[CIG-MC] ConMan issues report

Wed Aug 24 16:51:26 PDT 2016

Dear all,

Thanks for all the help. I downloaded ConMan via Thorsten Becker virtualbox and checked what a variable viscosity solution should be yielding.

Based on that, I determined that my code (2D Cartesian finite difference, iterative with multigrid) is doing the correct thing but cannot go beyond a small variation in viscosity (grad(eta) ~ 10) before crashing (resolution Nx=Nz=256).

Before abandoning this approach and move to using one of the several codes already available, I would like to understand why is it that this method is failing. In other words, I'm still puzzled as to how exactly were the software from the 90's able to solve the problem of variable viscosity. Is it better conservation in the finite element method as opposed to finite differences?

I'm using a very high order FDM (6th order in space, 3rd in time) and I'm seeing results still similar to if I use low (2nd) order in space.  In the Blankenbach et al 1989 benchmark several codes were FD.

Cheers,

Wlad

==================================

Dr Wladimir Lyra, Assistant Professor

California State University, Northridge

Dept of Physics and Astronomy

18111 Nordhoff St, Northridge, CA 91330

Phone : +1 818 677 7464

web: http://www.wladimirlyra.com

________________________________
From: Shijie Zhong <shijie.zhong at colorado.edu>
Sent: Thursday, August 18, 2016 10:40:20 AM
To: cig-mc at geodynamics.org
Cc: Lyra, Wladimir
Subject: Re: [CIG-MC] ConMan issues report

Just to add a comment on 2D direct vs iterative solvers. What Scott said is certainly true for most cases, especially for 1 time step Stokes flow solve. However, for time-dependent convection problems with time-dependent viscosity (due to temperature), iterative solvers may run faster than direct solvers due to the use of previous solutions as the initial guessed solution, especially if one has to compute for tens of thousands of time steps.

Hope you all have had a nice summer.

Shijie

Shijie Zhong, Professor
Department of Physics
University of Colorado at Boulder
Boulder, CO 80309
http://mathis.colorado.edu/szhong<https://urldefense.proofpoint.com/v2/url?u=http-3A__mathis.colorado.edu_szhong&d=DQQGaQ&c=Oo8bPJf7k7r_cPTz1JF7vEiFxvFRfQtp-j14fFwh71U&r=betAI_WKi5c6efJqRXXEeDH07uoTxe7Vp010C6-tIlg&m=7gDE9rf695IujYwNjjKMGT_i1usQL4cvGw0qTIBpMtA&s=MWvx35gwD9FpduHD0NywK4-amNEtLlP6h1ykRRQ0Gac&e=>
Tel: 303-735-5095; Fax: 303-492-7935

From: CIG-MC on behalf of John Naliboff
Reply-To: "cig-mc at geodynamics.org<mailto:cig-mc at geodynamics.org>"
Date: Thursday, August 18, 2016 at 11:32 AM
To: "cig-mc at geodynamics.org<mailto:cig-mc at geodynamics.org>"
Cc: "Lyra, Wladimir"
Subject: Re: [CIG-MC] ConMan issues report

Hi Scott, Hi Thorsten,

Speed of ConMan vs ASPECT

Similar findings to Scott.  For 2-D models of lithospheric deformation, I have found that ASPECT is indeed slower than the code I used previously (Fortran, direct solver).  This of course changes in 3D.  Perhaps it would be worth having a direct solver option (MUMPS) in ASPECT for 2D problems?

ConMan development

Scott, thank you for the update.  If the community is interested, the new version of ConMan certainly seems worth making available rather than fixing up the old version.  Completely understand about the time issue regards to writing updated documentation.  I will speak to Louise and Lorraine and see what they think.  At minimum, ConMan is an excellent tool for teaching and benchmarking 2-D convection problems.

ASPECT installation

Yes, it can definitely eat up a good deal of time.   However, for newer versions of Mac OS X (Yosemite, El Capitan) a  deal.II binary is now available.  Basically, the binary installs all of ASPECT’s dependencies and then all one has to do is install ASPECT through the terminal launched by the deal.ii application.  Quite straightforward.

There are also a few new methods to streamline the deal.II installation on Linux (https://github.com/dealii/candi<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_candi&d=DQMGaQ&c=Oo8bPJf7k7r_cPTz1JF7vEiFxvFRfQtp-j14fFwh71U&r=betAI_WKi5c6efJqRXXEeDH07uoTxe7Vp010C6-tIlg&m=7gDE9rf695IujYwNjjKMGT_i1usQL4cvGw0qTIBpMtA&s=MmU7xIE6J052duXWliqORBISB7m71wVHN3NXeVYt-2o&e=>, deal.II on home-brew).  I’m still installing piece by piece, but others in the group here at Davis have used “candi” with success.

Cheers,
John

*************************************************
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis

On Aug 17, 2016, at 4:36 PM, Scott King <sking07 at vt.edu<mailto:sking07 at vt.edu>> wrote:

Circa my geodynamics class of two years ago conman was faster than 2D citcom or Aspect.   For 2D problems iterative solvers don't have a large enough number of degrees of freedom to overcome the number of iterations needed to converge.   3D of course is a different story.

Scott

Sent from my iPhone

On Aug 17, 2016, at 7:12 PM, Thorsten Becker <twb at ig.utexas.edu<mailto:twb at ig.utexas.edu>> wrote:

I'd be curious how the speed of Aspect in 2D benchmark tests compares with ConMan for high Ra cases. From Aspect cookbook cases my student ran a while back it seemed the Aspect was quite resource demanding for high Ra at comparable resolved structure, though there might have been some user error.

Thorsten Becker - Jackson School of Geosciences, UT Austin<https://urldefense.proofpoint.com/v2/url?u=http-3A__www-2Dudc.ig.utexas.edu_external_becker_&d=DQMGaQ&c=Oo8bPJf7k7r_cPTz1JF7vEiFxvFRfQtp-j14fFwh71U&r=betAI_WKi5c6efJqRXXEeDH07uoTxe7Vp010C6-tIlg&m=7gDE9rf695IujYwNjjKMGT_i1usQL4cvGw0qTIBpMtA&s=Qq8DaVI_Y4CirsQwROSnrDPgBY2xn3zVnfpiZzVZyhI&e=>

On Wed, Aug 17, 2016 at 5:44 PM, John Naliboff <jbnaliboff at ucdavis.edu<mailto:jbnaliboff at ucdavis.edu>> wrote:
Dear Lyra,

Yes, we're running on a mac. I can try running on a linux if it's simpler, but what is the testing/debugging that is required?

It is just that we have successfully compiled ConMan on linux, but not on a mac recently.  The mac installation may work right away or additional issues may arise.  I would try compiling on your mac first with the 64 bit compiler, but then move to linux if that does not work.

Hm, interesting. We are in fact building our own code for specific problems in icy moons, and want to benchmark the code. We can get the isoviscous Blankenbach tests right, but we're running into some problems for variable viscosity (cases 2 and 3). We want to check the output of a code that does these cases right to see where we're doing wrong.

I know the isoviscous case has been tested successfully and I believe cases 2 and 3 have as well, but I will need to check on this.

Either ConMan or ASPECT will of course work for testing the Blankenbach cases.  ASPECT will definitely compile on the mac, though.

I should be able to get to the ConMan fix sometime tomorrow and will send an email as soon as it is updated.

Cheers,
John

*************************************************
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis

On Aug 17, 2016, at 3:35 PM, Lyra, Wladimir <wladimir.lyra at csun.edu<mailto:wladimir.lyra at csun.edu>> wrote:

Dear John

If you are running on a mac, more testing/debugging may be required.

Yes, we're running on a mac. I can try running on a linux if it's simpler, but what is the testing/debugging that is required?

A bit off topic, but is there a particular reason you choose ConMan?  ASPECT might be a better choice if you would like to run in parallel, do 3D simulations, use adaptive mesh refinement, etc. There is nothing you can do ConMan that cannot be  easily duplicated in ASPECT.  Happy to help you get setup with ASPECT if you would like to try it out.

Hm, interesting. We are in fact building our own code for specific problems in icy moons, and want to benchmark the code. We can get the isoviscous Blankenbach tests right, but we're running into some problems for variable viscosity (cases 2 and 3). We want to check the output of a code that does these cases right to see where we're doing wrong.

Did you benchmark ASPECT against the Blankenbach problems as well?

Cheers,
Wlad

==================================
Dr Wladimir Lyra, Assistant Professor
California State University, Northridge
Dept of Physics and Astronomy
18111 Nordhoff St, Northridge, CA 91330
Phone : +1 818 677 7464<tel:%2B1%20818%20677%207464>
web: http://www.wladimirlyra.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.wladimirlyra.com_&d=DQMGaQ&c=Oo8bPJf7k7r_cPTz1JF7vEiFxvFRfQtp-j14fFwh71U&r=betAI_WKi5c6efJqRXXEeDH07uoTxe7Vp010C6-tIlg&m=7gDE9rf695IujYwNjjKMGT_i1usQL4cvGw0qTIBpMtA&s=-S9JxaQLEdMctsys7edlQBvMySdg4E1cMxaOJkNtTpE&e=>

________________________________
From: John Naliboff <jbnaliboff at ucdavis.edu<mailto:jbnaliboff at ucdavis.edu>>
Sent: Wednesday, August 17, 2016 2:38:18 PM
To: cig-mc at geodynamics.org<mailto:cig-mc at geodynamics.org>
Cc: Lyra, Wladimir
Subject: Re: [CIG-MC] ConMan issues report

Dear Leondardo,

There is indeed an issue with the GitHub version of ConMan, thank you for the reminder ;)

We will push a patch to github in the next few days and let you know when it is ready to download and install.

On your end, what operating system are you trying to install ConMan on?  The updated version of ConMan should compile and run successfully on linux if you use the gfortran64 compiler and associated Makefile.

The code does compile successfully with the 32-bit compiler, but will crash upon execution.  This seems consistent with your error?

If you are running on a mac, more testing/debugging may be required.

A bit off topic, but is there a particular reason you choose ConMan?  ASPECT might be a better choice if you would like to run in parallel, do 3D simulations, use adaptive mesh refinement, etc.

There is nothing you can do ConMan that cannot be  easily duplicated in ASPECT.  Happy to help you get setup with ASPECT if you would like to try it out.

Anyhow, we will get ConMan updated in the next day or two.

Cheers,
John

*************************************************
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis

On Aug 16, 2016, at 4:34 PM, Leonardo S. Cassará <leonardo10 at astro.ufrj.br<mailto:leonardo10 at astro.ufrj.br>> wrote:

Dear ConMan developers and maintainers,

I am writing on mine and Professor Wladimir Lyra’s behalf, currently researching on icy convection.

We downloaded and installed ConMan from both the git repository conman.git and via the direct tar linkhttps://geodynamics.org/cig/software/conman/ConMan-2.0.0.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__geodynamics.org_cig_software_conman_ConMan-2D2.0.0.tar.gz&d=DQMFaQ&c=Oo8bPJf7k7r_cPTz1JF7vEiFxvFRfQtp-j14fFwh71U&r=betAI_WKi5c6efJqRXXEeDH07uoTxe7Vp010C6-tIlg&m=-SjoKD3I2cgpC0-lR2OFWlbaIaO4ml-VdNEZ7nzJf4E&s=x9fwriz_-ajoIC28JmsCNTLf3nT679rikpXcvR-YamI&e=>. However, both ways gave us issues that I would like to address here:

1- When installing via the git repository, the src directory lacks the libs folder, which we had to take from the installation via tar in order to compile.

2- After compiling (using the git repository installation + libs folder from tar), we could not run the code by following the instructions. Here is the output of our trial:

:~/ConMan/conman/cookbook1$ ../src/conman.pic < run.bb1a50
Segmentation fault (core dumped)

We are either missing something or there is an installation problem that we alone cannot solve. I hope this report helps the ConMan team to make the code even better. We appreciate any attention given to this case.

Thanks in advance,
Leonardo S. Cassara

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