Re: Gadget crashes at IC readin

From: Sylvia Ploeckinger <ploeckinger_at_strw.leidenuniv.nl>
Date: Fri, 27 Nov 2015 15:03:24 +0100

Hi Volker,

     thanks a lot for pointing me in this direction!

It was not the missing density block that caused the code to complain,
but the missing internal energy block.
As it is an isolated galaxy with an initial uniform temperature, that
was not necessary to define.

I found that there is a flag NO_UTHERM_IN_IC_FILE in the Gadget version
that I am using and if I use it,
the code reads in the IC file without problems and sets the gas
temperature to the value of InitGasTemp,
which is perfect! I guess this flag was introduced relatively recently.
It was not used in some
of the previous versions with the same IC files.

But in any case: It works! Now the fun begins!

Thanks again!

Greetings,

Sylvia


On 26/11/15 21:24, Volker Springel wrote:
> Hmm… looks like your IC file doesn’t contain the density block for the SPH particles. These values are not really needed for the ICs (as they are recalculated) and Gadget2 doesn’t require them to be present. Your version of Gadget3 (whichever it is - lot’s of people fiddled with it extensively) apparently tries to read in these density values however. The only solution is to either fixing your IC file by appending a dummy block with these densities, or changing the Gadget3 code. The latter requires editing the file read_ic.c, and replacing
>
> for(bnr = 0; bnr < 1000; bnr++)
> {
> blocknr = (enum iofields) bnr;
>
> with
>
> for(bnr = 0; bnr < 1000; bnr++)
> {
> blocknr = (enum iofields) bnr;
>
> if(RestartFlag == 0 && blocknr == IO_RHO)
> continue;
>
> Volker
>
>
> On Nov 26, 2015, at 4:14 PM, Sylvia Ploeckinger <ploeckinger_at_strw.leidenuniv.nl> wrote:
>
>> Hi all,
>>
>> I tried out a few more things.
>>
>> First of all:
>> I installed now also the public Gadget-2 version on my system and it works!
>> It reads my IC file without problems when I compile the code with the default Makefile (therefore also without LONGIDS).
>> (Thanks a lot to Matthias Kühtreiber for testing my .icl file first!)
>>
>> I tried it again with Gadget-3 with the same Makefile options as in the default Gadget-2 Makefile:
>>
>> PERIODIC
>> UNEQUALSOFTENINGS
>> PEANOHILBERT
>> WALLCLOCK
>> PMGRID=128
>> DOUBLEPRECISION
>> DOUBLEPRECISION_FFTW
>> SYNCHRONIZATION
>> HAVE_HDF5
>>
>> but it failed again with the same error message. The parameter files for both tests are identical,
>> I only commented out a few parameter from Gadget 3 that Gadget 2 doesn't have.
>>
>> Did something change between Gadget 2 and Gadget 3 in terms of how the IC files are read in that could be responsible for this?
>>
>> Thanks everyone for helping with that!
>>
>> Sylvia
>>
>>
>>
>> On 26/11/15 14:05, Sylvia Ploeckinger wrote:
>>> Hi Volker,
>>>
>>> thanks for your reply! I set LONGIDS in the code and now it is crashing a little bit earlier.
>>>
>>> Instead of (without LONDIDs):
>>> task=0 blocknr=0 bytes_per_blockelement=12 npart=288018
>>> task=0 blocknr=2 bytes_per_blockelement=12 npart=288018
>>> task=0 blocknr=3 bytes_per_blockelement=4 npart=288018
>>> task=0 blocknr=4 bytes_per_blockelement=4 npart=0
>>> task=0 blocknr=6 bytes_per_blockelement=4 npart=6445
>>> task=0 blocknr=7 bytes_per_blockelement=4 npart=6445
>>> I/O error (fread) on task=0 has occured: end of file
>>> nread = 0, nmemb = 1
>>> fread = 0
>>> size = 4
>>> task 0: endrun called with an error level of 778
>>>
>>> I now get (with LONGIDs):
>>>
>>> task=0 blocknr=0 bytes_per_blockelement=12 npart=288018
>>> task=0 blocknr=2 bytes_per_blockelement=12 npart=288018
>>> task=0 blocknr=3 bytes_per_blockelement=8 npart=288018
>>> I/O error (fread) on task=0 has occured: end of file
>>> nread = 140788, nmemb = 262773
>>> fread = 0
>>> size = 8
>>> task 0: endrun called with an error level of 778
>>>
>>> Please find attached the complete output file for additional information.
>>>
>>> I try to set up an isolated galaxy for some tests with new cooling tables I am working on.
>>> To do that, I got the IC generator and the parameter file that a colleague of mine was
>>> using for his isolated galaxies. In his paper he says:
>>>
>>> "The initial conditions that we use are based on the model of Springel et al. (2005),
>>> and were generated using a modified version of a code that was kindly provided to us
>>> by Volker Springel."
>>>
>>> I guess that the general structure of the ICs should be alright.
>>> Is there a way to check whether the problem is somewhere in creating the ICs or with the read-in?
>>>
>>> Some more information:
>>> - compiler version: gcc (GCC) 4.9.2 20150212 (Red Hat 4.9.2-6)
>>> - compiler options for the ICs: gcc -m64 -O3
>>> - compiler options for the Code:
>>> CC = mpicc
>>> ifeq ($(SYSTYPE), "paracluster")
>>> OPTIMIZE = -g -O3 -Wall -DH5_USE_16_API
>>> [...]
>>> endif
>>>
>>> mpicc -show:
>>> gcc -m64 -O2 -fPIC -Wl,-z,noexecstack -I/usr/include/mpich-x86_64 -L/usr/lib64/mpich/lib -Wl,-rpath -Wl,/usr/lib64/mpich/lib -lmpich -lopa -lmpl -lrt -lpthread
>>>
>>> (I also tried to set all compiler optimization to -O2 but it didn't change anything.)
>>>
>>>
>>> Sylvia
>>>
>>>
>>>
>>> On 26/11/15 11:17, Volker Springel wrote:
>>>> Hi Sylvia,
>>>>
>>>> Presumably you have an IC file with 64-bit IDs but use gadget with 32-bit IDs. This could be resolved by activating LONGIDS in the code. Alternatively you recreate the ICs with 32-bit IDs.
>>>>
>>>> Alternatively the IC file has an incorrect structure, but it’s hard to diagnose this without information where this file comes from.
>>>>
>>>> Volker
>>>>
>>>>
>>>>
>>>> On Nov 26, 2015, at 10:42 AM, Sylvia Ploeckinger
>>>> <ploeckinger_at_strw.leidenuniv.nl>
>>>> wrote:
>>>>
>>>>
>>>>> Hi Michael,
>>>>>
>>>>> thanks a lot for your input!
>>>>> The compiler on my system should use 64bit as default,
>>>>> but to be sure I included the -m64 flag for both the IC generator
>>>>> as well as the code itself. Unfortunately it still doesn't work.
>>>>>
>>>>> Do you remember which flags you used to get it to work again after this error occurred?
>>>>> Was it also -m64 or did you use something else?
>>>>>
>>>>> Greets,
>>>>>
>>>>> Sylvia
>>>>>
>>>>>
>>>>> On 25/11/15 19:13, Michael Hansen wrote:
>>>>>
>>>>>> HI Sylvia.
>>>>>>
>>>>>> I had the same problem some while ago. Check that you are compiling both code and IC generator with or without 64 bit compatibility.
>>>>>>
>>>>>> Cheers,
>>>>>> Michael
>>>>>>
>>>>>> Sent from my iPhone
>>>>>>
>>>>>> On 25 Nov 2015, at 17:32, Sylvia Ploeckinger
>>>>>> <ploeckinger_at_strw.leidenuniv.nl>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> as the subject line already gives away, Gadget crashes when I try to read in an input file.
>>>>>>>
>>>>>>> The error is:
>>>>>>> I/O error (fread) on task=0 has occured: end of file
>>>>>>> task 0: endrun called with an error level of 778
>>>>>>>
>>>>>>> I found a posting in this mailing list from 2006(!) with the same error:
>>>>>>>
>>>>>>> http://wwwmpa.mpa-garching.mpg.de/gadget/gadget-list/0098.html
>>>>>>>
>>>>>>>
>>>>>>> but the solution seems to include some magic:
>>>>>>> "So, the good news is that Gadget2 runs with the LCDM gas simulation, but I don't have a clue why it didn't before!"
>>>>>>> (from the above posting)
>>>>>>>
>>>>>>> Did anyone else in the last 9 years have the same problem and knows how to fix it?
>>>>>>> I included the following extra lines in the routine my_fread to get some extra information:
>>>>>>> printf("nread = %zd, nmemb = %zd\n", nread, nmemb);
>>>>>>> printf("fread = %zd\n", fread(ptr, size, nmemb, stream));
>>>>>>> printf("size = %zd\n", size);
>>>>>>>
>>>>>>> and in the file read_ic.c, I included this line (as suggested by Volker in the 2006 discussion)
>>>>>>>
>>>>>>> printf("task=%d blocknr=%d bytes_per_blockelement=%d npart=%d\n",
>>>>>>> ThisTask, blocknr, bytes_per_blockelement, npart);
>>>>>>> fflush(stdout);
>>>>>>>
>>>>>>>
>>>>>>> Please find below the corresponding output. It comes from a one core test run, but it crashes with the same error message when I run it on 4 cores.
>>>>>>> The IC file seems to be okay, but is there an easy way to find out if the file is damaged to exclude this possibility?
>>>>>>>
>>>>>>> Thanks in advance!
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Sylvia
>>>>>>>
>>>>>>>
>>>>>>> Allocated 129 MByte for FFT kernel(s).
>>>>>>>
>>>>>>>
>>>>>>> Allocated 84.4627 MByte for particle storage.
>>>>>>>
>>>>>>> Allocated 1.47507 MByte for storage of SPH data.
>>>>>>>
>>>>>>>
>>>>>>> reading file `/net/para35/data2/ploeckinger/IC_Gadget/output/m1e11f30.ics' on task=0 (contains 288018 particles.)
>>>>>>> distributing this file to tasks 0-0
>>>>>>> Type 0 (gas): 6445 (tot= 0000006445) masstab=5.28564e-06
>>>>>>> Type 1 (halo): 262773 (tot= 0000262773) masstab=2.6309e-05
>>>>>>> Type 2 (disk): 15040 (tot= 0000015040) masstab=5.28505e-06
>>>>>>> Type 3 (bulge): 3760 (tot= 0000003760) masstab=5.28505e-06
>>>>>>> Type 4 (stars): 0 (tot= 0000000000) masstab=0
>>>>>>> Type 5 (bndry): 0 (tot= 0000000000) masstab=0
>>>>>>>
>>>>>>> task=0 blocknr=0 bytes_per_blockelement=12 npart=288018
>>>>>>> task=0 blocknr=2 bytes_per_blockelement=12 npart=288018
>>>>>>> task=0 blocknr=3 bytes_per_blockelement=4 npart=288018
>>>>>>> task=0 blocknr=4 bytes_per_blockelement=4 npart=0
>>>>>>> task=0 blocknr=6 bytes_per_blockelement=4 npart=6445
>>>>>>> task=0 blocknr=7 bytes_per_blockelement=4 npart=6445
>>>>>>> I/O error (fread) on task=0 has occured: end of file
>>>>>>> nread = 0, nmemb = 1
>>>>>>> fread = 0
>>>>>>> size = 4
>>>>>>> task 0: endrun called with an error level of 778
>>>>>>>
>>>>>>>
>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 778) - process 0
>>>>>>>
>>>>>>> ===================================================================================
>>>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>>> = PID 16587 RUNNING AT para37.strw.leidenuniv.nl
>>>>>>> = EXIT CODE: 10
>>>>>>> = CLEANING UP REMAINING PROCESSES
>>>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>>> ===================================================================================
>>>>>>>
>>>>>>> --
>>>>>>> Sylvia Ploeckinger
>>>>>>> Sterrewacht Leiden
>>>>>>> The Netherlands
>>>>>>>
>>>>>>> Room Nr. 438
>>>>>>> email:
>>>>>>>
>>>>>>> ploeckinger_at_strw.leidenuniv.nl
>>>>>>>
>>>>>>>
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>> If you wish to unsubscribe from this mailing, send mail to
>>>>>>>
>>>>>>> minimalist_at_MPA-Garching.MPG.de
>>>>>>> with a subject of: unsubscribe gadget-list
>>>>>>> A web-archive of this mailing list is available here:
>>>>>>>
>>>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
>>>>> --
>>>>> Sylvia Ploeckinger
>>>>> Sterrewacht Leiden
>>>>> The Netherlands
>>>>>
>>>>> Room Nr. 438
>>>>> email:
>>>>>
>>>>> ploeckinger_at_strw.leidenuniv.nl
>>>>>
>>>>>
>>>>> -----------------------------------------------------------
>>>>>
>>>>> If you wish to unsubscribe from this mailing, send mail to
>>>>>
>>>>> minimalist_at_MPA-Garching.MPG.de
>>>>> with a subject of: unsubscribe gadget-list
>>>>> A web-archive of this mailing list is available here:
>>>>>
>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
>>>>
>>>> -----------------------------------------------------------
>>>>
>>>> If you wish to unsubscribe from this mailing, send mail to
>>>>
>>>> minimalist_at_MPA-Garching.MPG.de
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>>>>
>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
>>> --
>>> Sylvia Ploeckinger
>>> Sterrewacht Leiden
>>> The Netherlands
>>>
>>> Room Nr. 438
>>> email:
>>> ploeckinger_at_strw.leidenuniv.nl
>> --
>> Sylvia Ploeckinger
>> Sterrewacht Leiden
>> The Netherlands
>>
>> Room Nr. 438
>> email:
>> ploeckinger_at_strw.leidenuniv.nl
>>
>> -----------------------------------------------------------
>>
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>
>
>
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-- 
Sylvia Ploeckinger
Sterrewacht Leiden
The Netherlands
Room Nr. 438
email: ploeckinger_at_strw.leidenuniv.nl


Received on 2015-11-27 15:03:34

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