[FLASH-USERS] Fwd: how to use parallel VisIt on Ubuntu?

[Scott Feister]

Hi Simon,

Sorry, I'm stumped. Maybe it's your Paramesh software configuration? Maybe
try ParaView visualization software instead of VisIt? Maybe try re-posting
your question to a forum for your Paramesh software or the VisIt users
forum?

Good luck!

Scott


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

On Thu, Sep 22, 2016 at 11:45 PM, simondonxq <simondonxq at gmail.com> wrote:

> Thank you dear Scott Feister.
>
> I use my PARAMESH program, run two cases to do output. one with one
> processor, the other with four processors.
> The HDF5 files from these two cases have exactly the same file size.
>
> Then I use VisIt (I think I install it just as you mentioned: *serial *version
> 2.10.2,  run install script, and start "visit" command) to visual these two
> files.
> The one from one processor is opened and the display is nice. As to
> the one from four processors, I can open it, but visibly only a small part
> of meshs are displayed.
> I am really confused.
>
> As to the mpi and HDF5 libraries, I test the below commands and am told
> that the computer has already have these installed.
> # MPI, HDF5 (parallel)
> sudo apt-get install mpi-default-dev
> sudo apt-get install openmpi-bin
> sudo apt-get install libhdf5-openmpi-dev # NOTE: I originally used
> "libhdf5-dev", but changed later to libhdf5-openmpi-dev for parallel I/O.
>
> ------------------------------
> simondonxq
>
> *From:* Scott Feister <sfeister at gmail.com>
> *Date:* 2016-09-22 12:05
> *To:* Simon Don <simondonxq at gmail.com>
> *CC:* flash-users <flash-users at flash.uchicago.edu>
> *Subject:* Re: [FLASH-USERS] Fwd: how to use parallel VisIt on Ubuntu?
> Hi Simon,
>
> If you're still stuck, I may be able to help a bit. In the past, I have
> successfully used the *serial *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.
>
> 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?
>
> 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 *sudo apt-get install **libhdf5-openmpi-dev
> *(parallel hdf5 library) rather than *libhdf5-dev* (serial hdf5 library).
>
>
> *Scott's notes on installing FLASH 4.3 in Ubuntu 14.04.3*
> *My installation followed the FLASH documentation.*
>
> 1. Installed FLASH dependencies, including optional parallel HDF5, using
> the package manager.
>
> # Going down the list at: http://flash.uchicago.edu/site
> /flashcode/user_support/flash4_ug_4p3/node5.html
> sudo apt-get update
> sudo apt-get upgrade
>
> # GCC and GNU Make
> sudo apt-get install build-essential
>
> # Fortran90
> sudo apt-get install gfortran
>
> # MPI, HDF5 (parallel)
> sudo apt-get install mpi-default-dev
> sudo apt-get install openmpi-bin
> sudo apt-get install libhdf5-openmpi-dev # NOTE: I originally used
> "libhdf5-dev", but changed later to libhdf5-openmpi-dev for parallel I/O.
>
>
> 2. Installed HYPRE dependency from source, into its own folder.
>
> # Download HYPRE 2.8 source code (2.10 does not work with FLASH 4.3), and
> unzip.
> tar -xvf hypre-2.8.0b.tar.gz
> # Navigate into the unzipped folder, and then make the library from source:
> cd src
> ./configure
> make
> make install
>
> 3. Download and unzip FLASH 4.3, and give your computer a Makefile.h in
> the "sites" directory.
>
> tar -xvf FLASH4.3.tar.gz
> cd FLASH4.3/sites
> mkdir virtuoso # Make a new folder named after your computer. Here, my
> computer's name is "virtuoso".
> cp Prototypes/Linux/Makefile.h virtuoso/Makefile.h # Copy the Linux
> makefile prototype
> # Now, change the Makefile.h to point to appropriate locations.
> nano virtuoso/Makefile.h
>
> *The beginning few lines of the copied Makefile.h should be modified to be
> similar to what's shown below.*
> *Each of those folders (no ending slash) must contain the subfolders
> called “lib” and/or “bin”.*
> *The HYPRE_PATH is where you just installed it.*
> *Find path of MPI_PATH by examining the output of: “type mpicc”*
> *Find path of HDF5_PATH by examining the output of: “echo $HDF5_C_LIBS”*
>
> *After modification, first few lines of …/sites/virtuoso/Makefile.h look
> like:*
>
> MPI_PATH   = /usr
>
> HDF4_PATH  =
>
> HDF5_PATH  = /usr
>
> HYPRE_PATH = /home/joeblow/hypre-2.8.0b/src/hypre
>
> ZLIB_PATH  =
>
> PAPI_PATH  =
>
> PAPI_FLAGS =
>
> NCMPI_PATH =
>
> MPE_PATH   =
>
> 4. Test the installation with WindTunnel (does not use Hypre) or LaserSlab
> (does use Hypre)
> ./setup WindTunnel -auto
> # Ends with “SUCCESS”
> cd object
> make -j 4 (runs on all four cores)
> # Ends with “SUCCESS”
> # Before running the simulation, edit flash.par to include some plotting
> variables (better test I/O); e.g. add the line:
> plot_var_1 = “dens”
> # Run the simulation and create outputs
> mpirun -np 4 flash4
>
>
> *Note: To test LaserSlab, you could start instead with something like:*
> ./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
>
>
>
>
> *Scott's notes on installing VisIt 2.9.2 in Ubuntu 14.04.3*1. Downloaded
> the VisIt 2.9.2 tarball for Ubuntu 14.04 64-bit Linux:
> “visit2_9_2.linux-x86_64-ubuntu14.tar.gz” from:
> https://wci.llnl.gov/simulation/computer-codes/visit/executables
>
>    - Downloaded and read the “VisIt install notes” for VisIt 2.9.2 at the
>    same website
>    - 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
>
> 2. Made the install script executable: “sudo chmod +x visit-install”
> 3. Ran the install script:
>
>    - “sudo ./visit-install 2.9.2 linux-x86_64-ubuntu14 /usr/local/visit”
>    - Note that the syntax is “sudo ./visit-install version platform
>    directory”
>    - When prompted, selected “No affiliation” or “no site” (choice 1)
>
> 4. Added the newly-created binaries folder to my user path:
>
>    - Edited (home)/.bashrc and added the following line at the bottom:
>    - “export PATH=$PATH:/usr/local/visit/bin”
>    - Then, restarted terminal
>
> 5. Can now open VisIt by typing “visit” at the terminal window
>
> Best,
>
> Scott
>
>
> Scott Feister, Ph.D.
> Postdoctoral Researcher, Flash Center for Computational Science
> University of Chicago, Department of Astronomy and Astrophysics
>
> On Wed, Sep 21, 2016 at 9:29 AM, Simon Don <simondonxq at gmail.com> wrote:
>
>> Thank you very much. In fact my code is now just using PARAMESH amr
>> package and the HDF5 files is generated by papamesh 's parallel HDF5
>> I/O. We have not finished the shift from paramesh to flash.
>>
>> 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.
>>
>> That the situation and why I am asking parallel visit things.
>>
>> Regards.
>>
>> 2016年9月21日星期三，Scott Feister <sfeister at gmail.com> 写道：
>>
>>> Hi Simon,
>>>
>>> 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 *itself*? Or both?
>>>
>>> Best,
>>>
>>> Scott
>>>
>>>
>>>
>>> Scott Feister, Ph.D.
>>> Postdoctoral Researcher, Flash Center for Computational Science
>>> University of Chicago, Department of Astronomy and Astrophysics
>>>
>>> On Wed, Sep 21, 2016 at 8:25 AM, Simon Don <simondonxq at gmail.com> wrote:
>>>
>>>> Dear all:
>>>>
>>>> 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.
>>>>
>>>> I downloaded the built executable
>>>> <https://wci.llnl.gov/simulation/computer-codes/visit/executables>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.
>>>>
>>>> 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?
>>>>
>>>> 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?
>>>>
>>>> Anyone who is familiar with this? Thank you very much!!
>>>>
>>>> Shimon
>>>
>>>
>>>
>>
>
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