CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > Software User Forums > SU2

Parallelizing SU2 in PBS

Register Blogs Members List Search Today's Posts Mark Forums Read

Reply
 
LinkBack Thread Tools Search this Thread Display Modes
Old   July 29, 2019, 10:06
Post Parallelizing SU2 in PBS
  #1
New Member
 
Nadeem Kever
Join Date: Jul 2019
Posts: 4
Rep Power: 6
NKever is on a distinguished road
Hi,

I am trying to run the shape_optimization.py script and use all my available nodes in PBS and I don't think I am doing this right.

Here is my script:

Code:
#PBS -q devel

##PBS -q long

##PBS -q normal

#PBS -W group_list=a1489

#PBS -lselect=50:ncpus=28:model=bro,walltime=02:00:00

##PBS -lselect=80:ncpus=28:model=bro,walltime=08:00:00

##PBS -lselect=80:ncpus=28:model=bro,walltime=50:00:00

#PBS -N test_su2

#

# Request that regular output and terminal output go to the same file

#PBS -j oe

#PBS -m n

# go to where the qsub was performed.

cd $PBS_O_WORKDIR

# Running Program

export SU2_RUN="/home6/nkever/su2/install/SU2/bin"

export SU2_HOME="/home6/nkever/su2/src/SU2"

export PATH=$PATH:$SU2_RUN

export PYTHONPATH=$PYTHONPATH:$SU2_RUN

module load mpi-sgi/mpt

module load python/2.7.15

module load comp-intel/2018.0.128

./shape_optimization.py -g CONTINUOUS_ADJOINT -o SLSQP -f inv_NACA0012_basic.cfg -n 400

echo "finished mpirun"

So I think the issue may be the -n, my interpretation is that the number of partitions tells su2 the amount of nodes. How do I use all my nodes?

I've seen this thread already, but I'm not sure it addresses my question. Thank you!
NKever is offline   Reply With Quote

Old   August 8, 2019, 16:39
Default
  #2
New Member
 
Jayant Mukhopadhaya
Join Date: Jul 2018
Posts: 3
Rep Power: 7
jayantmukho is on a distinguished road
Hey Nadeem,

Is your issue that PBS doesn't use the different nodes and just tries to start all 400 processes on 1 node?

I had this particular issue when I was trying to run using openmpi with PBS. In that case, the openmpi installation that I was using wasn't configured to work with torque/pbs (https://www.open-mpi.org/faq/?category=tm). It required a particular option to be set when configuring openmpi.

I haven't used SGI MPT before so I am not certain if there is a similar issue that would need to be rectified.
jayantmukho is offline   Reply With Quote

Old   August 25, 2019, 05:42
Default
  #3
pcg
Senior Member
 
Pedro Gomes
Join Date: Dec 2017
Posts: 465
Rep Power: 13
pcg is on a distinguished road
Hi Nadeem,

The problem might be that all nodes are executing the shape optimization script, and only one should since it is not an mpi-ready program (I think).

The simplest way to do this kind of thing would be to wrap the SU2 execution in a script that submits an individual job per SU2 run and waits for results.

Cheers,
Pedro
pcg is offline   Reply With Quote

Reply

Tags
pbs, su2

Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are Off
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
Problem running SU2 using PBS jzhen SU2 11 July 25, 2019 14:10
Introducing SU2 International Developers Society (IDS) fpalacios SU2 News & Announcements 1 June 17, 2019 23:38
Running SU2 Pyhton Script in Parallel with PBS Torque andromeda91 SU2 1 October 20, 2014 15:25
parallel computation with PBS error tsevine SU2 4 July 4, 2014 07:21
Fluent jobs through pbs ibnkureshi FLUENT 5 June 9, 2011 14:43


All times are GMT -4. The time now is 08:57.