error while loading shared libraries: libtbb.so.2

[rungitta]

The installation from Bioconda seems to work. But when running Sina I get this error:

(sina) $ sina --help
sina: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory

conda list gives me:

_libgcc_mutex             0.1                        main
_openmp_mutex             4.5                       1_gnu
arb-bio-tools             6.0.6                haa8b8d8_8    bioconda
boost-cpp                 1.70.0               ha2d47e9_1    conda-forge
bzip2                     1.0.8                h7b6447c_0
gettext                   0.21.0               hf68c758_0
glib                      2.68.2               h36276a3_0
icu                       58.2                 he6710b0_3
libarbdb                  6.0.6                haa8b8d8_8    bioconda
libffi                    3.3                  he6710b0_2
libgcc-ng                 9.3.0               h5101ec6_17
libgomp                   9.3.0               h5101ec6_17
libstdcxx-ng              9.3.0               hd4cf53a_17
libxml2                   2.9.12               h03d6c58_0
pcre                      8.45                 h295c915_0
sina                      1.7.2                h9aa86b4_0    bioconda
tbb                       2021.2.0             hff7bd54_0
xz                        5.2.5                h7b6447c_0
zlib                      1.2.11               h7b6447c_3

I try find this file and get this:

(sina) $ find . -name libtbb*
./lib/libtbbmalloc.so.2
./lib/libtbb.so.12
./lib/libtbbmalloc_proxy.so.2.2
./lib/libtbbmalloc.so.2.2
./lib/libtbbmalloc_proxy.so.2
./lib/libtbb.so.12.2

[lucaz88]

I had the same problem and could solve it by simply downgrading the tbb library: conda install tbb=2020.2

[Jeltje]

Your system is missing the tbb library. I fixed mine (on Ubuntu) like so

sudo apt-get install libtbb2

[epruesse]

When SINA is installed from Bioconda, there shouldn't be any client libraries like TBB that come from the system. It's nice that it works for you, @Jeltje, but I'm still considering this a bug. Just need to somehow scrounge up the time to figure it out...

[mapoNW]

I had the same problem. This is how I installed SINA today.

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda create --prefix /vol/tools/sina
conda activate /vol/tools/sina
conda install -c bioconda sina

Arb files were downloaded from SILVA (https://www.arb-silva.de/no_cache/download/archive/release_138.1/ARB_files/) and gunzip, folder in env folder

then I got the same error message as rungitta Then I use the fixe from Jeltje. sudo apt-get install libtbb2 sina --search-cover=all -p 10 --log-file=/path/08_SINA/log_SINA_SSU-query.log -i /path/possible_RNA.fasta -r /path/SILVA_138.1_SSURef_NR99_12_06_20_opt.arb -o /path/SINA_SSUarb_query.csv Then SINA 1.7.2 started to run. I use a deNBI simpleVM with 28 VCPUs (threads) and 256GB RAM. Hope this leads you to the solution.

[adeep028]

I had the same issue after installing fiona module on ubuntu. My earlier rasterio based code as well gdal_translate cli stopped working and started throwing the below error.

from rasterio._base import gdal_version ImportError: libtbb.so.2: cannot open shared object file: No such file or directory

gdal_translate: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory

Executing sudo apt-get install libtbb2 fixed the problem. Thank you @Jeltje

[Daydream0929]

Your system is missing the tbb library. I fixed mine (on Ubuntu) like so

sudo apt-get install libtbb2

thanks a lot, I fixed it on Ubuntu22.04 LTS