[Users] Error to write PittNull during checkpointing

Sun Jul 29 15:31:57 CDT 2012

On 07/28/2012 07:38 AM, Jakob Hansen wrote:
> Hi all,
>
> Thanks for fast replys ^^
>
> 2012/7/27 Yosef Zlochower <yosef at astro.rit.edu 
> <mailto:yosef at astro.rit.edu>>
>
>     Hi,
>
>      SphericalHarmonicDecomp should not be writing output at the
>     same time as a checkpoint. Are you using an NFS mount? 
>
>
> No, we're using Lustre filesystem.
>
>
>     I noticed
>     issues with NFS servers becoming unresponsive (due to a large number
>     of blocking io operations) during a checkpoint. Perhaps right after
>     a checkpoint, the server is still too busy.
>
>
> Well, indeed this happens just after checkpointing, however not at 
> every checkpoint and not for all output. I experienced this error 
> twice on two different simulations, once for each simulation. In each 
> case it affected the metric_obs_0_Decomp.h5 right after checkpointing :
>
> Case 1 : Output from ascii_output > gxx.asc :
> 2.7627600000000001e+02 -7.1882256506489145e-05 1.5746413856874709e-05
> 2.7640800000000002e+02 -7.1881310717781865e-05 1.5759232641588166e-05
>                  nan 0.0000000000000000e+00 0.0000000000000000e+00
> 2.7667200000000003e+02 -7.1875929421365471e-05 1.5784711415784759e-05
> 2.7680400000000003e+02 -7.1871563990008602e-05 1.5797542778149928e-05
>
> In this case there was a checkpoint at time 276.408 : INFO 
> (CarpetIOHDF5): Dumping periodic checkpoint at iteration 268032, 
> simulation time 276.408
>
The NaN is just the way ascii_ouput let's you know it couldn't read the 
data.

>
> Case 2: Output from ascii_output > gxx.asc :
> 3.2010000000000002e+02 -6.7572912816444132e-05 2.1144268516557760e-05
> 3.2023200000000003e+02 -6.7570803118733184e-05 2.1156692762978387e-05
>                  nan 0.0000000000000000e+00 0.0000000000000000e+00
> 3.2049600000000004e+02 -6.7568973330671772e-05 2.1182079214383173e-05
> 3.2062800000000004e+02 -6.7569118827631724e-05 2.1194791416536239e-05
>
> With a checkpoint at time 320.232 :  INFO (CarpetIOHDF5): Dumping 
> periodic checkpoint at iteration 310528, simulation time 320.232
>
>
> Also, in both cases it only affected the metric_obs_0_Decomp.h5 file, 
> the other detection radius files, _1 and _2, had all data.
>
>
Do the  Caltech fixes help?  If that doesn't work, then it may be
that your IO system is saturated. Perhaps then a crude workaround would be
to put a delay in after a checkpoint to give the IO system time to 
process its
backlog of IO requests.
> <snip>
>
>
>
> 2012/7/28 Erik Schnetter <schnetter at cct.lsu.edu 
> <mailto:schnetter at cct.lsu.edu>>
>
>     Jakob
>
>     I have not heard about such a problem before.
>
>     When an HDF5 file is not properly closed, its content may be
>     corrupted. (This will be addressed in the next major release.)
>     There may be two reasons for this: either the file is not closed
>     (which would be an error in the code), or there is a write error
>     (e.g. you run out of disk space). The latter is the major reason
>     for people encountering corrupted HDF5 files. Since you don't see
>     error messages, this is either not the case, or these HDF5 output
>     routines suppress these errors.
>
>     The thorn SphericalHarmonicDecomp implements its own HDF5 output
>     routines and does not use Cactus. I see that it uses a
>     non-standard way to determine whether the file exists, and that it
>     does not check for errors when writing or closing. I think that
>     HDF5 errors should cause prominent warnings in stdout and stderr
>     (did you check?), and if you don't see these, the writing should
>     have succeeded.
>
>
> The errors I see on stderr are the ones I mentioned in my first mail :
>
>
>
> HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
> #000: H5F.c line 1509 in H5Fopen(): unable to open file
> major: File accessability
> minor: Unable to open file
> #001: H5F.c line 1300 in H5F_open(): unable to read superblock
> major: File accessability
> minor: Read failed
>
> .... etc.
>
> stdout does not produce any errors or warnings related to this.
>
>
>     You mention checkpointing. Are you experiencing these problems
>     right after recovery, i.e. during the first
>     SphericalHarmonicDecomp HDF5 output afterwards?
>
>
> No, this happened during the first run, not related to recovery.
>
>     In this case, did you maybe switch to a new directory where this
>     file doesn't exist?
>
>     If not, then it may be the non-standard way in which the code
>     determines whether the file already exists, combined with
>     something that may be special about your file system.
>
>     (The "standard" way operates as follows: open the file as if it
>     existed; if this fails, open it by creating it. The code works
>     differently: it opens the file as binary file. If this fails, the
>     HDF5 file is created; if it succeeds, the file is closed and
>     re-openend as HDF5 file. Maybe the quick closing-then-reopening
>     causes problems?)
>
>     -erik
>
>
>
>
> 2012/7/28 Roland Haas <roland.haas at physics.gatech.edu 
> <mailto:roland.haas at physics.gatech.edu>>
>
>     Hello all,
>
>     >> I have not heard about such a problem before.
>     I believe Nick Taylor at Caltech had similar issues. Bela has since
>     fixed some bugs but had trouble actually committing them (he just saw
>     your emails). I'll grab his changes and commit them.
>
>
> Sounds interesting, I'm looking forward to appying the changes and see 
> if the problem disappears.
>
> Cheers,
> Jakob
>
>
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-- 
Dr. Yosef Zlochower
Center for Computational Relativity and Gravitation
Assistant Professor
School of Mathematical Sciences
Rochester Institute of Technology
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Rochester, NY 14623

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Phone: +1 585-475-6103

yosef at astro.rit.edu

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