[torqueusers] Accelrys Material Studio Submission Script Example

[Chris Vaughan]

Hi,


I'm currently working with a customer on getting their jobs to run with Moab/Torque and I was wondering if anyone has an example Accelrys Material Studio job submission script they would be willing to share?


I saw the following post but no example job submission script.


http://www.clusterresources.com/pipermail/torqueusers/2006-January/003015.html




Many thanks in advance,
--
Chris Vaughan | Technical Consultant - EMEA

3000 Cathedral Hill | Guildford GU2 7YB | United Kingdom





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[Michael Robbert]

We use Materials Studio at our site, but do not work directly with submission scripts. The user submits their job from within the Materials Studio GUI and a submission script along with job data is all magically submitted to Torque behind the scenes. I have looked at the scripts that are generated and they are of little use without the data if I remember correctly. One thing to note though is that since that 2006 thread Accelrys has come out with Version 5 which has official support for Torque. We are still testing that version, but have 4.3 and 4.4 running without any problems.
If you have any questions for me please feel free to contact my directly.

Thanks,
Mike Robbert, HPC & Networking Engineer
Colorado School of Mines

On Mar 8, 2010, at 12:04 PM, Chris Vaughan wrote:

Hi,

I'm currently working with a customer on getting their jobs to run with Moab/Torque and I was wondering if anyone has an example Accelrys Material Studio job submission script they would be willing to share?

I saw the following post but no example job submission script.

http://www.clusterresources.com/pipermail/torqueusers/2006-January/003015.html


Many thanks in advance,

--
Chris Vaughan | Technical Consultant - EMEA
3000 Cathedral Hill | Guildford GU2 7YB | United Kingdom



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[Reddy, John]

Allow me to jump on the "If you've got a Materials Studio 5.0 job
submission script, please let me know" band wagon.



-John



---

John Reddy

Technology Architect

Information Technology Division - Unix Services

Brookhaven National Laboratory

jreddy at bnl.gov - 631-344-3284



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[Chris Samuel]

Post by Michael Robbert
Accelrys has come out with Version 5 which has official support for Torque

I remember when I was at VPAC having to patch Material Studio to not do stupid
things like assuming that any failure of the qstat command meant the job it
was querying had finished, they just needed to check for the right exit
status.

Hopefully things like that have been sorted out now!

cheers!
Chris
--
Chris Samuel : http://www.csamuel.org/ : Melbourne, VIC

This email may come with a PGP signature as a file. Do not panic.
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[John Koskie]

Chris,

I have had some success getting Materials Studio to run on our systems
with moab/torque. Materials Studio works entirely with torque, so the
following should work with any scheduler.

Please note that I am not a developer for Accelrys, I am just sharing
what I have found works.

First, you need to configure your gateway as described in their
manual:in the section "Installing Materials Studio on a server with a
queuing system", except substitute "TORQUE/dsd_torque" for LSF/dsd_lsf.

Now when you send a job to the gateway, MS will create a command file
for torque and then submit it via a qsub command, as given in the
comments in the script. If you have a fairly simple torque setup, this
may work. However, torque has many features not supported by MS

In our case, we require Accounting information and a maximum wall time
when submitting a job. To do this I had to do the following:
Adding the accounting line was simple. To do this, modify the file
$ACCELRYSDIR/Accelrys/MaterialsStudio50/etc/Gateway/root_default/dsd/commands/queues/TORQUE/torque.cfg
Uncomment the "params =" line and change it to "params = -A accountname".

Adding wall time, or any other parameters required a small hack to the
perl script
$ACCELRYSDIR/Accelrys/MaterialsStudio50/etc/Gateway/root_default/dsd/commands/queues/TORQUE/dsd_torque.pm
as follows:
diff dsd_torque.pm dsd_torque.pm.dist
90c90
< $params .= ",walltime=24:00:00 " ; #added by JEK for UMaine
torque install

These modifications worked, but as you can see, the drawback is that
users cant modify the variables at job submission time. You have to
user moab/maui commands after submission to do that.

cheers

John
--
John Koskie, Ph.D.
University of Maine
Advanced Computing Research Lab
20 Godfrey Dr.
Orono, ME 04473
207-866-6511
www.clusters.umaine.edu

Post by Chris Vaughan
Hi,
I'm currently working with a customer on getting their jobs to run
with Moab/Torque and I was wondering if anyone has an example Accelrys
Material Studio job submission script they would be willing to share?
I saw the following post but no example job submission script.
http://www.clusterresources.com/pipermail/torqueusers/2006-January/003015.html
Many thanks in advance,
--
*Chris Vaughan* | Technical Consultant - EMEA
3000 Cathedral Hill | Guildford GU2 7YB | United Kingdom
http://www.adaptivecomputing.com/sig.png
_______________________________________________
torqueusers mailing list
torqueusers at supercluster.org <mailto:torqueusers at supercluster.org>
http://www.supercluster.org/mailman/listinfo/torqueusers
------------------------------------------------------------------------
Hi,
I'm currently working with a customer on getting their jobs to run
with Moab/Torque and I was wondering if anyone has an example Accelrys
Material Studio job submission script they would be willing to share?
I saw the following post but no example job submission script.
http://www.clusterresources.com/pipermail/torqueusers/2006-January/003015.html
Many thanks in advance,
--
*Chris Vaughan* | Technical Consultant - EMEA
3000 Cathedral Hill | Guildford GU2 7YB | United Kingdom

[Prakash Velayutham]

Post by John Koskie
Chris,
I have had some success getting Materials Studio to run on our systems
with moab/torque. Materials Studio works entirely with torque, so the
following should work with any scheduler.
Please note that I am not a developer for Accelrys, I am just sharing
what I have found works.
First, you need to configure your gateway as described in their
manual:in the section "Installing Materials Studio on a server with a
queuing system", except substitute "TORQUE/dsd_torque" for LSF/
dsd_lsf.
Now when you send a job to the gateway, MS will create a command file
for torque and then submit it via a qsub command, as given in the
comments in the script. If you have a fairly simple torque setup, this
may work. However, torque has many features not supported by MS
In our case, we require Accounting information and a maximum wall time
Adding the accounting line was simple. To do this, modify the file
$ACCELRYSDIR/Accelrys/MaterialsStudio50/etc/Gateway/root_default/dsd/
commands/queues/TORQUE/torque.cfg
Uncomment the "params =" line and change it to "params = -A
accountname".
Adding wall time, or any other parameters required a small hack to the
perl script
$ACCELRYSDIR/Accelrys/MaterialsStudio50/etc/Gateway/root_default/dsd/
commands/queues/TORQUE/dsd_torque.pm
diff dsd_torque.pm dsd_torque.pm.dist
90c90
< $params .= ",walltime=24:00:00 " ; #added by JEK for UMaine
torque install
These modifications worked, but as you can see, the drawback is that
users cant modify the variables at job submission time. You have to
user moab/maui commands after submission to do that.
cheers
John
--
John Koskie, Ph.D.
University of Maine
Advanced Computing Research Lab
20 Godfrey Dr.
Orono, ME 04473
207-866-6511
www.clusters.umaine.edu

Post by Chris Vaughan
Hi,
I'm currently working with a customer on getting their jobs to run
with Moab/Torque and I was wondering if anyone has an example
Accelrys
Material Studio job submission script they would be willing to share?
I saw the following post but no example job submission script.
http://www.clusterresources.com/pipermail/torqueusers/2006-January/003015.html
Many thanks in advance,
--
*Chris Vaughan* | Technical Consultant - EMEA
3000 Cathedral Hill | Guildford GU2 7YB | United Kingdom
http://www.adaptivecomputing.com/sig.png
_______________________________________________
torqueusers mailing list
torqueusers at supercluster.org <mailto:torqueusers at supercluster.org>
http://www.supercluster.org/mailman/listinfo/torqueusers
------------------------------------------------------------------------
Hi,
I'm currently working with a customer on getting their jobs to run
with Moab/Torque and I was wondering if anyone has an example
Accelrys
Material Studio job submission script they would be willing to share?
I saw the following post but no example job submission script.
http://www.clusterresources.com/pipermail/torqueusers/2006-January/003015.html
Many thanks in advance,
--
*Chris Vaughan*

Hi John,

Which version of MS are you referring to in this email?

Thanks,
Prakash

[John Koskie]

Prakash,

Version 5, their latest

John

Post by John Koskie
Chris,
I have had some success getting Materials Studio to run on our systems
with moab/torque. Materials Studio works entirely with torque, so the
following should work with any scheduler.
Please note that I am not a developer for Accelrys, I am just sharing
what I have found works.
First, you need to configure your gateway as described in their
manual:in the section "Installing Materials Studio on a server with a
queuing system", except substitute "TORQUE/dsd_torque" for LSF/
dsd_lsf.
Now when you send a job to the gateway, MS will create a command file
for torque and then submit it via a qsub command, as given in the
comments in the script. If you have a fairly simple torque setup, this
may work. However, torque has many features not supported by MS
In our case, we require Accounting information and a maximum wall time
Adding the accounting line was simple. To do this, modify the file
$ACCELRYSDIR/Accelrys/MaterialsStudio50/etc/Gateway/root_default/dsd/
commands/queues/TORQUE/torque.cfg
Uncomment the "params =" line and change it to "params = -A accountname".
Adding wall time, or any other parameters required a small hack to the
perl script
$ACCELRYSDIR/Accelrys/MaterialsStudio50/etc/Gateway/root_default/dsd/
commands/queues/TORQUE/dsd_torque.pm
diff dsd_torque.pm dsd_torque.pm.dist
90c90
< $params .= ",walltime=24:00:00 " ; #added by JEK for UMaine
torque install
These modifications worked, but as you can see, the drawback is that
users cant modify the variables at job submission time. You have to
user moab/maui commands after submission to do that.
cheers
John
--
John Koskie, Ph.D.
University of Maine
Advanced Computing Research Lab
20 Godfrey Dr.
Orono, ME 04473
207-866-6511
www.clusters.umaine.edu

Post by Chris Vaughan
Hi,
I'm currently working with a customer on getting their jobs to run
with Moab/Torque and I was wondering if anyone has an example Accelrys
Material Studio job submission script they would be willing to share?
I saw the following post but no example job submission script.

"ttp://www.clusterresources.com/pipermail/torqueusers/2006-January/003015.html

Post by John Koskie

Post by Chris Vaughan
Many thanks in advance,
--
*Chris Vaughan* | Technical Consultant - EMEA
3000 Cathedral Hill | Guildford GU2 7YB | United Kingdom
"ttp://www.adaptivecomputing.com/sig.png
_______________________________________________
torqueusers mailing list
torqueusers at supercluster.org <mailto:torqueusers at supercluster.org>
"ttp://www.supercluster.org/mailman/listinfo/torqueusers
------------------------------------------------------------------------
Hi,
I'm currently working with a customer on getting their jobs to run
with Moab/Torque and I was wondering if anyone has an example Accelrys
Material Studio job submission script they would be willing to share?
I saw the following post but no example job submission script.

"ttp://www.clusterresources.com/pipermail/torqueusers/2006-January/003015.html

Post by John Koskie

Post by Chris Vaughan
Many thanks in advance,
--
*Chris Vaughan*

Hi John,
Which version of MS are you referring to in this email?
Thanks,
Prakash