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(Before You Go The First Time)
 
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{{Template:CCDelete}}
 
{{Software
 
{{Software
|package_name=LUMERICAL
+
|package_name=FDTD
 
|package_description=Providing photonic and optoelectronic TCAD device simulation and photonic integrated circuit design products
 
|package_description=Providing photonic and optoelectronic TCAD device simulation and photonic integrated circuit design products
 
|package_idnumber=34
 
|package_idnumber=34
 
}}
 
}}
 +
{{Template:GrahamUpdate}}
  
==Licensing Information==
+
=Introduction=
  
 
As of February 2013, SHARCNET no long holds the FDTD Solutions (also known as front end or GUI) licence. Users who need to use FDTD Solutions for their model construction and data analysis must obtain their own licences.  
 
As of February 2013, SHARCNET no long holds the FDTD Solutions (also known as front end or GUI) licence. Users who need to use FDTD Solutions for their model construction and data analysis must obtain their own licences.  
Line 11: Line 13:
 
<font color="red">Users who previously used CAD - the Unix port of FDTD Solution GUI for model construction and data analysis - must now either possess a licence (a FLEX managed licence) that allows them to use CAD on SHARCNET systems, or use FDTD Solutions on their own computers.</font>
 
<font color="red">Users who previously used CAD - the Unix port of FDTD Solution GUI for model construction and data analysis - must now either possess a licence (a FLEX managed licence) that allows them to use CAD on SHARCNET systems, or use FDTD Solutions on their own computers.</font>
  
Thanks to the kind donation of FDTD Engine licences by Lumerical solutions, Inc., SHARCNET will continue to support the serial farming and parallel processing of FDTD simulations on SHARCNET systems.
+
Thanks to the kind donation of FDTD Engine licences by Lumerical solutions, Inc., SHARCNET will continue to support the serial farming and parallel processing of FDTD simulations on SHARCNET systems. Note the FDTD engines are the only components that are supported. We no longer have the licence for the frontend FDTD Solutions.
 
+
==Version Changes==
+
 
+
The latest release is 8.5.3 and this is the only version supported. The licences to the older versions have expired.
+
 
+
Note the FDTD engines are the only components that are supported. We no longer have the licence for the frontend FDTD Solutions.
+
  
 
==The Workflow==
 
==The Workflow==
Line 30: Line 26:
  
 
To transfer data between one's computers and SHARCNET systems, one may use the common secure file transfer client software such as SSH Secure File Transfer Client, WinSCP, putty-sftp, etc. Users are referred to the [https://www.sharcnet.ca/help/index.php/SSH tutorials] on using these tools.
 
To transfer data between one's computers and SHARCNET systems, one may use the common secure file transfer client software such as SSH Secure File Transfer Client, WinSCP, putty-sftp, etc. Users are referred to the [https://www.sharcnet.ca/help/index.php/SSH tutorials] on using these tools.
<!--
 
==Account Preparation (version 6 only)==
 
  
Before running lumerical on <b>requin</b> or <b>rainbow</b> verify that the following "ini" file exists and contains the server and type line as shown.  If it doesnt exist created it.  Note that if you have been running version 7 jobs the "ini" file might be corrupted and need to be re-created:
+
=Version Selection=
  
1)  First create the directory using the following command:
+
<pre>
 +
module load fdtd/8.19.1466
 +
</pre>
  
mkdir -p ~/.config/Lumerical
+
==License Configuration==
  
2)  Using an editor (such as vi) open the "ini" file:
+
First check if you have a folder named <tt>.config/Lumerical</tt> in your home directory. Use command
  
  vi .config/Lumerical/"FDTD Solutions.ini"
+
  cd
 +
ls -a
  
3) Paste in the following 3 lines and save the file:
+
to list all files including the normally "hidden" files with a leading '.'
  
[license]
+
If the folder doesn't exist, create it:
server\host=db.uwo.sharcnet
+
type=floating
+
-->
+
  
==Loading Lumerical and Support Library Modules==
+
mkdir -p ~/.config/Lumerical
  
Before you can run Lumerical, you must load the Lumerical module:
+
If the folder exists and contains the license file <tt>FDTD Solutions.ini</tt> remove the license file:
  
<pre>
+
cd ~/.config/Lumerical
module load lumerical
+
rm -f "FDTD Solutions.ini"
</pre>
+
  
As well one must perform the following
+
OR rename it to something like <tt>FDTD Solutions.ini.bak</tt>. Note there is a space in the filename between FDTD and Solutions.ini hence why quotes are being used.  Removing this file should clean the cache of any corrupted Lumerical license information from previous versions, then it will remain to simply recreate the file using a text editor by copying in the following text:
  
<pre>
+
[roberpj@saw-login2:~] nano ~/.config/Lumerical/"FDTD Solutions.ini"
module unload openmpi intel compile
+
[license]
module load gcc/4.3.4
+
type=flex
module load openmpi/gcc/1.4.2
+
flexserver\host=27015@license2.sharcnet.ca
</pre>
+
  
==Before You Go==
+
The licence file can also be created with the following commands
  
Before you run Lumerical simulations for the first time, remove the existing configuration file in your home directory, if any:
+
echo [license] > "FDTD Solutions.ini"
 +
echo type=flex >> "FDTD Solutions.ini"
 +
echo "flexserver\host=27015@license2.sharcnet.ca" >> "FDTD Solutions.ini"
  
cd ~/.config
+
Another option for creating or updating the <tt>FDTD Solutions.ini</tt> file is to load the lumerical module and then run the <i>fdtd-config-license</i> script. Specify license2.sharcnet.ca for the server, and specify 27015 for the port. The result will be the same as the previous stanza.  If you want to use your own license, replace the contents of <tt>FDTD Solutions.ini</tt> with your own license information.
  rm FDTD\ Solutions.ini
+
  
or rename it, e.g. as <tt>"FDTD Solutions.ini.bak"</tt>. Note there is a space in the file name and you will need to use '\' followed by a space for the file name.
+
=Examples=
  
This cleans the cached or corrupted Lumerical licencing infomation for previous versions. Then, recreate the file again, put the following lines in it and save it
+
==Queue Usage==
+
[license]
+
type=flex
+
flexserver\host=license2.uwo.sharcnet
+
flexserver\port=27015
+
  
You should be ready to go.
+
o First copy the examples into your account:
  
Note: If you are using your own licence, then, you should replace this file with your own licence file, while keeping the file name <tt>"FDTD Solutions.ini.bak"</tt>.
+
mkdir 8.19.1466-examples
 +
cp /opt/sharcnet/fdtd/8.19.1466/examples/* 8.19.1466-examples
 +
cd 8.19.1466-examples
  
==Using FDTD Solutions GUI CAD==
+
===Submit Serial Job===
  
This section is for those who want to build simulation models and prepare data files using Lumerical graphic user interface on SHARCNET systems using their own licence.
+
o To demonstrate howto submit <i>nanowire.fsp</i> to the serial queue:
  
Without your own licence for FDTD Solutions (also named CAD for Unix), you will not be able to use it on SHARCNET systems.
+
module load fdtd/8.19.1466
 +
sqsub -q serial -r 1.5h -o ofile.%J fdtd-engine-mpich2nem nanowire.fsp
  
As of February 2013, SHARCNET no longer has the licence to the front end GUI (CAD for Linux). Users who previously used CAD - the Unix port of FDTD Solution GUI for model construction and data analysis - must now either possess a licence (a FLEX managed licence) that allows them to use CAD on SHARCNET systems, or use FDTD Solutions on their own computers.
+
===Submit Parallel Job===
  
If one pursues to use CAD on SHARCNET systems using their own licence, he/she must first contact the [mailto:bge@sharcnet.ca administrator] for technical arrangements.
+
o To demonstrate howto submit <i>paralleltest.fsp</i> into the mpi queue:
  
To run CAD remotely on SHARCNET systems (login nodes or visualization systems) from a Windows desktop, one needs an X server running on Windows. We recommend using [https://www.sharcnet.ca/help/index.php/Remote_Graphical_Connections#Xming_Software Xming + Putty] or [http://www.cygwin.com Cygwin/X]. They are all free. Or if your connecting from a linux desktop then run the "ssh -X clustername" command for instance:
+
module unload intel openmpi
 +
module load fdtd/8.19.1466 intel/12.1.3 openmpi/intel/1.6.2
 +
export LD_LIBRARY_PATH=/opt/sharcnet/openmpi/1.6.2/intel/lib:$LD_LIBRARY_PATH
 +
sqsub -r 1h -q mpi -n 4 --mpp 1g -o ofile.%J fdtd-engine-ompi-lcl paralleltest.fsp
  
<pre>
+
==Interactive Usage==
ssh -X viz4-uwo.sharcnet.ca
+
module load lumerical
+
cd /scratch/$USER
+
cp /opt/sharcnet/lumerical/version/examples/paralleltest.fsp .
+
CAD paralleltest.fsp
+
</pre>
+
  
==Submitting A Serial Job==
+
This section describes howto run fdte compute jobs from the command line useful for testing before submitting a production job into the queue.
  
One must load necessary modules before submitting a job. Loading a module sets the environment variables needed for the running executables. The environment variables set will be inherited on the compute nodes automatically
+
===Run Serial Test===
  
module load lumerical
+
o To run a serial (single core) interactive test on vdi or iqaluk do:
sqsub -q serial -r 1.5h -o <i>output</i>%J fdtd-engine-mpich2nem <i>simulation</i>.fsp
+
  
==Submitting A Parallel Job==
+
ssh vdi-centos6.user.sharcnet.ca
 +
or ssh iqaluk.sharcnet.ca
 +
module load fdtd/8.7.3
 +
fdtd-engine-mpich2nem nanowire.fsp
  
Starting with version <b>7</b> the lumerical module must be loaded first before submitting a job or running the CAD command for instance as follows:
+
===Run Parallel Test===
<!--
+
 
 +
o To run a parallel interactive test on vdi-centos6 or iqaluk do:
 +
 
 +
ssh vdi-centos6.user.sharcnet.ca
 +
or ssh iqaluk.sharcnet.ca
 
  module unload intel openmpi
 
  module unload intel openmpi
  module load intel/11.0.083 openmpi/intel/1.4.2
+
  module load fdtd/8.7.3 intel/12.1.3 openmpi/intel/1.6.2
  module load lumerical/7.5.6
+
  export LD_LIBRARY_PATH=/opt/sharcnet/openmpi/1.6.2/intel/lib:$LD_LIBRARY_PATH
-->
+
  mpirun -np 4 --bind-to-core fdtd-engine-ompi-lcl paralleltest.fsp
module load lumerical
+
  sqsub -q mpi -r 1.5h -n <i>num_procs</i> -o <i>output</i>%J fdtd-engine-ompi-lcl <i>parallel_simulation</i>.fsp
+
  
For further details about <i>Distributed simulation testing</i> please refer to the documentation on Lumerical's web site which can be found here[http://www.lumerical.com/fdtd_online_help/user_guide_distributed_simulations.php].
+
o To run a parallel interactive test on a sharcnet viz station (running fedora) do :
  
See also [http://docs.lumerical.com/en/fdtd/user_guide.html Lumerical's User Guide]
+
ssh viz10-uwo.sharcnet.ca
 +
module load fdtd/8.7.3
 +
/usr/lib64/openmpi/bin/mpirun -np 8 -bind-to core fdtd-engine-ompi-lcl paralleltest.fsp
 +
 
 +
o  To run a parallel interactive test on the sharcnet vdi machine do:
 +
 
 +
ssh vdi-centos6.user.sharcnet.ca
 +
module load fdtd/8.7.3
 +
/usr/lib64/openmpi/bin/mpirun -np 8 -bind-to-core fdtd-engine-ompi-lcl paralleltest.fsp
 +
 
 +
=General Notes=
 +
 
 +
==Using FDTD Solutions GUI CAD==
 +
 
 +
This section is for those who want to build simulation models and prepare data files using Lumerical graphic user interface on SHARCNET systems using their own licence.
 +
 
 +
Without your own licence for FDTD Solutions (also named CAD for Unix), you will be unable to use the GUI on SHARCNET systems.  As of February 2013, SHARCNET no longer has the licence to the front end GUI (CAD for Linux).  Users who previously used CAD - the Unix port of FDTD Solution GUI for model construction and data analysis - must now either possess a licence (a FLEX managed licence) that allows them to use CAD on SHARCNET systems, or use FDTD Solutions on their own computers.  If you try to run CAD withoutyour own license, and error message box will pop up such as:
 +
 
 +
<pre>
 +
                    Error: Unable to check out a FlexNet license.
 +
                    The flexNet error code is: -18, which corresponds to the error:
 +
                    License server system does not support this feature.
 +
                    And so forth
 +
</pre>
 +
 
 +
 
 +
If one pursues to use CAD on SHARCNET systems using their own licence, he/she must first contact the [mailto:bge@sharcnet.ca administrator] for technical arrangements.
 +
 
 +
To run CAD remotely on a SHARCNET login or devel node from a Windows desktop, one needs a X server running on Windows. We recommend using [https://www.sharcnet.ca/help/index.php/Remote_Graphical_Connections#Xming_Software Xming + Putty] or [http://www.cygwin.com Cygwin/X] which are all free. Or if your connecting from a linux desktop then run the "ssh -X clustername" command.  To establish a graphical capable session on a sharcnet Visualization machine, start a remote desktop by clicking the blue icon beside vdi-centos6 on https://www.sharcnet.ca/my/systems.  Once connected do the following:
 +
 
 +
<pre>
 +
module load fdtd/8.7.3
 +
cd /scratch/$USER
 +
cp /opt/sharcnet/fdtd/8.7.3/examples/paralleltest.fsp .
 +
CAD paralleltest.fsp
 +
</pre>
  
 
==Using A Script to Submit Batch Jobs==
 
==Using A Script to Submit Batch Jobs==
Line 162: Line 189:
 
     sqsub -q serial -r 1.5h -o output%J fdtd-engine-mpich2nem simulation$i.fsp
 
     sqsub -q serial -r 1.5h -o output%J fdtd-engine-mpich2nem simulation$i.fsp
 
     i=$((i+1))
 
     i=$((i+1))
 +
done
 +
</pre>
 +
 +
One may also use a C/C++ like syntax for the above loop
 +
 +
<pre>
 +
#!/bin/sh
 +
n=100
 +
 +
for((i=1;i<=n;i++)); do
 +
    sqsub -q serial -r 1.5h -o output%J fdtd-engine-mpich2nem simulation$i.fsp
 
done
 
done
 
</pre>
 
</pre>
Line 167: Line 205:
 
Note the examples shown above are not just for serial jobs, it can be used for parallel jobs too. One only needs to replace the sqsub options with those relevant to parallel jobs.
 
Note the examples shown above are not just for serial jobs, it can be used for parallel jobs too. One only needs to replace the sqsub options with those relevant to parallel jobs.
  
==References==
+
==Show Sharcnet License Usage==
 +
 
 +
<pre>
 +
[roberpj@orc-login2:~] module load fdtd
 +
 
 +
[roberpj@orc-login2:~] fdtdstat
 +
lmutil - Copyright (c) 1989-2013 Flexera Software LLC. All Rights Reserved.
 +
Flexible License Manager status on Wed 3/1/2017 18:39
 +
License server status: 27015@license2.sharcnet.ca
 +
    License file(s) on license2.sharcnet.ca: licenses/LUMERICL/FDTD_Solutions_engine_2015_2016.lic:licenses/LUMERICL/FDTD_Solutions_engine_2016_2017.lic:licenses/LUMERICL/start.lic:licenses/LUMERICL/FDTD_Solutions_engine_2016_2017.lic:
 +
license2.sharcnet.ca: license server UP v11.12
 +
Vendor daemon status (on license2):
 +
  LUMERICL: UP v11.12
 +
Feature usage info:
 +
Users of FDTD_Solutions_engine:  (Total of 10 licenses issued;  Total of 2 licenses in use)
 +
  "FDTD_Solutions_engine" v1.0, vendor: LUMERICL
 +
  floating license
 +
    hfoy orc98 /dev/tty (v1.0) (license2.sharcnet.ca/27015 542), start Wed 3/1 15:47
 +
    hfoy orc303 /dev/tty (v1.0) (license2.sharcnet.ca/27015 280), start Wed 3/1 16:26
 +
Users of start:  (Total of 1 license issued;  Total of 0 licenses in use)
 +
</pre>
 +
 
 +
=References=
  
 
o Lumerical Homepage<br>
 
o Lumerical Homepage<br>
http://www.lumerical.com/
+
http://www.lumerical.com
<!--
+
 
o Primer to Use Lumerical FDTD Solutions on SHARCNET
+
o Parallel Engine Issues<br>
<a href="/Documents/tutorials/Lumerical/Lumerical_FDTD_Instructions-HJ-JS.pdf">/Documents/tutorials/Lumerical/Lumerical_FDTD_Instructions-HJ-JS.pdf</a>
+
http://docs.lumerical.com/en/install_linux_install_faq.html
-->
+
 
 +
o Run FDTD in Single Processor Mode<br>
 +
http://docs.lumerical.com/en/index.html?ref_scripts_run.html
 +
 
 +
<!--checked2016-->

Latest revision as of 10:08, 6 June 2019

This page is scheduled for deletion because it is either redundant with information available on the CC wiki, or the software is no longer supported.
FDTD
Description: Providing photonic and optoelectronic TCAD device simulation and photonic integrated circuit design products
SHARCNET Package information: see FDTD software page in web portal
Full list of SHARCNET supported software


Note: Some of the information on this page is for our legacy systems only. The page is scheduled for an update to make it applicable to Graham.


Introduction

As of February 2013, SHARCNET no long holds the FDTD Solutions (also known as front end or GUI) licence. Users who need to use FDTD Solutions for their model construction and data analysis must obtain their own licences.

Users who previously used CAD - the Unix port of FDTD Solution GUI for model construction and data analysis - must now either possess a licence (a FLEX managed licence) that allows them to use CAD on SHARCNET systems, or use FDTD Solutions on their own computers.

Thanks to the kind donation of FDTD Engine licences by Lumerical solutions, Inc., SHARCNET will continue to support the serial farming and parallel processing of FDTD simulations on SHARCNET systems. Note the FDTD engines are the only components that are supported. We no longer have the licence for the frontend FDTD Solutions.

The Workflow

In general, one conducts FDTD simulations in following steps:

  • Constructing model, preparing data (.fsp files), this is typically done on one's local computers, not SHARCNET clusters;
  • Bringing data files to SHARCNET;
  • Running simulations on SHARCNET using FDTD engines;
  • Getting results back and performing analysis and modifications on local computers

It is assumed that users prepare their simulation files on their own computers with FDTD Solutions and then carry on large scale simulations--being large number of cases or large size of problems that are not feasible on their computers--on SHARCNET systems through serial farming or parallel processing. Typically this will involve transferring simulation files to SHARCNET and copying computed results back to their local computers for analysis.

To transfer data between one's computers and SHARCNET systems, one may use the common secure file transfer client software such as SSH Secure File Transfer Client, WinSCP, putty-sftp, etc. Users are referred to the tutorials on using these tools.

Version Selection

module load fdtd/8.19.1466

License Configuration

First check if you have a folder named .config/Lumerical in your home directory. Use command

cd
ls -a

to list all files including the normally "hidden" files with a leading '.'

If the folder doesn't exist, create it:

mkdir -p ~/.config/Lumerical

If the folder exists and contains the license file FDTD Solutions.ini remove the license file:

cd ~/.config/Lumerical
rm -f "FDTD Solutions.ini"

OR rename it to something like FDTD Solutions.ini.bak. Note there is a space in the filename between FDTD and Solutions.ini hence why quotes are being used. Removing this file should clean the cache of any corrupted Lumerical license information from previous versions, then it will remain to simply recreate the file using a text editor by copying in the following text:

[roberpj@saw-login2:~] nano ~/.config/Lumerical/"FDTD Solutions.ini"
[license]
type=flex
flexserver\host=27015@license2.sharcnet.ca

The licence file can also be created with the following commands

echo [license] > "FDTD Solutions.ini"
echo type=flex >> "FDTD Solutions.ini"
echo "flexserver\host=27015@license2.sharcnet.ca" >> "FDTD Solutions.ini"

Another option for creating or updating the FDTD Solutions.ini file is to load the lumerical module and then run the fdtd-config-license script. Specify license2.sharcnet.ca for the server, and specify 27015 for the port. The result will be the same as the previous stanza. If you want to use your own license, replace the contents of FDTD Solutions.ini with your own license information.

Examples

Queue Usage

o First copy the examples into your account:

mkdir 8.19.1466-examples
cp /opt/sharcnet/fdtd/8.19.1466/examples/* 8.19.1466-examples
cd 8.19.1466-examples

Submit Serial Job

o To demonstrate howto submit nanowire.fsp to the serial queue:

module load fdtd/8.19.1466
sqsub -q serial -r 1.5h -o ofile.%J fdtd-engine-mpich2nem nanowire.fsp

Submit Parallel Job

o To demonstrate howto submit paralleltest.fsp into the mpi queue:

module unload intel openmpi
module load fdtd/8.19.1466 intel/12.1.3 openmpi/intel/1.6.2
export LD_LIBRARY_PATH=/opt/sharcnet/openmpi/1.6.2/intel/lib:$LD_LIBRARY_PATH
sqsub -r 1h -q mpi -n 4 --mpp 1g -o ofile.%J fdtd-engine-ompi-lcl paralleltest.fsp

Interactive Usage

This section describes howto run fdte compute jobs from the command line useful for testing before submitting a production job into the queue.

Run Serial Test

o To run a serial (single core) interactive test on vdi or iqaluk do:

ssh vdi-centos6.user.sharcnet.ca
or ssh iqaluk.sharcnet.ca
module load fdtd/8.7.3
fdtd-engine-mpich2nem nanowire.fsp

Run Parallel Test

o To run a parallel interactive test on vdi-centos6 or iqaluk do:

ssh vdi-centos6.user.sharcnet.ca
or ssh iqaluk.sharcnet.ca
module unload intel openmpi
module load fdtd/8.7.3 intel/12.1.3 openmpi/intel/1.6.2
export LD_LIBRARY_PATH=/opt/sharcnet/openmpi/1.6.2/intel/lib:$LD_LIBRARY_PATH
mpirun -np 4 --bind-to-core fdtd-engine-ompi-lcl paralleltest.fsp

o To run a parallel interactive test on a sharcnet viz station (running fedora) do :

ssh viz10-uwo.sharcnet.ca
module load fdtd/8.7.3
/usr/lib64/openmpi/bin/mpirun -np 8 -bind-to core fdtd-engine-ompi-lcl paralleltest.fsp

o To run a parallel interactive test on the sharcnet vdi machine do:

ssh vdi-centos6.user.sharcnet.ca
module load fdtd/8.7.3
/usr/lib64/openmpi/bin/mpirun -np 8 -bind-to-core fdtd-engine-ompi-lcl paralleltest.fsp

General Notes

Using FDTD Solutions GUI CAD

This section is for those who want to build simulation models and prepare data files using Lumerical graphic user interface on SHARCNET systems using their own licence.

Without your own licence for FDTD Solutions (also named CAD for Unix), you will be unable to use the GUI on SHARCNET systems. As of February 2013, SHARCNET no longer has the licence to the front end GUI (CAD for Linux). Users who previously used CAD - the Unix port of FDTD Solution GUI for model construction and data analysis - must now either possess a licence (a FLEX managed licence) that allows them to use CAD on SHARCNET systems, or use FDTD Solutions on their own computers. If you try to run CAD withoutyour own license, and error message box will pop up such as:

                     Error: Unable to check out a FlexNet license.
                     The flexNet error code is: -18, which corresponds to the error:
                     License server system does not support this feature.
                     And so forth


If one pursues to use CAD on SHARCNET systems using their own licence, he/she must first contact the administrator for technical arrangements.

To run CAD remotely on a SHARCNET login or devel node from a Windows desktop, one needs a X server running on Windows. We recommend using Xming + Putty or Cygwin/X which are all free. Or if your connecting from a linux desktop then run the "ssh -X clustername" command. To establish a graphical capable session on a sharcnet Visualization machine, start a remote desktop by clicking the blue icon beside vdi-centos6 on https://www.sharcnet.ca/my/systems. Once connected do the following:

module load fdtd/8.7.3
cd /scratch/$USER
cp /opt/sharcnet/fdtd/8.7.3/examples/paralleltest.fsp .
CAD paralleltest.fsp

Using A Script to Submit Batch Jobs

Suppose you have a number of jobs you want to process at once, and you want to avoid typing job submission command multiple times, the simplest way is to put the commands in a shell script and run the shell script instead. To create a script, use an editor to create a file, say "runsim.sh", and put the following lines

#!/bin/sh
sqsub -q serial -r 1.5h -o output%J fdtd-engine-mpich2nem simulation1.fsp
sqsub -q serial -r 1.5h -o output%J fdtd-engine-mpich2nem simulation2.fsp
... ...
sqsub -q serial -r 1.5h -o output%J fdtd-engine-mpich2nem simulationN.fsp

and save it.

To make this shell script executable, use command

chmod +x runsim.sh

To run the simulations 1 to N, as specified in the script, simply execute the command at the command line

./runsim.sh

If you have a large number of jobs and each of the .fsp files follows some pattern, e.g. a case number in ascending consecutive integer, then, you may simplify the script using a loop. The following shows an example of a script "runsims.sh" that submits 100 jobs in a loop

#!/bin/sh
n=100

i=1
while [ $i -le $n ]; do
    sqsub -q serial -r 1.5h -o output%J fdtd-engine-mpich2nem simulation$i.fsp
    i=$((i+1))
done

One may also use a C/C++ like syntax for the above loop

#!/bin/sh
n=100

for((i=1;i<=n;i++)); do
    sqsub -q serial -r 1.5h -o output%J fdtd-engine-mpich2nem simulation$i.fsp
done

Note the examples shown above are not just for serial jobs, it can be used for parallel jobs too. One only needs to replace the sqsub options with those relevant to parallel jobs.

Show Sharcnet License Usage

[roberpj@orc-login2:~] module load fdtd

[roberpj@orc-login2:~] fdtdstat
lmutil - Copyright (c) 1989-2013 Flexera Software LLC. All Rights Reserved.
Flexible License Manager status on Wed 3/1/2017 18:39
License server status: 27015@license2.sharcnet.ca
    License file(s) on license2.sharcnet.ca: licenses/LUMERICL/FDTD_Solutions_engine_2015_2016.lic:licenses/LUMERICL/FDTD_Solutions_engine_2016_2017.lic:licenses/LUMERICL/start.lic:licenses/LUMERICL/FDTD_Solutions_engine_2016_2017.lic:
license2.sharcnet.ca: license server UP v11.12
Vendor daemon status (on license2):
  LUMERICL: UP v11.12
Feature usage info:
Users of FDTD_Solutions_engine:  (Total of 10 licenses issued;  Total of 2 licenses in use)
  "FDTD_Solutions_engine" v1.0, vendor: LUMERICL
  floating license
    hfoy orc98 /dev/tty (v1.0) (license2.sharcnet.ca/27015 542), start Wed 3/1 15:47
    hfoy orc303 /dev/tty (v1.0) (license2.sharcnet.ca/27015 280), start Wed 3/1 16:26
Users of start:  (Total of 1 license issued;  Total of 0 licenses in use)

References

o Lumerical Homepage
http://www.lumerical.com

o Parallel Engine Issues
http://docs.lumerical.com/en/install_linux_install_faq.html

o Run FDTD in Single Processor Mode
http://docs.lumerical.com/en/index.html?ref_scripts_run.html