Re: running Gadget 2 simulation on stampede

From: Andre Bubel <kontakt_at_andre-bubel.de>
Date: Sun, 20 Nov 2016 05:17:58 +0100

Hi,

I haven't worked with Gadget for a while, and don't have access to your
cluster, but I would check two things:

1. Does your InitCondFile path end with 'galaxy.param'? Looking at the
error message it seems that you only have specified the directory, not
the file itself.

2. Are the paths to your files the same on the cluster nodes as on the
machine you are submitting from? I.e. you might want to check *if you
can access the files on the computing nodes, e.g. with a mpi job that
just calls 'ls' on the directory.

Hope that helps. :)

Best,
Andre Bubel
*
On 19.11.2016 05:33, turhan nasri wrote:
> Hi people,
>
> I am trying to run an example Gadget simulation on stampede machine.
> While I have successfully created the executable Gadget 2 , made a new
> directory called /galaxy, copied galaxy.param and executable Gadget2
> to that directory. I have also made relavant changes to the file
> galaxy.param , changing the InitCondFile :
> the/path/to/gadget-2.0.7/Ics/galaxy_littleendian.dat
> and the output directory as well.
>
> however, when I submit the run with 16 processor with stampede, I get
> a following error:
>
> TACC: Starting up job 7877179
> TACC: Setting up parallel environment for MVAPICH2+mpispawn.
> TACC: Starting parallel tasks...
>
> This is Gadget, version `2.0'.
>
> Running on 16 processors.
>
> Allocated 25 MByte communication buffer per processor.
>
> Communication buffer has room for 504122 particles in gravity computation
> Communication buffer has room for 204800 particles in density computation
> Communication buffer has room for 163840 particles in hydro computation
> Communication buffer has room for 163840 particles in domain decomposition
>
>
> Hubble (internal units) = 0.1
> G (internal units) = 43007.1
> UnitMass_in_g = 1.989e+43
> UnitTime_in_s = 3.08568e+16
> UnitVelocity_in_cm_per_s = 100000
> UnitDensity_in_cgs = 6.76991e-22
> UnitEnergy_in_cgs = 1.989e+53
>
>
> *Can't find initial conditions file.neither as
> '/scratch/03858/thaque56/umassd-hpc-tazkerahaque/Final_Project/Gadget-2.0.7/ICs/galaxy_littleendian.d/scratch/03858/thaque56/umassd-hpc-tazkerahaque/Final_Project/Gadget-2.0.7/galaxy/.0'
> nor as
> '/scratch/03858/thaque56/umassd-hpc-tazkerahaque/Final_Project/Gadget-2.0.7/ICs/galaxy_littleendian.d/scratch/03858/thaque56/umassd-hpc-tazkerahaque/Final_Project/Gadget-2.0.7/galaxy/'
> *
> TACC: Shutdown complete. Exiting.*
> *
>
> I checked it miltiple times whether I have given the right path to the
> /ICs dir and it's obviuosly OK, I just don't see why It cannot locate
> the file. I did the same thing in my local machine with 4 processor
> and I got it running and produced output files. If anyone see what's
> going wrong here, would be very useful to notify me. thanks
>
Received on 2016-11-20 05:18:02