[FLASH-USERS] creating executable error

[Scott Feister]

Hi Isabella,

>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 :-)

Your Makefile that you sent me starts with the lines:

MPI_PATH   = /usr/local/
HDF4_PATH  =
HDF5_PATH  = /home/isabella/hdf5
HYPRE_PATH = /home/isabella/hypre-2.11.2/src/hypre

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 *Hypre *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.

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.

____________

*EXAMPLE INSTALLATION OF FLASH ON UBUNTU 14.04*
*1. Install several packages from the Ubuntu package repository, to satisfy
FLASH dependencies.*
I went down the list of dependencies in the user guide for the version I
was using: http://flash.uchicago.edu/site/flashcode/user_support/
flash4_ug_4p3/node5.html














*sudo apt-get updatesudo apt-get upgrade# GCC and GNU Makesudo apt-get
install build-essential# Fortran90sudo apt-get install gfortran# MPI, HDF5
(parallel)sudo apt-get install mpi-default-devsudo apt-get install
openmpi-binsudo apt-get install libhdf5-openmpi-dev*

*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.*



*cd /home/scott/hypre-2.8.0b/src./configuremakemake install*

*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.*
*cd <flashdirectory>/sites*
*mkdir scottpc*
*cp Prototypes/Linux/Makefile.h scottpc/*

*4. Modify the top lines of your new Makefile.h
(<flashdirectory>/sites/scottpc/Makefile.h) to point to your MPI, HDF5, and
HYPRE libraries:*



*MPI_PATH   = /usrHDF4_PATH  =HDF5_PATH  = /usrHYPRE_PATH =
/home/scott/hypre-2.8.0b/src/hypre*

*Notes on this step:*
* Each of those folders (no ending slash) must contain the subfolders
called “lib” and/or “bin”.
* Find your own path of MPI_PATH by examining the output of: “type mpicc”
* Find your own path of HDF5_PATH by examining the output of: “echo
$HDF5_C_LIBS”

*5. Test your installation. E.g. call FLASH setup and explicitly point to
your Makefile*
*./setup WindTunnel -auto -site=scottpc*
Ends with “SUCCESS”

*cd object*
*make -j 4 *[runs make on four cores]
Ends with “SUCCESS”

Edit flash.par to include plotting variables; e.g. add the line:
*plot_var_1 = “dens”*

*mpirun -np 4 flash4*
[Check that it runs and that generated HDF5 files are readable]


________________________________


I hope this helps you find your issue!

Best,

Scott


Scott Feister, Ph.D.
Postdoctoral Researcher, Flash Center for Computational Science
University of Chicago, Department of Astronomy and Astrophysics

On Tue, Jul 10, 2018 at 2:05 PM, Scott Feister <sfeister at gmail.com> wrote:

> Hi Isabella,
>
> Are you specifying a custom Makefile in your setup command with the
> "-site=" flag? If you send your Makefile, I can take a look.
>
> Best,
>
> Scott
>
>
> Scott Feister, Ph.D.
> Postdoctoral Researcher, Flash Center for Computational Science
> University of Chicago, Department of Astronomy and Astrophysics
>
> On Tue, Jul 10, 2018 at 12:59 PM, Isabella M Pagano <ipagano at utexas.edu>
> wrote:
>
>> Hi,
>> 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.
>> Thanks!
>> --
>> Bella
>>
>
>
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