Re: Need help to start running Gadget

From: Yves Revaz <yves.revaz_at_epfl.ch>
Date: Thu, 19 Jun 2014 10:18:51 +0200

Hum,

after the line corresponding to the
memory allocation of the BH tree, you should have something like:


start domain decomposition...
NTopleaves= 512
work-load balance=1 memory-balance=1
exchange of 0000196608 particles
domain decomposition done.
begin Peano-Hilbert order...
Peano-Hilbert done.
Begin Ngb-tree construction.
Ngb-Tree contruction finished
...








On 06/19/2014 12:42 AM, Yahya Alivov wrote:
>
> In addition to what I said, the code generates filesenergy.txt,
> info.txt, timings.txt, cpu.txt after start, as it should, but all
> these files stay empty as program runs, when I would expect they would
> be filling with the text.
>
> In previous e-mail I copied by accident old messages too from the
> screen, so please ignore beginning of the copy. Thanks again!
>
> Yahya
>
>
>
> On Wed, Jun 18, 2014 at 2:01 PM, Yahya Alivov <alivov.y_at_gmail.com
> <mailto:alivov.y_at_gmail.com>> wrote:
>
> 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
> <mailto: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 <tel:%2B41%2022%20379%2024%2028>
> 51. Ch. des Maillettes Fax :+41 22 379 22 05 <tel:%2B41%2022%20379%2022%2005>
> 1290 Sauverny e-mail :Yves.Revaz_at_epfl.ch <mailto:Yves.Revaz_at_epfl.ch>
> SWITZERLAND Web :http://people.epfl.ch/yves.revaz
> ---------------------------------------------------------------------
>
>
>
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-- 
---------------------------------------------------------------------
   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
---------------------------------------------------------------------
Received on 2014-06-19 10:29:32

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