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 <[email protected]> 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 .
pgpW9CkQjijGm.pgp
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