Re: Problem "incorrect header format", but only on SUN SunFire V440 server.

From: James Himer <james.himer_at_oracle.com>
Date: Tue, 17 Jan 2012 11:52:30 -0700

Just a thought. Any roadmap plans to add support for netCDF to
gadget to make it more endian agnostic? Many scientific codes
made such a transition many years ago.

Clear Skies -- JTH

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On 01/17/12 10:38, Nathan Goldbaum wrote:
> Hi Christer,
>
> If you're using gcc to compile your code, you may be able to compile with the -mlittle-endian option. That will make
> the gadget executable do the conversion automatically.
>
> If that doesn't work I can regenerate those initial conditions files in big-endian format. Let me know if you're
> still having trouble and I will put the files on my website later today.
>
> Best
> Nathan Goldbaum
>
>
>
> On Jan 17, 2012, at 9:14 AM, Christer Eriksson <agkbill_at_gmail.com <mailto:agkbill_at_gmail.com>> wrote:
>
>>
>> Ok, so that is the reason why I get "incorrect header format" the bit order is not correct.
>>
>> Is there any easy way to convert the input file? I have not made any input files myself, only used the one in the SIC
>> example.
>>
>> /Christer
>>
>>
>>
>> On Tue, Jan 17, 2012 at 6:04 PM, Jay Jay Billings <jayjaybillings_at_gmail.com <mailto:jayjaybillings_at_gmail.com>> wrote:
>>
>> The V440 is a 64-bit big-endian chip. Christer, you will have to convert your input file or run on a
>> little-endian system.
>>
>> Jay
>>
>>
>> On Tue, Jan 17, 2012 at 11:57 AM, Christer Eriksson <agkbill_at_gmail.com <mailto:agkbill_at_gmail.com>> wrote:
>>
>>
>> I found that Sun Fire SPARC platforms use the big-endian format to store and operate on their data.
>>
>>
>>
>>
>>
>> On Tue, Jan 17, 2012 at 5:52 PM, christer eriksson <agkbill_at_gmail.com <mailto:agkbill_at_gmail.com>> wrote:
>>
>>
>> Hi Max,
>>
>> I am unfortunately not familiar with big-endian and little-endian.
>> How do I find out? Will google and se what I can find on V440.
>>
>> /Christer
>>
>>
>>
>>
>>
>>
>>
>> On 01/17/2012 05:47 PM, max kondel wrote:
>>> Hi Christer,
>>>
>>> Is V440 big-endian and your IC file little-endian?
>>>
>>> -Max
>>>
>>> On Tue, Jan 17, 2012 at 11:35 AM, Christer Eriksson <agkbill_at_gmail.com <mailto:agkbill_at_gmail.com>> wrote:
>>>
>>>
>>>
>>>
>>> Dear GADGET2 users,
>>>
>>> I have been following a guide at
>>> "http://astrobites.com/2011/06/11/running-your-first-sph-simulation/" as well as instructions at
>>> "http://www.mpa-garching.mpg.de/gadget/".
>>>
>>> I never managed to get Linux up and running OK on the server, tried with Gentoo but it was always
>>> something that did not work. FreeBSD and OpenBSD on the outher hand was very easy to get up and running.
>>>
>>> I have managed to install and build GADGET2 but have problems.
>>>
>>> When I start a simulation on my SunFire V440 it looks like this:
>>>
>>> ------------------------------------------------------------------------------------------------------------
>>> [christer_at_V440 /usr/home/christer/GADGET2/SICtest]$ mpirun -np 4 ./Gadget2 15/SIC_015.param
>>>
>>> This is Gadget, version `2.0'.
>>>
>>> Running on 4 processors.
>>> application called MPI_Abort(MPI_COMM_WORLD, 890) - process 0
>>> rank 0 in job 1 V440_51366 caused collective abort of all ranks
>>> exit status of rank 0: killed by signal 9
>>>
>>> Allocated 25 MByte communication buffer per processor.
>>>
>>> Communication buffer has room for 436906 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) = 3.49333e-06
>>> G (internal units) = 1.23414
>>> UnitMass_in_g = 1.98992e+33
>>> UnitTime_in_s = 1.07793e+12
>>> UnitVelocity_in_cm_per_s = 46385.2
>>> UnitDensity_in_cgs = 1.59194e-17
>>> UnitEnergy_in_cgs = 4.28148e+42
>>>
>>> incorrect header format
>>> task 0: endrun called with an error level of 890
>>>
>>>
>>> [christer_at_V440 /usr/home/christer/GADGET2/SICtest]$
>>> ---------------------------------------------------------------------------------------------------------------
>>>
>>>
>>> Then I copy the Makefile to my Linux PC and also the SICtest/15 folder with following files:
>>>
>>> SIC_015.dat
>>> SIC_015.param-usedvalues
>>> energy.txt
>>> parameters-usedvalues
>>> SIC_015.param
>>> cpu.txt
>>> info.txt
>>> timings.txt
>>>
>>>
>>>
>>> ###############################################
>>>
>>>
>>>
>>> Now everything runs OK, starting with:
>>>
>>> [christer_at_Arch SICtest]$ mpirun -np 2 ./Gadget2 15/SIC_015.param
>>>
>>> This is Gadget, version `2.0'.
>>>
>>> Running on 2 processors.
>>>
>>> Allocated 25 MByte communication buffer per processor.
>>>
>>> Communication buffer has room for 436906 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) = 3.49333e-06
>>> G (internal units) = 1.23414
>>> UnitMass_in_g = 1.98992e+33
>>> UnitTime_in_s = 1.07793e+12
>>> UnitVelocity_in_cm_per_s = 46385.2
>>> UnitDensity_in_cgs = 1.59194e-17
>>> UnitEnergy_in_cgs = 4.28148e+42
>>>
>>>
>>> Allocated 1.59375 MByte for particle storage. 68
>>>
>>> Allocated 1.96875 MByte for storage of SPH data. 84
>>>
>>>
>>> reading file `./15/SIC_015.dat' on task=0 (contains 32768 particles.)
>>> distributing this file to tasks 0-1
>>> Type 0 (gas): 32768 (tot= 0000032768) masstab=0
>>> Type 1 (halo): 0 (tot= 0000000000) masstab=0
>>> Type 2 (disk): 0 (tot= 0000000000) masstab=0
>>> 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 : 0000032768
>>>
>>> allocated 0.0762939 Mbyte for ngb search.
>>>
>>> Allocated 2.22545 MByte for BH-tree. 68
>>>
>>> domain decomposition...
>>> NTopleaves= 120
>>> work-load balance=1.00043 memory-balance=1.00043
>>> exchange of 0000016413 particles
>>> domain decomposition done.
>>> begin Peano-Hilbert order...
>>> Peano-Hilbert done.
>>> Begin Ngb-tree construction.
>>> Ngb-Tree contruction finished
>>> ngb iteration 1: need to repeat for 0000030189 particles.
>>> ngb iteration 2: need to repeat for 0000004023 particles.
>>> ngb iteration 3: need to repeat for 0000003197 particles.
>>> ngb iteration 4: need to repeat for 0000002915 particles.
>>> ngb iteration 5: need to repeat for 0000001626 particles.
>>>
>>> Setting next time for snapshot file to Time_next= 0
>>>
>>>
>>> writing snapshot file...
>>> done with snapshot.
>>>
>>> Setting next time for snapshot file to Time_next= 0.0025
>>>
>>>
>>> Begin Step 0, Time: 0, Systemstep: 0
>>> domain decomposition...
>>> NTopleaves= 120
>>> work-load balance=1.00043 memory-balance=1.00043
>>> domain decomposition done.
>>> begin Peano-Hilbert order...
>>> Peano-Hilbert done.
>>> Start force computation...
>>> Tree construction.
>>> Tree construction done.
>>> Begin tree force.
>>>
>>>
>>> ######################################
>>>
>>>
>>>
>>>
>>> Any idea why it does not work on the SUN server?
>>>
>>> All input most appreciated, would be great to get GADGET2 up and running OK.
>>>
>>>
>>> Thank you.
>>>
>>> Best reagrds,
>>> /Christer
>>>
>>>
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>>
>>
>>
>>
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Received on 2012-01-17 19:53:11

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