[Beowulf] Anyone else seeing write(2) occasionally failing with -EINVAL under GPFS 3.5.0.12?

Christopher Samuel samuel at unimelb.edu.au
Thu Sep 26 17:20:22 PDT 2013


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Hi folks,

We have recently had to upgrade from GPFS 3.5.0.10 to 3.5.0.12 to avoid
a deadlock bug we were hitting and we are now seeing issues with
programs such as GROMACS occasionally failing, reporting:

- -------------------------------------------------------
Program mdrun_mpi, VERSION 4.6.1
Source code file: /usr/local/src/GROMACS/gromacs-4.6.1/src/mdlib/stat.c, line: 699

File input/output error:
Cannot write trajectory; maybe you are out of disk space?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
- -------------------------------------------------------

Running it under strace we see a write fail with -EINVAL, thus:

write(21, "\276\224\315\271>X\3537=\231\220y>u\35\365>4,\370>\0039\272>\234 \271>\6F\372"..., 23008) = -1 EINVAL (Invalid argument)

Is anyone else seeing odd file writing issues under 3.5.0.12?

cheers,
Chris
- -- 
 Christopher Samuel        Senior Systems Administrator
 VLSCI - Victorian Life Sciences Computation Initiative
 Email: samuel at unimelb.edu.au Phone: +61 (0)3 903 55545
 http://www.vlsci.org.au/      http://twitter.com/vlsci

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