Re: Need help to start running Gadget

From: Yahya Alivov <alivov.y_at_gmail.com>
Date: Wed, 18 Jun 2014 15:42:24 -0700

In addition to what I said, the code generates files energy.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> 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> 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 2014-06-19 00:42:27

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