paraview: error while loading shared libraries: libpdal_base.so.13: cannot open shared object file

gazzafield · February 23, 2024, 10:20am

I have installed Paraview Version 10 on Ubuntu v22.04LTS

When attempting to run Paraview for the first time:-

./bin/pvserver

The following error occurs:-

paraview: error while loading shared libraries: libpdal_base.so.13: cannot open shared object file: No such file or directory

I have tried to install libpdal_base13 however Ubuntu proudly reports that the latest version is already installed whixh is libpdal_base15.

mwestphal · February 23, 2024, 10:25am

Please use latest ParaView binary release from https://paraview.org/download

gazzafield · February 23, 2024, 11:35am

Download latest release candidate. Extracted the file.

Entered the directory that was created:- ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64

cd bin
./paraview

No change. Same error.

mwestphal · February 23, 2024, 1:00pm

what is the output of printenv ?

ben.boeckel · February 26, 2024, 1:50am

I do not see any reference to libpdal_base.so.13 in the 5.12.0-RC3 package. Does running with the --dr flag work (i.e., paraview --dr)? If so, your configuration may be trying to load a plugin that was compiled against an older ParaView (where libpdal_base.so.13 did exist).

gazzafield · February 29, 2024, 8:10am

Output of printenv:-

SHELL=/bin/bash
LANGUAGE=en_GB:en
GTK_MODULES=appmenu-gtk-module
PWD=/media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64/bin
LOGNAME=tech
XDG_SESSION_TYPE=tty
MOTD_SHOWN=pam
HOME=/media/8TB-LOCAL-VOLUME/User_Homes/tech
LANG=en_GB.UTF-8
SSH_CONNECTION=130.209.26.149 49753 130.209.26.216 22
XDG_SESSION_CLASS=user
TERM=xterm-256color
LIBVIRT_DEFAULT_URI=qemu:///system
USER=tech
SHLVL=1
UBUNTU_MENUPROXY=1
XDG_SESSION_ID=357
XDG_RUNTIME_DIR=/run/user/1000
SSH_CLIENT=130.209.26.149 49753 22
XDG_DATA_DIRS=/media/8TB-LOCAL-VOLUME/User_Homes/tech/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share:/var/lib/snapd/desktop
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
SSH_TTY=/dev/pts/0
OLDPWD=/media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64
_=/usr/bin/printenv

gazzafield · February 29, 2024, 8:12am

Running pvserver or paravieww qith --dr makes no difference.

This is a fresh installation of Ubuntu v22.04 LTS (MATE) on a new Workstation with many and varied Apps and all updates installed. I have installed Paraview v5.10, which did not run correctly, and have downloaded the latest Release Candidate and tried that as suggested.

ben.boeckel · February 29, 2024, 11:20am

That is strange…we need to find what thinks it needs libpdal_base.so.13. Do you see any reference in the ParaView tree (grep -alR pdal_base /path/to/pv/extracted/package may result in some files; their paths and the output of readelf -d $path on each would be useful)?

If that comes up empty, tracing loaded libraries with LD_DEBUG=libs in the environment may provide hints as to what wants it in its output.

gazzafield · March 4, 2024, 3:17pm

Output of grep:-

grep -alR pdal_base /media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64
/media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64/lib/libvtkIOPDAL-pv5.12.so.1
/media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64/lib/libvtkIOPDAL-pv5.12.so.5.12
/media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64/lib/libpdal_base.so.15
/media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64/lib/libvtkIOPDAL-pv5.12.so
/media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64/lib/libpdal_base.so.15.6.0
/media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64/lib/libpdal_base.so

Is the command LD_DEBUG=libs simply run as that? If so, it returned nothing at all.

ben.boeckel · March 4, 2024, 5:33pm

OK; can you provide readelf -d $path on each result? These should all be .so.15, not .so.13.

gazzafield · March 5, 2024, 1:31pm

There’s A LOT of info on these so I have supplied the result of the first two:-

tech@Ubuntu-MATE-22:~$ readelf -d /media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64/lib/libvtkIOPDAL-pv5.12.so.1

Dynamic section at offset 0x13c30 contains 46 entries:
Tag Type Name/Value
0x0000000000000001 (NEEDED) Shared library: [libc.so.6]
0x0000000000000001 (NEEDED) Shared library: [libvtkFiltersGeneral-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libpdal_base.so.15]
0x0000000000000001 (NEEDED) Shared library: [libvtkFiltersCore-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonExecutionModel-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonDataModel-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonMisc-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonTransforms-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonMath-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkkissfft-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonCore-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtktoken-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libpthread.so.0]
0x0000000000000001 (NEEDED) Shared library: [libtbb.so.12]
0x0000000000000001 (NEEDED) Shared library: [libgomp.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtksys-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libdl.so.2]
0x0000000000000001 (NEEDED) Shared library: [libpdal_util.so.15]
0x0000000000000001 (NEEDED) Shared library: [libstdc++.so.6]
0x0000000000000001 (NEEDED) Shared library: [libm.so.6]
0x0000000000000001 (NEEDED) Shared library: [libgcc_s.so.1]
0x000000000000000e (SONAME) Library soname: [libvtkIOPDAL-pv5.12.so.1]
0x000000000000000f (RPATH) Library rpath: [$ORIGIN:ORIGIN/../lib] 0x000000000000000c (INIT) 0x6000 0x000000000000000d (FINI) 0x10e78 0x0000000000000019 (INIT_ARRAY) 0x147b0 0x000000000000001b (INIT_ARRAYSZ) 16 (bytes) 0x000000000000001a (FINI_ARRAY) 0x147c0 0x000000000000001c (FINI_ARRAYSZ) 8 (bytes) 0x000000006ffffef5 (GNU_HASH) 0x260 0x0000000000000005 (STRTAB) 0x1790 0x0000000000000006 (SYMTAB) 0x338 0x000000000000000a (STRSZ) 8631 (bytes) 0x000000000000000b (SYMENT) 24 (bytes) 0x0000000000000003 (PLTGOT) 0x15000 0x0000000000000002 (PLTRELSZ) 2904 (bytes) 0x0000000000000014 (PLTREL) RELA 0x0000000000000017 (JMPREL) 0x4970 0x0000000000000007 (RELA) 0x3bc0 0x0000000000000008 (RELASZ) 3504 (bytes) 0x0000000000000009 (RELAENT) 24 (bytes) 0x000000006ffffffe (VERNEED) 0x3b00 0x000000006fffffff (VERNEEDNUM) 4 0x000000006ffffff0 (VERSYM) 0x3948 0x000000006ffffff9 (RELACOUNT) 43 0x0000000000000000 (NULL) 0x0 tech@Ubuntu-MATE-22:~ readelf -d /media/8TB-LOCAL-VOLUME/User_Homes/tech/Downloads/ParaView-5.12.0-RC3-MPI-Linux-Python3.10-x86_64/lib/libvtkIOPDAL-pv5.12.so.5.12

Dynamic section at offset 0x13c30 contains 46 entries:
Tag Type Name/Value
0x0000000000000001 (NEEDED) Shared library: [libc.so.6]
0x0000000000000001 (NEEDED) Shared library: [libvtkFiltersGeneral-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libpdal_base.so.15]
0x0000000000000001 (NEEDED) Shared library: [libvtkFiltersCore-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonExecutionModel-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonDataModel-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonMisc-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonTransforms-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonMath-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkkissfft-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtkCommonCore-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtktoken-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libpthread.so.0]
0x0000000000000001 (NEEDED) Shared library: [libtbb.so.12]
0x0000000000000001 (NEEDED) Shared library: [libgomp.so.1]
0x0000000000000001 (NEEDED) Shared library: [libvtksys-pv5.12.so.1]
0x0000000000000001 (NEEDED) Shared library: [libdl.so.2]
0x0000000000000001 (NEEDED) Shared library: [libpdal_util.so.15]
0x0000000000000001 (NEEDED) Shared library: [libstdc++.so.6]
0x0000000000000001 (NEEDED) Shared library: [libm.so.6]
0x0000000000000001 (NEEDED) Shared library: [libgcc_s.so.1]
0x000000000000000e (SONAME) Library soname: [libvtkIOPDAL-pv5.12.so.1]
0x000000000000000f (RPATH) Library rpath: [$ORIGIN:ORIGIN/../lib] 0x000000000000000c (INIT) 0x6000 0x000000000000000d (FINI) 0x10e78 0x0000000000000019 (INIT_ARRAY) 0x147b0 0x000000000000001b (INIT_ARRAYSZ) 16 (bytes) 0x000000000000001a (FINI_ARRAY) 0x147c0 0x000000000000001c (FINI_ARRAYSZ) 8 (bytes) 0x000000006ffffef5 (GNU_HASH) 0x260 0x0000000000000005 (STRTAB) 0x1790 0x0000000000000006 (SYMTAB) 0x338 0x000000000000000a (STRSZ) 8631 (bytes) 0x000000000000000b (SYMENT) 24 (bytes) 0x0000000000000003 (PLTGOT) 0x15000 0x0000000000000002 (PLTRELSZ) 2904 (bytes) 0x0000000000000014 (PLTREL) RELA 0x0000000000000017 (JMPREL) 0x4970 0x0000000000000007 (RELA) 0x3bc0 0x0000000000000008 (RELASZ) 3504 (bytes) 0x0000000000000009 (RELAENT) 24 (bytes) 0x000000006ffffffe (VERNEED) 0x3b00 0x000000006fffffff (VERNEEDNUM) 4 0x000000006ffffff0 (VERSYM) 0x3948 0x000000006ffffff9 (RELACOUNT) 43 0x0000000000000000 (NULL) 0x0 tech@Ubuntu-MATE-22:~

mwestphal · March 7, 2024, 1:44pm

I confirm that the libs in the package are pointing to the right libpdal_base.so.15

Something else must be amiss in @gazzafield environnement.