<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:DengXian;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:"\@DengXian";
panose-1:2 1 6 0 3 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 2.0cm 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="blue" vlink="purple" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal">Hi Matt, Roland and others,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">@ Roland, I can create the Vec in Petsc, but want to load it with external data. I can arrange that data in what ever way with Python. It is about two vectors, each of length 4.6 x10^6 entries.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have created a hdf5 file with Python and try to load it into PETSc which gives me some errors. I added the small test script I am using. The error I am getting is:
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">error: ‘PetscViewerHDF5Open’ was not declared in this scope; did you mean ‘PetscViewerVTKOpen’?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Am I using the wrong header?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best, <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thijs<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Matthew Knepley <knepley@gmail.com>
<br>
<b>Sent:</b> 03 March 2021 23:02<br>
<b>To:</b> Smit Thijs <thijs.smit@hest.ethz.ch><br>
<b>Cc:</b> petsc-users@mcs.anl.gov<br>
<b>Subject:</b> Re: [petsc-users] Loading external array data into PETSc<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Wed, Mar 3, 2021 at 4:23 PM Smit Thijs <<a href="mailto:thijs.smit@hest.ethz.ch">thijs.smit@hest.ethz.ch</a>> wrote:<o:p></o:p></p>
</div>
<div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi All,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I would like to readin a fairly large external vector into PETSc to be used further. My idea was to write a hdf5 file using Python with the vector data. Then read that hdf5 file
into PETSc using PetscViewerHDF5Open and VecLoad. Is this the advised way or is there a better alternative to achieve the same (getting this external array data into PETSc)?<o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I think there are at least two nice ways to do this:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">1) Use HDF5. Here you have to name your vector to match the HDF5 object<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">2) Use raw binary. This is a specific PETSc format, but it is fast and simple.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"> Thanks,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"> Matt<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#24292E">Best regards,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#24292E"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#24292E">Thijs Smit</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#24292E"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#24292E">PhD Candidate</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#24292E">ETH Zurich</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#24292E">Institute for Biomechanics</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">-- <o:p></o:p></p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>