Re: LCDM_gas simulation aborts in initialization

From: <ROBERT.J.MORGAN_at_asu.edu>
Date: Tue, 06 Jun 2006 10:13:51 -0700 (MST)

Dear Volker,

Thanks for the code. Installing it confirmed that EOF condition occurred. Also,
checked IC file for lcdm_gas and it was 1966376 bytes long. Downloaded new
Gadget-2.0.3 code and extracted files. Did "diff" on that lcdm_gas IC file
and "old" (Gadget-2.0) IC file and were identical. (No diferences.) Just to be
sure, also tried runing simulation with "new" IC file with same result as
before. Complete text of output follows. Also, same result on single or dual
processors. (Two compute nodes connected by LAN.) Also checked "param" file to
make sure were the same. (Aside from path changes needed since I was running in
separate new sub-directory.) I think call to my_fread() for CommBuffer "file"
is part of loop checking on information for particle types. Although it has
already found the 65,536 particles in the IC file, the code seems to expect
more info or data in CommBuffer. Do you have any suggestions for what else I
could try or check to get this simulation to run or find out why it doesn't ?

Thank you,
Bob Morgan
ASU


Output of Gadget2, lcdm_gas simulation run :


This is Gadget, version `2.0'.

Running on 2 processors.

found 5 times in output-list.

Allocated 30 MByte communication buffer per processor.

Communication buffer has room for 714938 particles in gravity computation
Communication buffer has room for 245760 particles in density computation
Communication buffer has room for 196608 particles in hydro computation
Communication buffer has room for 182890 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 3.99994 MByte for particle storage. 80

Allocated 2.09997 MByte for storage of SPH data. 84


reading file `../ICs/lcdm_gas_littleendian.dat' on task=0 (contains 65536
particles.)
distributing this file to tasks 0-1
Type 0 (gas): 32768 (tot= 0000032768) masstab=4.23508
Type 1 (halo): 32768 (tot= 0000032768) masstab=27.528
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

I/O error (fread) on task=0 has occurred: end of file
task 0: endrun called with an error level of 778


[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_25749: p4_error: : 778
Killed by signal 2.
p0_25749: (4.391097) net_send: could not write to fd=4, errno = 32
++ exitstatus=1
++ '[' 0 '!=' 1 ']'
++ '[' 0 = 1 ']'
++ '[' 0 = 1 -a no = yes ']'
++ rm /home/bob/Gadget-2.0/COSMO/PI25665
++ '[' '' = yes ']'
++ '[' '' '!=' no -a '' = shared ']'
++ exit 1

.. end of output ..


Quoting Volker Springel <volker_at_MPA-Garching.MPG.DE>:

>
> ROBERT.J.MORGAN_at_asu.edu wrote:
> > Am trying to run the lcdm_gas simualtion. Runs aborts in
> initialization with
> > messages:
> > "reading file '../ICs/lcdm_gas_littleendian.dat on task=0 (contains
> 65536
> > particles.)
> > distributing this file to tasks 0-0
> > ... (then follows listing of types 0-5 particles) ...
> >
> > I/O error (fread) on task=0 has occured: no such file or directory
> > task 0: endrun called with an error level of 778
> >
> > [0] MPI Abort by user Aborting program !
> > [0] Aborting program!
> > p0_11987: p4_error: :778 "
> >
> >
> > Using gdb, problem seems to occur when read_file() in read_ic.c issues
>
> > my_fread(CommBuffer, ...) at line 485 and my_fread() in io.c issues
> and fread()
> > and gets nread=1 instead of nmemb=32768 and treats this as I/O error
> and calls
> > endrun.
>
> fread doen't distinguish between EOF and other errors when reading. From
> the
> viewpoint of gadget, both are equally bad and the run needs to be
> terminated. To see whether you are dealing with an end-of-file or
> another
> error you can replace the line
>
> printf("I/O error (fread) on task=%d has occured: end of file\n",
>
> ThisTask);
>
> with
> if(feof(stream))
> printf("I/O error (fread) on task=%d has occured: end of
> file\n",
> ThisTask);
> else
> printf("I/O error (fread) on task=%d has occured: %s\n",
> ThisTask,
> strerror(errno));
>
> I think you will likely see an end-of-file error now, i.e. your IC file
> is
> corrupt somehow. (It should have a length of 1966376.)
>
> > This seems questionable since an EOF can result in a short read
> (unless nmemb
> > data had previously been written to file.)
> >
> > Am running on a single processor (for this run) on an AMD Athlon and
> Centos 4.1
> > (Linux) OS. Not using mpirun though mpich is configured and loaded.
> Using
> > lcdm_gas_littleendian.dat and lcdm_gas.param files (supplied
> w/download.)
> >
> > Have previously run the collisionless galaxy simulations on both
> single and
> > multiple processors. But that doesn't use SPH which uses the
> CommBuffer.
> >
> > Should I just skip my_fread() and use fread() in initialization code
> for
> > CommBuffer? Info fread doesn't seem to distinguish between IO error
> and EOF
> > conditions, so is there some way to tell if actual I/O error?
>
> Yes, see above.
>
> Replacing my_fread with read will make the code ignore the I/O error. I
>
> wouldn't recommend that since then some of the initial data is undefined
>
> with unpredictable outcome.
>
> Volker
>
>
>
> > Thanks,
> >
> > Bob Morgan
> >
> > Arizona State University
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
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Received on 2006-06-06 20:28:05

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