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

Tue Jul 11 13:39:06 PDT 2017

Hi Marine,

I have attempted to install ASPECT on a Cray XC30 (Archer HPC in the UK) with no success. The HPC admin team has not had any success either. Please keep up posted on your progress.

I can compile and build dealii and aspect, but most dealii tests fail:

  4 - mpi.debug (Failed)

  6 - p4est.debug (Failed)

  7 - step-trilinos.debug (Failed)

I will have another go this week.

Phil

Philip J. Heron
Junior Research Fellow
Dept. of Earth Sciences
Durham University
web: http://philheron.com<http://philheron.com/>

________________________________
From: Aspect-devel <aspect-devel-bounces at geodynamics.org> on behalf of Timo Heister <heister at clemson.edu>
Sent: 11 July 2017 14:00:09
To: aspect-devel
Subject: Re: [aspect-devel] Fwd: [CIG-MC] Installing ASPECT on Cray XC30

Marine,

1. can you post your detailed.log from your ASPECT directory?

2. can you try to call
cmake -D ASPECT_USE_FP_EXCEPTIONS=OFF .

inside your aspect build directory, and then "make" again? This should
disable the floating point exceptions (we use this as a tool to find
errors and bugs), but you will likely run into other problems then.
But maybe this is enough to make things work.

On Tue, Jul 11, 2017 at 2:09 AM, Marine Lasbleis
<marine.lasbleis at elsi.jp> wrote:
> 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
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__members.elsi.jp_-7Emarine.lasbleis_&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=zrvFCXon07qCkF8qXzZ6rHu6CjY30e55CUFHopV1Hm8&s=LoLdd_1ebxXqVRRXpWavR7d1dGghq8WrxfMfJW5bv90&e=
> https://urldefense.proofpoint.com/v2/url?u=http-3A__elsi.jp_en_&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=zrvFCXon07qCkF8qXzZ6rHu6CjY30e55CUFHopV1Hm8&s=7qmW2cZqp2dDQA8f55NM9FLl5v83q1G1A8WVaCxGC14&e=
>
>
> 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>
> 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:
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__dealii.narkive.com_jCU1oGdB_deal-2Dii-2Dget-2Derrors-2Dwhen-2Dinstalling-2Ddealii-2Don-2Dopensuse-2Dleap-2D42-2D1-2Dby-2Dusing-2Dcandi&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=zrvFCXon07qCkF8qXzZ6rHu6CjY30e55CUFHopV1Hm8&s=3hIE02zdEMfEZQ-54THur4-xXpYPz_X9QkkDRViqAOc&e=
>> )
>>
>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_candi&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=zrvFCXon07qCkF8qXzZ6rHu6CjY30e55CUFHopV1Hm8&s=PNy4RPfYtSh0YwU5s31LHSfmZj0RgQv3wznnVVHjRXw&e=
>> 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
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mcs.anl.gov_petsc_documentation_faq.html-23valgrind&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=zrvFCXon07qCkF8qXzZ6rHu6CjY30e55CUFHopV1Hm8&s=EwRL-vfnsOaRgZyq9yA5cgFyGt6wyqbxmPnUR8DEnjo&e=
>> Try option -start_in_debugger or -on_error_attach_debugger
>> [1]PETSC ERROR: [3]PETSC ERROR: or try https://urldefense.proofpoint.com/v2/url?u=http-3A__valgrind.org&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=zrvFCXon07qCkF8qXzZ6rHu6CjY30e55CUFHopV1Hm8&s=ozKrZdv65t35wUP3q4s5YnSV27_oA6xmJCjsqYFNx3s&e=  on GNU/linux
>> and Apple Mac OS X to find memory corruption errors
>> or see https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mcs.anl.gov_petsc_documentation_faq.html-23valgrind&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=zrvFCXon07qCkF8qXzZ6rHu6CjY30e55CUFHopV1Hm8&s=EwRL-vfnsOaRgZyq9yA5cgFyGt6wyqbxmPnUR8DEnjo&e=
>> [1]PETSC ERROR: [3]PETSC ERROR: configure using --with-debugging=yes,
>> recompile, link, and run
>> or try https://urldefense.proofpoint.com/v2/url?u=http-3A__valgrind.org&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=zrvFCXon07qCkF8qXzZ6rHu6CjY30e55CUFHopV1Hm8&s=ozKrZdv65t35wUP3q4s5YnSV27_oA6xmJCjsqYFNx3s&e=  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
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_cig-2Dmc&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=zrvFCXon07qCkF8qXzZ6rHu6CjY30e55CUFHopV1Hm8&s=7tnjS3DwD11pd0Hw_1BkS8zxpTVmv_DKo8iWlM7fRuE&e=
>
>
>
>
> --
> ---------------------------------
> Max Rudolph
> Assistant Professor, Earth and Planetary Sciences, UC Davis
> webpage
> _______________________________________________
> CIG-MC mailing list
> CIG-MC at geodynamics.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_cig-2Dmc&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=zrvFCXon07qCkF8qXzZ6rHu6CjY30e55CUFHopV1Hm8&s=7tnjS3DwD11pd0Hw_1BkS8zxpTVmv_DKo8iWlM7fRuE&e=
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIGaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=R5lvg9JC99XvuTgScgbY_QFS80R7PEA2q0EPwDy7VQw&m=-Akgl8D9XHMqGKMmF_ZJUPsW7I_-1G6mLeoE2Wpszrc&s=0Gsi6keZz8ri0Vnr9RwBCIGZqCsFqbzuDynW8S3C41U&e=

--
Timo Heister
http://www.math.clemson.edu/~heister/
_______________________________________________
Aspect-devel mailing list
Aspect-devel at geodynamics.org
http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/aspect-devel/attachments/20170711/4e048077/attachment-0001.html>