<div dir="ltr">Hi Roland,<div><br></div><div>Hi Erik,<br></div><div><br></div><div>Thanks again for your email, these are very helpful.</div><div><br></div><div>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 (<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.</div><div>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.</div><div>But now I get a new error, when I try to load rho.xy.h5 directly on the VisIt GUI:</div><div>- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -</div><div>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)</div><div>- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -</div><div><div>Along with the RHEL version we also tried Fedora and CentOS just because they are related, but getting the same error.</div><div><br></div><div>I think this error of "libfabric.so" missing is because the VisIt files from here (<a href="https://wci.llnl.gov/simulation/computer-codes/visit/executables">https://wci.llnl.gov/simulation/computer-codes/visit/executables</a>) 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.</div><div><br></div><div>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.</div><div><br></div><div>Yours sincerely,</div><div>Atul.</div><div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">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></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>
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>
visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libECarpetHDF5Database_ser.so<br>
<br>
visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libECarpetHDF5Database_par.so<br>
<br>
visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libICarpetHDF5Database.so<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 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 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>
> > <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>
> > visit3_1_0.linux-x86_64/3.1.0/linux-x86_64/plugins/databases/libMCarpetHDF5Database.so <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 about<br>
> reading Carpet HDF5 files.<br>
> <br>
> <br>
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -<br>
> - - - - - - - - - - - - - - - - - - - - - - - - - - - -<br>
> VisIt: Error - VisIt could not read from the file "/afs/<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>
> <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>
> 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>
> 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>
> VisIt could not read from the file "/afs/<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>
> <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>
> 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>
> 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>
</blockquote></div>