HDFView fails to find input files on command line when using relative paths

[lee218llnl]

I initially thought this was a bug in https://github.com/spack/spack/issues/42153, but I think this may be an hdfview issue. When using the "# Default invocation when using modules" execution line in the hdfview.sh script, it appears that the argument -Dhdfview.root="$INSTALLDIR" causes hdfview to look in $INSTALLDIR for input files with a relative path. More concretely, if I run hdfview file.h5, I can see via strace that hdfview ends up looking for $INSTALLDIR/file.h5. It works OK if I run using the full path to the input file, such as hdfview $PWD/file.h5.

[byrnHDF]

Can you look at the https://github.com/HDFGroup/hdfview/blob/master/docs/WorkingDirectory.txt file and see if there is a workable solution for you, or we would welcome a suggestion.

[lee218llnl]

I tried various things include changing the java invocation line to:

"$JAVABIN/java" "$JAVAOPTS" -Djava.library.path="$INSTALLDIR:$INSTALLDIR/ext" -Dhdfview.root="$INSTALLDIR" -cp "$INSTALLDIR/*" hdf.view.HDFView -Dhdfview.workdir=$PWD startDir=$PWD "$@"

and it still does not look in $PWD for the specified file:

[lee218@oslic8:h5py]$ strace -f -s 999 ~/myhdfview2 dummy.h5 |& grep dummy.h5
execve("/g/g0/lee218/myhdfview2", ["/g/g0/lee218/myhdfview2", "dummy.h5"], 0x7fffffffaf20 /* 115 vars */) = 0
write(2, "+ /usr/tce/packages/openjdk/openjdk-11.0.15_10/bin/java -Xmx1024M -Djava.library.path=/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh:/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/ext -Dhdfview.root=/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh -cp '/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/*' hdf.view.HDFView -Dhdfview.workdir=/g/g0/lee218/test/python/h5py startDir=/g/g0/lee218/test/python/h5py dummy.h5\n", 678+ /usr/tce/packages/openjdk/openjdk-11.0.15_10/bin/java -Xmx1024M -Djava.library.path=/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh:/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/ext -Dhdfview.root=/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh -cp '/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/*' hdf.view.HDFView -Dhdfview.workdir=/g/g0/lee218/test/python/h5py startDir=/g/g0/lee218/test/python/h5py dummy.h5
[pid 4074792] execve("/usr/tce/packages/openjdk/openjdk-11.0.15_10/bin/java", ["/usr/tce/packages/openjdk/openjdk-11.0.15_10/bin/java", "-Xmx1024M", "-Djava.library.path=/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh:/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/ext", "-Dhdfview.root=/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh", "-cp", "/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/*", "hdf.view.HDFView", "-Dhdfview.workdir=/g/g0/lee218/test/python/h5py", "startDir=/g/g0/lee218/test/python/h5py", "dummy.h5"], 0x55555588ced0 /* 116 vars */) = 0
[pid 4074793] read(29, "/usr/tce/packages/openjdk/openjdk-11.0.15_10/bin/java\0-Xmx1024M\0-Djava.library.path=/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh:/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/ext\0-Dhdfview.root=/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh\0-cp\0/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/*\0hdf.view.HDFView\0-Dhdfview.workdir=/g/g0/lee218/test/python/h5py\0startDir=/g/g0/lee218/test/python/h5py\0dummy.h5\0", 4096) = 674
[pid 4074793] stat("/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/dummy.h5", 0x15555551e6c0) = -1 ENOENT (No such file or directory)
[pid 4074793] stat("/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/dummy.h5", 0x15555551e6c0) = -1 ENOENT (No such file or directory)
[pid 4074793] stat("/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/dummy.h5", 0x15555551e6c0) = -1 ENOENT (No such file or directory)
[pid 4074793] stat("/usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/dummy.h5", 0x15555551e6f0) = -1 ENOENT (No such file or directory)
[pid 4074793] read(34, "#Thu Jan 25 09:40:18 PST 2024\nmodule.treeview=Default\nusers.guide=/usr/tce/backend/installations/linux-rhel8-x86_64/intel-2021.6.0/hdfview-3.3.0-7im76vfgbwfezxpxwoydpswyamramxzz/share/doc/UsersGuide/index.html\nmodule.metadataview=Default\nmodule.paletteview=Default\nmodule.imageview=Default\nmodule.fileformat.HDF4=hdf.object.h4.H4File\nmodule.fileformat.NetCDF3=hdf.object.nc2.NC2File\nmodule.fileformat.HDF5=hdf.object.h5.H5File\nmodule.fileformat.FITS=hdf.object.fits.FitsFile\nimage.contrast=general\nrecent.file3=/g/g0/lee218/test/hdf5/test.h5\nmodule.tableview=Default\nrecent.file4=/g/g0/lee218/e3sm_hang.pdf\nrecent.file1=/g/g0/lee218/test/python/h5py/dummy.h5\nrecent.file2=/usr/WS2/lee218/test/hdf5/test.h5\nrecent.file0=/usr/WS2/lee218/test/python/h5py/dummy.h5\n", 8192) = 761
[pid 4074793] stat("/usr/WS2/lee218/test/python/h5py/dummy.h5",  <unfinished ...>
[pid 4074793] stat("/g/g0/lee218/test/python/h5py/dummy.h5",  <unfinished ...>
[pid 4074793] write(34, "#Thu Jan 25 09:41:50 PST 2024\nmodule.treeview=Default\nusers.guide=/usr/tce/backend/installations/linux-rhel8-x86_64/intel-2021.6.0/hdfview-3.3.0-7im76vfgbwfezxpxwoydpswyamramxzz/share/doc/UsersGuide/index.html\nmodule.metadataview=Default\nmodule.paletteview=Default\nmodule.imageview=Default\nmodule.fileformat.HDF4=hdf.object.h4.H4File\nmodule.fileformat.NetCDF3=hdf.object.nc2.NC2File\nmodule.fileformat.HDF5=hdf.object.h5.H5File\nmodule.fileformat.FITS=hdf.object.fits.FitsFile\nimage.contrast=general\nrecent.file3=/g/g0/lee218/test/hdf5/test.h5\nmodule.tableview=Default\nrecent.file4=/g/g0/lee218/e3sm_hang.pdf\nrecent.file1=/g/g0/lee218/test/python/h5py/dummy.h5\nrecent.file2=/usr/WS2/lee218/test/hdf5/test.h5\nrecent.file0=/usr/WS2/lee218/test/python/h5py/dummy.h5\n", 761) = 761

It looks like it is still looking for the specified "dummy.h5" in /usr/tce/backend/installations/linux-rhel8-x86_64/oneapi-2022.1.0/hdfview-3.3.0-olq4dtqra45vclrqmym5gwijzokox6vh/dummy.h5, which is the installation directory, rather than $PWD. Note that the strace output where it actually finds the proper location is just because its in my "recent file" history.

Let me know if I am specifying the start/work directory incorrectly.

[byrnHDF]

The -D define should go before the program clas - see the hdfview.root define location. Also make sure that the ini file does not override your command line. You should be able to open the user options preferences to see what everything is set to (without a file).

We do test these options but maybe I am doing something different, But startDir should have worked. Did you get a log file, you can enable that by adding some defines, the USING_logging.txt file.

I will check my test history.

[lee218llnl]

I moved the -Dhdfview.workdir=$PWD arg to before the hdf.view.HDFVIEW arg and it still did not work. Can you reproduce the behavior that I reported and do some testing and send me the script that works for you so I don't have to keep fumbling around? Thanks.

[byrnHDF]

Note that I did use the latest 3.3.1 version however everything worked with the define on the command line -Dhdfview.workdir="$PWD" <---- note the quotes or adding $PWD to the HDFView.cfg file with the launcher. I did not try the startdir option.

[byrnHDF]

The launcher worked (after edit) without any other changes. However, the supplied hdfview.sh does need to set the the INSTALLDIR up two dirs from the .sh location (export INSTALLDIR=$dir/../..).

[lee218llnl]

still no luck with me when I run:

"$JAVABIN/java" "$JAVAOPTS" -Djava.library.path="$INSTALLDIR:$INSTALLDIR/ext" -Dhdfview.root="$INSTALLDIR" -cp "$INSTALLDIR/*" -Dhdfview.workdir="$PWD" hdf.view.HDFView "$@"

This is an hdfview 3.3.0 installation, if that makes a difference. Also, in my strace, I don't see it accessing an HDFView.cfg file.

[byrnHDF]

I don't think this workdir process changed from 3.3.0 but I will check. There are two ways to invoke HDFView, from the launcher in the $INSTALLDIR/bin folder or the script from the $INSTALLDIR/lib/app folder. The Launcher uses the cfg file.

[byrnHDF]

Looks like we fixed the workdir option in 3.3.1 and forgot to announce it in the release notes. Please try 3.3.1.

[lee218llnl]

still fails for me with 3.3.1 (installed with spack, but added new version and checksum).

I have my script run this command:

"$JAVABIN/java" "$JAVAOPTS" -Djava.library.path="$INSTALLDIR:$INSTALLDIR/ext" -Dhdfview.root="$INSTALLDIR" -cp "$INSTALLDIR/*" -Dhdfview.workdir="$PWD" hdf.view.HDFView "$@"

and it does not appear to be looking for an HDFview.cfg file:

[lee218@rzwhippet18:spack]$ strace -f -s 9999 /usr/WS2/lee218/delete/spack/opt/spack/linux-rhel8-ivybridge/gcc-10.3.1/hdfview-3.3.1-ziimwueprhe3m5adhnl35ca3jgifkc4t/bin/hdfview $PWD/data.h5 |& grep -i hdfview.cfg [lee218@rzwhippet18:spack]$ echo $? 1

[byrnHDF]

and it does not appear to be looking for an HDFview.cfg file: The shell script would not use the .cfg, only the launcher binary.

I'm guessing you appending the filename to script, that I did not try. After launching HDFView I went to open file menu and the PWD was the selected folder.

I will need to try, but imagine that the HDFView argument processing may be not prepending the workdir.

[lee218llnl]

please read the initial issue report, where I explicitly stated that the issue was opening a file with a relative path from the command line. I hope you can appreciate that I have wasted a fair amount of time on this.

[byrnHDF]

Actually, have you tried to add the "-start=$PWD" to the command;

... hdf.view.HDFView -start="$PWD" "$@"

[byrnHDF]

See WorkingDirectory.txt for a description of arguments to HDFView. (-start is at line 16)

[lee218llnl]

still no luck:

[lee218@rzwhippet18:spack]$ tail -n 1 /usr/WS2/lee218/delete/spack/opt/spack/linux-rhel8-ivybridge/gcc-10.3.1/hdfview-3.3.1-ziimwueprhe3m5adhnl35ca3jgifkc4t/bin/hdfview 
"$JAVABIN/java" "$JAVAOPTS" -Djava.library.path="$INSTALLDIR:$INSTALLDIR/ext" -Dhdfview.root="$INSTALLDIR" -cp "$INSTALLDIR/*" -Dhdfview.workdir="$PWD" hdf.view.HDFView -start="$PWD" "$@"
[lee218@rzwhippet18:spack]$ echo $PWD
/usr/workspace/lee218/delete/spack
[lee218@rzwhippet18:spack]$ strace -f -s 9999 /usr/WS2/lee218/delete/spack/opt/spack/linux-rhel8-ivybridge/gcc-10.3.1/hdfview-3.3.1-ziimwueprhe3m5adhnl35ca3jgifkc4t/bin/hdfview data.h5  |& grep data.h5 | grep stat | head -n 4
[pid 421255] stat("/usr/WS2/lee218/delete/spack/opt/spack/linux-rhel8-ivybridge/gcc-10.3.1/hdfview-3.3.1-ziimwueprhe3m5adhnl35ca3jgifkc4t/data.h5", 0x15555551c6c0) = -1 ENOENT (No such file or directory)
[pid 421255] stat("/usr/WS2/lee218/delete/spack/opt/spack/linux-rhel8-ivybridge/gcc-10.3.1/hdfview-3.3.1-ziimwueprhe3m5adhnl35ca3jgifkc4t/data.h5", 0x15555551c6c0) = -1 ENOENT (No such file or directory)
[pid 421255] stat("/usr/WS2/lee218/delete/spack/opt/spack/linux-rhel8-ivybridge/gcc-10.3.1/hdfview-3.3.1-ziimwueprhe3m5adhnl35ca3jgifkc4t/data.h5", 0x15555551c6c0) = -1 ENOENT (No such file or directory)
[pid 421255] stat("/usr/WS2/lee218/delete/spack/opt/spack/linux-rhel8-ivybridge/gcc-10.3.1/hdfview-3.3.1-ziimwueprhe3m5adhnl35ca3jgifkc4t/data.h5", 0x15555551c6f0) = -1 ENOENT (No such file or directory)

Can you please do the testing yourself and let me know when you have a proper fix?

[byrnHDF]

The simple workaround is to add "$PWD" to the "$@" -> "$PWD/$@"

[lee218llnl]

modifying the hdfview launcher script to modify the user's args to "$PWD/$@" would break things if the user specifies a full path or wants to specify any other command-line arguments. I already told my users that they can run hdfview $PWD/file.h5 from the command line, so that is our workaround. If you decide that this is something you want to fix, then please let me know. I don't plan on spending any more time on this.

[byrnHDF]

Will try to fix it in the next release this spring as it looks like it is an implementation bug. It seems to not consider the startDir setting(looks like multiple ways of setting it as well) and tries to pull the dir from the file.

[lee218llnl]

any updates on a fix and release?

[byrnHDF]

Changes completed - Having trouble signing the packages.

[byrnHDF]

Completed for next release