View Issue Details

IDProjectCategoryView StatusLast Update
0004126OpenFOAMBugpublic2024-08-13 12:09
Reporterpeth Assigned To 
PrioritynormalSeverityminorReproducibilityalways
Status newResolutionopen 
PlatformGNU/LinuxOSarch linuxOS Version(please specify)
Product Version12 
Summary0004126: bashrc source error
DescriptionOpenFOAM-12 produces the following issue when the bashrc file is sourced before the compile process.
    command: source OpenFOAM-12/etc/bashrc
    command message:
        not a dynamic executable
        dirname: missing operand
        Try 'dirname --help' for more information.

The bashrc file is not modified compared to the GitHub version.
Steps To Reproduce#download from GitHub repository
git clone https://github.com/OpenFOAM/OpenFOAM-12
git clone https://github.com/OpenFOAM/ThirdParty-12

#source OF variables
source OpenFOAM-12/etc/bashrc
TagsNo tags attached.

Activities

cgoessni

2024-08-05 13:02

reporter   ~0013336

I also saw such kind of errors in the past, this is due to OpenFOAM picking up ParaView if it is in your $PATH with v12, thus, the following is executed in etc/config.sh/paraview (assuming that you use bash):

    # Look for a paraview installation
    if pvserverExe=$(which pvserver 2> /dev/null)
    then
        paraviewBinDir=$(dirname $pvserverExe)
        paraviewBinDir=$(cd $paraviewBinDir && pwd -P)
    fi

    # Set the environment
    if [ -d "$paraviewBinDir" ]
    then
        export ParaView_DIR=$(dirname $paraviewBinDir)
        export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
*** ldd $paraviewBinDir/pvserver | \
                                  grep -o "/.*/libpqCore-pv.*.so" | \
                                  xargs dirname)
        ...

Note that I had to change paraview to pvserver in the line marked ***, since I installed the headless ParaView which does not incude paraview executable. However, the grep would return nothing since ldd does not find, at least on my system, the libpqCore-pv.so object:

$ ldd /opt/paraview5.12/bin/pvserver
        linux-vdso.so.1 => (0x00007ffc843b7000)
        libvtksys-pv5.12.so.1 => /opt/paraview5.12/bin/../lib/libvtksys-pv5.12.so.1 (0x00007ff2ca6ff000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007ff2ca341000)
        libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007ff2ca039000)
        libm.so.6 => /lib64/libm.so.6 (0x00007ff2c9d37000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007ff2c9b21000)
        libc.so.6 => /lib64/libc.so.6 (0x00007ff2c9753000)
        /lib64/ld-linux-x86-64.so.2 (0x00007ff2ca545000)

In your case, paraview seems to not be an executable? Could you run:

ls -l $(which paraview)
ldd $(which paraview)

cgoessni

2024-08-05 13:03

reporter   ~0013337

So if you don't want to see such errors, you could exclude the paraview path from your $PATH - that's what I did.

chris

2024-08-05 15:09

manager   ~0013338

One issue is that on an installation of ParaView on a headless machine, there is no 'paraview' executable.
Following discussions with @cgoessni, it seems like the following could reliably replace the 'export ParaView_LIB_DIR=' sections starting at line 67
        export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
                                  ldd $paraviewBinDir/pvserver | \
                                  grep -o "/.*/libvtksys-pv.*.so" | \
                                  xargs dirname)

This looks for the path to the library libvtksys-pv5.10.so.1 (for v5.10), which seems to be present even in the most stripped down installation of ParaView

peth

2024-08-05 15:45

reporter   ~0013339

Thanks for explanation @cgoessni. I have pre-installed paraview indeed (independently from OpenFOAM). In my case the paraview executable is located at
    /usr/bin/
so it may not good excluding this lib from the $PATH as many other applications are also located here.
As suggested, it seems that the problematic line in etc/config.sh/paraview is:
    ldd $paraviewBinDir/paraview | \
    grep -o "/.*/libpqCore-pv.*.so" | \
    xargs dirname)
as in my case
    ldd /usr/bin/paraview
results in "not a dynamic executable", which causes problem for the further "dirname" command too.
I think a possible workaround can be to set
    ParaView_TYPE=none
in etc/bashrc to exclude this part.

cgoessni

2024-08-05 17:26

reporter   ~0013340

@perth, could you run

file $(which paraview)

It seems like your paraview is statically linked, is that correct?

peth

2024-08-05 19:02

reporter   ~0013343

I installed paraview with arch linux's package manager pacman.
I checked it now, these are the contents:
/usr/bin/paraview:
    #!/bin/sh

    exec paraview-wrapper paraview "$@"

where the "/usr/bin/paraview_wrapper" script is:
    #!/bin/sh

    export PATH=/opt/paraview/bin:"${PATH}"
    export PYTHONPATH=/opt/paraview/lib/python3.12/site-packages/:"${PYTHONPATH}"
    export LD_LIBRARY_PATH=/opt/paraview/lib/:"${LD_LIBRARY_PATH}"

    exec /opt/paraview/bin/"$@"

Based on these I guess
1. the "real" paraview executable is found at
    /opt/paraview/bin/paraview
and the ldd works on it (I checked it now). The executable is called via the /usr/bin/paraview and paraview-wrapper scripts.

2. However at the /etc/config.sh/paraview the following lines
        if pvserverExe=$(which pvserver 2> /dev/null)
        then
            paraviewBinDir=$(dirname $pvserverExe)
            paraviewBinDir=$(cd $paraviewBinDir && pwd -P)
        fi

    results in the following:
        echo $paraviewBinDir
            /usr/bin

    where later the ldd is called as
        ldd $paraviewBinDir/paraview

    i.e. ldd called for the /usr/bin/paraview and not for the /opt/paraview/bin/paraview

This probably means that the original problem (ldd results in "not a dynamic executable") is limited only to arch linux, when paraview is installed with pacman.

cgoessni

2024-08-05 19:28

reporter   ~0013344

Interesing, pwd -P should "avoid all symlinks".

Could you try this:

         if pvserverExe=$(which pvserver 2> /dev/null)
        then
            paraviewBinDir=$(dirname $pvserverExe)
            paraviewBinDir=$(realpath $paraviewBinDir)
        fi

What is $paraviewBinDir then?

peth

2024-08-05 19:37

reporter   ~0013345

The suggested script results in "/usr/bin" for $paraviewBinDir

cgoessni

2024-08-05 19:42

reporter   ~0013346

Oh I see now, sorry for not reading your response carefully. /usr/bin/paraview is a shell script that calls another shell script, so there is nothing that realpath / pwd -P can do about this.

chris

2024-08-06 08:24

manager   ~0013347

pwd -P refers to the path (directory).
It is dealing with the situation that the directory is a link.
In particular /bin
Try it: ls -ld /bin - /bin is a link to /usr/bin. We want /usr/bin.

chris

2024-08-06 08:27

manager   ~0013348

@peth What about 'pvserver' on archlinux? Is there an additional script for that?

chris

2024-08-06 08:33

manager   ~0013349

Just checked here https://archlinux.org/packages/extra/x86_64/paraview/
There is a /usr/bin/pvserver
These scripts are partially reproducing what OpenFOAM's configuration file does.
We need to bypass them somehow

peth

2024-08-06 08:42

reporter   ~0013351

Dear @chris,regarding comment 13348:
    It seems "/usr/bin/pvserver" using the same wrapper as the "/usr/bin/paraview" script described in my previous post:

    cat /usr/bin/pvserver
        #!/bin/sh

        exec paraview-wrapper pvserver "$@"

    This means "/usr/bin/paraview" calls the "/opt/paraview/bin/pvserver" executable via the wrapper.

and to comment 13350:
    The requested command results in
        which -a pvserver
            /usr/bin/pvserver
            /bin/pvserver

chris

2024-08-06 08:49

manager   ~0013352

Yes, I could see that happening, given the paraview-wrapper script.
When you source OpenFOAM's .bashrc file, what happens if you prepend the real paraview path into PATH before sourcing

PATH=/opt/paraview/bin/:$PATH source OpenFOAM-12/etc/bashrc

peth

2024-08-06 09:24

reporter   ~0013353

Inserting /opt/bin/paraview into the PATH before the bashrc source resolves the path issue, i.e. the $paraviewBinDir variable in /etc/config.sh/paraview now is set to
    echo $paraviewBinDir
        /opt/paraview/bin

However the
        export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
                              ldd $paraviewBinDir/paraview | \
                              grep -o "/.*/libpqCore-pv.*.so" | \
                              xargs dirname)
line works until the ldd part, i.e. the shared libraries are now printed, but for some reason the "libpqCore-pv.*.so" is not found in my case, so the "dirname" still prints: "missing operand Try 'dirname --help' for more information."

cgoessni

2024-08-06 09:42

reporter   ~0013354

Could you try this:

         export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
                                  ldd $paraviewBinDir/pvserver | \
                                  grep -o "/.*/libvtksys-pv.*.so" | \
                                  xargs dirname)

Note that the library search pattern changed.

peth

2024-08-06 10:44

reporter   ~0013355

I checked with the proposed modification, but the dirname issue is still there, i.e. the libvtksys-pv.*.so is also not found in the shared library list.

cgoessni

2024-08-06 10:53

reporter   ~0013356

What does

ldd /opt/paraview/bin/pvserver

yield?

Could you also try this if this works:

         export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
                                  ldd $paraviewBinDir/pvserver | \
                                  grep -o "/.*/libvtksys.*.so" | \
                                  xargs dirname)

According to arch linux, there is a opt/paraview/lib/libvtksys.so file installed.

peth

2024-08-06 11:07

reporter   ~0013357

I attach the sorted ldd lists of both paraview and pvserver. They were generated with the following commands:
ldd /opt/paraview/bin/paraview | sort > ldd_paraview_arch_linux
ldd /opt/paraview/bin/pvserver | sort > ldd_pvserver_arch_linux

libvtksys.so is in the list of pvserver, so running the proposed script results in:
echo $ParaView_LIB_DIR
    /opt/paraview/bin/../lib
ldd_pvserver_arch_linux (39,143 bytes)   
	/lib64/ld-linux-x86-64.so.2 => /usr/lib64/ld-linux-x86-64.so.2 (0x00007fb67378d000)
	libabsl_base.so.2401.0.0 => /usr/lib/libabsl_base.so.2401.0.0 (0x00007fb664cc9000)
	libabsl_city.so.2401.0.0 => /usr/lib/libabsl_city.so.2401.0.0 (0x00007fb661ff3000)
	libabsl_cord_internal.so.2401.0.0 => /usr/lib/libabsl_cord_internal.so.2401.0.0 (0x00007fb661fe0000)
	libabsl_cord.so.2401.0.0 => /usr/lib/libabsl_cord.so.2401.0.0 (0x00007fb669b20000)
	libabsl_cordz_functions.so.2401.0.0 => /usr/lib/libabsl_cordz_functions.so.2401.0.0 (0x00007fb661fd4000)
	libabsl_cordz_handle.so.2401.0.0 => /usr/lib/libabsl_cordz_handle.so.2401.0.0 (0x00007fb661fce000)
	libabsl_cordz_info.so.2401.0.0 => /usr/lib/libabsl_cordz_info.so.2401.0.0 (0x00007fb669b19000)
	libabsl_crc32c.so.2401.0.0 => /usr/lib/libabsl_crc32c.so.2401.0.0 (0x00007fb658333000)
	libabsl_crc_cord_state.so.2401.0.0 => /usr/lib/libabsl_crc_cord_state.so.2401.0.0 (0x00007fb661fd9000)
	libabsl_crc_internal.so.2401.0.0 => /usr/lib/libabsl_crc_internal.so.2401.0.0 (0x00007fb648b80000)
	libabsl_debugging_internal.so.2401.0.0 => /usr/lib/libabsl_debugging_internal.so.2401.0.0 (0x00007fb65832d000)
	libabsl_demangle_internal.so.2401.0.0 => /usr/lib/libabsl_demangle_internal.so.2401.0.0 (0x00007fb64ab56000)
	libabsl_die_if_null.so.2401.0.0 => /usr/lib/libabsl_die_if_null.so.2401.0.0 (0x00007fb66ae6c000)
	libabsl_examine_stack.so.2401.0.0 => /usr/lib/libabsl_examine_stack.so.2401.0.0 (0x00007fb66609e000)
	libabsl_exponential_biased.so.2401.0.0 => /usr/lib/libabsl_exponential_biased.so.2401.0.0 (0x00007fb6586a1000)
	libabsl_hash.so.2401.0.0 => /usr/lib/libabsl_hash.so.2401.0.0 (0x00007fb669b43000)
	libabsl_int128.so.2401.0.0 => /usr/lib/libabsl_int128.so.2401.0.0 (0x00007fb660a06000)
	libabsl_kernel_timeout_internal.so.2401.0.0 => /usr/lib/libabsl_kernel_timeout_internal.so.2401.0.0 (0x00007fb660a15000)
	libabsl_log_globals.so.2401.0.0 => /usr/lib/libabsl_log_globals.so.2401.0.0 (0x00007fb66332c000)
	libabsl_log_internal_check_op.so.2401.0.0 => /usr/lib/libabsl_log_internal_check_op.so.2401.0.0 (0x00007fb669b65000)
	libabsl_log_internal_conditions.so.2401.0.0 => /usr/lib/libabsl_log_internal_conditions.so.2401.0.0 (0x00007fb669b60000)
	libabsl_log_internal_format.so.2401.0.0 => /usr/lib/libabsl_log_internal_format.so.2401.0.0 (0x00007fb664cc3000)
	libabsl_log_internal_globals.so.2401.0.0 => /usr/lib/libabsl_log_internal_globals.so.2401.0.0 (0x00007fb664cae000)
	libabsl_log_internal_log_sink_set.so.2401.0.0 => /usr/lib/libabsl_log_internal_log_sink_set.so.2401.0.0 (0x00007fb664cb3000)
	libabsl_log_internal_message.so.2401.0.0 => /usr/lib/libabsl_log_internal_message.so.2401.0.0 (0x00007fb669b53000)
	libabsl_log_internal_nullguard.so.2401.0.0 => /usr/lib/libabsl_log_internal_nullguard.so.2401.0.0 (0x00007fb669b4e000)
	libabsl_log_internal_proto.so.2401.0.0 => /usr/lib/libabsl_log_internal_proto.so.2401.0.0 (0x00007fb664cbe000)
	libabsl_log_sink.so.2401.0.0 => /usr/lib/libabsl_log_sink.so.2401.0.0 (0x00007fb659f1c000)
	libabsl_low_level_hash.so.2401.0.0 => /usr/lib/libabsl_low_level_hash.so.2401.0.0 (0x00007fb661fee000)
	libabsl_malloc_internal.so.2401.0.0 => /usr/lib/libabsl_malloc_internal.so.2401.0.0 (0x00007fb660a0e000)
	libabsl_raw_hash_set.so.2401.0.0 => /usr/lib/libabsl_raw_hash_set.so.2401.0.0 (0x00007fb669b48000)
	libabsl_raw_logging_internal.so.2401.0.0 => /usr/lib/libabsl_raw_logging_internal.so.2401.0.0 (0x00007fb669ae1000)
	libabsl_spinlock_wait.so.2401.0.0 => /usr/lib/libabsl_spinlock_wait.so.2401.0.0 (0x00007fb669aee000)
	libabsl_stacktrace.so.2401.0.0 => /usr/lib/libabsl_stacktrace.so.2401.0.0 (0x00007fb661fc9000)
	libabsl_statusor.so.2401.0.0 => /usr/lib/libabsl_statusor.so.2401.0.0 (0x00007fb66a047000)
	libabsl_status.so.2401.0.0 => /usr/lib/libabsl_status.so.2401.0.0 (0x00007fb669b37000)
	libabsl_strerror.so.2401.0.0 => /usr/lib/libabsl_strerror.so.2401.0.0 (0x00007fb664cb9000)
	libabsl_str_format_internal.so.2401.0.0 => /usr/lib/libabsl_str_format_internal.so.2401.0.0 (0x00007fb668fca000)
	libabsl_strings_internal.so.2401.0.0 => /usr/lib/libabsl_strings_internal.so.2401.0.0 (0x00007fb660a00000)
	libabsl_strings.so.2401.0.0 => /usr/lib/libabsl_strings.so.2401.0.0 (0x00007fb668fa8000)
	libabsl_symbolize.so.2401.0.0 => /usr/lib/libabsl_symbolize.so.2401.0.0 (0x00007fb6586a6000)
	libabsl_synchronization.so.2401.0.0 => /usr/lib/libabsl_synchronization.so.2401.0.0 (0x00007fb669b08000)
	libabsl_throw_delegate.so.2401.0.0 => /usr/lib/libabsl_throw_delegate.so.2401.0.0 (0x00007fb669ae8000)
	libabsl_time.so.2401.0.0 => /usr/lib/libabsl_time.so.2401.0.0 (0x00007fb669af3000)
	libabsl_time_zone.so.2401.0.0 => /usr/lib/libabsl_time_zone.so.2401.0.0 (0x00007fb668fe5000)
	libacl.so.1 => /usr/lib/libacl.so.1 (0x00007fb64ab93000)
	libadios2_atl.so.2.10 => /usr/lib/../lib/libadios2_atl.so.2.10 (0x00007fb64ab9c000)
	libadios2_core_mpi.so.2.10 => /usr/lib/libadios2_core_mpi.so.2.10 (0x00007fb65838c000)
	libadios2_core.so.2.10 => /usr/lib/libadios2_core.so.2.10 (0x00007fb64d000000)
	libadios2_cxx11_mpi.so.2.10 => /usr/lib/libadios2_cxx11_mpi.so.2.10 (0x00007fb667f66000)
	libadios2_cxx11.so.2.10 => /usr/lib/libadios2_cxx11.so.2.10 (0x00007fb6620bd000)
	libadios2_dill.so.2.10 => /usr/lib/../lib/../lib/libadios2_dill.so.2.10 (0x00007fb647e58000)
	libadios2_evpath.so.2.10 => /usr/lib/../lib/libadios2_evpath.so.2.10 (0x00007fb648c32000)
	libadios2_ffs.so.2.10 => /usr/lib/../lib/libadios2_ffs.so.2.10 (0x00007fb648bcb000)
	libadios2_perfstubs.so.2.10 => /usr/lib/libadios2_perfstubs.so.2.10 (0x00007fb64ad34000)
	libaec.so.0 => /usr/lib/libaec.so.0 (0x00007fb65c551000)
	libaom.so.3 => /usr/lib/libaom.so.3 (0x00007fb658800000)
	libarchive.so.13 => /usr/lib/libarchive.so.13 (0x00007fb657d31000)
	libavcodec.so.61 => /usr/lib/libavcodec.so.61 (0x00007fb663400000)
	libavformat.so.61 => /usr/lib/libavformat.so.61 (0x00007fb664a00000)
	libavtdatabase_par.so.1 => /opt/paraview/bin/../lib/libavtdatabase_par.so.1 (0x00007fb668e4d000)
	libavtdbatts.so.1 => /opt/paraview/bin/../lib/libavtdbatts.so.1 (0x00007fb667a49000)
	libavtmath.so.1 => /opt/paraview/bin/../lib/libavtmath.so.1 (0x00007fb6609f2000)
	libavtpipeline_par.so.1 => /opt/paraview/bin/../lib/libavtpipeline_par.so.1 (0x00007fb667ae9000)
	libavutil.so.59 => /usr/lib/libavutil.so.59 (0x00007fb662200000)
	libblkid.so.1 => /usr/lib/libblkid.so.1 (0x00007fb647df1000)
	libblosc.so.1 => /usr/lib/libblosc.so.1 (0x00007fb6586df000)
	libbluray.so.2 => /usr/lib/libbluray.so.2 (0x00007fb65c5a3000)
	libboost_thread.so.1.83.0 => /usr/lib/libboost_thread.so.1.83.0 (0x00007fb65e25f000)
	libbrotlicommon.so.1 => /usr/lib/libbrotlicommon.so.1 (0x00007fb648b86000)
	libbrotlidec.so.1 => /usr/lib/libbrotlidec.so.1 (0x00007fb6586ae000)
	libbrotlienc.so.1 => /usr/lib/libbrotlienc.so.1 (0x00007fb64ae42000)
	libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x00007fb65d314000)
	libcairo-gobject.so.2 => /usr/lib/libcairo-gobject.so.2 (0x00007fb64ecf4000)
	libcairo.so.2 => /usr/lib/libcairo.so.2 (0x00007fb65917f000)
	libcap.so.2 => /usr/lib/libcap.so.2 (0x00007fb64877f000)
	libcgns.so.4.4 => /usr/lib/libcgns.so.4.4 (0x00007fb6678a2000)
	libcom_err.so.2 => /usr/lib/libcom_err.so.2 (0x00007fb64874c000)
	libcryptopp.so.8 => /usr/lib/libcryptopp.so.8 (0x00007fb64ca00000)
	libcrypto.so.3 => /usr/lib/libcrypto.so.3 (0x00007fb65a400000)
	libc.so.6 => /usr/lib/libc.so.6 (0x00007fb673547000)
	libcurl.so.4 => /usr/lib/libcurl.so.4 (0x00007fb65de5c000)
	libdatrie.so.1 => /usr/lib/libdatrie.so.1 (0x00007fb647de8000)
	libdav1d.so.7 => /usr/lib/libdav1d.so.7 (0x00007fb659a21000)
	libdeflate.so.0 => /usr/lib/libdeflate.so.0 (0x00007fb659f29000)
	libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fb669ada000)
	libdouble-conversion.so.3 => /usr/lib/libdouble-conversion.so.3 (0x00007fb669b87000)
	libdrm.so.2 => /usr/lib/libdrm.so.2 (0x00007fb65a8da000)
	libdvdnav.so.4 => /usr/lib/libdvdnav.so.4 (0x00007fb65de45000)
	libdvdread.so.8 => /usr/lib/libdvdread.so.8 (0x00007fb65d327000)
	libEGL.so.1 => /usr/lib/libEGL.so.1 (0x00007fb66051f000)
	libevent_core-2.1.so.7 => /usr/lib/libevent_core-2.1.so.7 (0x00007fb660556000)
	libevent_pthreads-2.1.so.7 => /usr/lib/libevent_pthreads-2.1.so.7 (0x00007fb661fc4000)
	libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00007fb668f7f000)
	libfabric.so.1 => /usr/lib/libfabric.so.1 (0x00007fb65cc00000)
	libffi.so.8 => /usr/lib/libffi.so.8 (0x00007fb64ce34000)
	libfmt.so.10 => /usr/lib/libfmt.so.10 (0x00007fb66610e000)
	libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0x00007fb64bdb0000)
	libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0x00007fb660a1b000)
	libfreexl.so.1 => /usr/lib/libfreexl.so.1 (0x00007fb64ab5f000)
	libfribidi.so.0 => /usr/lib/libfribidi.so.0 (0x00007fb64814f000)
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	linux-vdso.so.1 (0x00007fb67378b000)
ldd_pvserver_arch_linux (39,143 bytes)   
ldd_paraview_arch_linux (41,014 bytes)   
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	libabsl_cordz_info.so.2401.0.0 => /usr/lib/libabsl_cordz_info.so.2401.0.0 (0x0000726598e70000)
	libabsl_crc32c.so.2401.0.0 => /usr/lib/libabsl_crc32c.so.2401.0.0 (0x0000726589540000)
	libabsl_crc_cord_state.so.2401.0.0 => /usr/lib/libabsl_crc_cord_state.so.2401.0.0 (0x000072658bc44000)
	libabsl_crc_internal.so.2401.0.0 => /usr/lib/libabsl_crc_internal.so.2401.0.0 (0x000072657e521000)
	libabsl_debugging_internal.so.2401.0.0 => /usr/lib/libabsl_debugging_internal.so.2401.0.0 (0x0000726587b63000)
	libabsl_demangle_internal.so.2401.0.0 => /usr/lib/libabsl_demangle_internal.so.2401.0.0 (0x000072657eb1d000)
	libabsl_die_if_null.so.2401.0.0 => /usr/lib/libabsl_die_if_null.so.2401.0.0 (0x000072659a1b8000)
	libabsl_examine_stack.so.2401.0.0 => /usr/lib/libabsl_examine_stack.so.2401.0.0 (0x000072658cfe8000)
	libabsl_exponential_biased.so.2401.0.0 => /usr/lib/libabsl_exponential_biased.so.2401.0.0 (0x0000726587e08000)
	libabsl_hash.so.2401.0.0 => /usr/lib/libabsl_hash.so.2401.0.0 (0x0000726598e77000)
	libabsl_int128.so.2401.0.0 => /usr/lib/libabsl_int128.so.2401.0.0 (0x000072658bc1d000)
	libabsl_kernel_timeout_internal.so.2401.0.0 => /usr/lib/libabsl_kernel_timeout_internal.so.2401.0.0 (0x000072658bc2e000)
	libabsl_log_globals.so.2401.0.0 => /usr/lib/libabsl_log_globals.so.2401.0.0 (0x000072658bc65000)
	libabsl_log_internal_check_op.so.2401.0.0 => /usr/lib/libabsl_log_internal_check_op.so.2401.0.0 (0x00007265998d4000)
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	libabsl_log_internal_format.so.2401.0.0 => /usr/lib/libabsl_log_internal_format.so.2401.0.0 (0x000072658cfe2000)
	libabsl_log_internal_globals.so.2401.0.0 => /usr/lib/libabsl_log_internal_globals.so.2401.0.0 (0x000072658bc6b000)
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	libabsl_log_internal_message.so.2401.0.0 => /usr/lib/libabsl_log_internal_message.so.2401.0.0 (0x00007265992ce000)
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	libabsl_log_sink.so.2401.0.0 => /usr/lib/libabsl_log_sink.so.2401.0.0 (0x00007265898cd000)
	libabsl_low_level_hash.so.2401.0.0 => /usr/lib/libabsl_low_level_hash.so.2401.0.0 (0x000072658bc5b000)
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	libabsl_raw_logging_internal.so.2401.0.0 => /usr/lib/libabsl_raw_logging_internal.so.2401.0.0 (0x000072659741c000)
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	libabsl_status.so.2401.0.0 => /usr/lib/libabsl_status.so.2401.0.0 (0x0000726596d59000)
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	libabsl_strings_internal.so.2401.0.0 => /usr/lib/libabsl_strings_internal.so.2401.0.0 (0x000072658bc17000)
	libabsl_strings.so.2401.0.0 => /usr/lib/libabsl_strings.so.2401.0.0 (0x000072659623c000)
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	libabsl_time.so.2401.0.0 => /usr/lib/libabsl_time.so.2401.0.0 (0x000072659693f000)
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	libadios2_atl.so.2.10 => /usr/lib/../lib/libadios2_atl.so.2.10 (0x0000726571777000)
	libadios2_core_mpi.so.2.10 => /usr/lib/libadios2_core_mpi.so.2.10 (0x000072657cb8c000)
	libadios2_core.so.2.10 => /usr/lib/libadios2_core.so.2.10 (0x0000726571e00000)
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	libavformat.so.61 => /usr/lib/libavformat.so.61 (0x0000726583e00000)
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	libavtdbatts.so.1 => /opt/paraview/bin/../lib/libavtdbatts.so.1 (0x0000726589560000)
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	libavutil.so.59 => /usr/lib/libavutil.so.59 (0x0000726581600000)
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	libblosc.so.1 => /usr/lib/libblosc.so.1 (0x000072657d122000)
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	libcairo.so.2 => /usr/lib/libcairo.so.2 (0x000072657decd000)
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	libvtkParallelMPI.so.1 => /usr/lib/libvtkParallelMPI.so.1 (0x0000726593b05000)
	libvtkPVVTKExtensionsAMR.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsAMR.so.1 (0x000072658f6ce000)
	libvtkPVVTKExtensionsCore.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsCore.so.1 (0x000072659a551000)
	libvtkPVVTKExtensionsExtractionPython.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsExtractionPython.so.1 (0x000072658f5e6000)
	libvtkPVVTKExtensionsExtraction.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsExtraction.so.1 (0x000072658f5ee000)
	libvtkPVVTKExtensionsFiltersGeneralMPI.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsFiltersGeneralMPI.so.1 (0x000072658fd0b000)
	libvtkPVVTKExtensionsFiltersGeneral.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsFiltersGeneral.so.1 (0x000072658f729000)
	libvtkPVVTKExtensionsFiltersMaterialInterface.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsFiltersMaterialInterface.so.1 (0x000072658fd16000)
	libvtkPVVTKExtensionsFiltersParallelDIY2.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsFiltersParallelDIY2.so.1 (0x00007265902d0000)
	libvtkPVVTKExtensionsFiltersPython.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsFiltersPython.so.1 (0x000072658fd6d000)
	libvtkPVVTKExtensionsFiltersRendering.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsFiltersRendering.so.1 (0x0000726593d1f000)
	libvtkPVVTKExtensionsFiltersStatistics.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsFiltersStatistics.so.1 (0x00007265902dc000)
	libvtkPVVTKExtensionsInteractionStyle.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsInteractionStyle.so.1 (0x000072658f661000)
	libvtkPVVTKExtensionsIOAMR.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsIOAMR.so.1 (0x00007265902f6000)
	libvtkPVVTKExtensionsIOCGNSWriter.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsIOCGNSWriter.so.1 (0x00007265902fe000)
	libvtkPVVTKExtensionsIOCore.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsIOCore.so.1 (0x000072658f67d000)
	libvtkPVVTKExtensionsIOEnSight.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsIOEnSight.so.1 (0x000072658fd90000)
	libvtkPVVTKExtensionsIOExodus.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsIOExodus.so.1 (0x000072659031d000)
	libvtkPVVTKExtensionsIOGeneral.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsIOGeneral.so.1 (0x000072658fccd000)
	libvtkPVVTKExtensionsIOImage.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsIOImage.so.1 (0x0000726591f94000)
	libvtkPVVTKExtensionsIOParallelCGNSWriter.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsIOParallelCGNSWriter.so.1 (0x0000726590328000)
	libvtkPVVTKExtensionsIOSPCTH.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsIOSPCTH.so.1 (0x0000726590334000)
	libvtkPVVTKExtensionsMisc.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsMisc.so.1 (0x000072658f611000)
	libvtkPVVTKExtensionsPoints.so.1 => /opt/paraview/bin/../lib/libvtkPVVTKExtensionsPoints.so.1 (0x000072659037f000)
	libvtkPythonInterpreter.so.1 => /opt/paraview/bin/../lib/libvtkPythonInterpreter.so.1 (0x000072659b47d000)
	libvtkqttesting.so.1 => /opt/paraview/bin/../lib/libvtkqttesting.so.1 (0x000072659b58a000)
	libvtkRemotingAnimation.so.1 => /opt/paraview/bin/../lib/libvtkRemotingAnimation.so.1 (0x0000726598a41000)
	libvtkRemotingApplication.so.1 => /opt/paraview/bin/../lib/libvtkRemotingApplication.so.1 (0x0000726592000000)
	libvtkRemotingClientServerStream.so.1 => /opt/paraview/bin/../lib/libvtkRemotingClientServerStream.so.1 (0x000072659b444000)
	libvtkRemotingCore.so.1 => /opt/paraview/bin/../lib/libvtkRemotingCore.so.1 (0x000072659ad19000)
	libvtkRemotingExport.so.1 => /opt/paraview/bin/../lib/libvtkRemotingExport.so.1 (0x00007265998dd000)
	libvtkRemotingLive.so.1 => /opt/paraview/bin/../lib/libvtkRemotingLive.so.1 (0x000072659932c000)
	libvtkRemotingMisc.so.1 => /opt/paraview/bin/../lib/libvtkRemotingMisc.so.1 (0x00007265992fa000)
	libvtkRemotingServerManagerPython.so.1 => /opt/paraview/bin/../lib/libvtkRemotingServerManagerPython.so.1 (0x000072659038c000)
	libvtkRemotingServerManager.so.1 => /opt/paraview/bin/../lib/libvtkRemotingServerManager.so.1 (0x000072659a200000)
	libvtkRemotingSettings.so.1 => /opt/paraview/bin/../lib/libvtkRemotingSettings.so.1 (0x000072659bcea000)
	libvtkRemotingViewsPython.so.1 => /opt/paraview/bin/../lib/libvtkRemotingViewsPython.so.1 (0x000072659039e000)
	libvtkRemotingViews.so.1 => /opt/paraview/bin/../lib/libvtkRemotingViews.so.1 (0x0000726591c00000)
	libvtkRenderingAnnotation.so.1 => /opt/paraview/bin/../lib/libvtkRenderingAnnotation.so.1 (0x0000726591837000)
	libvtkRenderingCellGrid.so.1 => /usr/lib/libvtkRenderingCellGrid.so.1 (0x000072658f27d000)
	libvtkRenderingContext2D.so.1 => /opt/paraview/bin/../lib/libvtkRenderingContext2D.so.1 (0x000072659b48e000)
	libvtkRenderingContextOpenGL2.so.1 => /usr/lib/libvtkRenderingContextOpenGL2.so.1 (0x000072658f2a2000)
	libvtkRenderingCore.so.1 => /opt/paraview/bin/../lib/libvtkRenderingCore.so.1 (0x0000726598c00000)
	libvtkRenderingFreeType.so.1 => /opt/paraview/bin/../lib/libvtkRenderingFreeType.so.1 (0x0000726591795000)
	libvtkRenderingGL2PSOpenGL2.so.1 => /usr/lib/libvtkRenderingGL2PSOpenGL2.so.1 (0x000072658ec5b000)
	libvtkRenderingHyperTreeGrid.so.1 => /opt/paraview/bin/../lib/libvtkRenderingHyperTreeGrid.so.1 (0x000072659bc9e000)
	libvtkRenderingLabel.so.1 => /usr/lib/libvtkRenderingLabel.so.1 (0x000072658f340000)
	libvtkRenderingLICOpenGL2.so.1 => /usr/lib/libvtkRenderingLICOpenGL2.so.1 (0x000072658f2da000)
	libvtkRenderingMatplotlib.so.1 => /usr/lib/libvtkRenderingMatplotlib.so.1 (0x000072658f3c3000)
	libvtkRenderingOpenGL2.so.1 => /opt/paraview/bin/../lib/libvtkRenderingOpenGL2.so.1 (0x0000726599600000)
	libvtkRenderingParallelLIC.so.1 => /usr/lib/libvtkRenderingParallelLIC.so.1 (0x000072658f45b000)
	libvtkRenderingParallel.so.1 => /usr/lib/libvtkRenderingParallel.so.1 (0x000072658f425000)
	libvtkRenderingRayTracing.so.1 => /opt/paraview/bin/../lib/libvtkRenderingRayTracing.so.1 (0x000072659748f000)
	libvtkRenderingSceneGraph.so.1 => /usr/lib/libvtkRenderingSceneGraph.so.1 (0x000072658ea24000)
	libvtkRenderingUI.so.1 => /opt/paraview/bin/../lib/libvtkRenderingUI.so.1 (0x000072659b431000)
	libvtkRenderingVolumeAMR.so.1 => /usr/lib/libvtkRenderingVolumeAMR.so.1 (0x000072658f566000)
	libvtkRenderingVolumeOpenGL2.so.1 => /usr/lib/libvtkRenderingVolumeOpenGL2.so.1 (0x000072658f4c4000)
	libvtkRenderingVolume.so.1 => /usr/lib/libvtkRenderingVolume.so.1 (0x000072658e200000)
	libvtkRenderingVtkJS.so.1 => /usr/lib/libvtkRenderingVtkJS.so.1 (0x000072658ea3b000)
	libvtksys.so.1 => /opt/paraview/bin/../lib/libvtksys.so.1 (0x0000726599caa000)
	libvtkTestingRendering.so.1 => /opt/paraview/bin/../lib/libvtkTestingRendering.so.1 (0x0000726598a27000)
	libvtktoken.so.1 => /opt/paraview/bin/../lib/libvtktoken.so.1 (0x000072659a493000)
	libvtkUtilitiesPythonInitializer.so.1 => /opt/paraview/bin/../lib/libvtkUtilitiesPythonInitializer.so.1 (0x000072659c194000)
	libvtkViewsContext2D.so.1 => /usr/lib/libvtkViewsContext2D.so.1 (0x000072659ac84000)
	libvtkViewsCore.so.1 => /usr/lib/libvtkViewsCore.so.1 (0x000072658f573000)
	libvtkvpic.so.1 => /usr/lib/libvtkvpic.so.1 (0x00007265898e4000)
	libvtkWebCore.so.1 => /usr/lib/libvtkWebCore.so.1 (0x000072658f5ca000)
	libvtkWebGLExporter.so.1 => /usr/lib/libvtkWebGLExporter.so.1 (0x000072658f596000)
	libvtkWrappingPythonCore3.12.so.1 => /opt/paraview/bin/../lib/libvtkWrappingPythonCore3.12.so.1 (0x000072659a1bf000)
	libvtkxdmf2.so.1 => /usr/lib/libvtkxdmf2.so.1 (0x00007265858f0000)
	libvtkxdmf3.so.1 => /usr/lib/libvtkxdmf3.so.1 (0x000072658550f000)
	libvtkxdmfcore.so.1 => /usr/lib/libvtkxdmfcore.so.1 (0x0000726584f03000)
	libwebpmux.so.3 => /usr/lib/libwebpmux.so.3 (0x000072657ffac000)
	libwebp.so.7 => /usr/lib/libwebp.so.7 (0x000072657d191000)
	libX11.so.6 => /usr/lib/libX11.so.6 (0x0000726599359000)
	libX11-xcb.so.1 => /usr/lib/libX11-xcb.so.1 (0x0000726572606000)
	libx264.so.164 => /usr/lib/libx264.so.164 (0x0000726573c00000)
	libx265.so.209 => /usr/lib/libx265.so.209 (0x0000726572800000)
	libXau.so.6 => /usr/lib/libXau.so.6 (0x000072658adbd000)
	libxcb-dri3.so.0 => /usr/lib/libxcb-dri3.so.0 (0x000072657178c000)
	libxcb-render.so.0 => /usr/lib/libxcb-render.so.0 (0x0000726571c6b000)
	libxcb-shm.so.0 => /usr/lib/libxcb-shm.so.0 (0x0000726573afb000)
	libxcb.so.1 => /usr/lib/libxcb.so.1 (0x0000726593698000)
	libXcursor.so.1 => /usr/lib/libXcursor.so.1 (0x0000726596230000)
	libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x000072658a861000)
	libxerces-c-3.2.so => /usr/lib/libxerces-c-3.2.so (0x0000726571400000)
	libXext.so.6 => /usr/lib/libXext.so.6 (0x0000726571c7a000)
	libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x000072658a869000)
	libxml2.so.2 => /usr/lib/libxml2.so.2 (0x0000726584134000)
	libXrender.so.1 => /usr/lib/libXrender.so.1 (0x000072658adc2000)
	libxvidcore.so.4 => /usr/lib/libxvidcore.so.4 (0x000072657c6f3000)
	libyaml-cpp.so.0.8 => /usr/lib/../lib/libyaml-cpp.so.0.8 (0x00007265706cd000)
	libzfp.so.1 => /usr/lib/../lib/libzfp.so.1 (0x0000726570877000)
	libzmq.so.5 => /usr/lib/../lib/libzmq.so.5 (0x00007265708c7000)
	libz.so.1 => /usr/lib/libz.so.1 (0x0000726597476000)
	libzstd.so.1 => /usr/lib/libzstd.so.1 (0x0000726590727000)
	linux-vdso.so.1 (0x000072659c4be000)
ldd_paraview_arch_linux (41,014 bytes)   

wyldckat

2024-08-12 16:51

updater   ~0013365

So in principle, the necessary change for a clean path is this:

         export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
                                  ldd $paraviewBinDir/pvserver | \
                                  grep -o "/.*/libvtksys.*.so" | \
                                  xargs dirname | \
                                  xargs realpath)

@peth: If you modify this in the file 'OpenFOAM-12/etc/config.sh/paraview' then run the source command, does it work well, while using Chris' suggestion?
Namely to run the source command like this:

    PATH=/opt/paraview/bin/:$PATH source OpenFOAM-12/etc/bashrc

peth

2024-08-13 10:12

reporter   ~0013369

Yes, sourcing the /etc/bashrc with the proposed modification in /etc/config.sh/paraview script and the suggested PATH extension with /opt/paraview/bin produces no errors. I think in the script it also works with paraview instead of pvserver, i.e.
                export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
                                  ldd $paraviewBinDir/paraview | \
                                  grep -o "/.*/libvtksys.*.so" | \
                                  xargs dirname | \
                                  xargs realpath)

results in also
        echo $ParaView_LIB_DIR/
        /opt/paraview/lib/

as libvtksys can be found in the shared libraries of paraview too.

cgoessni

2024-08-13 11:57

reporter   ~0013371

Yes, but as we anticipated before, headless installs as downloaded from ParaView.org wouldn't contain paraview executable, only pvserver, so going for pvserver seems safer than paraview

wyldckat

2024-08-13 12:07

updater   ~0013372

@peth: Then if 'paraview' works, then we might as well change to something similar to the original search, namely look for 'libpqCore':

                export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
                                  ldd $paraviewBinDir/paraview | \
                                  grep -o "/.*/libpqCore.*.so" | \
                                  xargs dirname | \
                                  xargs realpath)


@chris: So following Peth's feedback, the code I wrote just above should work more generally for system-wide installations of ParaView.

I added the 'realpath' command so that it would unroll the relative paths, as shown at the end of comment #13357: https://bugs.openfoam.org/view.php?id=4126#c13357

All that is missing is some kind of check for whether the 'paraview' binary should be checked with 'ldd' or not. One way to check for it is to use the the 'file' application:

    $ file -b --mime-type $(which paraview)
    application/x-executable

    $ file -b --mime-type Allwmake
    text/x-shellscript

So the check would be something like this:

    pv_filetype=$(file -b --mime-type $paraviewBinDir/paraview)
    if [ "${pv_filetype}" = " ${pv_filetype/application/}" ]
    then

        echo "Warning: '$paraviewBinDir/paraview' is not an application."
        echo "First add to the PATH variable the path to where paraview is installed, then source OpenFOAM's bashrc file again."

        export ParaView_LIB_DIR=

    else

        export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
                          ldd $paraviewBinDir/paraview | \
                          grep -o "/.*/libpqCore.*.so" | \
                          xargs dirname | \
                          xargs realpath)

    fi
    unset pv_filetype

wyldckat

2024-08-13 12:09

updater   ~0013373

@cgoessni: Good point... here is the revised code:

    pv_filetype=$(file -b --mime-type $paraviewBinDir/pvserver)
    if [ "${pv_filetype}" = " ${pv_filetype/application/}" ]
    then

        echo "Warning: '$paraviewBinDir/pvserver' is not an application."
        echo "First add to the PATH variable the path to where 'pvserver' is installed, then source OpenFOAM's bashrc file again."

        export ParaView_LIB_DIR=

    else

        export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
                          ldd $paraviewBinDir/pvserver | \
                          grep -o "/.*/libvtksys.*.so" | \
                          xargs dirname | \
                          xargs realpath)

    fi
    unset pv_filetype

Issue History

Date Modified Username Field Change
2024-08-05 11:17 peth New Issue
2024-08-05 13:02 cgoessni Note Added: 0013336
2024-08-05 13:03 cgoessni Note Added: 0013337
2024-08-05 15:09 chris Note Added: 0013338
2024-08-05 15:45 peth Note Added: 0013339
2024-08-05 17:26 cgoessni Note Added: 0013340
2024-08-05 19:02 peth Note Added: 0013343
2024-08-05 19:28 cgoessni Note Added: 0013344
2024-08-05 19:37 peth Note Added: 0013345
2024-08-05 19:42 cgoessni Note Added: 0013346
2024-08-06 08:24 chris Note Added: 0013347
2024-08-06 08:27 chris Note Added: 0013348
2024-08-06 08:33 chris Note Added: 0013349
2024-08-06 08:42 peth Note Added: 0013351
2024-08-06 08:49 chris Note Added: 0013352
2024-08-06 09:24 peth Note Added: 0013353
2024-08-06 09:42 cgoessni Note Added: 0013354
2024-08-06 10:44 peth Note Added: 0013355
2024-08-06 10:53 cgoessni Note Added: 0013356
2024-08-06 11:07 peth Note Added: 0013357
2024-08-06 11:07 peth File Added: ldd_pvserver_arch_linux
2024-08-06 11:07 peth File Added: ldd_paraview_arch_linux
2024-08-12 16:51 wyldckat Note Added: 0013365
2024-08-13 10:12 peth Note Added: 0013369
2024-08-13 11:57 cgoessni Note Added: 0013371
2024-08-13 12:07 wyldckat Note Added: 0013372
2024-08-13 12:09 wyldckat Note Added: 0013373