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Bug #4330

New installation on Ubuntu missing libblas3gf and libjpeg62

Added by Brian Burns over 1 year ago. Updated 12 months ago.

Status:
Closed
Priority:
Normal
Assignee:
Kris Becker
Category:
Installation
Target version:
-
Impact:
Test Reviewer:

Description

I just installed ISIS 3.4.13.7091 on Xubuntu 16.04 using the installer from https://isis.astrogeology.usgs.gov/documents/InstallGuide/assets/isisInstall.sh, but all the commands were returning

error while loading shared libraries: libblas.so.3gf: cannot open shared object file: No such file or directory

I'm a bit new to Linux so apologies if I'm missing something obvious - as far as I know Xubuntu is the same as Ubuntu, apart from the desktop UI.

I tried this, but it couldn't find the package

$ sudo apt-get install libblas3gf

but I eventually found it and installed it -

$ curl http://mirrors.kernel.org/ubuntu/pool/main/b/blas/libblas3gf_1.2.20110419-2ubuntu1_amd64.deb -o foo.deb
$ sudo dpkg -i foo.deb

Then got

error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory

so installed that also

$ sudo apt-get install libjpeg62

and now things seem to be working.

So somehow the installation for Ubuntu seems to be missing those libraries.


Related issues

Related to ISIS - Bug #3881: Resolve external installation issues with findfeatures and OpenCV Closed

History

#1 Updated by Brian Burns over 1 year ago

Some more dependencies - I realize I could be doing something wrong here...

$ findfeatures listall=true
findfeatures: error while loading shared libraries: libswscale.so.2: cannot open shared object file: No such file or directory

So I tried installing these packages with gdebi -
http://packages.ubuntu.com/precise/amd64/libswscale2/download
http://packages.ubuntu.com/precise/amd64/libavutil51/download
http://packages.ubuntu.com/precise/amd64/libavutil-extra-51/download

but get a different error -

$ findfeatures listall=true
findfeatures: error while loading shared libraries: libdsklib.so: cannot map zero-fill pages

#2 Updated by Tammy Becker over 1 year ago

  • Status changed from New to Acknowledged

#3 Updated by Kris Becker over 1 year ago

  • Related to Bug #3881: Resolve external installation issues with findfeatures and OpenCV added

#4 Updated by Kris Becker over 1 year ago

  • Status changed from Acknowledged to Feedback
  • Assignee set to Kris Becker

Hi Brian...

Part of the problem may be that you are attempting to install ISIS on a Xubuntu 16.01 distribution, which is not supported. Our development and officially support system is Ubuntu 12.04, which is two releases before and including 16.01. ISIS also runs on Ubuntu 14.04 but 16.01 is has not been tested.

The last error you posted regarding libdsk.so may indicate an incomplete or corrupted ISIS download - you could reinstall ISIS. Also check your disk space as the device you are installing ISIS in may be out of space. And, it is not recommended to attempt to install ISIS in a virtual machine where the installation directory is a (network mounted) host device/disk (attach a virtual disk). Some OSes cannot support symbolic links (e.g. Windows) which is used for library versioning.

One way to determined missing libraries is using the ldd command. Run the command ldd $ISISROOT/bin/findfeatures. This command will list all the runtime dynamic library dependencies. Here is the result of the command on our Ubuntu 12.04 development machine:

prog10[37]: ldd $ISISROOT/bin/findfeatures 
        linux-vdso.so.1 =>  (0x00007fffb41ff000)
        libisis3.4.13.so => /usgs/pkgs/isis3.4.13/isis/bin/../lib/libisis3.4.13.so (0x00007f14b513a000)
        libQtXml.so.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libQtXml.so.4 (0x00007f14b4ef5000)
        libQtSql.so.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libQtSql.so.4 (0x00007f14b4cb3000)
        libQtGui.so.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libQtGui.so.4 (0x00007f14b3faf000)
        libQtCore.so.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libQtCore.so.4 (0x00007f14b3aca000)
        libQtWebKit.so.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libQtWebKit.so.4 (0x00007f14b1f87000)
        libQtDBus.so.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libQtDBus.so.4 (0x00007f14b1d05000)
        libqwt.so.6 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libqwt.so.6 (0x00007f14b1a15000)
        libxerces-c-3.1.so => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libxerces-c-3.1.so (0x00007f14b1462000)
        libgeotiff.so.2 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libgeotiff.so.2 (0x00007f14b122f000)
        libdsklib.so => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libdsklib.so (0x00007f1489f47000)
        libcspice.so => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libcspice.so (0x00007f14845ee000)
        libgeos-3.3.2.so => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libgeos-3.3.2.so (0x00007f14840cb000)
        libgeos_c.so.1 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libgeos_c.so.1 (0x00007f1483e8d000)
        libgsl.so.0 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libgsl.so.0 (0x00007f1483a50000)
        libgslcblas.so.0 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libgslcblas.so.0 (0x00007f148380b000)
        libprotobuf.so.7 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libprotobuf.so.7 (0x00007f1483522000)
        libkdu_a63R.so => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libkdu_a63R.so (0x00007f1483183000)
        libcholmod.so => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libcholmod.so (0x00007f1482e9c000)
        libamd.so => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libamd.so (0x00007f1482c92000)
        libcolamd.so => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libcolamd.so (0x00007f1482a8a000)
        liblapack.so => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/liblapack.so (0x00007f14820dd000)
        libblas.so.3gf => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libblas.so.3gf (0x00007f1481e43000)
        libgfortran.so.3 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libgfortran.so.3 (0x00007f1481b2b000)
        libopencv_calib3d.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_calib3d.so.2.4 (0x00007f1481887000)
        libopencv_contrib.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_contrib.so.2.4 (0x00007f1481595000)
        libopencv_core.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_core.so.2.4 (0x00007f148114d000)
        libopencv_features2d.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_features2d.so.2.4 (0x00007f1480ea1000)
        libopencv_highgui.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_highgui.so.2.4 (0x00007f1480abf000)
        libopencv_imgproc.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_imgproc.so.2.4 (0x00007f14805f2000)
        libopencv_ml.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_ml.so.2.4 (0x00007f1480370000)
        libopencv_nonfree.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_nonfree.so.2.4 (0x00007f1480151000)
        libopencv_superres.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_superres.so.2.4 (0x00007f147ff27000)
        libopencv_video.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_video.so.2.4 (0x00007f147fccf000)
        libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f147f9b4000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f147f6b7000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f147f4a1000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f147f284000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f147eec4000)
        libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007f147ebcf000)
        libpng12.so.0 => /lib/x86_64-linux-gnu/libpng12.so.0 (0x00007f147e9a7000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f147e78f000)
        libfreetype.so.6 => /usr/lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007f147e4f2000)
        libgobject-2.0.so.0 => /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0 (0x00007f147e2a3000)
        libSM.so.6 => /usr/lib/x86_64-linux-gnu/libSM.so.6 (0x00007f147e09a000)
        libICE.so.6 => /usr/lib/x86_64-linux-gnu/libICE.so.6 (0x00007f147de80000)
        libXrender.so.1 => /usr/lib/x86_64-linux-gnu/libXrender.so.1 (0x00007f147dc76000)
        libfontconfig.so.1 => /usr/lib/x86_64-linux-gnu/libfontconfig.so.1 (0x00007f147da3f000)
        libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f147d82e000)
        libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f147d4f9000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f147d2f4000)
        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f147d0ec000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f14b5ec7000)
        libQtNetwork.so.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libQtNetwork.so.4 (0x00007f147cd99000)
        libQtSvg.so.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libQtSvg.so.4 (0x00007f147cb41000)
        libtiff.so.5 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/../lib/libtiff.so.5 (0x00007f147c8d1000)
        libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f147c69a000)
        libopencv_flann.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_flann.so.2.4 (0x00007f147c42b000)
        libtbb.so.2 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libtbb.so.2 (0x00007f147c1df000)
        libopencv_objdetect.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_objdetect.so.2.4 (0x00007f147bf5f000)
        libGL.so.1 => /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1 (0x00007f147bcfe000)
        libjpeg.so.8 => /usr/lib/x86_64-linux-gnu/libjpeg.so.8 (0x00007f147baae000)
        libavcodec.so.53 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libavcodec.so.53 (0x00007f147ac9b000)
        libavformat.so.53 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libavformat.so.53 (0x00007f147a99a000)
        libavutil.so.51 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libavutil.so.51 (0x00007f147a77a000)
        libswscale.so.2 => /usr/lib/x86_64-linux-gnu/libswscale.so.2 (0x00007f147a533000)
        libQtOpenGL.so.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libQtOpenGL.so.4 (0x00007f147a232000)
        libQtTest.so.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libQtTest.so.4 (0x00007f147a00c000)
        libopencv_gpu.so.2.4 => /usgs/pkgs/isis3.4.13/isis/bin/../3rdParty/lib/libopencv_gpu.so.2.4 (0x00007f1479dcb000)
        libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f1479b8e000)
        libffi.so.6 => /usr/lib/x86_64-linux-gnu/libffi.so.6 (0x00007f1479985000)
        libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007f1479780000)
        libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f1479555000)
        libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f1479337000)
        libjpeg.so.62 => /usr/lib/x86_64-linux-gnu/libjpeg.so.62 (0x00007f1479111000)
        libglapi.so.0 => /usr/lib/x86_64-linux-gnu/libglapi.so.0 (0x00007f1478eec000)
        libXdamage.so.1 => /usr/lib/x86_64-linux-gnu/libXdamage.so.1 (0x00007f1478ce8000)
        libXfixes.so.3 => /usr/lib/x86_64-linux-gnu/libXfixes.so.3 (0x00007f1478ae2000)
        libX11-xcb.so.1 => /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1 (0x00007f14788e0000)
        libxcb-glx.so.0 => /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0 (0x00007f14786c8000)
        libXxf86vm.so.1 => /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1 (0x00007f14784c3000)
        libdrm.so.2 => /usr/lib/x86_64-linux-gnu/libdrm.so.2 (0x00007f14782b8000)
        libvpx.so.1 => /usr/lib/libvpx.so.1 (0x00007f1478012000)
        libvorbisenc.so.2 => /usr/lib/x86_64-linux-gnu/libvorbisenc.so.2 (0x00007f1477b43000)
        libvorbis.so.0 => /usr/lib/x86_64-linux-gnu/libvorbis.so.0 (0x00007f1477917000)
        libtheoraenc.so.1 => /usr/lib/x86_64-linux-gnu/libtheoraenc.so.1 (0x00007f14776d9000)
        libtheoradec.so.1 => /usr/lib/x86_64-linux-gnu/libtheoradec.so.1 (0x00007f14774be000)
        libspeex.so.1 => /usr/lib/x86_64-linux-gnu/libspeex.so.1 (0x00007f14772a5000)
        libschroedinger-1.0.so.0 => /usr/lib/libschroedinger-1.0.so.0 (0x00007f1476ff1000)
        libgsm.so.1 => /usr/lib/libgsm.so.1 (0x00007f1476de3000)
        libva.so.1 => /usr/lib/x86_64-linux-gnu/libva.so.1 (0x00007f1476bcd000)
        libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f14769bc000)
        libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f14767b9000)
        libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f14765b2000)
        libogg.so.0 => /usr/lib/x86_64-linux-gnu/libogg.so.0 (0x00007f14763ab000)
        liborc-0.4.so.0 => /usr/lib/x86_64-linux-gnu/liborc-0.4.so.0 (0x00007f147612f000)

Library paths containing /usgs/pkgs/isis3.4.13/isis are ones that should be found in your ISIS installation, but in your $ISISROOT install directory/path. All others come from system libraries that are part of the system installation. For Ubuntu 12.04 and 14.04, I suggest installing the OpenCV2 package to resolve findfeatures dependencies. If you don't have system admin privileges, run the command and let us know which libraries are not found. I do not know if OpenCV2 can be installed in Ubuntu 16.01 as it appears to provide OpenCV3.

#5 Updated by Brian Burns over 1 year ago

Thanks Kris, the installation page at https://isis.astrogeology.usgs.gov/documents/InstallGuide/ didn't mention an Ubuntu version number, so I thought it would work with the latest version. That's okay though - I'll see if I can get it to work with 16.04, and write down what I do here.

Your hint about running out of disk space led me to check on that - I'm using VirtualBox on Windows 8.1 - it had plenty of space but I hadn't paid much attention to the memory when I created the VM - it had defaulted to only 768KB of memory, so I increased it to 2GB and the libdsklib.so error went away. And then...

$ findfeatures listall=true
findfeatures: error while loading shared libraries: libvpx.so.1: cannot open shared object file: No such file or directory

$ apt-cache search vpx
libvpx-dev - VP8 and VP9 video codec (development files)
libvpx-doc - VP8 and VP9 video codec (API documentation)
libvpx3 - VP8 and VP9 video codec (shared library)
libvpx3-dbg - VP8 and VP9 video codec (debugging symbols)
vpx-tools - VP8 and VP9 video codec encoding/decoding tools

# tried these but got same error
$ sudo apt-get install libvpx-dev
$ sudo apt-get install vpx-tools
$ sudo apt-get install libvpx3

# at some point I tried installing opencv version 2, 
# as apparently you can install both and switch between them, 
# but got same error
$ sudo apt-get install libopencv-dev

# found libvpx1 and installed that
$ curl -O http://ftp.us.debian.org/debian/pool/main/libv/libvpx/libvpx1_1.3.0-3_amd64.deb
$ sudo dpkg -i libvpx1_1.3.0-3_amd64.deb

# it worked!
$ findfeatures listall=true
Object = Algorithms
  OpenCVVersion = 2.4.6.1

  Object = Algorithm
    Name                  = BackgroundSubtractor.GMG
    backgroundPrior       = 0.8
...

So if I run into any more dependency issues I'll post them here.

#6 Updated by Kris Becker about 1 year ago

  • Status changed from Feedback to Resolved

I will mark this resolved for the time being.

#7 Updated by Kris Becker 12 months ago

  • Status changed from Resolved to Closed

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