From ljhwang at ucdavis.edu Wed Nov 9 13:10:31 2016
From: ljhwang at ucdavis.edu (Lorraine Hwang)
Date: Wed, 9 Nov 2016 13:10:31 -0800
Subject: [CIG-LONG] CIG Webinar: TOMRROW @ 2pm featuring Renee Gassmoeller
Message-ID: <9AB35B8D-4ABF-493C-89C8-69A7873FBAE0@ucdavis.edu>
Don’t miss a chance to learn from the expert...
Rene Gassmoeller will be delivering tomorrow’s CIG webinar Thursday November 10 @ 2pm PT talking to us about a key feature of ASPECT - particle implementation.
Intricacies of particle-in-cell methods in convection models with adaptive meshes: Using ASPECT's particle implementation
Rene Gassmoeller, CSU Fort Collins
Particle-in-cell methods have a long history in modeling of mantle convection, lithospheric deformation and crustal dynamics. However, their efficient parallel implementation and application in models - in particular combined with adaptive meshes - is involved due to the complex reassignment of particles to cells and frequent parallel communication.
In this webinar, I present the implementation of a flexible, scalable and efficient particle-in-cell method for the massively parallel finite-element code ASPECT. I discuss the complexity of the implemented algorithms, present scaling tests and discuss load-balancing strategies like balanced repartitioning for particles in adaptive meshes with their strengths and weaknesses. Additionally, I will show an application tutorial on how to convert a model with compositional fields into one using the particle advection scheme, and which consequences follow from this conversion for model runtime and accuracy.
Connect: http://uc-d.adobeconnect.com/r28i3av93ti/
Best,
-Lorraine
*****************************
Lorraine Hwang, Ph.D.
Associate Director, CIG
530.752.3656
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From david.boutelier at newcastle.edu.au Wed Nov 9 16:23:18 2016
From: david.boutelier at newcastle.edu.au (David Boutelier)
Date: Thu, 10 Nov 2016 00:23:18 +0000
Subject: [CIG-LONG] Compiling Gale 2 on Ubuntu 16.04
Message-ID:
Hi,
I am trying to compile Gale-2_0_1 on a Ubuntu 16.04 workstation to get the benefit of parallel acceleration.
I do have the libxml2 library but the configure script does not find it.
This where my libxml is:
david at CG106-3XZ3TF2:/usr/lib/x86_64-linux-gnu$ pwd
/usr/lib/x86_64-linux-gnu
david at CG106-3XZ3TF2:/usr/lib/x86_64-linux-gnu$ ls -la libxml2*
-rw-r--r-- 1 root root 2947916 Jun 4 02:57 libxml2.a
lrwxrwxrwx 1 root root 16 Jun 4 02:57 libxml2.so -> libxml2.so.2.9.3
lrwxrwxrwx 1 root root 16 Oct 21 20:37 libxml2.so.2 -> libxml2.so.2.9.3
-rw-r--r-- 1 root root 1805560 Jun 4 02:57 libxml2.so.2.9.3
So I started compiling with the argument libxml2-lib-dir like this
david at CG106-3XZ3TF2:~/Gale-2_0_1$ ./configure.sh --libxml2-lib-dir='/usr/lib/x86_64-linux-gnu'
scons: Reading SConscript files ...
Checking whether the C++ compiler worksyes
Checking for package libXML2... no
**** ERROR ****
Failed to locate required package libXML2.
Details in 'config.log'
************************************
If you require help, send the files:
config.log
config.cfg (if it exists)
to: cig-long at geodynamics.org
and this is the content of the config.log
file /home/david/Gale-2_0_1/config/config.py,line 66:
Configure(confdir = .sconf_temp)
Configuring using:
config/scons/scons.py --config=force -f SConfigure --libxml2-lib-dir=/usr/lib/x86_64-linux-gnu
file /home/david/Gale-2_0_1/config/cxx.py,line 11:
Configure(confdir = .sconf_temp)
scons: Configure: Checking whether the C++ compiler works
.sconf_temp/conftest_0.cpp <-
|
|int main()
|{
| return 0;
|}
|
g++ -o .sconf_temp/conftest_0.o -c .sconf_temp/conftest_0.cpp
scons: Configure: yes
Failed to find static or shared libraries for 'libXML2'.
Static missing: ['xml2']
Shared missing: ['xml2']
Looked in: ['/usr/lib']
Failed to find static or shared libraries for 'libXML2'.
Static missing: ['xml2']
Shared missing: ['xml2']
Looked in: ['/usr/lib']
Failed to find static or shared libraries for 'libXML2'.
Static missing: ['xml2']
Shared missing: ['xml2']
Looked in: ['/usr/lib64']
Failed to find static or shared libraries for 'libXML2'.
Static missing: ['xml2']
Shared missing: ['xml2']
Looked in: ['/usr/lib64']
Failed to find static or shared libraries for 'libXML2'.
Static missing: ['xml2']
Shared missing: ['xml2']
Looked in: ['/usr/local/lib']
Failed to find static or shared libraries for 'libXML2'.
Static missing: ['xml2']
Shared missing: ['xml2']
Looked in: ['/usr/local/lib']
Failed to find static or shared libraries for 'libXML2'.
Static missing: ['xml2']
Shared missing: ['xml2']
Looked in: ['/usr/local/lib64']
Failed to find static or shared libraries for 'libXML2'.
Static missing: ['xml2']
Shared missing: ['xml2']
Looked in: ['/usr/local/lib64']
I am perplexed. Can you guide me ? What I am missing?
Thanks
David
________________________________
DAVID BOUTELIER
School of Environmental and Life Sciences,
The University of Newcastle, University Drive, Callaghan 2304 NSW
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From jbnaliboff at ucdavis.edu Wed Nov 9 17:42:16 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Wed, 9 Nov 2016 17:42:16 -0800
Subject: [CIG-LONG] Compiling Gale 2 on Ubuntu 16.04
In-Reply-To:
References:
Message-ID:
Hi David,
Long story short, I strongly recommend not using GALE.
Gale is currently not compiling successfully on the CIG automated build
machine (ubuntu 14.04) and we officially stopped supporting it a while
ago. Without going into detail, there is a reason for this and there
are better options available.
If you are accustomed to using GALE and it is a good match for the
processes you are examining, my first recommendation is to check out
Underworld2 (http://www.underworldcode.org/).
GALE was originally based off an earlier version of Underworld, so the
transition from GALE to Underworld2 should not be too much of a hassle.
Underworld2 is also a significant improvement over GALE in terms of the
user interface and underlying code.
Depending on what kind of problem you want to examine, the CIG code
ASPECT may also be suitable. I've been testing how ASPECT does with
lithospheric deformation problems and the results so far are very
encouraging. If you would like to give ASPECT a shot, feel free to
email me independently or via this email list so we can discuss it further.
Additional 3D codes for modeling lithospheric deformation exist, but I'm
not sure if they are officially available yet. Members of the
community, please chime in with more options or suggestions.
Cheers,
John
*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis
On 11/09/2016 04:23 PM, David Boutelier wrote:
>
> Hi,
>
>
> I am trying to compile Gale-2_0_1 on a Ubuntu 16.04 workstation to get
> the benefit of parallel acceleration.
>
>
> I do have the libxml2 library but the configure script does not find it.
>
>
> This where my libxml is:
>
>
> david at CG106-3XZ3TF2:/usr/lib/x86_64-linux-gnu$ pwd
> /usr/lib/x86_64-linux-gnu
>
> david at CG106-3XZ3TF2:/usr/lib/x86_64-linux-gnu$ ls -la libxml2*
> -rw-r--r-- 1 root root 2947916 Jun 4 02:57 libxml2.a
> lrwxrwxrwx 1 root root 16 Jun 4 02:57 libxml2.so -> libxml2.so.2.9.3
> lrwxrwxrwx 1 root root 16 Oct 21 20:37 libxml2.so.2 ->
> libxml2.so.2.9.3
> -rw-r--r-- 1 root root 1805560 Jun 4 02:57 libxml2.so.2.9.3
>
> So I started compiling with the argument libxml2-lib-dir like this
>
>
> david at CG106-3XZ3TF2:~/Gale-2_0_1$ ./configure.sh
> --libxml2-lib-dir='/usr/lib/x86_64-linux-gnu'
> scons: Reading SConscript files ...
> Checking whether the C++ compiler worksyes
> Checking for package libXML2... no
>
> **** ERROR ****
> Failed to locate required package libXML2.
> Details in 'config.log'
>
>
> ************************************
> If you require help, send the files:
> config.log
> config.cfg (if it exists)
> to: cig-long at geodynamics.org
>
>
> and this is the content of the config.log
>
>
> file /home/david/Gale-2_0_1/config/config.py,line 66:
> Configure(confdir = .sconf_temp)
>
> Configuring using:
> config/scons/scons.py --config=force -f SConfigure
> --libxml2-lib-dir=/usr/lib/x86_64-linux-gnu
>
> file /home/david/Gale-2_0_1/config/cxx.py,line 11:
> Configure(confdir = .sconf_temp)
> scons: Configure: Checking whether the C++ compiler works
> .sconf_temp/conftest_0.cpp <-
> |
> |int main()
> |{
> | return 0;
> |}
> |
> g++ -o .sconf_temp/conftest_0.o -c .sconf_temp/conftest_0.cpp
> scons: Configure: yes
>
>
> Failed to find static or shared libraries for 'libXML2'.
> Static missing: ['xml2']
> Shared missing: ['xml2']
> Looked in: ['/usr/lib']
> Failed to find static or shared libraries for 'libXML2'.
> Static missing: ['xml2']
> Shared missing: ['xml2']
> Looked in: ['/usr/lib']
> Failed to find static or shared libraries for 'libXML2'.
> Static missing: ['xml2']
> Shared missing: ['xml2']
> Looked in: ['/usr/lib64']
> Failed to find static or shared libraries for 'libXML2'.
> Static missing: ['xml2']
> Shared missing: ['xml2']
> Looked in: ['/usr/lib64']
> Failed to find static or shared libraries for 'libXML2'.
> Static missing: ['xml2']
> Shared missing: ['xml2']
> Looked in: ['/usr/local/lib']
> Failed to find static or shared libraries for 'libXML2'.
> Static missing: ['xml2']
> Shared missing: ['xml2']
> Looked in: ['/usr/local/lib']
> Failed to find static or shared libraries for 'libXML2'.
> Static missing: ['xml2']
> Shared missing: ['xml2']
> Looked in: ['/usr/local/lib64']
> Failed to find static or shared libraries for 'libXML2'.
> Static missing: ['xml2']
> Shared missing: ['xml2']
> Looked in: ['/usr/local/lib64']
>
>
> I am perplexed. Can you guide me ? What I am missing?
>
>
> Thanks
>
> David
>
> ------------------------------------------------------------------------
> *DAVID BOUTELIER*
> School of Environmental and Life Sciences,
> The University of Newcastle, University Drive, Callaghan 2304 NSW
>
>
>
>
> _______________________________________________
> CIG-LONG mailing list
> CIG-LONG at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-long
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