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

From: Christer Eriksson <agkbill_at_gmail.com>
Date: Tue, 17 Jan 2012 20:42:58 +0100

Thank you,

I will try with adding -mlittle-endian option.

Is it correct that I do that by adding at OPTIMIZE in the Makefile?

-------------------------------------------------------------------------------
CC = mpicc
OPTIMIZE = -O3 -Wall -mlittle-endian
GSL_INCL = -I/usr/local/include
GSL_LIBS = -L/usr/local/lib -Wl,"-R /usr/local/lib"
FFTW_INCL= -I/usr/local/include
FFTW_LIBS= -L/usr/local/lib
MPICHLIB = -L/usr/local/lib
#HDF5INCL =
#HDF5LIB = -lhdf5 -lz
endif
-------------------------------------------------------------------------------

FreeBSD 9.0 use "gcc version 4.2.1 20070831 patched [FreeBSD]"

It did not work to add -mlittle-endian like I did, maybe 4.2.1 it to old. I
am now building 4.4, will see how that work.

Best regards,
/Christer



On Tue, Jan 17, 2012 at 7:52 PM, James Himer <james.himer_at_oracle.com> wrote:

> 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
>
> [image: Oracle] <http://www.oracle.com>
> Jim Himer | Principal Application Developer
> Phone: +14037752860 | |
> Oracle Strategic Applications Engineering
> ORACLE Canada | Suite 801, 401-9th Avenue SW, Calgary, AB | T2P3C5
> [image: Green Oracle] <http://www.oracle.com/commitment> Oracle is
> committed to developing practices and products that help protect the
> environment
>
> 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> 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> 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>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>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>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 20:43:00

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