[aspect-devel] Fwd: [CIG-MC] Installing ASPECT on Cray XC30

Mon Jul 10 23:09:07 PDT 2017

Hi all, 

Sorry, it appears I used the wrong mailing list! 
Let me know if someone has experience building ASPECT (and required libraries) on a CRAY XC30. 

Best, 
Marine

Marine Lasbleis

=====
ELSI Research Scientist
Earth Life Science Institute
Tokyo Institute of Technology
Tokyo, Japan
+81 70 1572 5070
marine.lasbleis at elsi.jp <mailto:marine.lasbleis at elsi.jp>

https://members.elsi.jp/~marine.lasbleis/ <https://members.elsi.jp/~marine.lasbleis/> 
http://elsi.jp/en/ <http://elsi.jp/en/> 

> Begin forwarded message:
> 
> From: Max Rudolph <maxrudolph at ucdavis.edu>
> Subject: Re: [CIG-MC] Installing ASPECT on Cray XC30
> Date: 11 Jul 2017 11:52:51 GMT+9
> To: <cig-mc at geodynamics.org>
> Reply-To: cig-mc at geodynamics.org
> 
> Marine,
> You may want to post this on the aspect-devel mailing list if you haven't done so already.
> 
> Max
> 
> On Mon, Jul 10, 2017 at 5:00 PM, Marine Lasbleis <marine.lasbleis at gmail.com <mailto:marine.lasbleis at gmail.com>> wrote:
> Hi all, 
> 
> This is my first message here, I hope it’s OK. 
> I’m started to work on ASPECT, and installed it already on a desktop computer (debian with 8 cores). But would like to install it on the available clusters. (I have access to 3 different clusters. Not sure which one is the best for that… And definitely no real admin for the clusters. They are “self-organised”, which is not always for the best)
> 
> I’m trying to install ASPECT on the ELSI cluster, which is a CRAY CX30, and while having problems, I found that you may have done the same a couple of weeks ago (I saw this conversation: http://dealii.narkive.com/jCU1oGdB/deal-ii-get-errors-when-installing-dealii-on-opensuse-leap-42-1-by-using-candi <http://dealii.narkive.com/jCU1oGdB/deal-ii-get-errors-when-installing-dealii-on-opensuse-leap-42-1-by-using-candi> )
> 
> For now, what we’ve done: (before seeing candi installation)
> - switch to PrgEnv-gnu 
> - try to install p4est. But it seems that we need to use “ftn” and not fortran or others, so he can’t do anything, and stop very soon. I tried to modify by hand the configure file (adding ftn where I could find the system was looking for fortran of mpif77.) But I guess it’s definitely not a good idea, and I am obviously still missing a couple of call because I still got the same error. 
> 
> So, with the conversation, I guessed that https://github.com/dealii/candi <https://github.com/dealii/candi> can actually install everything for me. 
> Since I’m using a slightly different cluster (CRAY XC30), I will try to give you updates on my progress. 
> I’m not familiar with candi, but I decided to give a try, so please excuse me if I am doing obvious mistakes. 
> 
> I changed the configuration as requested, and loaded the required modules and defined new variables for the info on the compilers. 
> In this particular cluster, we need to be careful with the path where to install (the default one is on a drive that is very slow to access, and compilation takes forever), so I had to use a -p path option. Also, I think I used first too many cores to compile, and got a memory error (internal compiler error raised, which seems to be related to available memory)
> 
> So, from my day trying to install: 
> - I finished the candi.sh script, apparently everything correctly installed. 
> - I built ASPECT (with this particular cluster, be careful with cmake. By default, the cmake is not up-to-date, and in particular even after installation with candi.sh, the available cmake is not the one that was installed)
> I got a couple of warnings, mostly about PETSc, that I thought were only warnings and not problems.
> Most of them were along the line of this one: 
> warning: 'dealii::PETScWrappers::MPI::Vector::supports_distributed_data' is deprecated [-Wdeprecated-declarations] , for either PETSc or Trilinos.
> 
> - I’ve run a couple of examples from the cookbook. None are working. 
> 
> I got this from running ASPEC using aprun -n4 ../aspect burnman.prm
> -----------------------------------------------------------------------------
> -- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion.
> --     . version 1.5.0
> --     . running in DEBUG mode
> --     . running with 4 MPI processes
> --     . using Trilinos
> -----------------------------------------------------------------------------
> 
> [0]PETSC ERROR: [1]PETSC ERROR: [3]PETSC ERROR: [2]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: ------------------------------------------------------------------------
> ------------------------------------------------------------------------
> [2]PETSC ERROR: ------------------------------------------------------------------------
> [1]PETSC ERROR: [3]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero
> [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> Caught signal number 8 FPE: Floating Point Exception,probably divide by zero
> [1]PETSC ERROR: [3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind <http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>
> Try option -start_in_debugger or -on_error_attach_debugger
> [1]PETSC ERROR: [3]PETSC ERROR: or try http://valgrind.org <http://valgrind.org/> on GNU/linux and Apple Mac OS X to find memory corruption errors
> or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind <http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>
> [1]PETSC ERROR: [3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
> or try http://valgrind.org <http://valgrind.org/> on GNU/linux and Apple Mac OS X to find memory corruption errors
> [1]PETSC ERROR: [3]PETSC ERROR: to get more information on the crash.
> configure using --with-debugging=yes, recompile, link, and run
> [3]PETSC ERROR: to get more information on the crash.
> [1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> Caught signal number 8 FPE: Floating Point Exception,probably divide by zero
> 
> 
> 
> 
> 
> Any idea where this could come from? 
> (any additional files I should show you?) 
> 
> 
> Thanks! (and many thanks to the person who did the candi.sh script for Cray XC40 :-) )
> Marine
> 
> 
> 
> 
> 
> _______________________________________________
> CIG-MC mailing list
> CIG-MC at geodynamics.org <mailto:CIG-MC at geodynamics.org>
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc>
> 
> 
> 
> -- 
> ---------------------------------
> Max Rudolph
> Assistant Professor, Earth and Planetary Sciences, UC Davis
> webpage <http://www.maxrudolph.org/>
> _______________________________________________
> CIG-MC mailing list
> CIG-MC at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-mc

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/aspect-devel/attachments/20170711/45303a8c/attachment.html>