Von mises stress calculation of elasticity

General
1

Hi, everyone. I followed The FEniCSx tutorial to study how to calculate the displacement and the von Mises stress of an elastic body. I got the same deformation result as shown in the example, but when I calculated the stress I met some errors below:
HDF5-DIAG: Error detected in HDF5 (1.14.3) MPI-process 0:
#000: H5F.c line 660 in H5Fcreate(): unable to synchronously create file
major: File accessibility
minor: Unable to create file
#001: H5F.c line 614 in H5F__create_api_common(): unable to create file
major: File accessibility
minor: Unable to open file
#002: H5VLcallback.c line 3605 in H5VL_file_create(): file create failed
major: Virtual Object Layer
minor: Unable to create file
#003: H5VLcallback.c line 3571 in H5VL__file_create(): file create failed
major: Virtual Object Layer
minor: Unable to create file
#004: H5VLnative_file.c line 94 in H5VL__native_file_create(): unable to create file
major: File accessibility
minor: Unable to open file
#005: H5Fint.c line 2018 in H5F_open(): unable to read superblock
major: File accessibility
minor: Read failed
#006: H5Fsuper.c line 392 in H5F__super_read(): file signature not found
major: File accessibility
minor: Not an HDF5 file
Traceback (most recent call last):
File “/mnt/fghs/share/linearelasticity_code.py”, line 138, in
with io.XDMFFile(domain.comm, “deformation.xdmf”, “w”) as xdmf:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: Failed to create HDF5 file.
I use FEniCSx v0.7.0 which was installed by conda with the help of the code on the FEniCS Download webpage. Any advice for this problem?

2

That sounds like an error when trying to create the file itself. Is the disk mounted with the correct permissions? Is there enough free space?

3

Hi Wen, I found a post here which has a solution from hyjin86. It looks like the file is locked or protected. Hope it works!

4

I use a virtual machine in Win and run the code in root. I use the command ‘’ df -h’’ which shows that there is enough space.

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5

You seem to be running the code in a mounted disk whgfs-fuse. Try running the same code in your home: if the error is not there anymore, then it is due to the mount options you chose.

6

Thank you for your help!! It works and there is no error now. But I still cant get the image of the stress, the result I get like this:

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图片1189×835 51.6 KB

which is far from the result shown in the tutorial

7

Thanks for your advice. I changed the position and the code runs without error, but the result seems not right like this；

图片
图片1189×835 51.6 KB

8

You may try Paraview, but your image looks nothing like the one in tutorial (assume we’re talking about the same demo):

image
image963×590 74.6 KB

Also you could print out some numbers.

9

It seems that we are talking about different ones. The result is like this:

图片
图片1085×748 37.8 KB

I’ll learn how to use Paraview, thanks for your help.

10

You might be interested in this: Visual representation (interpolation) of a 2nd order tensor in a 3D space (recipe)

11

It is totally unexpected that I have exactly the same problem, I sourced export HDF5_USE_FILE_LOCKING=FALSE in .bash_profile, but nothing happened, the errors were still there. This is wired. Both 2019.1.0 docker image and standalone 2019.2.0.dev show same error. So may I ask what did you do?

12

I just gave up using Pyvista after trying many times. I export the result as a .xdmf file to visualize it in Paraview

13

I’m saying the HDF5 error, sorry.