<div dir="ltr"><div>Hi Isabella,</div><div><br></div><div>From your screenshot it looks like you're going to be running FLASH in Ubuntu. Is that right? I think I recognize that font and color scheme :-)<br></div><div><br></div><div>Your Makefile that you sent me starts with the lines:</div><div>
<pre class="m_4401470553912757714gmail-aLF-aPX-K0-aPE">MPI_PATH = /usr/local/
HDF4_PATH =
HDF5_PATH = /home/isabella/hdf5
HYPRE_PATH = /home/isabella/hypre-2.11.2/<wbr>src/hypre</pre>
Did you build HDF5 and MPI libraries yourself? It's a lot of work, and can have pitfalls! If you're using Ubuntu, I recommend downloading all your dependencies except <i>Hypre </i>from Ubuntu's package repositories. After you've done this, in my experience, the Linux Makefile.h does not work without further modification to locate your installation of MPI and HDF5.<br><div><br></div>
Maybe it can help you if I describe the way I installed FLASH on Ubuntu last year. When I installed FLASH in Ubuntu 14.04, I did the following.</div><div><br></div><div>____________</div><div><br></div><div><u><b>EXAMPLE INSTALLATION OF FLASH ON UBUNTU 14.04</b></u><br></div><div><b>1. Install several packages from the Ubuntu package repository, to satisfy FLASH dependencies.</b><br></div><div>I went down the list of dependencies in the user guide for the version I was using: <a href="http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p3/node5.html" target="_blank">http://flash.uchicago.edu/<wbr>site/flashcode/user_support/<wbr>flash4_ug_4p3/node5.html</a></div><div><i><br></i></div><div><i>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<br></i></div><div><br></div><div><b>2. Build hypre from source (I used hypre-2.8.0b, since this was the most recent having compatibility to my FLASH version at the time), and make note of the build directory.</b><br></div><div><i>cd
/home/scott/hypre-2.8.0b/src<br>./configure<br>make<br>make install</i><br><br></div><div><b>3. Make a new directory in sites, e.g. in my case called "scottpc" under the FLASH code "sites" directory. You can call this folder anything, but best practice is to call it the hostname of your PC, since you can later exclude the "-site=" flag in FLASH setup. Then copy the default Linux Makefile.h into that folder.</b></div><div><i>cd <flashdirectory>/sites</i></div><div><i>mkdir scottpc</i><br></div><div><i></i></div><div><i>cp Prototypes/Linux/Makefile.h scottpc/</i><br><br></div><div><b>4. Modify the top lines of your new Makefile.h (<i><flashdirectory>/sites/<wbr>scottpc/Makefile.h</i>)<i> </i>to point to your MPI, HDF5, and HYPRE libraries:</b><br></div><div><i>MPI_PATH = /usr<br>HDF4_PATH =<br>HDF5_PATH = /usr<br>HYPRE_PATH = /home/scott/hypre-2.8.0b/src/<wbr>hypre</i><br></div><div><br></div><div><b>Notes on this step:</b></div><div>* Each of those folders (no ending slash) must contain the subfolders called “lib” and/or “bin”.<br>* Find your own path of MPI_PATH by examining the output of: “type mpicc”<br>* Find your own path of HDF5_PATH by examining the output of: “echo $HDF5_C_LIBS”<br></div><div><br></div><div><b>5. Test your installation. E.g. call FLASH setup and explicitly point to your Makefile</b></div><div><i>./setup WindTunnel -auto -site=scottpc</i><i><br></i>Ends with “SUCCESS”<i><br></i></div><div><i><br></i>
</div><div><i>cd object</i></div><div><i>make -j 4 </i>[runs make on four cores]<i><br></i>Ends with “SUCCESS”</div><div><i><br></i></div><div><i></i>Edit flash.par to include plotting variables; e.g. add the line:<i><br>plot_var_1 = “dens”</i></div><div><i><br></i></div><div><i>mpirun -np 4 flash4</i></div><div>[Check that it runs and that generated HDF5 files are readable]<br></div><div><br></div><div><br></div><div>______________________________<wbr>__</div><div><br></div><div><br></div><div>I hope this helps you find your issue!<br></div><div><br></div><div>Best,</div><div><br></div><div>Scott<br></div><div class="gmail_extra"><br clear="all"><div><div class="m_4401470553912757714gmail_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 Tue, Jul 10, 2018 at 2:05 PM, Scott Feister <span dir="ltr"><<a href="mailto:sfeister@gmail.com" target="_blank">sfeister@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 dir="ltr"><div>Hi Isabella,</div><div><br></div><div>Are you specifying a custom Makefile in your setup command with the "-site=" flag? If you send your Makefile, I can take a look.</div><div><br></div><div>Best,</div><div><br></div><div>Scott<br></div></div><div class="gmail_extra"><br clear="all"><div><div class="m_4401470553912757714m_7178886499132422737gmail_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><div><div class="m_4401470553912757714h5">
<br><div class="gmail_quote">On Tue, Jul 10, 2018 at 12:59 PM, Isabella M Pagano <span dir="ltr"><<a href="mailto:ipagano@utexas.edu" target="_blank">ipagano@utexas.edu</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">Hi, <br clear="all"><div>I'm trying to compile the executable for the laserslab included problem, but I keep getting an error that corresponds to (I think) the linkages between the compilers? I've tried altering the path files, but it didn't seem to help fix this particular error. (screenshot attached.) Any tips would be appreciated. </div><div>Thanks! </div><span class="m_4401470553912757714m_7178886499132422737HOEnZb"><font color="#888888">-- <br><div dir="ltr" class="m_4401470553912757714m_7178886499132422737m_4680537023411038836gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Bella </div></div></font></span></div>
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