Octree example failure

[lperozzi]

I tried the octree in the examples folder and works as expected. However, when I modify the input file and try to generate stochastic families (1 for elliptical, 1 for rectangular) it fails with the following error:

Traceback (most recent call last):
  File "../test/dfnWorks/examples/octree/run_octree.py", line 24, in <module>
    DFN.map_to_continuum(l=0.1,orl=3)
  File "/usr/local/lib/python3.6/dist-packages/pydfnworks-2.5-py3.6.egg/pydfnworks/dfnGen/meshing/udfm/map2continuum.py", line 109, in map_to_continuum
    lagrit_run(self, num_poly, path, dir_name)
  File "/usr/local/lib/python3.6/dist-packages/pydfnworks-2.5-py3.6.egg/pydfnworks/dfnGen/meshing/udfm/map2continuum.py", line 724, in lagrit_run
    mh.run_lagrit_script("driver_octree_start.lgi")
  File "/usr/local/lib/python3.6/dist-packages/pydfnworks-2.5-py3.6.egg/pydfnworks/dfnGen/meshing/mesh_dfn_helper.py", line 532, in run_lagrit_script
    sys.stderr.write(error)
NameError: name 'sys' is not defined

The same file has been used to generate stochastic families (without UFDM) and worked. Maybe someone has a hint?

[hymanjd]

Hi Lorenzo,

Add import sys

to the header of pydfnworks/dfnGen/meshing/mesh_dfn_helper.py and re-install pydfnworks. Thanks for finding that for us. I’ll include this in the next update.

Jeffrey

-- Jeffrey Hyman PhD Staff Scientist Earth & Environmental Sciences Division (EES-16) Los Alamos National Laboratory Office: +1 (505) 665 2074 https://dfnworks.lanl.gov/ (Pronouns: he, him, his)

From: Lorenzo Perozzi @.> Reply-To: lanl/dfnWorks @.> Date: Friday, October 8, 2021 at 7:47 AM To: lanl/dfnWorks @.> Cc: Subscribed @.> Subject: [EXTERNAL] [lanl/dfnWorks] Octree example failure (#16)

I tried the octree in the examples folder and works as expected. However, when I modify the input file and try to generate stochastic families (1 for elliptical, 1 for rectangular) it fails with the following error:

Traceback (most recent call last):

File "../test/dfnWorks/examples/octree/run_octree.py", line 24, in

DFN.map_to_continuum(l=0.1,orl=3)

File "/usr/local/lib/python3.6/dist-packages/pydfnworks-2.5-py3.6.egg/pydfnworks/dfnGen/meshing/udfm/map2continuum.py", line 109, in map_to_continuum

lagrit_run(self, num_poly, path, dir_name)

File "/usr/local/lib/python3.6/dist-packages/pydfnworks-2.5-py3.6.egg/pydfnworks/dfnGen/meshing/udfm/map2continuum.py", line 724, in lagrit_run

mh.run_lagrit_script("driver_octree_start.lgi")

File "/usr/local/lib/python3.6/dist-packages/pydfnworks-2.5-py3.6.egg/pydfnworks/dfnGen/meshing/mesh_dfn_helper.py", line 532, in run_lagrit_script

sys.stderr.write(error)

NameError: name 'sys' is not defined

The same file has been used to generate stochastic families (without UFDM) and worked. Maybe someone has a hint?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/lanl/dfnWorks/issues/16, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEKOGDDVKTO3ICM2K6LY4BLUF3Y6BANCNFSM5FTVG3SQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[lperozzi]

Hi Jeffrey,

thanks for the prompt reply. I'm using the docker container, so I'm not sure how (neither if it is possible) to re-install pydfnworks. Should I install dfnWorks locally?

Lorenzo

[hymanjd]

I’m working on a new container push today. I’ll let you know when it’s up. I’ll include this in the update.

It’s up to you about doing a native build. If you want to discuss the pros/cons send me a direct email. J

-- Jeffrey Hyman PhD Staff Scientist Earth & Environmental Sciences Division (EES-16) Los Alamos National Laboratory Office: +1 (505) 665 2074 https://dfnworks.lanl.gov/ (Pronouns: he, him, his)

From: Lorenzo Perozzi @.> Reply-To: lanl/dfnWorks @.> Date: Friday, October 8, 2021 at 7:54 AM To: lanl/dfnWorks @.> Cc: Jeffrey Hyman @.>, Comment @.***> Subject: [EXTERNAL] Re: [lanl/dfnWorks] Octree example failure (#16)

Hi Jeffrey,

thanks for the prompt reply. I'm using the docker container, so I'm not sure how (neither if it is possible) to re-install pydfnworks. Should I install dfnWorks locally?

Lorenzo

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/lanl/dfnWorks/issues/16#issuecomment-938662237, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEKOGDADY5CMO2YW6IMBWQDUF3ZX5ANCNFSM5FTVG3SQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[lperozzi]

I'll waiting for the new container ... many thanks

[hymanjd]

Just pushed. Please pull, give it a shot, and let me know how it goes.

---

Jeffrey Hyman Computational Earth Science (EES-16) Los Alamos National Laboratory 1 - (505) - 665 - 2074 @.***

---

From: Lorenzo Perozzi @.***> Sent: Friday, October 8, 2021 7:59:46 AM To: lanl/dfnWorks Cc: Hyman, Jeffrey De'Haven; Comment Subject: [EXTERNAL] Re: [lanl/dfnWorks] Octree example failure (#16)

I'll waiting for the new container ... many thanks

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/lanl/dfnWorks/issues/16#issuecomment-938666507, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEKOGDA6DGEW4VGGP4SNOQTUF32NFANCNFSM5FTVG3SQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[lperozzi]

I pulled the new container and executed an octree test but end up with the following error

 THE PSET  prefine  HAS    2733220 POINTS
#
# If one wants anisotropic mesh refinement, then the
# variable REFINE_AMR can be set in parameters_octree_dfn.mlgi
#
refine/constant/imt1/linear/element/pset,get,prefine/-1.,0.,0./exclusive/amr REF
INE_AMR
refine elements:
Killed
ERROR running LaGriT on script driver_octree_start.lgi. Exiting Program.

is maybe something wrong with my input file? However, the same file works to generate a simple DFN. Many thanks for helping

[hymanjd]

It looks like your machine (or docker instance) ran out of memory. Please email me directly and we can try to sort it out.

J

-- Jeffrey Hyman PhD Staff Scientist Earth & Environmental Sciences Division (EES-16) Los Alamos National Laboratory Office: +1 (505) 665 2074 https://dfnworks.lanl.gov/ (Pronouns: he, him, his)

From: Lorenzo Perozzi @.> Reply-To: lanl/dfnWorks @.> Date: Monday, October 11, 2021 at 1:16 AM To: lanl/dfnWorks @.> Cc: Jeffrey Hyman @.>, Comment @.***> Subject: [EXTERNAL] Re: [lanl/dfnWorks] Octree example failure (#16)

I pulled the new container and executed an octree test but end up with the following error

THE PSET prefine HAS 2733220 POINTS

#

If one wants anisotropic mesh refinement, then the

variable REFINE_AMR can be set in parameters_octree_dfn.mlgi

#

refine/constant/imt1/linear/element/pset,get,prefine/-1.,0.,0./exclusive/amr REF

INE_AMR

refine elements:

Killed

ERROR running LaGriT on script driver_octree_start.lgi. Exiting Program.

is maybe something wrong with my input file? However, the same file works to generate a simple DFN. Many thanks for helping

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/lanl/dfnWorks/issues/16#issuecomment-939753846, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEKOGDHJL3MUCKWMY6EVCS3UGKFMLANCNFSM5FTVG3SQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.