Installation on Amazon Cloud Computing Instance (AWS)

Discussion about building and installing Elmer
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gschrank
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Installation on Amazon Cloud Computing Instance (AWS)

Post by gschrank » 07 Apr 2018, 18:55

Good morning! I've been attempting to install elmer on an AWS instance of Ubuntu 16.04. I've successfully installed the code locally and, for about a year now, have been testing the integration of some custom modules. I recently found that I'm memory-bound trying to do the computations locally, so I thought I'd try installing and running on AWS for the boost in resources.

I can successfully compile elmer with my custom modules. However, when I run the ctests I get the following output:

Code: Select all

Test project /home/ubuntu/elmer/build
        Start   1: 1dtests
  1/575 Test   #1: 1dtests .................................................***Exception: Child aborted  0.27 sec
        Start   2: 1sttime
  2/575 Test   #2: 1sttime .................................................***Exception: Child aborted  0.12 sec
        Start   3: 2ndtime
  3/575 Test   #3: 2ndtime .................................................***Exception: Child aborted  0.12 sec
        Start   4: AdvDiffFCT
  4/575 Test   #4: AdvDiffFCT ..............................................***Exception: Child aborted  0.12 sec
        Start   5: AdvReactDG
  5/575 Test   #5: AdvReactDG ..............................................***Exception: Child aborted  0.12 sec
        Start   6: AdvReactDG_np6
  6/575 Test   #6: AdvReactDG_np6 ..........................................***Exception: Child aborted  0.12 sec
        Start   7: AdvReactDG_P
  7/575 Test   #7: AdvReactDG_P ............................................***Exception: Child aborted  0.12 sec
        Start   8: AnalyticalTest
  8/575 Test   #8: AnalyticalTest ..........................................***Exception: Child aborted  0.12 sec
        Start   9: AngleMetisLayer
  9/575 Test   #9: AngleMetisLayer .........................................***Exception: Child aborted  0.12 sec
        Start  10: AngleMetisLayer_np2
 10/575 Test  #10: AngleMetisLayer_np2 .....................................***Exception: Child aborted  0.12 sec
        Start  11: AngleMetisLayer_np3
 11/575 Test  #11: AngleMetisLayer_np3 .....................................***Exception: Child aborted  0.12 sec
        Start  12: AngleMetisLayer_np4
 12/575 Test  #12: AngleMetisLayer_np4 .....................................***Exception: Child aborted  0.12 sec
        Start  13: AnglePartitionLayer_np4
 13/575 Test  #13: AnglePartitionLayer_np4 .................................***Exception: Child aborted  0.12 sec
        Start  14: ArteryOutlet
 14/575 Test  #14: ArteryOutlet ............................................***Exception: Child aborted  0.12 sec
        Start  15: BDM2D
 15/575 Test  #15: BDM2D ...................................................***Exception: Child aborted  0.12 sec
        Start  16: BDM3D
 16/575 Test  #16: BDM3D ...................................................***Exception: Child aborted  0.12 sec
        Start  17: BlockLinElast1
 17/575 Test  #17: BlockLinElast1 ..........................................***Exception: Child aborted  0.12 sec
        Start  18: BlockLinElast2
 18/575 Test  #18: BlockLinElast2 ..........................................***Exception: Child aborted  0.12 sec
        Start  19: BlockLinElast2b
 19/575 Test  #19: BlockLinElast2b .........................................***Exception: Child aborted  0.12 sec
        Start  20: BlockLinElast3
 20/575 Test  #20: BlockLinElast3 ..........................................***Exception: Child aborted  0.12 sec
        Start  21: BlockLinElast3b
 21/575 Test  #21: BlockLinElast3b .........................................***Exception: Child aborted  0.12 sec
        Start  22: BlockLinElast3c
 22/575 Test  #22: BlockLinElast3c .........................................***Exception: Child aborted  0.12 sec
        Start  23: BlockLinElast3d
 23/575 Test  #23: BlockLinElast3d .........................................***Exception: Child aborted  0.12 sec
        Start  24: BlockPoisson1
 24/575 Test  #24: BlockPoisson1 ...........................................***Exception: Child aborted  0.12 sec
        Start  25: BlockPoisson2
 25/575 Test  #25: BlockPoisson2 ...........................................***Exception: Child aborted  0.12 sec
        Start  26: BlockPoisson3
 26/575 Test  #26: BlockPoisson3 ...........................................***Exception: Child aborted  0.12 sec
        Start  27: BlockRotatingBCPoisson3D
 27/575 Test  #27: BlockRotatingBCPoisson3D ................................***Exception: Child aborted  0.12 sec
        Start  28: BoundaryFluxes
 28/575 Test  #28: BoundaryFluxes ..........................................***Exception: Child aborted  0.12 sec
        Start  29: BoundaryFluxes2
 29/575 Test  #29: BoundaryFluxes2 .........................................***Exception: Child aborted  0.12 sec
        Start  30: CapacitanceMatrix
 30/575 Test  #30: CapacitanceMatrix .......................................***Exception: Child aborted  0.12 sec
etc. I've stopped the tests before they complete because the behavior looks to be the same for all of them. I've never seen this "***Exception:Child aborted" behavior before, and I don't know what it means.

I tried forging ahead and just tried running one of the models I was working with locally. Elmer will launch and start running. However, it gets to a portion of the mesh preparation and give a SEG FAULT error:

Code: Select all

ElmerAsciiMesh: Performing step: 5
NonNodalElements: Requested elements require creation of edges
FindMeshEdges: Determining faces in 3D mesh
FindMeshFaces3D: Number of faces found: 647114
FindMeshEdges: Determining edges in 3D mesh

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7ff0df0d1cc2
#1  0x7ff0df0d0f90
#2  0x7ff0ded214af
#3  0x7ff0df4e0d14
#4  0x7ff0df67b9d6
#5  0x7ff0df67f022
#6  0x7ff0df68b08c
#7  0x7ff0df6904ef
#8  0x7ff0df692866
#9  0x7ff0df4dd14a
#10  0x7ff0df7b34a2
#11  0x401045
#12  0x400dae
#13  0x7ff0ded0c82f
#14  0x400de8
#15  0xffffffffffffffff
Segmentation fault (core dumped)
It does not do this when I run locally with the same sif and mesh files.

Since it is Ubuntu, I tried installing elmer from the repo just to make sure I wasn't forgetting something in my system configuration (like a vital library or a line in the bashrc or something). After confirming that the command line version of ElmerSolver was referring to the version of elmer installed from the repo and not what was in my home directory, I tried restarting the ctests, and I observed the same behavior. I can't run the repo version of my models because it lacks the custom modules that I've authored, so I didn't try that.

I'm wondering if anyone else has tried installing elmer on an AWS instance and can share their experience.

Thanks much!

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