<div dir="ltr">Hi body! <div><br></div><div><p style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:rgb(0,0,0);text-decoration:none">>>HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0 for parallel output</span></p><p style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:rgb(0,0,0);text-decoration:none">>>either HDF5/1.10.2-GCC-7.2.0 for serial one</span></p></div><div>I'm not sure about your problem, but at least in my case I haven't had to install hdf5 libreries twice, </div><div>one for serial outputs and another for parallel outputs. Instead just one. </div><div><br></div><div>During the <span style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">hdf5</span> installation I made something like this: </div><div><br></div><div> $ ./configure -h</div><div> $ ./configure --enable-parallel --enable-static --enable-shared --enable-fortran</div><div> $ make</div><div> $ make install</div><div><br></div><div>Hope this help!</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr">El jue., 21 jun. 2018 a las 7:14, <a href="mailto:t_schlegel@t-online.de">t_schlegel@t-online.de</a> (<<a href="mailto:t_schlegel@t-online.de">t_schlegel@t-online.de</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">Hello,<br></span></p>
<p style="margin:0px"> </p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">I have installed the modules:</span></p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"> 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></p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">hypre/2.11.2-OpenMPI-3.0.0-GCC-7.2.0</span></p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0 for parallel output</span></p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">either HDF5/1.10.2-GCC-7.2.0 for serial one</span></p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">parallel_netcdf/1.9.0-OpenMPI-3.0.0-GCC-7.2.0 on our cluster.<br></span></p>
<p style="margin:0px"> </p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">The Sedov example with serial HDF5 works as expected, </span></p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">but using the HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0 module instead of serial IO </span></p>
<p style="margin:0px"> </p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">(./setup Sedov -auto +parallelio, putting the right path for HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0</span></p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">in Makefile.h)</span></p>
<p style="margin:0px"> </p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">the job will be aborted at first write of a ckeckpoint file. <br></span></p>
<p style="margin:0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">Part of the error output:</span></p>
<p style="margin:0px 5px 0px 0px">HDF5-DIAG: Error detected in HDF5 (1.10.1) MPI-process 3:<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #000: H5Ddeprec.c line 187 in H5Dopen1(): not a location<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Invalid arguments to routine<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Inappropriate type<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #001: H5Gloc.c line 251 in H5G_loc(): invalid object ID<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Invalid arguments to routine<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Bad value<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span>flash4: io_h5_attribute.c:49: io_h5_attribute_create: Assertion `dsetID >= 0' failed.</p>
<p style="margin:0px 5px 0px 0px">Program received signal SIGABRT: Process abort signal.<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span></p>
<p style="margin:0px 5px 0px 0px"> </p>
<p style="margin:0px 5px 0px 0px">A similar situation I observed with the more complex example LaserSlab:</p>
<p style="margin:0px 5px 0px 0px"> </p>
<p style="margin:0px 5px 0px 0px">HDF5-DIAG: Error detected in HDF5 (1.10.1) MPI-process 4:<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #000: H5Dio.c line 269 in H5Dwrite(): can't prepare for writing data<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Dataset<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #001: H5Dio.c line 345 in H5D__pre_write(): can't write data<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Dataset<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #002: H5Dio.c line 791 in H5D__write(): can't write data<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Dataset<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #003: H5Dmpio.c line 527 in H5D__contig_collective_write(): couldn't finish shared collective MPI-IO<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Low-level I/O<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #004: H5Dmpio.c line 1398 in H5D__inter_collective_io(): couldn't finish collective MPI-IO<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Low-level I/O<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Can't get value<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #005: H5Dmpio.c line 1442 in H5D__final_collective_io(): optimized write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Dataset<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #006: H5Dmpio.c line 295 in H5D__mpio_select_write(): can't finish collective parallel write<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Low-level I/O<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #007: H5Fio.c line 195 in H5F_block_write(): write through page buffer failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Low-level I/O<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #008: H5PB.c line 1041 in H5PB_write(): write through metadata accumulator failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Page Buffering<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #009: H5Faccum.c line 834 in H5F__accum_write(): file write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Low-level I/O<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #010: H5FDint.c line 308 in H5FD_write(): driver write request failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Virtual File Layer<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> #011: H5FDmpio.c line 1864 in H5FD_mpio_write(): file write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> major: Low-level I/O<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span> minor: Write failed<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span>flash4: io_h5_xfer_mesh_dataset.c:210: io_h5_xfer_mesh_dataset: Assertion `err >= 0' failed.</p>
<p style="margin:0px 5px 0px 0px">Program received signal SIGABRT: Process abort signal.<span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none"><br></span></p>
<p style="margin:0px 5px 0px 0px"> </p>
<p style="margin:0px 5px 0px 0px"><span style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;text-decoration:none">How can I overcome these problems? </span></p>
<p style="margin:0px 5px 0px 0px">Thanks in advancce,</p>
<p style="margin:0px 5px 0px 0px">Theo</p></div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font face="monospace, monospace"><i><font color="#000000">Ernesto Zurbriggen</font></i><i> </i></font><div><font face="monospace, monospace"><i><br></i></font><div><font face="monospace, monospace"><i><font color="#444444">Consejo Nacional de Investigaciones Científicas y Técnicas </font></i></font><i style="font-size:12.8px;font-family:monospace,monospace"><font color="#274e13">(CONICET)</font></i><i style="font-family:monospace,monospace;font-size:12.8px"><font color="#444444">, Instituto de Astronomía Teórica y Experimental </font><font color="#274e13">(IATE)</font><font color="#444444">. </font></i></div><div><i style="font-size:12.8px;color:rgb(68,68,68);font-family:monospace,monospace"><br></i></div><div><i style="font-size:12.8px;color:rgb(68,68,68);font-family:monospace,monospace">Universidad Nacional de Córdoba </i><i style="font-size:12.8px;font-family:monospace,monospace"><font color="#274e13">(UNC)</font></i><i style="font-size:12.8px;color:rgb(68,68,68);font-family:monospace,monospace">, </i><font face="monospace, monospace" style="font-size:12.8px"><i><font color="#444444">Observatorio Astronómico de Córdoba </font></i></font><i style="font-size:12.8px;font-family:monospace,monospace"><font color="#274e13">(OAC)</font></i><i style="font-size:12.8px;color:rgb(68,68,68);font-family:monospace,monospace">. </i></div></div><div><i style="color:rgb(68,68,68);font-family:monospace,monospace;font-size:12.8px"><br></i></div><div><i style="color:rgb(68,68,68);font-family:monospace,monospace;font-size:12.8px">Teléfono: +54 0351 4331064-5, interno 222. </i></div><div><span style="font-size:12.8px"><i><font color="#444444">Laprida 854, Bº Observatorio (CP 5000), Córdoba, Argentina.<br></font></i></span><font color="#444444"><br><br></font></div></div></div></div></div></div></div></div></div></div></div></div></div>