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<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Hi HPC & Spear users,</span></div>
<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><br>
We have completed upgrading all HPC, Spear, and Login nodes to Alma8.6. We appreciate your patience during this upgrade.<br>
<br>
Due to the large scope and the many moving parts of this project, we are still cleaning up some residual issues.
<a href="mailto:support@rcc.fsu.edu" id="OWA7bf175ac-528f-f7a3-d08f-31a4591c0861" class="OWAAutoLink" data-loopstyle="linkonly">
Let us know</a> if you experience any problems after the upgrade.<br>
<br>
</span></div>
<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Most libraries are available, but we are working on lesser used ones. Please review
the list and recommended workarounds below the signature line in this email. Our Apps specialists will be working through the list in the coming days. Please
<a href="mailto:support@rcc.fsu.edu" id="OWA66d08453-be3e-4d06-efd7-c41093123b22" class="OWAAutoLink" data-loopstyle="linkonly">
contact us</a> if you need us to prioritize any package in that list.</span></div>
<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><br>
Important notes:</span></div>
<ul style="list-style-type: disc;">
<li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">We upgraded the GNU GCC compiler from v8.3 to v8.5. If you use that compiler, your code will likely need to be recompiled
for the new software stack. As with any software upgrade, shared libraries have changed; some have been removed in favor of newer alternatives, and some have new versions. Please let us know if you need help recompiling your code.</span></li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">OpenMPI is currently available only with the GNU v8.5.0 and Intel v21 compilers.</span></li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">We upgraded our CUDA libraries and installed both v11.8 and v12.1. Load the
<code>cuda/12.1</code> module to use the newer version.</span></li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">If you need a version of Python newer than v3.6.8, we recommend installing it in a Conda environment. You can install
any version up to and including v3.12. Instructions or on <a href="https://docs.rcc.fsu.edu/software/python/#using-newer-versions-of-python-on-the-hpc" id="OWA10f01f28-7192-f279-a3cb-b2a99366acb5" class="OWAAutoLink" data-loopstyle="linkonly">
our website</a>.</span></li></ul>
<div><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">For those of you who have outstanding software installation or upgrade requests, we
appreciate your patience. In our triage process, we are prioritizing existing packages before attending to new software requests. This will be the case for the next few weeks.<br>
<br>
If you have any questions or comments, please let us know: <a href="mailto:support@rcc.fsu.edu" id="OWA59634a1e-59d3-b131-c945-ecf80cfe147e" class="OWAAutoLink" data-loopstyle="linkonly">
support@rcc.fsu.edu</a>.<br>
<br>
Best regards,<br>
The RCC Team</span></div>
<hr>
<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><br>
</span></div>
<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">The following libraries and executables are not yet available. Please
<a href="mailto:support@rcc.fsu.edu" id="LPlnk183131" class="OWAAutoLink" title="mailto:support@rcc.fsu.edu" data-loopstyle="linkonly">
let us know</a> if you need any of the following packages:</span></div>
<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><br>
</span></div>
<table id="tableSelected0" data-editing-info="{"topBorderColor":"#CCCCCC","bottomBorderColor":"#CCCCCC","verticalBorderColor":"#CCCCCC","hasHeaderRow":false,"hasFirstColumn":false,"hasBandedRows":false,"hasBandedColumns":false,"bgColorEven":null,"bgColorOdd":"#CCCCCC20","headerRowColor":"#CCCCCC","tableBorderFormat":0,"verticalAlign":null}" style="box-sizing: border-box; height: 563px;">
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<td style="width: 161.81px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Package<br>
</span></td>
<td style="width: 168.089px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><b>Compilers</b><br>
</span></td>
<td style="width: 510px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><b>Workaround</b></span></div>
</td>
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<td style="width: 161.81px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">GNU Compilers v4.8.5<br>
</span></td>
<td style="width: 168.089px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">-<br>
</span></td>
<td style="width: 510px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Use 8.5.0 (default)</span></div>
</td>
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<td style="width: 161.81px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">OpenMPI v4.1.3<br>
</span></td>
<td style="width: 168.089px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">All GNU and Intel<br>
</span></td>
<td style="width: 510px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Use OpenMPI 4.1.0</span></div>
</td>
</tr>
<tr>
<td style="width: 161.81px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">MVAPICH2 v2.3.7<br>
</span></td>
<td style="width: 168.089px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">All GNU and Intel<br>
</span></td>
<td style="width: 510px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Use MVAPICH2 2.3.5</span></div>
</td>
</tr>
<tr>
<td style="width: 161.81px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">NetCDF v4.7.0<br>
</span></td>
<td style="width: 168.089px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">All GNU and Intel<br>
</span></td>
<td style="width: 510px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Use NetCDF 4.8.0</span></div>
</td>
</tr>
<tr>
<td style="width: 161.81px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">NetCDF-Fortran v4.4.5<br>
</span></td>
<td style="width: 168.089px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">All GNU and Intel<br>
</span></td>
<td style="width: 510px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Use NetCDF-Fortran 4.5.3</span></div>
</td>
</tr>
<tr>
<td style="width: 161.81px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">RELION 3.13<br>
</span></td>
<td style="width: 168.089px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">GNU 8.5.0 + CUDA 11.8<br>
</span></td>
<td style="width: 510px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Contact
<a href="mailto:support@rcc.fsu.edu" id="OWA840fb1c1-7a8c-40fe-a4ac-177da3d60af9" class="OWAAutoLink" data-loopstyle="linkonly">
support@rcc.fsu.edu</a></span></div>
</td>
</tr>
<tr>
<td style="width: 161.81px; height: 55px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">bcl2fastq v2.20.0<br>
</span></td>
<td style="width: 168.089px; height: 55px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">GNU<br>
</span></td>
<td style="width: 510px; height: 55px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Use a
<a href="https://docs.rcc.fsu.edu/software/python/#using-newer-versions-of-python-on-the-hpc" id="OWA525c3554-30b9-de95-4811-54402b22d8db" class="OWAAutoLink" data-loopstyle="linkonly">
Conda</a> environment:<br>
<code>conda install -c dranew bcl2fastq</code></span></div>
</td>
</tr>
<tr>
<td style="width: 161.81px; height: 55px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">blat v34<br>
</span></td>
<td style="width: 168.089px; height: 55px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">GNU<br>
</span></td>
<td style="width: 510px; height: 55px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Use a
<a href="https://docs.rcc.fsu.edu/software/conda/" id="OWA5d415cfd-1c0e-6ff9-9c75-7aaa60b4b2d2" class="OWAAutoLink" data-loopstyle="linkonly">
Conda</a> environment:<br>
<code>conda install -c bioconda blat</code></span></div>
</td>
</tr>
<tr>
<td style="width: 161.81px; height: 55px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Python >=3.6.8<br>
</span></td>
<td style="width: 168.089px; height: 55px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">-<br>
</span></td>
<td style="width: 510px; height: 55px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Use a
<a href="https://docs.rcc.fsu.edu/software/conda/" id="OWA141904f6-7764-d059-5ea1-a814c1cae031" class="OWAAutoLink" data-loopstyle="linkonly">
Conda</a> environment:<br>
<code>conda install python=3.10</code></span></div>
</td>
</tr>
<tr>
<td style="width: 161.81px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">HDF5 v1.12.2<br>
</span></td>
<td style="width: 168.089px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">All GNU and Intel<br>
</span></td>
<td style="width: 510px; height: 29.0047px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Use HDF5 1.12.0</span></div>
</td>
</tr>
<tr>
<td style="width: 161.81px; height: 77.9968px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">NCL v6.6.2<br>
</span></td>
<td style="width: 168.089px; height: 77.9968px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Intel<br>
</span></td>
<td style="width: 510px; height: 77.9968px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Use a
<a href="https://docs.rcc.fsu.edu/software/conda/" id="OWA0aecdda5-b38c-9675-688e-6c41b36fbe1e" class="OWAAutoLink" data-loopstyle="linkonly">
Conda</a> environment:<br>
<code>conda install -c conda-forge ncl</code><br>
<br>
</span></div>
</td>
</tr>
<tr>
<td style="width: 161.81px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">FreeFEM++ v4.7<br>
</span></td>
<td style="width: 168.089px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box;">
<span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">GNU<br>
</span></td>
<td style="width: 510px; height: 28.9978px; border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204); box-sizing: border-box; word-break: break-word; white-space: normal;">
<div style="white-space: normal;"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Contact
<a href="mailto:support@rcc.fsu.edu" id="OWA8896f779-4b21-ad59-abde-fedbd9b951e3" class="OWAAutoLink" data-loopstyle="linkonly">
support@rcc.fsu.edu</a></span></div>
</td>
</tr>
<tr>
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