Ubuntu install doesn't find libQt5Core

[nategarver-daniels]

Trying to install the .deb package in Ubuntu 22.04, and running fastpathology indicates a missing libQt5Core.so.5. The library is in /opt/fastpathology/lib, as are other libraries that the binary is linked against and finds. Any chance this is something others have seen?

[smistad]

Sounds like there might be something wrong with the rpath. I can take a look at this tomorrow. Maybe you can do: ldd /opt/fastpathology/bin/fastpathology to see which libraries it is unable to find. And also objdump -x /opt/fastpathology/bin/fastpathology | grep 'R.*PATH' to check if the rpath is set.

[nategarver-daniels]

Thanks for the quick response. This is the only missing library:

ldd /opt/fastpathology/bin/fastpathology | grep not | sort -u libQt5Core.so.5 => not found

and

The runpath appears to be relative:

objdump -x /opt/fastpathology/bin/fastpathology | grep 'R.*PATH' RUNPATH $ORIGIN/../lib

And other libraries that are installed in the fastpathology path are found:

libFAST.so.4 => /opt/fastpathology/bin/./../lib/libFAST.so.4 (0x00007f76d0800000) libOpenCL.so.1 => /opt/fastpathology/bin/./../lib/libOpenCL.so.1 (0x00007f76d0400000) libQt5Core.so.5 => not found libQt5Widgets.so.5 => /opt/fastpathology/bin/./../lib/libQt5Widgets.so.5 (0x00007f76cfa00000) libQt5Gui.so.5 => /opt/fastpathology/bin/./../lib/libQt5Gui.so.5 (0x00007f76cf000000) libQt5OpenGL.so.5 => /opt/fastpathology/bin/./../lib/libQt5OpenGL.so.5 (0x00007f76cec00000) libQt5Network.so.5 => /opt/fastpathology/bin/./../lib/libQt5Network.so.5 (0x00007f76ce800000)

I'll admit that this one is stumping me. I thought perhaps libQt5Core.so.5 was missing a dependency, but it looks OK as well:

ldd ../lib/libQt5Core.so.5 linux-vdso.so.1 (0x00007ffea3b6e000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f125d99a000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f125d995000) libglib-2.0.so.0 => /opt/fastpathology/bin/../lib/../lib/libglib-2.0.so.0 (0x00007f125cc00000) libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f125c9d4000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f125c8ed000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f125d973000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f125c6c5000) /lib64/ld-linux-x86-64.so.2 (0x00007f125d9ac000) libpcre.so.3 => /opt/fastpathology/bin/../lib/../lib/../lib/libpcre.so.3 (0x00007f125c400000)

On Mon, Aug 21, 2023 at 3:45 PM Erik Smistad @.***> wrote:

Sounds like there might be something wrong with the rpath. I can take a look at this tomorrow. Maybe you can do: ldd /opt/fastpathology/bin/fastpathology to see which libraries it is unable to find. And also objdump -x /opt/fastpathology/bin/fastpathology | grep 'R.*PATH' to check if the rpath is set.

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[smistad]

Can you confirm that it is the latest release you have tried (1.1.1) https://github.com/AICAN-Research/FAST-Pathology/releases/tag/v1.1.1

I tried installing this on my ubuntu 20.04, and it works fine.

Could you paste the entire output of ldd /opt/fastpathology/bin/fastpathology?

[nategarver-daniels]

Thanks Erik. this is with v1.1.1 on 22.04 LTS. I am installing it in a singularity container, so it's possible that is the issue as well. Here's the full ldd output:

ldd /opt/fastpathology/bin/fastpathology linux-vdso.so.1 (0x00007fffdadfc000) libFAST.so.4 => /opt/fastpathology/bin/../lib/libFAST.so.4 (0x00007fa373e00000) libOpenCL.so.1 => /opt/fastpathology/bin/../lib/libOpenCL.so.1 (0x00007fa373a00000) libQt5Core.so.5 => not found libQt5Widgets.so.5 => /opt/fastpathology/bin/../lib/libQt5Widgets.so.5 (0x00007fa373000000) libQt5Gui.so.5 => /opt/fastpathology/bin/../lib/libQt5Gui.so.5 (0x00007fa372600000) libQt5OpenGL.so.5 => /opt/fastpathology/bin/../lib/libQt5OpenGL.so.5 (0x00007fa372200000) libQt5Network.so.5 => /opt/fastpathology/bin/../lib/libQt5Network.so.5 (0x00007fa371e00000) libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fa371bd4000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fa373d19000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fa3745e0000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa3719ac000) libQt5Core.so.5 => not found libQt5Multimedia.so.5 => /opt/fastpathology/bin/../lib/../lib/libQt5Multimedia.so.5 (0x00007fa371600000) libz.so.1 => /opt/fastpathology/bin/../lib/../lib/libz.so.1 (0x00007fa371200000) libtiff.so.5 => /opt/fastpathology/bin/../lib/../lib/libtiff.so.5 (0x00007fa370e00000) libopenslide.so => /opt/fastpathology/bin/../lib/../lib/libopenslide.so (0x00007fa370a00000) libhdf5_cpp.so.103 => /opt/fastpathology/bin/../lib/../lib/libhdf5_cpp.so.103 (0x00007fa370600000) libJKQTPlotterSharedLib_Release.so.4.0.0 => /opt/fastpathology/bin/../lib/../lib/libJKQTPlotterSharedLib_Release.so.4.0.0 (0x00007fa370000000) libOpenGL.so.0 => /lib/x86_64-linux-gnu/libOpenGL.so.0 (0x00007fa3745b4000) libGLX.so.0 => /lib/x86_64-linux-gnu/libGLX.so.0 (0x00007fa374580000) libX11.so.6 => /lib/x86_64-linux-gnu/libX11.so.6 (0x00007fa3724c0000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fa37497c000) libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007fa374536000) /lib64/ld-linux-x86-64.so.2 (0x00007fa374994000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fa374975000) libQt5Core.so.5 => not found libQt5Core.so.5 => not found libGL.so.1 => /lib/x86_64-linux-gnu/libGL.so.1 (0x00007fa373c92000) libQt5Core.so.5 => not found libQt5Core.so.5 => not found libssl.so.1.1 => /opt/fastpathology/bin/../lib/../lib/libssl.so.1.1 (0x00007fa36fc00000) libcrypto.so.1.1 => /opt/fastpathology/bin/../lib/../lib/libcrypto.so.1.1 (0x00007fa36f600000) libQt5Core.so.5 => not found libjpeg.so.8 => /opt/fastpathology/bin/../lib/../lib/../lib/libjpeg.so.8 (0x00007fa36f200000) libpixman-1.so.0 => /opt/fastpathology/bin/../lib/../lib/../lib/libpixman-1.so.0 (0x00007fa36ee00000) libglib-2.0.so.0 => /opt/fastpathology/bin/../lib/../lib/../lib/libglib-2.0.so.0 (0x00007fa36ea00000) libcairo.so.2 => /lib/x86_64-linux-gnu/libcairo.so.2 (0x00007fa3714d8000) libgdk_pixbuf-2.0.so.0 => /opt/fastpathology/bin/../lib/../lib/../lib/libgdk_pixbuf-2.0.so.0 (0x00007fa36e600000) libopenjp2.so.7 => /opt/fastpathology/bin/../lib/../lib/../lib/libopenjp2.so.7 (0x00007fa36e200000) libsqlite3.so.0 => /opt/fastpathology/bin/../lib/../lib/../lib/libsqlite3.so.0 (0x00007fa36de00000) libxml2.so.2 => /opt/fastpathology/bin/../lib/../lib/../lib/libxml2.so.2 (0x00007fa36da00000) libpng16.so.16 => /opt/fastpathology/bin/../lib/../lib/../lib/libpng16.so.16 (0x00007fa36d600000) libgobject-2.0.so.0 => /opt/fastpathology/bin/../lib/../lib/../lib/libgobject-2.0.so.0 (0x00007fa36d200000) libgio-2.0.so.0 => /opt/fastpathology/bin/../lib/../lib/../lib/libgio-2.0.so.0 (0x00007fa36ce00000) libhdf5.so.103 => /opt/fastpathology/bin/../lib/../lib/../lib/libhdf5.so.103 (0x00007fa36c800000) libQt5Svg.so.5 => /opt/fastpathology/bin/../lib/../lib/../lib/libQt5Svg.so.5 (0x00007fa36c400000) libJKQTMathTextSharedLib_Release.so.4.0.0 => /opt/fastpathology/bin/../lib/../lib/../lib/libJKQTMathTextSharedLib_Release.so.4.0.0 (0x00007fa36c000000) libJKQTCommonSharedLib_Release.so.4.0.0 => /opt/fastpathology/bin/../lib/../lib/../lib/libJKQTCommonSharedLib_Release.so.4.0.0 (0x00007fa36bc00000) libQt5PrintSupport.so.5 => /opt/fastpathology/bin/../lib/../lib/../lib/libQt5PrintSupport.so.5 (0x00007fa36b800000) libQt5Core.so.5 => not found libGLdispatch.so.0 => /lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007fa373948000) libxcb.so.1 => /lib/x86_64-linux-gnu/libxcb.so.1 (0x00007fa373c68000) libpcre.so.3 => /opt/fastpathology/bin/../lib/../lib/../lib/../lib/libpcre.so.3 (0x00007fa36b400000) libfontconfig.so.1 => /lib/x86_64-linux-gnu/libfontconfig.so.1 (0x00007fa373c1e000) libfreetype.so.6 => /lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007fa371138000) libxcb-shm.so.0 => /lib/x86_64-linux-gnu/libxcb-shm.so.0 (0x00007fa373c19000) libxcb-render.so.0 => /lib/x86_64-linux-gnu/libxcb-render.so.0 (0x00007fa373939000) libXrender.so.1 => /lib/x86_64-linux-gnu/libXrender.so.1 (0x00007fa373c0c000) libXext.so.6 => /lib/x86_64-linux-gnu/libXext.so.6 (0x00007fa373924000) libgmodule-2.0.so.0 => /opt/fastpathology/bin/../lib/../lib/../lib/../lib/libgmodule-2.0.so.0 (0x00007fa36b000000) libicuuc.so.60 => /opt/fastpathology/bin/../lib/../lib/../lib/../lib/libicuuc.so.60 (0x00007fa36ac00000) liblzma.so.5 => /opt/fastpathology/bin/../lib/../lib/../lib/../lib/liblzma.so.5 (0x00007fa36a800000) libffi.so.6 => /opt/fastpathology/bin/../lib/../lib/../lib/../lib/libffi.so.6 (0x00007fa36a400000) libselinux.so.1 => /lib/x86_64-linux-gnu/libselinux.so.1 (0x00007fa3738f8000) libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007fa3738e4000) libmount.so.1 => /lib/x86_64-linux-gnu/libmount.so.1 (0x00007fa372fbc000) libQt5Core.so.5 => not found libQt5Core.so.5 => not found libQt5Xml.so.5 => /opt/fastpathology/bin/../lib/../lib/../lib/../lib/libQt5Xml.so.5 (0x00007fa36a000000) libQt5Core.so.5 => not found libQt5Core.so.5 => not found libXau.so.6 => /lib/x86_64-linux-gnu/libXau.so.6 (0x00007fa372fb4000) libXdmcp.so.6 => /lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007fa372fac000) libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007fa372f7b000) libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007fa372f72000) libbrotlidec.so.1 => /lib/x86_64-linux-gnu/libbrotlidec.so.1 (0x00007fa372f62000) libicudata.so.60 => /opt/fastpathology/bin/../lib/../lib/../lib/../lib/../lib/libicudata.so.60 (0x00007fa368400000) libpcre2-8.so.0 => /lib/x86_64-linux-gnu/libpcre2-8.so.0 (0x00007fa371441000) libblkid.so.1 => /lib/x86_64-linux-gnu/libblkid.so.1 (0x00007fa372489000) libQt5Core.so.5 => not found libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007fa372471000) libbrotlicommon.so.1 => /lib/x86_64-linux-gnu/libbrotlicommon.so.1 (0x00007fa3721dd000) libmd.so.0 => /lib/x86_64-linux-gnu/libmd.so.0 (0x00007fa372464000)

On Tue, Aug 22, 2023 at 4:35 AM Erik Smistad @.***> wrote:

Can you confirm that it is the latest release you have tried (1.1.1) https://github.com/AICAN-Research/FAST-Pathology/releases/tag/v1.1.1

I tried installing this on my ubuntu 20.04, and it works fine.

Could you paste the entire output of ldd /opt/fastpathology/bin/fastpathology?

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[smistad]

Very strange.. Have you tried outside singularity?

You could also try to do LD_LIBRARY_PATH=/opt/fastpathology/lib/ /opt/fastpathology/bin/fastpathology Since the libQt5Core.so.5 should lie in /opt/fastpathology/lib/

[nategarver-daniels]

I am working on doing it outside of Singularity, but I've also tried explicitly setting LD_LIBRARY_PATH, etc. to no avail. Since it works for you, I'm definitely suspecting this is a me problem, and as such the issue can likely be closed.

On Tue, Aug 22, 2023 at 8:39 AM Erik Smistad @.***> wrote:

Very strange.. Have you tried outside singularity?

You could also try to do LD_LIBRARY_PATH=/opt/fastpathology/lib/ /opt/fastpathology/bin/fastpathology Since the libQt5Core.so.5 should lie in /opt/fastpathology/lib/

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[nategarver-daniels]

Another note, this happens even if I add the /opt/fastpathology/lib directory to the system shared library path with ldconfig. So definitely a me problem : )

[nategarver-daniels]

Ok, last comment and I'll close it. Thanks for nudging me in the right direction. Running ldconfig -p after adding the libraries showed:

`Singularity> ldconfig -p | grep Core

libQt5Core.so.5 (libc6,x86-64, OS ABI: Linux 3.17.0) => /opt/fastpathology/lib/libQt5Core.so.5 libQt5Core.so (libc6,x86-64, OS ABI: Linux 3.17.0) => /opt/fastpathology/lib/libQt5Core.so`

and none of the other libraries had ABI tags. The kernel the underlying system was using did not have the same ABI tag, which (to my understanding) was preventing the shared library from being used. Using strip to remove the ABI tag like so:

strip --remove-section=.note.ABI-tag /opt/fastpathology/lib/libQt5Core.so.5.15.2

seems to have cleared things up. Thanks again for the help, I appreciate it.

[smistad]

Hm, I have never noticed this tag before. Does it mean that your singularity container was using a very old linux kernel? The Qt5 binaries here were compiled on ubuntu 18.04

We should then probably consider adding this fix ourselves

[nategarver-daniels]

The OS where the container was running was a RHEL7.9 system, so it's kernel as presented to the container was 3.10, which was the problem. Here is a very long thread about it on the microsoft WSL github: https://github.com/microsoft/WSL/issues/3023

[smistad]

Ok, thanks for the info.