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<p class="MsoNormal">Hi everybody,<o:p></o:p></p>
<p class="MsoNormal">I am having a (perhaps) similar issue on Mac with the following versions:<o:p></o:p></p>
<p class="MsoNormal">FLASH4.5 <o:p></o:p></p>
<p class="MsoNormal">mpich-3.2.1<o:p></o:p></p>
<p class="MsoNormal">hdf5-1.8.20<o:p></o:p></p>
<p class="MsoNormal">hypre-2.11.2<o:p></o:p></p>
<p class="MsoNormal">parallel-netcdf-1.9.0<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal">[ 06-22-2018 13:05:22.498 ] [IO_writeCheckpoint] open: type=checkpoint name=lasslab_hdf5_chk_0000<o:p></o:p></p>
<p class="MsoNormal">[ 06-22-2018 13:05:22.533 ] [io_writeData]: wrote 58 blocks<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">And the end of the console output is<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">Hydro initialized</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">Gravity initialized</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">Initial dt verified</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">Program received signal SIGSEGV: Segmentation fault - invalid memory reference.</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">Backtrace for this error:</span><o:p></o:p></p>
<p class="p1"><span class="s1">#0</span><span class="apple-converted-space"> </span>
<span class="s1">0x106649f3c</span><o:p></o:p></p>
<p class="p1"><span class="s1">#1</span><span class="apple-converted-space"> </span>
<span class="s1">0x1066492e3</span><o:p></o:p></p>
<p class="p1"><span class="s1">#2</span><span class="apple-converted-space"> </span>
<span class="s1">0x7fff79d38f59</span><o:p></o:p></p>
<p class="p1"><span class="s1">Segmentation fault: 11</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any help appreciated!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">-Alex<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><flash-users-bounces@flash.uchicago.edu> on behalf of "t_schlegel@t-online.de" <t_schlegel@t-online.de><br>
<b>Reply-To: </b>"t_schlegel@t-online.de" <t_schlegel@t-online.de><br>
<b>Date: </b>Thursday, June 21, 2018 at 3:14 AM<br>
<b>To: </b>"flash-users@flash.uchicago.edu" <flash-users@flash.uchicago.edu><br>
<b>Subject: </b>[FLASH-USERS] HDF5 IO problem<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">Hello,</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"> <o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">I have installed the modules:</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">GCC/7.2.0 5)<br>
OpenMPI/3.0.0-GCC-7.2.0 <br>
FLASH/4.5-OpenMPI-3.0.0-GCC-7.2.0</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">hypre/2.11.2-OpenMPI-3.0.0-GCC-7.2.0</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0 for parallel output</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">either HDF5/1.10.2-GCC-7.2.0 for serial one</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">parallel_netcdf/1.9.0-OpenMPI-3.0.0-GCC-7.2.0 on our cluster.</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"> <o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">The Sedov example with serial HDF5 works as expected, </span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">but using the HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0 module instead of serial IO
</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"> <o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">(./setup Sedov -auto +parallelio, putting the right path for HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">in Makefile.h)</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"> <o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">the job will be aborted at first write of a ckeckpoint file.
</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">Part of the error output:</span><o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
HDF5-DIAG: Error detected in HDF5 (1.10.1) MPI-process 3:<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#000: H5Ddeprec.c line 187 in H5Dopen1(): not a location<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Invalid arguments to routine<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Inappropriate type<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#001: H5Gloc.c line 251 in H5G_loc(): invalid object ID<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Invalid arguments to routine<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Bad value<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>flash4: io_h5_attribute.c:49: io_h5_attribute_create: Assertion `dsetID >= 0' failed.<o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
Program received signal SIGABRT: Process abort signal.<o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
<o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
A similar situation I observed with the more complex example LaserSlab:<o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
<o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
HDF5-DIAG: Error detected in HDF5 (1.10.1) MPI-process 4:<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#000: H5Dio.c line 269 in H5Dwrite(): can't prepare for writing data<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Dataset<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#001: H5Dio.c line 345 in H5D__pre_write(): can't write data<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Dataset<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#002: H5Dio.c line 791 in H5D__write(): can't write data<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Dataset<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#003: H5Dmpio.c line 527 in H5D__contig_collective_write(): couldn't finish shared collective MPI-IO<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Low-level I/O<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#004: H5Dmpio.c line 1398 in H5D__inter_collective_io(): couldn't finish collective MPI-IO<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Low-level I/O<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Can't get value<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#005: H5Dmpio.c line 1442 in H5D__final_collective_io(): optimized write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Dataset<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#006: H5Dmpio.c line 295 in H5D__mpio_select_write(): can't finish collective parallel write<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Low-level I/O<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#007: H5Fio.c line 195 in H5F_block_write(): write through page buffer failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Low-level I/O<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#008: H5PB.c line 1041 in H5PB_write(): write through metadata accumulator failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Page Buffering<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#009: H5Faccum.c line 834 in H5F__accum_write(): file write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Low-level I/O<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#010: H5FDint.c line 308 in H5FD_write(): driver write request failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Virtual File Layer<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>#011: H5FDmpio.c line 1864 in H5FD_mpio_write(): file write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>major: Low-level I/O<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>minor: Write failed<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"><br>
</span>flash4: io_h5_xfer_mesh_dataset.c:210: io_h5_xfer_mesh_dataset: Assertion `err >= 0' failed.<o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
Program received signal SIGABRT: Process abort signal.<o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
<o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
<span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">How can I overcome these problems?
</span><o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
Thanks in advancce,<o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:3.75pt;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
Theo<o:p></o:p></p>
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