[Users] NSNSTOHMNS(Gallery example) Plotting issues

Mon Feb 17 13:56:52 CST 2020

Hi Roland,

Thanks for this excellent suggestion.
We are working on getting Visit to work along with ffmpeg on our cluster.
We realized we have some ffmpeg required libraries that are missing on our
cluster.

A good news is that I am able to load files into the Visit GUI
successfully.

I will let you know when I have more definite issues.

best regards,
Atul

On Wed, Feb 5, 2020 at 2:57 PM Roland Haas <rhaas at illinois.edu> wrote:

> Hello Atul,
>
> the easiest way around this is likely to disable the "ADIOS2" database
> in the "Options/Plugin Manager" menu.
>
> You may even have to remove all
>
> /visit/3.1.0/3.1.0/linux-x86_64/plugins/databases/lib?ADIOS2Database.so
>
> where the ? stands for "M" or "E" or "I".
>
> libfabric is used for infiniband and some other network types and
> indeed I have seen that missing on (workstations mostly) before. It is
> usually used by MPI so I am not quite sure why lib?ADIOS2Database.so
> would use it (given that none of the Linux VisIt executables available
> for download seem MPI enabled).
>
> Yours,
> Roland
>
>
> > Hi Roland,
> >
> > Hi Erik,
> >
> > Thanks again for your email, these are very helpful.
> >
> > I found my mistake: previously we(me and my colleague at Notre Dame) had
> > installed the Debian version of visit 3.1.0(134a7fd ) on our RHEL
> cluster.
> > So we reinstalled the RHEL version from (
> > https://wci.llnl.gov/simulation/computer-codes/visit/executables) now.
> > So now, when I open VisIt, I do get CarpetHDF5 as a supported extension.
> > CarpetHDF5 is also enabled in "Options/Plugin Manager" menu. And my VisIt
> > GUI looks like the screenshot from Rolandlast email.
> > But now I get a new error, when I try to load rho.xy.h5 directly on the
> > VisIt GUI:
> > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> > Error opening plugin file: ...
> > /visit/3.1.0/3.1.0/linux-x86_64/plugins/databases/libMADIOS2Database.so
> > (libfabric.so.1: cannot open shared object file: No such file or
> directory)
> > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> > Along with the RHEL version we also tried Fedora and CentOS just because
> > they are related, but getting the same error.
> >
> > I think this error of "libfabric.so" missing is because the VisIt files
> > from here (
> https://wci.llnl.gov/simulation/computer-codes/visit/executables)
> > are pre-compiled on Intel machines, and our cluster is a different
> machine.
> > We are still trying to see if there is a workaround for "libfabric.so",
> or
> > if we can compile visit directly on our machine.
> >
> > I currently don't have the tool "h5format_convert". I will try to get it
> as
> > soon as we get the libfabric.so issue fixed.
> >
> > Yours sincerely,
> > Atul.
> >
> > On Mon, Feb 3, 2020 at 3:03 PM Roland Haas <rhaas at illinois.edu> wrote:
> >
> > > Hello Atul,
> > >
> > > as far as I can tell VisIt 3.1.0 binary available from the VisIt
> > > downloads page
> > > (https://wci.llnl.gov/simulation/computer-codes/visit/executables) for
> > > Linux (Debian 9.0 64bit specifically) does have the plugin included.
> > >
> > > To check you should see if there are files
> > >
> > >
> > >
> visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libECarpetHDF5Database_ser.so
> > >
> > >
> > >
> visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libECarpetHDF5Database_par.so
> > >
> > >
> > >
> visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libICarpetHDF5Database.so
> > >
> > >
> > >
> visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libMCarpetHDF5Database.so
> > >
> > > which are the compiled shared libraries (not the src files). I can
> > > confirm that that plugin can read in CarpetHDF5 files (did so today).
> > >
> > > This is for VisIt 3.1.0 git version 134a7fd (according to the about
> > > dialog).
> > >
> > > I would check that you have not disabled the CarpetHDF5 database
> > > plugin in the "Options/Plugin Manager" menu.
> > >
> > > Other than that I am not sure at all what could be happening. I have
> > > seem issues with HDF5 files being of too new a format (eg if ldd
> > > cactus_sim reports libhdf5.so.10 but "ls
> > > visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/lib/libhdf5.so.*" is less
> than
> > > 10) but that does not (as far as I know) affect Cactus since
> > > we ask the newer libraries to write files readable by the old versions.
> > >
> > > Just for completeness' sake I am attaching a screenshot showing where
> > > CarpetHDF5 shows up for me.
> > >
> > > Yours,
> > > Roland
> > >
> > > > Hi Roland,
> > > >
> > > > Thanks again for your email.
> > > >
> > > > > > I have VisIt 3 and ETK Mayer downloaded which I believe doesn't
> have
> > > > > > CarpetHDF5. How do I use the CarpetHDF5 reader? Do I need to
> install
> > > it
> > > > > > from https://bitbucket.org/rhaas80/carpethdf5/src/multifile/ or
> is
> > > > > there a
> > > > > > newer version?
> > > > > That is still the newest version. Though I do not know of that
> version
> > > > > will compile with VisIt 3 (it may have changed the plugin
> interfaces).
> > > > >
> > > > > I had a look at VisIt 3.1
> > > > > (
> > > > >
> > >
> https://github.com/visit-dav/visit/releases/download/v3.1.0/visit3_1_0.linux-x86_64-debian9.tar.gz
>
> > > > > since I run Debian) and as far as I can tell that one includes the
> > > > > CarpetHDF5 reader in
> > > > >
> > > > >
> > >
> visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libMCarpetHDF5Database.so
> > >
> > > >
> > > >
> > > > I installed VisIt 3.1.0 from the link. I tried running the
> visualization
> > > > script with it and that gives me errors. The issue still seems to
> be
> > > about
> > > > reading Carpet HDF5 files.
> > > >
> > > >
> > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> - -
> > > - -
> > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> > > > VisIt: Error - VisIt could not read from the file "/afs/
> > > >
> > >
> crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5
>
> > > > ".
> > > >
> > > > The generated error message was:
> > > >
> > > > There was an error opening /afs/
> > > >
> > >
> crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5
> > > .
> > > > It may be an invalid file.
> > > > VisIt tried using the following file format readers to open the
> file: <No
> > > > suitable plugins were identified>
> > > > VisIt: Error - Cannot create a plot until a database has been opened.
> > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> - -
> > > - -
> > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> > > >
> > > >
> > > > For assurance, I checked that the installed version of VisIt 3.1.0
> has a
> > > > folder on CarpetHDF5 in :
> > > > visit/3.1.0/visit3.1.0/src/databases/CarpetHDF5
> > > > Should this be the only folder with CarpetHDF5 created?
> > > >
> > > > > As to s.screenCapture, it was by default set to 0 , I have
> attached a
> > > > > > sample image.
> > > > > > setting s.screenCapture = 1 gives empty images, so does not fix
> the
> > > > > problem.
> > > > > I see. The first step will then be to try and see if you can load a
> > > > > Carpet HDF5 file in the GUI to make sure that at least in
> principle you
> > > > > should be able to load a file (as compared to there being a
> scripting
> > > > > issue).
> > > > >
> > > > > You should also make sure that when the script runs the file is
> > > > > actually opened by CarpetHDF5 and not some other plugin that can
> read
> > > > > HDF5 files (PIXIE is often doing this). I believe there is some
> output
> > > > > to screen about which reader is used.
> > > > >
> > > >
> > > > On trying to load a file on Visit GUI I get this error message:
> > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> - -
> > > - -
> > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> > > > VisIt could not read from the file "/afs/
> > > >
> > >
> crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5
>
> > > > ".
> > > >
> > > > The generated error message was:
> > > >
> > > > There was an error opening /afs/
> > > >
> > >
> crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5
> > > .
> > > > It may be an invalid file.
> > > > VisIt tried using the following file format readers to open the
> file: <No
> > > > suitable plugins were identified>
> > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> - -
> > > - -
> > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> > > > And when I'm selecting the file, there is no option for CarpetHDF5
> in the
> > > > dropdown list of supported file name/extension.
> > > >
> > > > Thank you for your help,
> > > > Atul
> > >
> > >
> > >
> > > --
> > > My email is as private as my paper mail. I therefore support encrypting
> > > and signing email messages. Get my PGP key from http://pgp.mit.edu .
> > >
>
>
>
> --
> My email is as private as my paper mail. I therefore support encrypting
> and signing email messages. Get my PGP key from http://pgp.mit.edu .
>
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