[FLASH-USERS] HDF5 IO problem

[Zylstra, Alex]

Hi everybody,
I am having a (perhaps) similar issue on Mac with the following versions:
FLASH4.5
mpich-3.2.1
hdf5-1.8.20
hypre-2.11.2
parallel-netcdf-1.9.0

Sedov with serial IO works fine for me, but when I try the laser slab problem I get a segmentation fault as it starts to write the initial checkpoint. From the log file:
[ 06-22-2018  13:05:22.498 ] [IO_writeCheckpoint] open: type=checkpoint name=lasslab_hdf5_chk_0000
[ 06-22-2018  13:05:22.533 ] [io_writeData]: wrote      58          blocks

And the end of the console output is

 Hydro initialized

 Gravity initialized

 Initial dt verified



Program received signal SIGSEGV: Segmentation fault - invalid memory reference.



Backtrace for this error:

#0  0x106649f3c

#1  0x1066492e3

#2  0x7fff79d38f59

Segmentation fault: 11

Any help appreciated!

-Alex

From: <flash-users-bounces at flash.uchicago.edu> on behalf of "t_schlegel at t-online.de" <t_schlegel at t-online.de>
Reply-To: "t_schlegel at t-online.de" <t_schlegel at t-online.de>
Date: Thursday, June 21, 2018 at 3:14 AM
To: "flash-users at flash.uchicago.edu" <flash-users at flash.uchicago.edu>
Subject: [FLASH-USERS] HDF5 IO problem


Hello,



I have installed the modules:

GCC/7.2.0 5)
OpenMPI/3.0.0-GCC-7.2.0
FLASH/4.5-OpenMPI-3.0.0-GCC-7.2.0

hypre/2.11.2-OpenMPI-3.0.0-GCC-7.2.0

HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0 for parallel output

either HDF5/1.10.2-GCC-7.2.0 for serial one

parallel_netcdf/1.9.0-OpenMPI-3.0.0-GCC-7.2.0       on our cluster.



The Sedov example with serial HDF5 works as expected,

but using the HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0 module instead of serial IO



(./setup Sedov -auto +parallelio, putting the right path for HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0

in Makefile.h)



the job will be aborted at first write of a ckeckpoint file.

Part of the error output:

HDF5-DIAG: Error detected in HDF5 (1.10.1) MPI-process 3:
#000: H5Ddeprec.c line 187 in H5Dopen1(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 251 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
flash4: io_h5_attribute.c:49: io_h5_attribute_create: Assertion `dsetID >= 0' failed.

Program received signal SIGABRT: Process abort signal.



A similar situation I observed with the more complex example LaserSlab:



HDF5-DIAG: Error detected in HDF5 (1.10.1) MPI-process 4:
#000: H5Dio.c line 269 in H5Dwrite(): can't prepare for writing data
major: Dataset
minor: Write failed
#001: H5Dio.c line 345 in H5D__pre_write(): can't write data
major: Dataset
minor: Write failed
#002: H5Dio.c line 791 in H5D__write(): can't write data
major: Dataset
minor: Write failed
#003: H5Dmpio.c line 527 in H5D__contig_collective_write(): couldn't finish shared collective MPI-IO
major: Low-level I/O
minor: Write failed
#004: H5Dmpio.c line 1398 in H5D__inter_collective_io(): couldn't finish collective MPI-IO
major: Low-level I/O
minor: Can't get value
#005: H5Dmpio.c line 1442 in H5D__final_collective_io(): optimized write failed
major: Dataset
minor: Write failed
#006: H5Dmpio.c line 295 in H5D__mpio_select_write(): can't finish collective parallel write
major: Low-level I/O
minor: Write failed
#007: H5Fio.c line 195 in H5F_block_write(): write through page buffer failed
major: Low-level I/O
minor: Write failed
#008: H5PB.c line 1041 in H5PB_write(): write through metadata accumulator failed
major: Page Buffering
minor: Write failed
#009: H5Faccum.c line 834 in H5F__accum_write(): file write failed
major: Low-level I/O
minor: Write failed
#010: H5FDint.c line 308 in H5FD_write(): driver write request failed
major: Virtual File Layer
minor: Write failed
#011: H5FDmpio.c line 1864 in H5FD_mpio_write(): file write failed
major: Low-level I/O
minor: Write failed
flash4: io_h5_xfer_mesh_dataset.c:210: io_h5_xfer_mesh_dataset: Assertion `err >= 0' failed.

Program received signal SIGABRT: Process abort signal.



How can I overcome these problems?

Thanks in advancce,

Theo
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