[FLASH-USERS] HDF5 IO problem

[ERNESTO ZURBRIGGEN]

Hi body!

>>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
I'm not sure about your problem, but at least in my case I haven't had to
install hdf5 libreries twice,
one for serial outputs and another for parallel outputs. Instead just one.

During the hdf5 installation I made something like this:

 $  ./configure -h
 $  ./configure --enable-parallel --enable-static --enable-shared
--enable-fortran
 $  make
 $  make install

Hope this help!


El jue., 21 jun. 2018 a las 7:14, t_schlegel at t-online.de (<
t_schlegel at t-online.de>) escribió:

> 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
> 
>


-- 
*Ernesto Zurbriggen*

*Consejo Nacional de Investigaciones Científicas y Técnicas **(CONICET)**,
Instituto de Astronomía Teórica y Experimental (IATE). *

*Universidad Nacional de Córdoba **(UNC)**, **Observatorio Astronómico de
Córdoba **(OAC)**. *

*Teléfono: +54 0351 4331064-5, interno 222. *

*Laprida 854, Bº Observatorio (CP 5000), Córdoba, Argentina.*
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