<div dir="ltr"><div><div>Hi Simon,<br><br></div>If you're still stuck, I may be able to help a bit. In the past, I have successfully used the <i>serial </i>version of VisIt in Ubuntu 14.04.3 to read HDF5 files created by FLASH's parallel I/O. I don't think the parallel VisIt installation is necessary.<br><br></div><div>One idea is that maybe it's not VisIt, but it's your HDF5 file. E.g., maybe the outputs are getting corrupted when you run in parallel. Were the HDF5 files made on Ubuntu, too?<br><br></div><div>Last year, I did a full setup on FLASH and VisIt in Ubuntu. I organized some notes for you in case they are of help. Especially relevant may be the choice of hdf5 libraries: I used <i>sudo apt-get install </i><b>libhdf5-openmpi-dev </b>(parallel hdf5 library) rather than <b>libhdf5-dev</b> (serial hdf5 library).<br></div><div><br></div><div><u><b><u><b><i>Scott's notes on installing FLASH 4.3 in Ubuntu 14.04.3<br></i></b></u></b></u></div><div><i>My installation followed the FLASH documentation<b>.</b></i><u><b><u><b><i><br><br></i></b></u></b></u></div><div>1. Installed FLASH dependencies, including optional parallel HDF5, using the package manager.<br><blockquote># Going down the list at: <a target="_blank" href="http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p3/node5.html">http://flash.uchicago.edu/<wbr>site/flashcode/user_support/<wbr>flash4_ug_4p3/node5.html</a><br>sudo apt-get update<br>sudo apt-get upgrade<br><br># GCC and GNU Make<br>sudo apt-get install build-essential<br><br># Fortran90<br>sudo apt-get install gfortran<br><br># MPI, HDF5 (parallel)<br>sudo apt-get install mpi-default-dev<br>sudo apt-get install openmpi-bin<br>sudo apt-get install libhdf5-openmpi-dev # NOTE: I originally used "libhdf5-dev", but changed later to libhdf5-openmpi-dev for parallel I/O.<br></blockquote><br></div><div>2. Installed HYPRE dependency from source, into its own folder.<br><blockquote># Download HYPRE 2.8 source code (2.10 does not work with FLASH 4.3), and unzip.<br>tar -xvf hypre-2.8.0b.tar.gz<br># Navigate into the unzipped folder, and then make the library from source:<br>cd src<br>./configure<br>make<br>make install<br></blockquote></div><div>3. Download and unzip FLASH 4.3, and give your computer a Makefile.h in the "sites" directory.<br></div><div><blockquote>tar -xvf FLASH4.3.tar.gz<br>cd FLASH4.3/sites<br>mkdir virtuoso # Make a new folder named after your computer. Here, my computer's name is "virtuoso".<br>cp Prototypes/Linux/Makefile.h virtuoso/Makefile.h # Copy the Linux makefile prototype<br># Now, change the Makefile.h to point to appropriate locations.<br>nano virtuoso/Makefile.h<br></blockquote><div style="margin-left:40px"><i>The beginning few lines of the copied Makefile.h should be modified to be similar to what's shown below.</i><br><i>Each of those folders (no ending slash) must contain the subfolders called “lib” and/or “bin”.</i><br><i><i>The HYPRE_PATH is where you just installed it.</i></i><br><i>Find path of MPI_PATH by examining the output of: “type mpicc”</i><br><i>Find path of HDF5_PATH by examining the output of: “echo $HDF5_C_LIBS”</i><br></div></div><div style="margin-left:40px"><br><i>After modification, first few lines of …/sites/virtuoso/Makefile.h look like:</i><br></div><div><div style="margin-left:40px">
</div><p style="margin-top:0pt;margin-bottom:0pt;margin-left:80px;text-align:left;word-break:normal"><span style="font-size:12pt;font-family:calibri;color:black">MPI_PATH<span>
</span></span><span style="font-size:12pt;font-family:calibri;color:black">= /</span><span style="font-size:12pt;font-family:calibri;color:black">usr</span></p><div style="margin-left:80px">
</div><p style="margin-top:0pt;margin-bottom:0pt;margin-left:80px;text-align:left;word-break:normal"><span style="font-size:12pt;font-family:calibri;color:black">HDF4_PATH<span>
</span>=</span></p><div style="margin-left:80px">
</div><p style="margin-top:0pt;margin-bottom:0pt;margin-left:80px;text-align:left;word-break:normal"><span style="font-size:12pt;font-family:calibri;color:black">HDF5_PATH<span>
</span>= /</span><span style="font-size:12pt;font-family:calibri;color:black">usr</span></p><div style="margin-left:80px">
</div><p style="margin-top:0pt;margin-bottom:0pt;margin-left:80px;text-align:left;word-break:normal"><span style="font-size:12pt;font-family:calibri;color:black">HYPRE_PATH = /home/</span><span style="font-size:12pt;font-family:calibri;color:black">joeblow</span><span style="font-size:12pt;font-family:calibri;color:black">/hypre-2.8.0b/</span><span style="font-size:12pt;font-family:calibri;color:black">src</span><span style="font-size:12pt;font-family:calibri;color:black"><wbr>/</span><span style="font-size:12pt;font-family:calibri;color:black">hypre<br></span></p><div style="margin-left:80px">
</div><p style="margin-top:0pt;margin-bottom:0pt;margin-left:80px;text-align:left;word-break:normal"><span style="font-size:12pt;font-family:calibri;color:black">ZLIB_PATH<span>
</span>=</span></p><div style="margin-left:80px">
</div><p style="margin-top:0pt;margin-bottom:0pt;margin-left:80px;text-align:left;word-break:normal"><span style="font-size:12pt;font-family:calibri;color:black">PAPI_PATH<span>
</span>=</span></p><div style="margin-left:80px">
</div><p style="margin-top:0pt;margin-bottom:0pt;margin-left:80px;text-align:left;word-break:normal"><span style="font-size:12pt;font-family:calibri;color:black">PAPI_FLAGS =</span></p><div style="margin-left:80px">
</div><p style="margin-top:0pt;margin-bottom:0pt;margin-left:80px;text-align:left;word-break:normal"><span style="font-size:12pt;font-family:calibri;color:black">NCMPI_PATH =</span></p><div style="margin-left:80px">
</div><p style="margin-top:0pt;margin-bottom:0pt;margin-left:80px;text-align:left;word-break:normal"><span style="font-size:12pt;font-family:calibri;color:black">MPE_PATH<span>
</span>=</span></p>
<br></div><div>4. Test the installation with WindTunnel (does not use Hypre) or LaserSlab (does use Hypre)<br><div style="margin-left:40px">./setup WindTunnel -auto<br># Ends with “SUCCESS”<br>cd object<br>make -j 4 (runs on all four cores)<br># Ends with “SUCCESS”<br># Before running the simulation, edit flash.par to include some plotting variables (better test I/O); e.g. add the line:<br>plot_var_1 = “dens”<br></div><div style="margin-left:40px"># Run the simulation and create outputs<br></div><div style="margin-left:40px">mpirun -np 4 flash4<br><br></div></div><div><i>Note: To test LaserSlab, you could start instead with something like:<br></i><div style="margin-left:40px">./setup -auto LaserSlab -2d +uhd3t +pm4dev +hdf5typeio +mgd mgd_meshgroups=30 -geometry=cylindrical -nxb=10 -nyb=10 +mtmmmt -maxblocks=8192 -without-unit=Particles species=cham,targ</div><i><br><br></i></div><div><u><b><u><b><i><br></i></b></u><i>Scott's notes on installing VisIt 2.9.2 in Ubuntu 14.04.3</i><br></b></u>1. Downloaded the VisIt 2.9.2 tarball for Ubuntu 14.04 64-bit Linux: “visit2_9_2.linux-x86_64-<wbr>ubuntu14.tar.gz” from: <a target="_blank" href="https://wci.llnl.gov/simulation/computer-codes/visit/executables">https://wci.llnl.gov/<wbr>simulation/computer-codes/<wbr>visit/executables</a><ul><li>Downloaded and read the “VisIt install notes” for VisIt 2.9.2 at the same website</li><li>Downloaded the “VisIt install script” for VisIt 2.9.2 from the same website, named it “visit-install” and put it in the same folder as the tarball</li></ul>2. Made the install script executable: “sudo chmod +x visit-install”<br>3. Ran the install script:<br><ul><li>“sudo ./visit-install <span style="color:rgb(255,0,0)">2.9.2</span> <span style="color:rgb(11,83,148)">linux-x86_64-ubuntu14</span> <span style="color:rgb(56,118,29)">/usr/local/visit</span>”</li><li>Note that the syntax is “sudo ./visit-install <span style="color:rgb(255,0,0)">version</span> <span style="color:rgb(11,83,148)">platform</span> <span style="color:rgb(56,118,29)">directory</span>”</li><li>When prompted, selected “No affiliation” or “no site” (choice 1)<br></li></ul></div><div>4. Added the newly-created binaries folder to my user path:<br><ul><li>Edited (home)/.bashrc and added the following line at the bottom:</li><li>“export PATH=$PATH:/usr/local/visit/<wbr>bin”</li><li>Then, restarted terminal</li></ul>5. Can now open VisIt by typing “visit” at the terminal window<br><br></div><div>Best,<br><br></div><div>Scott<br></div></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 Wed, Sep 21, 2016 at 9:29 AM, Simon Don <span dir="ltr"><<a href="mailto:simondonxq@gmail.com" target="_blank">simondonxq@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><span></span>Thank you very much. In fact my code is now just using PARAMESH amr package and the HDF5 files is generated by papamesh 's <font size="2"><span style="background-color:rgba(255,255,255,0)">parallel HDF5 I/O. We have not finished the shift from paramesh to flash.</span></font><div><font size="2"><span><br></span></font></div><div><font size="2"><span>Now I want to open these hdf5 files by visit. But I can only do this when the hdf5 file is written by only one processor. When the MPI is used to write the hdf5 file, my present visit on ubuntu can not open it rightly.</span></font></div><div><font size="2"><span><br></span></font></div><div><font size="2"><span>That the situation and why I am asking parallel visit things.</span></font></div><div><font size="2"><span><br></span></font></div><div><font size="2"><span>Regards.<span></span><br></span></font><br>2016年9月21日星期三，Scott Feister <<a>sfeister@gmail.com</a>> 写道：<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi Simon,<br><br></div>Just to clarify, are you having trouble when opening an HDF5 made by using FLASH's parallel HDF5 I/O, or trying to run a parallel installation VisIt <i>itself</i>? Or both?<br><br></div>Best,<br><br></div>Scott<br><div><div><br></div></div></div><div class="gmail_extra"><br clear="all"><div><div 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 Wed, Sep 21, 2016 at 8:25 AM, Simon Don <span dir="ltr"><<a>simondonxq@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all:<div><br></div><div>I now get some result data of AMR. It is written by Fujitsu MPI in hdf5 format. I want to use VisIt to visualize it. </div><div><br></div><div>I downloaded the built <a href="https://wci.llnl.gov/simulation/computer-codes/visit/executables" target="_blank">executable</a>s from the visit homepage and installed it on my ubuntu computer. When I use it to open hdf5 generated by one processor, it works well. We I open file generated by MPI, the display is not right or sometimes I can't open the file. </div><div><br></div><div>So my question is, now the executables of VisIt for ubuntu are without mpi and can't support MPI? In order to get a parallel VisIt on ubuntu, I need to install from the source code and build it by myself with the certain MPI library options?</div><div><br></div>As I said, the MPI used for calculations is Fujitsu MPI, so I have to build a parallel VisIt with Fujitsu MPi to open such a data file? Can i build a parallel visit using other mpi like openmpi and open a data file generated by Fujitsu mpi?<div><br></div><div>Anyone who is familiar with this? Thank you very much!!</div><div><br></div>Shimon
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