Fail to launch SimVascular for linux

[David Parker]

Hi Amirtaha,

You can run svsolver compute jobs on the server but which computer are you using that has a display and graphics card to run SimVascular? Is that now working?

Cheers,
Dave

[Amirtaha Taebi]

Hi David,

1. I have a windows machine with SimVascular installed. The display is connected to this computer. I can interact with the 3D model when I run SimVascular in my windows machine. I have nvidia Quadro P5000 on this machine.

2. I use MobaXterm to work with a server which is a Linux machine. As an output for the simvascular command in the MobaXterm terminal, the simvascular GUI pops up on my windows machine monitor. The 3D models are not shown in this GUI. I get errors (those that I had posted earlier) about the OpenGL in MobaXterm terminal, for example:

#6139.866# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0xa135e40):
#6139.870# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x3a15580): 1: #version 140

Thank you very much for your time and help.

Thanks,
Amirtaha

[David Parker]

Hi Amirtaha,

Now I understand (finally!). You will not be able to run SimVascular remotely on a computer that does not have a graphics card. The errors you are seeing about OpenGL occur when SimVascular tries to display the 3D geometry of a model but can't because there is no graphics card to run OpenGL on. The GUI can be displayed because it can use X windows directly.

You will need to generate the solver data files on your Windows computer and then move them over to the Linux server. You can then run a simulation from the command line using mpiexec. Does that make sense?

Cheers,
Dave

[Amirtaha Taebi]

Hi David,

Yes, I see, it completely makes sense. I was actually runnig a few simulations during the past few days this same way. Thank you very much for all the guidance and help in the last few days.


Thanks,
Amirtaha

[Amirtaha Taebi]

Hi David,

I installed the simvascular and all other stuff that we had discussed in this thread on a Linux machine. Once I run simvascular, I get this error and the software doesn't run. Can you please advise how to get around this?

Code: Select all

[1.268] [BlueBerry] LOG: Warning: Detected recursive attempt by part org.sv.views.datamanager to create itself (this is probably, but not necessarily, a bug)
!1.296! WARNING: The X11 connection broke: I/O error (code 1)
XIO:  fatal IO error 0 (Success) on X server "localhost:12.0"
      after 476 requests (476 known processed) with 0 events remaining.
/usr/local/bin/simvascular: line 113:  8417 Aborted                 (core dumped) $SV_HOME/bin/simvascular $*

Thank you very much,
Amirtaha

[David Parker]

Hi Amirtaha,

What OS/version are you running on? SV only runs on Ubuntu 16 and 18.

The X server "localhost:12.0 looks odd, this is typically :0 on Ubuntu. Are you running SV remotely on another computer?

Cheers,
Dave

[Amirtaha Taebi]

Hi David,

Yes, I want to run sv remotely on another computer with Ubuntu 18.

Thanks,
Amirtaha

[Amirtaha Taebi]

Hi David,

I would like to provide you more information about our environment. Actually we had sv running fine on this computer before. Then we made the following changes on the computer:

Before update:
Nvidia K80 Graphic card with the driver v395.xx
With that, we could do both GPU computing and sv.

After update:
Nvidia Tesla V100 with the driver v410.xx
sv is no longer working and the error message looks like

Code: Select all

[1.268] [BlueBerry] LOG: Warning: Detected recursive attempt by part org.sv.views.datamanager to create itself (this is probably, but not necessarily, a bug)
!1.296! WARNING: The X11 connection broke: I/O error (code 1)
XIO:  fatal IO error 0 (Success) on X server "localhost:12.0"
      after 476 requests (476 known processed) with 0 events remaining.
/usr/local/bin/simvascular: line 113:  8417 Aborted                 (core dumped) $SV_HOME/bin/simvascular $*

Also, it was giving me the following output for this command: glxinfo | grep -i opengl

Before update:

Code: Select all

OpenGL vendor string: VMware, Inc.
OpenGL renderer string: llvmpipe (LLVM 7.0, 256 bits)
OpenGL version string: 3.1 Mesa 18.2.8
OpenGL shading language version string: 1.40
OpenGL context flags: (none)
OpenGL extensions: 

After update:

Code: Select all

OpenGL vendor string: Mesa Project
OpenGL renderer string: Software Rasterizer
OpenGL version string: 1.4 (2.1 Mesa 10.5.4)
OpenGL extensions:

To confirm what the problem is, we uninstalled the Nvidia driver v410.xx and ran sv again. SimVascular works!

So the question is how can we install the Nvidia driver v410.xx for GPU computing and make sv working as before?

Thank you very much,
Amirtaha

[Amirtaha Taebi]

We solved this issue. For those might face the same issue in future:

After uninstalling the driver downloaded from Nvidia website, we installed the driver via apt-get and now sv is working.

[David Parker]

Good find!

I think installing the Nvidea driver from the website was setting the DISPLAY environment variable incorrectly to **localhost:12.0**.

Cheers,
Dave