<div dir="ltr"><div><div>Hi Mehrnoosh,<br></div><br>Did you create a site-specific Makefile for your cluster (in the "sites" directory) before calling setup? In that Makefile, do you point to the desired HDF5 and MPI library paths?<br><br>It's very important to use
the same version of fortran compilers and MPI to build FLASH as was used to build
HDF5. E.g. if you point to HDF5 libraries that were built with Intel compiler 12 and OpenMPI 2.3, you need to build FLASH with the same versions of these compilers. If you point to HDF5 libraries built with GNU compilers 6.1 and mvapich, same story. If you haven't verified that part, start there!<br></div><div><br></div><div>Good luck!<br><br></div><div>Best,<br></div><div><br></div>Scott<br></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><br>Scott Feister, Ph.D.<br>Postdoctoral Researcher, Flash Center for Computational Science<br></div><div>University of Chicago, Department of Astronomy and Astrophysics<br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Jun 9, 2017 at 6:01 PM, Mehrnoosh Tahani <span dir="ltr"><<a href="mailto:mtahani@ucalgary.ca" target="_blank">mtahani@ucalgary.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div id="m_-4418974710949467937divtagdefaultwrapper" dir="ltr" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols">
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">Hello there,</span></p>
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px"><br>
</span></p>
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">I am new to FLASH and I'm </span><span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">trying
to compile and run FLASH4.3 on </span><a href="https://wiki.scinet.utoronto.ca/wiki/index.php/GPC_Quickstart" style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px" target="_blank">SciNet(GPC)</a><span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">.
When I do 'make' in the object folder I receive the following error message:</span></p>
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px"><br>
</span></p>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span>mpicc -I /scinet/gpc/Libraries/HDF5-1.<wbr>8.11/v18-openmpi-intel/include -c -g -DMAXBLOCKS=500 -DNXB=8 -DNYB=8 -DNZB=8 -DN_DIM=3 io_h5_attribute.c</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span>io_h5_attribute.c(48): error #165: too few arguments in function call</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span> dsetID = H5Dopen(hFileID, datasetName);</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span> ^</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span></span><br>
</p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span>io_h5_attribute.c(55): error #165: too few arguments in function call</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span style="white-space:pre-wrap"> </span><span style="white-space:pre-wrap"></span> attDataspace, H5P_DEFAULT);</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span style="white-space:pre-wrap"> </span><span style="white-space:pre-wrap"></span> ^</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span></span><br>
</p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span>io_h5_attribute.c(101): error #165: too few arguments in function call</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span> dsetID = H5Dopen(hFileID, datasetName);</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span> ^</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span></span><br>
</p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span>compilation aborted for io_h5_attribute.c (code 2)</span></p>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span>make: *** [io_h5_attribute.o] Error 2</span></p>
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<br>
</div>
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I tried all the available versions of HDF5 and gcc in SciNet but I got the same error with each of them. I have FLASH working on my Mac with an old version of gcc which is not available on SciNet.</div>
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<br>
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I found <a href="http://flash.uchicago.edu/pipermail/flash-users/2013-September/001354.html" target="_blank">here</a> that my compilation command is probably not pointing to the right include directory for HDF5 headers. But I couldn't find anything wrong with the path. Could
you please help me on this? (<a href="http://flash.uchicago.edu/pipermail/flash-users/2013-September/001354.html" class="m_-4418974710949467937OWAAutoLink" id="m_-4418974710949467937LPlnk138653" target="_blank">http://flash.uchicago.edu/<wbr>pipermail/flash-users/2013-<wbr>September/001354.html</a>) </div>
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<br>
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Many thanks,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">
<br>
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Mehrnoosh</div>
<p></p>
<div id="m_-4418974710949467937Signature">
<div id="m_-4418974710949467937divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;background-color:rgb(255,255,255)">
<p style="color:rgb(0,0,0);font-size:12pt"><span style="font-family:"PT Sans",sans-serif;font-size:10pt;color:rgb(117,123,128)">~~~~~~~~~~~~~~~~~~~~~~~~~~~</span><br style="font-family:"PT Sans",sans-serif;font-size:13px">
<span style="font-size:10pt;color:rgb(117,123,128)"></span><span style="font-family:"PT Sans",sans-serif;font-size:10pt;color:rgb(117,123,128)">Mehrnoosh Tahani, MSc. (Physics)</span><br style="font-family:"PT Sans",sans-serif;font-size:13px">
<span style="font-size:10pt;color:rgb(117,123,128)"></span><span style="font-family:"PT Sans",sans-serif;font-size:10pt;color:rgb(117,123,128)">PhD Student, Astrophysics </span><br style="font-family:"PT Sans",sans-serif;font-size:13px">
<span style="font-size:10pt;color:rgb(117,123,128)"></span><span style="font-family:"PT Sans",sans-serif;font-size:10pt;color:rgb(117,123,128)">Department of Physics & Astronomy</span><br style="font-family:"PT Sans",sans-serif;font-size:13px">
<span style="font-size:10pt;color:rgb(117,123,128)"></span><span style="font-family:"PT Sans",sans-serif;font-size:10pt;color:rgb(117,123,128)">University of Calgary</span></p>
<p><span style="font-size:10pt;color:rgb(117,123,128);font-size:10pt"></span><span style="color:rgb(117,123,128);font-size:10pt;font-family:"PT Sans",sans-serif"><a href="mailto:mtahani@ucalgary.ca" target="_blank">mtahani@ucalgary.ca</a></span><br>
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</blockquote></div><br></div>