[Users] NSNSTOHMNS(Gallery example) Plotting issues

[Atul Kedia]

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 .
>
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