[Users] NSNSTOHMNS(Gallery example) Plotting issues

Roland Haas rhaas at illinois.edu
Wed Feb 5 13:57:02 CST 2020 

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 .
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 833 bytes
Desc: OpenPGP digital signature
Url : http://lists.einsteintoolkit.org/pipermail/users/attachments/20200205/f48dd6c2/attachment-0001.bin

More information about the Users mailing list