<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><br><div><div>On 5 Oct 2015, at 12:43, Geraint Pratten <<a href="mailto:g.pratten@sussex.ac.uk">g.pratten@sussex.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div class="gmail_default" style="font-family: arial, helvetica, sans-serif;">Hi,</div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif;"><br></div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif;">I am trying to run a simulation with the same output directory - though I've been removing the simulations after each run while trying to fix the above issue. I should have write access to the file and there should be sufficient storage. </div></div></blockquote><div><br></div><div>Can you check the standard output of the run and see if the number of processes and threads are what you expect? You should see something like "Carpet is running on N processes with M threads". Maybe there is a problem in MPI initialisation, and multiple processes are trying to write to the same HDF5 file at the same time.</div><div><br></div><br><blockquote type="cite"><div dir="ltr"><div class="gmail_default" style="font-family: arial, helvetica, sans-serif;"><br></div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif;">Geraint</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 5 October 2015 at 11:34, Ian Hinder <span dir="ltr"><<a href="mailto:ian.hinder@aei.mpg.de" target="_blank">ian.hinder@aei.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<br>
<div><span class="">
<div>On 1 Oct 2015, at 15:49, Erik Schnetter <<a href="mailto:schnetter@cct.lsu.edu" target="_blank">schnetter@cct.lsu.edu</a>> wrote:</div>
<br>
<blockquote type="cite">
<div dir="ltr">Geraint
<div><br>
</div>
<div>Some very fundamental HDF5 operations fail. This could be due to a file system problem; maybe you don't have write access to the file, or your disk is full. It could also be that there exists a corrupted HDF5 file, and you are trying to write to it (extend
it).</div>
<div><br>
</div>
<div>HDF5 files can get corrupted if you have opened it for writing, and then the application is interrupted or crashes, or you run out of disk space. Even if you make free space later, a corrupted file remains corrupted.</div>
</div>
</blockquote>
<div><br>
</div>
</span><div>Hi Geraint,</div>
<div><br>
</div>
<div>Are you trying to run a simulation with output in the same directory as one that was run before? </div>
<br>
<blockquote type="cite">
<div dir="ltr">
<div><br>
</div>
<div>-erik</div>
<div><br>
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</div>
<div class="gmail_extra"><br>
<div class="gmail_quote"><span class="">On Thu, Oct 1, 2015 at 9:30 AM, Geraint Pratten <span dir="ltr">
<<a href="mailto:g.pratten@sussex.ac.uk" target="_blank">g.pratten@sussex.ac.uk</a>></span> wrote:<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<div dir="ltr">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Hi all,</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">I recently built the latest release (Hilbert) on the local cluster and I've been getting a HDF5 error. I've tried building Cactus with both the local HDF5 package on the cluster as
well as letting Cactus build HDF5 from scratch. Does anyone have any insight into the error I've attached below (extract of a long chain of errors of the same form)?</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">I can dump the output to file or give configuration files if needed.</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Thanks in advance!</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Geraint</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">----------</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
#000: H5Ddeprec.c line 193 in H5Dcreate1(): unable to create dataset</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
major: Dataset</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
minor: Unable to initialize object</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
#001: H5Dint.c line 453 in H5D__create_named(): unable to create and link to dataset</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
major: Dataset</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
minor: Unable to initialize object</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
#002: H5L.c line 1638 in H5L_link_object(): unable to create new link to object</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
major: Links</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
minor: Unable to initialize object</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
#003: H5L.c line 1882 in H5L_create_real(): can't insert link</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
major: Symbol table</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
minor: Unable to insert object</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
#004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
major: Symbol table</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
minor: Object not found</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
#005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
major: Symbol table</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
minor: Callback failed</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
#006: H5L.c line 1674 in H5L_link_cb(): name already exists</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
major: Symbol table</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
minor: Object already exists</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
WARNING level 1 from host node207.cm.cluster process 0</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
while executing schedule bin (none), routine (no thorn)::(no routine)</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
in thorn CarpetIOHDF5, file /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/<a href="http://output.cc/" target="_blank">Output.cc</a>:677:</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
-> HDF5 call 'dataset = H5Dcreate (outfile, datasetname.str().c_str(), filedatatype, dataspace, plist)' returned error code -1</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
WARNING level 1 from host node207.cm.cluster process 0</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
while executing schedule bin (none), routine (no thorn)::(no routine)</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
in thorn CarpetIOHDF5, file /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/<a href="http://output.cc/" target="_blank">Output.cc</a>:689:</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
-> HDF5 call 'H5Dwrite (dataset, memdatatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, data)' returned error code -1</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
WARNING level 1 from host node207.cm.cluster process 0</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
while executing schedule bin (none), routine (no thorn)::(no routine)</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
in thorn CarpetIOHDF5, file /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/<a href="http://output.cc/" target="_blank">Output.cc</a>:725:</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
-> HDF5 call 'attr = H5Acreate (dataset, "level", H5T_NATIVE_INT, dataspace, H5P_DEFAULT)' returned error code -1</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
WARNING level 1 from host node207.cm.cluster process 0</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
while executing schedule bin (none), routine (no thorn)::(no routine)</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
in thorn CarpetIOHDF5, file /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/<a href="http://output.cc/" target="_blank">Output.cc</a>:726:</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
-> HDF5 call 'H5Awrite (attr, H5T_NATIVE_INT, &refinementlevel)' returned error code -1</div>
<div style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(245,245,245);background-color:rgb(0,0,0)">
WARNING level 1 from host node207.cm.cluster process 0</div>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div>--
<div>
<div>
<div dir="ltr">
<div dir="ltr">
<div dir="ltr"><span style="background-color:rgb(255,255,255)"><font color="#444444">Geraint Pratten</font></span></div>
<div dir="ltr"><span style="background-color:rgb(255,255,255)"><font color="#444444">Postdoctoral Research Associate<br>
<br>
Mobile: <a href="tel:%2B44%280%29%207581709282" value="+447581709282" target="_blank">
+44(0) 7581709282</a><br>
E-mail: <a href="mailto:G.Pratten@sussex.ac.uk" target="_blank">G.Pratten@sussex.ac.uk</a><br>
Skype: geraint.pratten<br>
<br>
School of Mathematical and Physical Sciences<br>
Pevensey 3 Building<br>
University of Sussex<br>
Falmer Campus<br>
Brighton</font></span>
<div><span style="background-color:rgb(255,255,255)"><font color="#444444">BN1 9QH<br>
United Kingdom</font></span><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br></div></div><span class="">
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<br>
</span></blockquote>
</div><span class="">
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>Erik Schnetter <<a href="mailto:schnetter@cct.lsu.edu" target="_blank">schnetter@cct.lsu.edu</a>><br>
<a href="http://www.perimeterinstitute.ca/personal/eschnetter/" target="_blank">http://www.perimeterinstitute.ca/personal/eschnetter/</a></div>
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</span></blockquote><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
<br>
<div>
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;">
<div>-- </div>
<div>Ian Hinder</div>
<div><a href="http://members.aei.mpg.de/ianhin" target="_blank">http://members.aei.mpg.de/ianhin</a></div>
</div>
</div>
</div>
</div>
</div>
<br>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="background-color:rgb(255,255,255)"><font color="#444444">Geraint Pratten</font></span></div><div dir="ltr"><span style="background-color:rgb(255,255,255)"><font color="#444444">Postdoctoral Research Associate<br><br>Mobile: +44(0) 7581709282<br>E-mail: <a href="mailto:G.Pratten@sussex.ac.uk" target="_blank">G.Pratten@sussex.ac.uk</a><br>Skype: geraint.pratten<br><br>School of Mathematical and Physical Sciences<br>Pevensey 3 Building<br>University of Sussex<br>Falmer Campus<br>Brighton</font></span><div><span style="background-color:rgb(255,255,255)"><font color="#444444">BN1 9QH<br>United Kingdom</font></span><br></div></div></div></div></div>
</div>
</blockquote></div><br><div apple-content-edited="true">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>-- </div><div>Ian Hinder</div><div><a href="http://members.aei.mpg.de/ianhin">http://members.aei.mpg.de/ianhin</a></div></div></div></div></div>
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