<div dir="ltr"><div>Great! Thanks!</div><div><br></div><div>I thought I would work through the notebooks for PyDarshan. I use Anaconda for my Python which is the source of the issue I think.</div><div><br></div><div>I used pip to install PyDarshan on my system (most of the time I can get pip installed Python modules to work with conda). I'm trying the 01_darsha_introduction notebook. I tried running the first cell and got the following error:</div><div><br></div><div><br></div><div><pre><span class="gmail-ansi-red-fg">---------------------------------------------------------------------------</span>
<span class="gmail-ansi-red-fg">ValueError</span> Traceback (most recent call last)
<span class="gmail-ansi-green-fg"><ipython-input-1-923d294d02c5></span> in <span class="gmail-ansi-cyan-fg"><module></span>
<span class="gmail-ansi-green-fg">----> 1</span><span class="gmail-ansi-red-fg"> </span><span class="gmail-ansi-green-fg">import</span> darshan
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 2</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 3</span> report <span class="gmail-ansi-blue-fg">=</span> darshan<span class="gmail-ansi-blue-fg">.</span>DarshanReport<span class="gmail-ansi-blue-fg">(</span><span class="gmail-ansi-blue-fg">"example-logs/example.darshan"</span><span class="gmail-ansi-blue-fg">,</span> read_all<span class="gmail-ansi-blue-fg">=</span><span class="gmail-ansi-green-fg">True</span><span class="gmail-ansi-blue-fg">)</span> <span class="gmail-ansi-red-fg"># Default behavior</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 4</span> report<span class="gmail-ansi-blue-fg">.</span>info<span class="gmail-ansi-blue-fg">(</span><span class="gmail-ansi-blue-fg">)</span>
<span class="gmail-ansi-green-fg">~/.local/lib/python3.8/site-packages/darshan/__init__.py</span> in <span class="gmail-ansi-cyan-fg"><module></span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 17</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 18</span> <span class="gmail-ansi-red-fg">#from darshan.backend.cffi_backend import *</span>
<span class="gmail-ansi-green-fg">---> 19</span><span class="gmail-ansi-red-fg"> </span><span class="gmail-ansi-green-fg">from</span> darshan<span class="gmail-ansi-blue-fg">.</span>report <span class="gmail-ansi-green-fg">import</span> DarshanReport
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 20</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 21</span>
<span class="gmail-ansi-green-fg">~/.local/lib/python3.8/site-packages/darshan/report.py</span> in <span class="gmail-ansi-cyan-fg"><module></span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 8</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 9</span>
<span class="gmail-ansi-green-fg">---> 10</span><span class="gmail-ansi-red-fg"> </span><span class="gmail-ansi-green-fg">import</span> darshan<span class="gmail-ansi-blue-fg">.</span>backend<span class="gmail-ansi-blue-fg">.</span>cffi_backend <span class="gmail-ansi-green-fg">as</span> backend
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 11</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 12</span> <span class="gmail-ansi-green-fg">import</span> json
<span class="gmail-ansi-green-fg">~/.local/lib/python3.8/site-packages/darshan/backend/cffi_backend.py</span> in <span class="gmail-ansi-cyan-fg"><module></span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 9</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 10</span> <span class="gmail-ansi-green-fg">import</span> numpy <span class="gmail-ansi-green-fg">as</span> np
<span class="gmail-ansi-green-fg">---> 11</span><span class="gmail-ansi-red-fg"> </span><span class="gmail-ansi-green-fg">import</span> pandas <span class="gmail-ansi-green-fg">as</span> pd
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 12</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 13</span> <span class="gmail-ansi-green-fg">import</span> logging
<span class="gmail-ansi-green-fg">~/anaconda3/lib/python3.8/site-packages/pandas/__init__.py</span> in <span class="gmail-ansi-cyan-fg"><module></span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 27</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 28</span> <span class="gmail-ansi-green-fg">try</span><span class="gmail-ansi-blue-fg">:</span>
<span class="gmail-ansi-green-fg">---> 29</span><span class="gmail-ansi-red-fg"> </span><span class="gmail-ansi-green-fg">from</span> pandas<span class="gmail-ansi-blue-fg">.</span>_libs <span class="gmail-ansi-green-fg">import</span> hashtable <span class="gmail-ansi-green-fg">as</span> _hashtable<span class="gmail-ansi-blue-fg">,</span> lib <span class="gmail-ansi-green-fg">as</span> _lib<span class="gmail-ansi-blue-fg">,</span> tslib <span class="gmail-ansi-green-fg">as</span> _tslib
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 30</span> <span class="gmail-ansi-green-fg">except</span> ImportError <span class="gmail-ansi-green-fg">as</span> e<span class="gmail-ansi-blue-fg">:</span> <span class="gmail-ansi-red-fg"># pragma: no cover</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 31</span> <span class="gmail-ansi-red-fg"># hack but overkill to use re</span>
<span class="gmail-ansi-green-fg">~/anaconda3/lib/python3.8/site-packages/pandas/_libs/__init__.py</span> in <span class="gmail-ansi-cyan-fg"><module></span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 11</span>
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 12</span>
<span class="gmail-ansi-green-fg">---> 13</span><span class="gmail-ansi-red-fg"> </span><span class="gmail-ansi-green-fg">from</span> pandas<span class="gmail-ansi-blue-fg">.</span>_libs<span class="gmail-ansi-blue-fg">.</span>interval <span class="gmail-ansi-green-fg">import</span> Interval
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 14</span> from pandas._libs.tslibs import (
<span class="gmail-ansi-green-intense-fg gmail-ansi-bold"> 15</span> NaT<span class="gmail-ansi-blue-fg">,</span>
<span class="gmail-ansi-green-fg">pandas/_libs/interval.pyx</span> in <span class="gmail-ansi-cyan-fg">init pandas._libs.interval</span><span class="gmail-ansi-blue-fg">()</span>
<span class="gmail-ansi-red-fg">ValueError</span>: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
</pre></div><div><br></div><div>I'm guessing this is an interaction issue between conda and pip due to the last line. Any thoughts on this? I could ask for a PyDarshan package for conda and I wish I could help but I would be less than worthless in that regard.</div><div><br></div><div>Thanks for any advice!</div><div><br></div><div>Jeff</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 14, 2021 at 10:02 AM Snyder, Shane <<a href="mailto:ssnyder@mcs.anl.gov">ssnyder@mcs.anl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Hi Jeff,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Fire away! This mailing list and issues on our GitHub page (<a href="https://github.com/darshan-hpc/darshan" id="gmail-m_-8781932659329392958LPlnk" target="_blank">https://github.com/darshan-hpc/darshan</a>) are the best place for both Darshan and PyDarshan issues.<br>
</div>
<div>
<div id="gmail-m_-8781932659329392958LPBorder_GTaHR0cHM6Ly9naXRodWIuY29tL2RhcnNoYW4taHBjL2RhcnNoYW4." style="width:100%;margin-top:16px;margin-bottom:16px;max-width:800px;min-width:424px">
<table id="gmail-m_-8781932659329392958LPContainer597864" role="presentation" style="padding:12px 36px 12px 12px;width:100%;border-width:1px;border-style:solid;border-color:rgb(200,200,200);border-radius:2px">
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<div id="gmail-m_-8781932659329392958LPImageContainer597864" style="margin-right:12px;height:120px;overflow:hidden;width:240px">
<a id="gmail-m_-8781932659329392958LPImageAnchor597864" href="https://github.com/darshan-hpc/darshan" target="_blank"><img id="gmail-m_-8781932659329392958LPThumbnailImageId597864" alt="" style="display: block;" src="https://opengraph.githubassets.com/9ddeb56c895b7ef4b0be59ea140c1eaeeda7a8341b43cf692edc557e7e6367a4/darshan-hpc/darshan" width="240" height="120"></a></div>
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<div id="gmail-m_-8781932659329392958LPTitle597864" style="font-size:21px;font-weight:300;margin-right:8px;font-family:"wf_segoe-ui_light","Segoe UI Light","Segoe WP Light","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif;margin-bottom:12px">
<a id="gmail-m_-8781932659329392958LPUrlAnchor597864" href="https://github.com/darshan-hpc/darshan" style="text-decoration:none" target="_blank">darshan-hpc/darshan</a></div>
<div id="gmail-m_-8781932659329392958LPDescription597864" style="font-size:14px;max-height:100px;color:rgb(102,102,102);font-family:"wf_segoe-ui_normal","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif;margin-bottom:12px;margin-right:8px;overflow:hidden">
Darshan I/O characterization tool. Contribute to darshan-hpc/darshan development by creating an account on GitHub.</div>
<div id="gmail-m_-8781932659329392958LPMetadata597864" style="font-size:14px;font-weight:400;color:rgb(166,166,166);font-family:"wf_segoe-ui_normal","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif">
<a href="http://github.com" target="_blank">github.com</a></div>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Thanks,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
--Shane<br>
</div>
<div id="gmail-m_-8781932659329392958appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-8781932659329392958divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Darshan-users <<a href="mailto:darshan-users-bounces@lists.mcs.anl.gov" target="_blank">darshan-users-bounces@lists.mcs.anl.gov</a>> on behalf of Jeffrey Layton <<a href="mailto:laytonjb@gmail.com" target="_blank">laytonjb@gmail.com</a>><br>
<b>Sent:</b> Wednesday, July 14, 2021 8:11 AM<br>
<b>To:</b> <a href="mailto:darshan-users@lists.mcs.anl.gov" target="_blank">darshan-users@lists.mcs.anl.gov</a> <<a href="mailto:darshan-users@lists.mcs.anl.gov" target="_blank">darshan-users@lists.mcs.anl.gov</a>><br>
<b>Subject:</b> [Darshan-users] PyDarshan issues</font>
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<div>Good morning,</div>
<div><br>
</div>
<div>Is this is a good place to bring up PyDarshan issues or is there a better one?</div>
<div><br>
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<div>Thanks!</div>
<div><br>
</div>
<div>Jeff</div>
<div><br>
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