Re: Need help to start running Gadget

From: Yahya Alivov <alivov.y_at_gmail.com>
Date: Wed, 18 Jun 2014 14:01:06 -0700

Hi Yves,

Thank you for your help, it helped! After typing '/' before 'home', it did
not give any error, and seems to start to calculate. However, it takes so
long to finish calculations, more than 12 hours with 2 processors working.
What is more confusing is that according to User's Guide it should print
out a bunch of log-messages that inform about the present steps taken by
the code, but no messages are printed on the screen, after some messages
were printed after beginning (see copy below). The cursor just stays on one
place blinking. Is this normal? Thank you very much for your help. Yahya.

*Next is copy from the screen:*

alivov_at_yahya:~/Downloads/Gadget-2.0.7/galaxy$ mpirun -np 2 ./Gadget2
galaxy.param

This is Gadget, version `2.0'.

Running on 2 processors.
Code was compiled with periodic boundary conditions switched on.
You must set `PeriodicBoundariesOn=1', or recompile the code.
alivov_at_yahya:~/Downloads/Gadget-2.0.7/galaxy$ mpirun -np 2 ./Gadget2
galaxy.param

This is Gadget, version `2.0'.

Running on 2 processors.
Code was compiled with periodic boundary conditions switched on.
You must set `PeriodicBoundariesOn=1', or recompile the code.
alivov_at_yahya:~/Downloads/Gadget-2.0.7/galaxy$ mpirun -np 2 ./Gadget2
galaxy.param

This is Gadget, version `2.0'.

Running on 2 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 152408 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

Task=0 FFT-Slabs=64
Task=1 FFT-Slabs=64

Allocated 3.43323 MByte for particle storage. 80


reading file
`/home/alivov/Downloads/Gadget-2.0.7/ICs/galaxy_littleendian.dat' on task=0
(contains 60000 particles.)
distributing this file to tasks 0-1
Type 0 (gas): 0 (tot= 0000000000) masstab=0
Type 1 (halo): 40000 (tot= 0000040000) masstab=0.00104634
Type 2 (disk): 20000 (tot= 0000020000) masstab=0.00023252
Type 3 (bulge): 0 (tot= 0000000000) masstab=0
Type 4 (stars): 0 (tot= 0000000000) masstab=0
Type 5 (bndry): 0 (tot= 0000000000) masstab=0

reading done.
Total number of particles : 0000060000

allocated 0.0762939 Mbyte for ngb search.

Allocated 3.30359 MByte for BH-tree. 64

^C[mpiexec_at_yahya] Sending Ctrl-C to processes as requested
[mpiexec_at_yahya] Press Ctrl-C again to force abort
alivov_at_yahya:~/Downloads/Gadget-2.0.7/galaxy$ ^C
alivov_at_yahya:~/Downloads/Gadget-2.0.7/galaxy$ mpirun -np 2 ./Gadget2
galaxy.param

This is Gadget, version `2.0'.

Running on 2 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 152408 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

Task=0 FFT-Slabs=64
Task=1 FFT-Slabs=64

Allocated 3.43323 MByte for particle storage. 80


reading file
`/home/alivov/Downloads/Gadget-2.0.7/ICs/galaxy_littleendian.dat' on task=0
(contains 60000 particles.)
distributing this file to tasks 0-1
Type 0 (gas): 0 (tot= 0000000000) masstab=0
Type 1 (halo): 40000 (tot= 0000040000) masstab=0.00104634
Type 2 (disk): 20000 (tot= 0000020000) masstab=0.00023252
Type 3 (bulge): 0 (tot= 0000000000) masstab=0
Type 4 (stars): 0 (tot= 0000000000) masstab=0
Type 5 (bndry): 0 (tot= 0000000000) masstab=0

reading done.
Total number of particles : 0000060000

allocated 0.0762939 Mbyte for ngb search.

Allocated 3.30359 MByte for BH-tree. 64





On Tue, Jun 17, 2014 at 6:14 AM, Yves Revaz <yves.revaz_at_epfl.ch> wrote:

> On 06/17/2014 02:40 PM, Yahya Alivov wrote:
>
> Dear Gadget users,
>
> I have problem in getting Gadget-2 work, I would appreciate if you could
> help me. My problem is as follows. I am working in Ubuntu, I successfully
> installed GSL, FFTW, and MPICH, and created Gadget2 executable. But when I
> run Gadget, I get message which is copy-pasted below, please see first
> message. This message says "cannot create regular file
> parameters-usedvalues"; but this not true, I do see file
> "parameters-usedvalues" in the folder, from which I run Gadget2. Second,
> this message says "You must set `PeriodicBoundariesOn=1"; following this
> guide I change "0" to "1" in parameter file, but I get another error
> message, which I also copy-pasted below, please see second message. Do you
> have any suggestions? I would appreciate your help. Thank you much in
> advance!
>
>
> Hi Yahya,
>
> there must be a simple problem with the path setup in your parameter file .
> Clearly, the directory
>
> "home/alivov/Downloads/Gadget-2.0.7/galaxy/"
>
> doesn't exists. This is maybe that a '/' is missing before 'home'.
>
> Cheers,
>
> yves
>
>
>
>
> Yahya.
>
> *First message:*
>
> This is Gadget, version `2.0'.
>
> Running on 2 processors.
> cp: cannot create regular file
> ‘home/alivov/Downloads/Gadget-2.0.7/galaxy/parameters-usedvalues’: No such
> file or directory
> Code was compiled with periodic boundary conditions switched on.
> You must set `PeriodicBoundariesOn=1', or recompile the code.
>
>
> ---------------------------------------------------------------------------------------------------------------------------------
> *Second message:*
>
> This is Gadget, version `2.0'.
>
> Running on 2 processors.
> cp: cannot create regular file
> ‘home/alivov/Downloads/Gadget-2.0.7/galaxy/parameters-usedvalues’: No such
> file or directory
>
> 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 152408 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
>
> error in opening file 'home/alivov/Downloads/Gadget-2.0.7/galaxy/cpu.txt'
> task 0: endrun called with an error level of 1
>
>
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
>
> ===================================================================================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> = PID 23795 RUNNING AT yahya
> = EXIT CODE: 1
> = CLEANING UP REMAINING PROCESSES
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
> ===================================================================================
>
>
>
>
>
> --
>
> ---------------------------------------------------------------------
> Dr. Yves Revaz
> Laboratory of Astrophysics
> Ecole Polytechnique Fédérale de Lausanne (EPFL)
> Observatoire de Sauverny Tel : +41 22 379 24 28
> 51. Ch. des Maillettes Fax : +41 22 379 22 05
> 1290 Sauverny e-mail : Yves.Revaz_at_epfl.ch
> SWITZERLAND Web : http://people.epfl.ch/yves.revaz
> ---------------------------------------------------------------------
>
>
>
> -----------------------------------------------------------
>
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Received on 2014-06-18 23:01:10

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