Learning Forum

[Jordi Lopez Leyva]

I ran a 3D FDTD simulation in Lumerical on HPC Linux. This simulation seems to work fine, giving all the results I want. However, in the shell window, I get told "unexpected end of file". What is this error, how can I solve this and do I need to solve this?

 

6.64173% complete. Elapsed simulation time: 6.64173e-15 secs. Max time remaining: 8 secs. Auto Shutoff: 1
15.4974% complete. Elapsed simulation time: 1.54974e-14 secs. Max time remaining: 7 secs. Auto Shutoff: 1
33.2087% complete. Elapsed simulation time: 3.32087e-14 secs. Max time remaining: 6 secs. Auto Shutoff: 1
50.9199% complete. Elapsed simulation time: 5.09199e-14 secs. Max time remaining: 4 secs. Auto Shutoff: 1
68.6312% complete. Elapsed simulation time: 6.86312e-14 secs. Max time remaining: 3 secs. Auto Shutoff: 1
86.3425% complete. Elapsed simulation time: 8.63425e-14 secs. Max time remaining: 1 secs. Auto Shutoff: 0.311047
100% complete. Elapsed simulation time: 1.00041e-13 secs. Max time remaining: 0 secs. Auto Shutoff: 0.264385
sh: switchml: line 1: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC_switchml'
sh: _module_raw: line 2: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC__module_raw'
sh: switchml: line 1: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC_switchml'
sh: _module_raw: line 2: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC__module_raw'
sh: switchml: line 1: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC_switchml'
sh: _module_raw: line 2: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC__module_raw'
sh: switchml: line 1: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC_switchml'
sh: _module_raw: line 2: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC__module_raw'
sh: switchml: line 1: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC_switchml'
sh: _module_raw: line 2: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC__module_raw'
sh: switchml: line 1: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC_switchml'
sh: _module_raw: line 2: syntax error: unexpected end of file
sh: error importing function definition for `BASH_FUNC__module_raw'

[Lito Yap]

@Jordi Lopez Leyva,

Sorry to hear that you are having issues running FDTD on your cluster. To troubleshoot, please assist us with the following:

• Which Linux distro and version are you running on? 
• Which version of Ansys Lumerical are you using? 
• Do you run/submit to a job scheduler using a script? 
• Does the simulation run successfully?
  You can check the "simulationfilename_p0.log" file if the simulation is completed. 
• Can you open the simulation on your local desktop to view the results? 
• Are you using the bundled MPICH2 to run the simulation?
• Please send the sample execution line you used to run the simulation on the cluster.

e.g. /opt/lumerical/v232/mpich2/nemesis/bin/mpiexec -n 32 /opt/lumerical/v232/bin/fdtd-engine-mpich2nem -t 1 simulationfile.fsp

Thanks!

[Jordi Lopez Leyva]

 

• Which Linux distro and version are you running on? 
  • CentOS Linux release 7.9.2009 (Core)

 

• Which version of Ansys Lumerical are you using? 
  • Ansys Lumerical 2023 R1.1

 

• Do you run/submit to a job scheduler using a script? 
  • No script, just command

 

• Does the simulation run successfully?
  You can check the “simulationfilename_p0.log” file if the simulation is completed. 
  • Simulation did complete succesfully

 

• Can you open the simulation on your local desktop to view the results? 
  • Yes

 

• Are you using the bundled MPICH2 to run the simulation?
  • I’m indeed using the bundled MPICH2 from the Lumerical installation

 

• Please send the sample execution line you used to run the simulation on the cluster.
  • /cm/shared/apps/lumerical/2023-R1.1/mpich2/nemesis/bin/mpiexec -n 4 -host tue-login002 -env HOME /home/”MyPath”/Lumerical/test /cm/shared/apps/lumerical/2023-R1.1/bin/fdtd-engine-mpich2nem -t 1 /home/”MyPath”/Lumerical/test/Nanobeam.fsp

[Lito Yap]

@Jordi Lopez Leyva,

From the command you provided,

/.../mpiexec -n 4 -host tue-login002 -env HOME /.../test /.../fdtd-engine-mpich2nem -t 1 /.../Nanobeam.fsp

Are you running the simulation remotely from a Linux machine to another Linux machine, 'tue-login002' ?

Are you able to log in to the Linux machine, 'tue-login002', and run it directly from there (not remotely)?

i.e. 
/cm/shared/apps/lumerical/2023-R1.1/mpich2/nemesis/bin/mpiexec -n 4 /cm/shared/apps/lumerical/2023-R1.1/bin/fdtd-engine-mpich2nem -t 1 /home/”MyPath”/Lumerical/test/Nanobeam.fsp

Otherwise, try the command below, without the '-env HOME' options for the MPI. Let me know if the issue persists even though the simulation ran successfully. 

/cm/shared/apps/lumerical/2023-R1.1/mpich2/nemesis/bin/mpiexec -n 4 -host tue-login002 /cm/shared/apps/lumerical/2023-R1.1/bin/fdtd-engine-mpich2nem -t 1 /home/”MyPath”/Lumerical/test/Nanobeam.fsp