET DEBIAN

  xorg-dev

PACKAGE, AND SECOND TO TELL THE ncview configure SCRIPT WHERE TO FIND x:

  ./configure --x-libraries=/usr/lib