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<DIV>Thank you dear Scott Feister.</DIV>
<DIV> </DIV>
<DIV>I use my PARAMESH program, run two cases to do output. one with
one processor, the other with four processors.</DIV>
<DIV>The HDF5 files from these two cases have exactly the same file
size.</DIV>
<DIV> </DIV>
<DIV>Then I use VisIt (I think I install it just as you mentioned: <EM>serial
</EM>version 2.10.2, run install script, and start "visit" command) to
visual these two files.</DIV>
<DIV>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.</DIV>
<DIV>I am really confused.</DIV>
<DIV> </DIV>
<DIV>As to the mpi and HDF5 libraries, I test the below commands and am told
that the computer has already have these installed.</DIV>
<DIV># 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. </DIV>
<DIV> </DIV>
<HR style="HEIGHT: 1px; WIDTH: 210px" align=left color=#b5c4df SIZE=1>
<DIV><SPAN>simondonxq</SPAN></DIV>
<DIV> </DIV>
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<DIV><B>From:</B> <A href="mailto:sfeister@gmail.com">Scott
Feister</A></DIV>
<DIV><B>Date:</B> 2016-09-22 12:05</DIV>
<DIV><B>To:</B> <A href="mailto:simondonxq@gmail.com">Simon Don</A></DIV>
<DIV><B>CC:</B> <A
href="mailto:flash-users@flash.uchicago.edu">flash-users</A></DIV>
<DIV><B>Subject:</B> Re: [FLASH-USERS] Fwd: how to use parallel VisIt on
Ubuntu?</DIV></DIV></DIV>
<DIV>
<DIV class=FoxDiv20160923132821057842 style="BACKGROUND-COLOR: white">
<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
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><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-BOTTOM: 0pt; WORD-BREAK: normal; TEXT-ALIGN: left; MARGIN-LEFT: 80px; MARGIN-TOP: 0pt"><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-BOTTOM: 0pt; WORD-BREAK: normal; TEXT-ALIGN: left; MARGIN-LEFT: 80px; MARGIN-TOP: 0pt"><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-BOTTOM: 0pt; WORD-BREAK: normal; TEXT-ALIGN: left; MARGIN-LEFT: 80px; MARGIN-TOP: 0pt"><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-BOTTOM: 0pt; WORD-BREAK: normal; TEXT-ALIGN: left; MARGIN-LEFT: 80px; MARGIN-TOP: 0pt"><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-BOTTOM: 0pt; WORD-BREAK: normal; TEXT-ALIGN: left; MARGIN-LEFT: 80px; MARGIN-TOP: 0pt"><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-BOTTOM: 0pt; WORD-BREAK: normal; TEXT-ALIGN: left; MARGIN-LEFT: 80px; MARGIN-TOP: 0pt"><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-BOTTOM: 0pt; WORD-BREAK: normal; TEXT-ALIGN: left; MARGIN-LEFT: 80px; MARGIN-TOP: 0pt"><SPAN
style="FONT-SIZE: 12pt; FONT-FAMILY: calibri; COLOR: black">PAPI_FLAGS
=</SPAN></P>
<DIV style="MARGIN-LEFT: 80px"></DIV>
<P
style="MARGIN-BOTTOM: 0pt; WORD-BREAK: normal; TEXT-ALIGN: left; MARGIN-LEFT: 80px; MARGIN-TOP: 0pt"><SPAN
style="FONT-SIZE: 12pt; FONT-FAMILY: calibri; COLOR: black">NCMPI_PATH
=</SPAN></P>
<DIV style="MARGIN-LEFT: 80px"></DIV>
<P
style="MARGIN-BOTTOM: 0pt; WORD-BREAK: normal; TEXT-ALIGN: left; MARGIN-LEFT: 80px; MARGIN-TOP: 0pt"><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 href="https://wci.llnl.gov/simulation/computer-codes/visit/executables"
target=_blank>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>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>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>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>“export PATH=$PATH:/usr/local/visit/<WBR>bin”
<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>
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<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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<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=>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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">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
</BLOCKQUOTE></DIV><BR></DIV></BLOCKQUOTE></DIV><BR></DIV></DIV></BLOCKQUOTE></DIV><BR></DIV></DIV></DIV></BODY></HTML>