[CIG-LONG] new install

[Matty Mookerjee]

Hello all,

I finally got Gale to compile.

Both Walter's and Zurab's help was invaluable.

I do think that a big part of my problem was that Petsc had been configured and reconfigure and recompiled so many times that there were "ghosts" of old version.  It seemed to be pretty helpful to just delete the whole folder and start fresh.

Zurab wrote up this whole procedure which, after a few tweeks, worked for my computer.  I hope it's helpful to others:

Let's start with building from scratch.
1. download and extract petsc
$ cd ~/Downloads
$ wget -c http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.2-p7.tar.gz
$ tar xfv petsc-3.2-p7.tar.gz
$ cd  petsc-3.2-p7/

2. configure petsc
$ ./configure --prefix=/usr/local --without-x
$ make PETSC_DIR=/home/matty/Downloads/petsc-3.2-p7 PETSC_ARCH=arch-linux2-c-debug all
$ sudo make PETSC_DIR=/home/matty/Downloads/petsc-3.2-p7 PETSC_ARCH=arch-linux2-c-debug install
$ make PETSC_DIR=/usr/local test

at this point if installation was successful you will see this message
	C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process
	C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes
	Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process
	Completed test examples

this means that you have petsc installed with locally available openmpi and lapack, blas libraries. 

3. now let's install Gale 
$ cd ~/Downloads
$ wget -c http://geodynamics.org/cig/software/gale/Gale-2_0_1.tgz
$ tar xfv Gale-2_0_1.tgz
$ cd Gale-2_0_1

4. configure Gale
$ ./configure.sh 

if successful, check the output of config.cfg

$ cat config.cfg | grep LIBS
LIBS = ['petsc', 'hdf5', 'xml2']

you will see that LIBS variable does not contain Lapack and BLAS libraries. This is bug in Gale configuration script and 
fastest way to fix it is to add libraries manually. 

replace  LIBS = ['petsc', 'hdf5', 'xml2']
with 
LIBS = ['petsc', 'hdf5', 'xml2', 'lapack', 'blas']

5. Build Gale
$ ./scons

and you should have everything working.
___________________________________________

Thanks again everyone for all of your help.

Matty

-----Original Message-----
From: cig-long-bounces at geodynamics.org [mailto:cig-long-bounces at geodynamics.org] On Behalf Of Walter Landry
Sent: Monday, February 04, 2013 8:58 PM
To: cig-long at geodynamics.org
Subject: Re: [CIG-LONG] new install

Matty Mookerjee <matty.mookerjee at sonoma.edu> wrote:
> Walter,
> 
> That seems entirely possible considering through this process I have 
> compiled petsc several/many times along with and without the two main 
> dependencies.
> 
> I certainly can delete the folder that had Petsc installed in it, but 
> will that completely remove it?  I suspect there is a more complete 
> way to uninstall it, but without using Synamptic (which doesn't 
> recognize this version of Petsc) I don't know the best way to 
> completely uninstall.

That should do it.  There is nothing in your path that is picking up a different MPI implementation.

Cheers,
Walter Landry
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