<div dir="ltr">Hi Roland,<div><br></div><div>Thanks for this excellent suggestion.</div><div>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.</div><div><br></div><div>A good news is that I am able to load files into the Visit GUI successfully. <br></div><div><br></div><div></div><div>I will let you know when I have more definite issues.</div><div><br></div><div>best regards,</div><div>Atul</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Feb 5, 2020 at 2:57 PM Roland Haas <<a href="mailto:rhaas@illinois.edu" target="_blank">rhaas@illinois.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hello Atul,<br>
<br>
the easiest way around this is likely to disable the "ADIOS2" database<br>
in the "Options/Plugin Manager" menu.<br>
<br>
You may even have to remove all <br>
<br>
/visit/3.1.0/3.1.0/linux-x86_64/plugins/databases/lib?ADIOS2Database.so<br>
<br>
where the ? stands for "M" or "E" or "I".<br>
<br>
libfabric is used for infiniband and some other network types and<br>
indeed I have seen that missing on (workstations mostly) before. It is<br>
usually used by MPI so I am not quite sure why lib?ADIOS2Database.so<br>
would use it (given that none of the Linux VisIt executables available<br>
for download seem MPI enabled).<br>
<br>
Yours,<br>
Roland<br>
<br>
<br>
> Hi Roland,<br>
> <br>
> Hi Erik,<br>
> <br>
> Thanks again for your email, these are very helpful.<br>
> <br>
> I found my mistake: previously we(me and my colleague at Notre Dame) had<br>
> installed the Debian version of visit 3.1.0(134a7fd ) on our RHEL cluster.<br>
> So we reinstalled the RHEL version from (<br>
> <a href="https://wci.llnl.gov/simulation/computer-codes/visit/executables" rel="noreferrer" target="_blank">https://wci.llnl.gov/simulation/computer-codes/visit/executables</a>) now.<br>
> So now, when I open VisIt, I do get CarpetHDF5 as a supported extension.<br>
> CarpetHDF5 is also enabled in "Options/Plugin Manager" menu. And my VisIt<br>
> GUI looks like the screenshot from Rolandlast email.<br>
> But now I get a new error, when I try to load rho.xy.h5 directly on the<br>
> VisIt GUI:<br>
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -<br>
> Error opening plugin file: ...<br>
> /visit/3.1.0/3.1.0/linux-x86_64/plugins/databases/libMADIOS2Database.so<br>
> (libfabric.so.1: cannot open shared object file: No such file or directory)<br>
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -<br>
> Along with the RHEL version we also tried Fedora and CentOS just because<br>
> they are related, but getting the same error.<br>
> <br>
> I think this error of "libfabric.so" missing is because the VisIt files<br>
> from here (<a href="https://wci.llnl.gov/simulation/computer-codes/visit/executables" rel="noreferrer" target="_blank">https://wci.llnl.gov/simulation/computer-codes/visit/executables</a>)<br>
> are pre-compiled on Intel machines, and our cluster is a different machine.<br>
> We are still trying to see if there is a workaround for "libfabric.so", or<br>
> if we can compile visit directly on our machine.<br>
> <br>
> I currently don't have the tool "h5format_convert". I will try to get it as<br>
> soon as we get the libfabric.so issue fixed.<br>
> <br>
> Yours sincerely,<br>
> Atul.<br>
> <br>
> On Mon, Feb 3, 2020 at 3:03 PM Roland Haas <<a href="mailto:rhaas@illinois.edu" target="_blank">rhaas@illinois.edu</a>> wrote:<br>
> <br>
> > Hello Atul,<br>
> ><br>
> > as far as I can tell VisIt 3.1.0 binary available from the VisIt<br>
> > downloads page<br>
> > (<a href="https://wci.llnl.gov/simulation/computer-codes/visit/executables" rel="noreferrer" target="_blank">https://wci.llnl.gov/simulation/computer-codes/visit/executables</a>) for<br>
> > Linux (Debian 9.0 64bit specifically) does have the plugin included.<br>
> ><br>
> > To check you should see if there are files<br>
> ><br>
> ><br>
> > visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libECarpetHDF5Database_ser.so<br>
> ><br>
> ><br>
> > visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libECarpetHDF5Database_par.so<br>
> ><br>
> ><br>
> > visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libICarpetHDF5Database.so<br>
> ><br>
> ><br>
> > visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libMCarpetHDF5Database.so<br>
> ><br>
> > which are the compiled shared libraries (not the src files). I can<br>
> > confirm that that plugin can read in CarpetHDF5 files (did so today).<br>
> ><br>
> > This is for VisIt 3.1.0 git version 134a7fd (according to the about<br>
> > dialog).<br>
> ><br>
> > I would check that you have not disabled the CarpetHDF5 database<br>
> > plugin in the "Options/Plugin Manager" menu.<br>
> ><br>
> > Other than that I am not sure at all what could be happening. I have<br>
> > seem issues with HDF5 files being of too new a format (eg if ldd<br>
> > cactus_sim reports libhdf5.so.10 but "ls<br>
> > visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/lib/libhdf5.so.*" is less than<br>
> > 10) but that does not (as far as I know) affect Cactus since<br>
> > we ask the newer libraries to write files readable by the old versions.<br>
> ><br>
> > Just for completeness' sake I am attaching a screenshot showing where<br>
> > CarpetHDF5 shows up for me.<br>
> ><br>
> > Yours,<br>
> > Roland<br>
> > <br>
> > > Hi Roland,<br>
> > ><br>
> > > Thanks again for your email.<br>
> > > <br>
> > > > > I have VisIt 3 and ETK Mayer downloaded which I believe doesn't have<br>
> > > > > CarpetHDF5. How do I use the CarpetHDF5 reader? Do I need to install <br>
> > it <br>
> > > > > from <a href="https://bitbucket.org/rhaas80/carpethdf5/src/multifile/" rel="noreferrer" target="_blank">https://bitbucket.org/rhaas80/carpethdf5/src/multifile/</a> or is <br>
> > > > there a <br>
> > > > > newer version? <br>
> > > > That is still the newest version. Though I do not know of that version<br>
> > > > will compile with VisIt 3 (it may have changed the plugin interfaces).<br>
> > > ><br>
> > > > I had a look at VisIt 3.1<br>
> > > > (<br>
> > > > <br>
> > <a href="https://github.com/visit-dav/visit/releases/download/v3.1.0/visit3_1_0.linux-x86_64-debian9.tar.gz" rel="noreferrer" target="_blank">https://github.com/visit-dav/visit/releases/download/v3.1.0/visit3_1_0.linux-x86_64-debian9.tar.gz</a> <br>
> > > > since I run Debian) and as far as I can tell that one includes the<br>
> > > > CarpetHDF5 reader in<br>
> > > ><br>
> > > > <br>
> > visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libMCarpetHDF5Database.so<br>
> > <br>
> > ><br>
> > ><br>
> > > I installed VisIt 3.1.0 from the link. I tried running the visualization<br>
> > > script with it and that gives me errors. The issue still seems to be <br>
> > about <br>
> > > reading Carpet HDF5 files.<br>
> > ><br>
> > ><br>
> > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <br>
> > - - <br>
> > > - - - - - - - - - - - - - - - - - - - - - - - - - - - -<br>
> > > VisIt: Error - VisIt could not read from the file "/afs/<br>
> > > <br>
> > <a href="http://crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5" rel="noreferrer" target="_blank">crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5</a> <br>
> > > ".<br>
> > ><br>
> > > The generated error message was:<br>
> > ><br>
> > > There was an error opening /afs/<br>
> > > <br>
> > <a href="http://crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5" rel="noreferrer" target="_blank">crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5</a><br>
> > . <br>
> > > It may be an invalid file.<br>
> > > VisIt tried using the following file format readers to open the file: <No<br>
> > > suitable plugins were identified><br>
> > > VisIt: Error - Cannot create a plot until a database has been opened.<br>
> > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <br>
> > - - <br>
> > > - - - - - - - - - - - - - - - - - - - - - - - - - - - -<br>
> > ><br>
> > ><br>
> > > For assurance, I checked that the installed version of VisIt 3.1.0 has a<br>
> > > folder on CarpetHDF5 in :<br>
> > > visit/3.1.0/visit3.1.0/src/databases/CarpetHDF5<br>
> > > Should this be the only folder with CarpetHDF5 created?<br>
> > > <br>
> > > > As to s.screenCapture, it was by default set to 0 , I have attached a <br>
> > > > > sample image.<br>
> > > > > setting s.screenCapture = 1 gives empty images, so does not fix the <br>
> > > > problem.<br>
> > > > I see. The first step will then be to try and see if you can load a<br>
> > > > Carpet HDF5 file in the GUI to make sure that at least in principle you<br>
> > > > should be able to load a file (as compared to there being a scripting<br>
> > > > issue).<br>
> > > ><br>
> > > > You should also make sure that when the script runs the file is<br>
> > > > actually opened by CarpetHDF5 and not some other plugin that can read<br>
> > > > HDF5 files (PIXIE is often doing this). I believe there is some output<br>
> > > > to screen about which reader is used.<br>
> > > > <br>
> > ><br>
> > > On trying to load a file on Visit GUI I get this error message:<br>
> > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <br>
> > - - <br>
> > > - - - - - - - - - - - - - - - - - - - - - - - - - - - -<br>
> > > VisIt could not read from the file "/afs/<br>
> > > <br>
> > <a href="http://crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5" rel="noreferrer" target="_blank">crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5</a> <br>
> > > ".<br>
> > ><br>
> > > The generated error message was:<br>
> > ><br>
> > > There was an error opening /afs/<br>
> > > <br>
> > <a href="http://crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5" rel="noreferrer" target="_blank">crc.nd.edu/user/a/akedia/simulations/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5</a><br>
> > . <br>
> > > It may be an invalid file.<br>
> > > VisIt tried using the following file format readers to open the file: <No<br>
> > > suitable plugins were identified><br>
> > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <br>
> > - - <br>
> > > - - - - - - - - - - - - - - - - - - - - - - - - - - - -<br>
> > > And when I'm selecting the file, there is no option for CarpetHDF5 in the<br>
> > > dropdown list of supported file name/extension.<br>
> > ><br>
> > > Thank you for your help,<br>
> > > Atul <br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > My email is as private as my paper mail. I therefore support encrypting<br>
> > and signing email messages. Get my PGP key from <a href="http://pgp.mit.edu" rel="noreferrer" target="_blank">http://pgp.mit.edu</a> .<br>
> > <br>
<br>
<br>
<br>
-- <br>
My email is as private as my paper mail. I therefore support encrypting<br>
and signing email messages. Get my PGP key from <a href="http://pgp.mit.edu" rel="noreferrer" target="_blank">http://pgp.mit.edu</a> .<br>
</blockquote></div>