ImportError: dlopen: cannot load any more object with static TLS

[mkolmus]

To Reproduce

conda create -n test1 python=3 gimmemotifs
conda activate test1 
gimme -h 

Traceback (most recent call last): File "/mbshome/mkolmus/anaconda3/envs/test1/bin/gimme", line 8, in from gimmemotifs.cli import cli File "/mbshome/mkolmus/anaconda3/envs/test1/lib/python3.6/site-packages/gimmemotifs/cli.py", line 11, in from gimmemotifs import commands, version File "/mbshome/mkolmus/anaconda3/envs/test1/lib/python3.6/site-packages/gimmemotifs/commands/init.py", line 15, in "{0}.{1}".format(name, cmdname), globals(), locals(), [cmdname], level File "/mbshome/mkolmus/anaconda3/envs/test1/lib/python3.6/site-packages/gimmemotifs/commands/background.py", line 8, in from gimmemotifs.background import create_background_file File "/mbshome/mkolmus/anaconda3/envs/test1/lib/python3.6/site-packages/gimmemotifs/background.py", line 36, in from gimmemotifs.utils import number_of_seqs_in_file, as_fasta File "/mbshome/mkolmus/anaconda3/envs/test1/lib/python3.6/site-packages/gimmemotifs/utils.py", line 36, in from gimmemotifs.rocmetrics import ks_pvalue File "/mbshome/mkolmus/anaconda3/envs/test1/lib/python3.6/site-packages/gimmemotifs/rocmetrics.py", line 14, in from sklearn.metrics import ( File "/mbshome/mkolmus/anaconda3/envs/test1/lib/python3.6/site-packages/sklearn/init.py", line 83, in from .utils._show_versions import show_versions File "/mbshome/mkolmus/anaconda3/envs/test1/lib/python3.6/site-packages/sklearn/utils/_show_versions.py", line 12, in from ._openmp_helpers import _openmp_parallelism_enabled ImportError: dlopen: cannot load any more object with static TLS

Installation information (please complete the following information):

• OS: Linux
• Installation conda

packages in environment at /mbshome/mkolmus/anaconda3/envs/test1:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 0_gnu conda-forge _py-xgboost-mutex 2.0 cpu_0 conda-forge alsa-lib 1.1.5 h516909a_1002 conda-forge appdirs 1.4.3 py_1 conda-forge arrow-cpp 0.15.1 py36h982ac2c_6 conda-forge attrs 19.3.0 py_0 conda-forge backcall 0.1.0 py_0 conda-forge backports 1.0 py_2 conda-forge bedtools 2.29.2 hc088bd4_0 bioconda biopython 1.76 py36h516909a_0 conda-forge bleach 3.1.0 py_0 conda-forge boltons 20.0.0 py_0 conda-forge boost-cpp 1.70.0 ha2d47e9_1 conda-forge brotli 1.0.7 he1b5a44_1000 conda-forge bucketcache 0.12.1 py36_1 conda-forge bzip2 1.0.8 h516909a_2 conda-forge c-ares 1.15.0 h516909a_1001 conda-forge ca-certificates 2019.11.28 hecc5488_0 conda-forge certifi 2019.11.28 py36_0 conda-forge cffi 1.13.2 py36h8022711_0 conda-forge chardet 3.0.4 py36_1003 conda-forge click 7.0 py_0 conda-forge configparser 3.7.3 py36_1 conda-forge cryptography 2.8 py36h72c5cf5_1 conda-forge curl 7.65.3 hf8cf82a_0 conda-forge cycler 0.10.0 py_2 conda-forge dbus 1.13.6 he372182_0 conda-forge decorator 4.4.1 py_0 conda-forge defusedxml 0.6.0 py_0 conda-forge dinamo 1.0 h78a066a_0 bioconda diskcache 4.0.0 py_0 conda-forge double-conversion 3.1.5 he1b5a44_2 conda-forge entrypoints 0.3 py36_1000 conda-forge expat 2.2.5 he1b5a44_1004 conda-forge feather-format 0.4.0 py_1003 conda-forge fontconfig 2.13.1 he4413a7_1000 conda-forge freetype 2.10.0 he983fc9_1 conda-forge future 0.18.2 py36_0 conda-forge gadem 1.3.1 h470a237_1 bioconda genomepy 0.7.1 py_0 bioconda gettext 0.19.8.1 hc5be6a0_1002 conda-forge gflags 2.2.2 he1b5a44_1002 conda-forge ghostscript 9.22 hf484d3e_1001 conda-forge giflib 5.2.1 h516909a_1 conda-forge gimmemotifs 0.14.1 py36h516909a_1 bioconda glib 2.58.3 py36h6f030ca_1002 conda-forge glog 0.4.0 he1b5a44_1 conda-forge grpc-cpp 1.25.0 h213be95_2 conda-forge gst-plugins-base 1.14.5 h0935bb2_0 conda-forge gstreamer 1.14.5 h36ae1b5_0 conda-forge homer 4.10 pl526hc9558a2_0 bioconda icu 58.2 hf484d3e_1000 conda-forge idna 2.8 py36_1000 conda-forge importlib_metadata 1.4.0 py36_0 conda-forge ipykernel 5.1.3 py36h5ca1d4c_0 conda-forge ipython 7.11.1 py36h5ca1d4c_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.5.1 py_0 conda-forge jedi 0.15.2 py36_0 conda-forge jinja2 2.10.3 py_0 conda-forge joblib 0.14.1 py_0 conda-forge jpeg 9c h14c3975_1001 conda-forge jsonschema 3.2.0 py36_0 conda-forge jupyter_client 5.3.4 py36_1 conda-forge jupyter_core 4.6.1 py36_0 conda-forge kiwisolver 1.1.0 py36hc9558a2_0 conda-forge krb5 1.16.4 h2fd8d38_0 conda-forge lcms2 2.9 hbd6801e_1 conda-forge libblas 3.8.0 14_openblas conda-forge libcblas 3.8.0 14_openblas conda-forge libcurl 7.65.3 hda55be3_0 conda-forge libdeflate 1.5 h516909a_0 conda-forge libedit 3.1.20170329 hf8c457e_1001 conda-forge libevent 2.1.10 h72c5cf5_0 conda-forge libffi 3.2.1 he1b5a44_1006 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 9.2.0 h24d8f2e_2 conda-forge libgfortran-ng 7.3.0 hdf63c60_4 conda-forge libgomp 9.2.0 h24d8f2e_2 conda-forge libiconv 1.15 h516909a_1005 conda-forge liblapack 3.8.0 14_openblas conda-forge libopenblas 0.3.7 h5ec1e0e_6 conda-forge libpng 1.6.37 hed695b0_0 conda-forge libprotobuf 3.11.0 h8b12597_0 conda-forge libsodium 1.0.17 h516909a_0 conda-forge libssh2 1.8.2 h22169c7_2 conda-forge libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge libtiff 4.1.0 hc3755c2_3 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxgboost 0.90 he1b5a44_4 conda-forge libxml2 2.9.9 h13577e0_2 conda-forge libxslt 1.1.32 hae48121_1003 conda-forge logbook 1.5.3 py36h516909a_0 conda-forge logomaker 0.8 py_0 bioconda lz4-c 1.8.3 he1b5a44_1001 conda-forge markupsafe 1.1.1 py36h516909a_0 conda-forge matplotlib 3.1.1 py36_0 conda-forge matplotlib-base 3.1.1 py36hfd891ef_0 conda-forge meme 5.0.5 py36pl526h19b89cf_0 bioconda mistune 0.8.4 py36h516909a_1000 conda-forge more-itertools 8.1.0 py_0 conda-forge mpi 1.0 openmpi conda-forge mysql-connector-c 6.1.11 hc9bbbdd_1005 conda-forge nbconvert 5.6.1 py36_0 conda-forge nbformat 5.0.3 py_0 conda-forge ncurses 6.1 hf484d3e_1002 conda-forge norns 0.1.5 py_0 bioconda nose 1.3.7 py36_1003 conda-forge notebook 6.0.2 py36_0 conda-forge numpy 1.17.5 py36h95a1406_0 conda-forge olefile 0.46 py_0 conda-forge openjdk 11.0.1 h600c080_1018 conda-forge openmpi 4.0.2 hd49bf07_2 conda-forge openssl 1.1.1d h516909a_0 conda-forge pandas 0.25.3 py36hb3f55d8_0 conda-forge pandoc 2.9.1.1 0 conda-forge pandocfilters 1.4.2 py_1 conda-forge parquet-cpp 1.5.1 2 conda-forge parso 0.5.2 py_0 conda-forge pathlib 1.0.1 py36_1 conda-forge patsy 0.5.1 py_0 conda-forge pcre 8.43 he1b5a44_0 conda-forge perl 5.26.2 h516909a_1006 conda-forge perl-algorithm-cluster 1.58 pl526h14c3975_0 bioconda perl-app-cpanminus 1.7044 pl526_1 bioconda perl-base 2.23 pl526_1 bioconda perl-carp 1.38 pl526_3 bioconda perl-cgi 4.44 pl526h14c3975_1 bioconda perl-common-sense 3.74 pl526_2 bioconda perl-constant 1.33 pl526_1 bioconda perl-dbi 1.642 pl526_0 bioconda perl-encode 2.88 pl526_1 bioconda perl-exporter 5.72 pl526_1 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-file-path 2.16 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-file-which 1.23 pl526_0 bioconda perl-html-parser 3.72 pl526h6bb024c_5 bioconda perl-html-tagset 3.20 pl526_3 bioconda perl-html-template 2.97 pl526_1 bioconda perl-html-tree 5.07 pl526_1 bioconda perl-json 4.02 pl526_0 bioconda perl-json-xs 2.34 pl526h6bb024c_3 bioconda perl-log-log4perl 1.49 pl526_0 bioconda perl-math-cdf 0.1 pl526h14c3975_5 bioconda perl-parent 0.236 pl526_1 bioconda perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-xml-namespacesupport 1.12 pl526_0 bioconda perl-xml-parser 2.44_01 pl526ha1d75be_1002 conda-forge perl-xml-sax 1.02 pl526_0 bioconda perl-xml-sax-base 1.09 pl526_0 bioconda perl-xml-sax-expat 0.51 pl526_3 bioconda perl-xml-simple 2.25 pl526_1 bioconda perl-xsloader 0.24 pl526_0 bioconda perl-yaml 1.29 pl526_0 bioconda pexpect 4.7.0 py36_0 conda-forge pickleshare 0.7.5 py36_1000 conda-forge pillow 7.0.0 py36hefe7db6_0 conda-forge pip 19.3.1 py36_0 conda-forge prometheus_client 0.7.1 py_0 conda-forge prompt_toolkit 3.0.2 py_0 conda-forge prosampler 1.0 hc9558a2_0 bioconda psutil 5.6.7 py36h516909a_0 conda-forge pthread-stubs 0.4 h14c3975_1001 conda-forge ptyprocess 0.6.0 py_1001 conda-forge py-xgboost 0.90 py36_4 conda-forge pyarrow 0.15.1 py36h8b68381_1 conda-forge pybedtools 0.8.1 py36he513fc3_0 bioconda pycparser 2.19 py36_1 conda-forge pyfaidx 0.5.8 py_1 bioconda pygments 2.5.2 py_0 conda-forge pyopenssl 19.1.0 py36_0 conda-forge pyparsing 2.4.6 py_0 conda-forge pyqt 5.9.2 py36hcca6a23_4 conda-forge pyrsistent 0.15.7 py36h516909a_0 conda-forge pysam 0.15.4 py36hbcae180_0 bioconda pysocks 1.7.1 py36_0 conda-forge python 3.6.7 h357f687_1006 conda-forge python-dateutil 2.8.1 py_0 conda-forge python-xxhash 1.4.1 py36h516909a_0 conda-forge pytz 2019.3 py_0 conda-forge pyyaml 5.1.2 py36h516909a_0 conda-forge pyzmq 18.1.1 py36h1768529_0 conda-forge qt 5.9.7 h52cfd70_2 conda-forge re2 2020.01.01 he1b5a44_0 conda-forge readline 8.0 hf8c457e_0 conda-forge represent 1.6.0 py36h516909a_0 conda-forge requests 2.22.0 py36_1 conda-forge scikit-learn 0.22.1 py36hcdab131_1 conda-forge scipy 1.4.1 py36h921218d_0 conda-forge seaborn 0.9.0 py_2 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 45.1.0 py36_0 conda-forge sip 4.19.8 py36hf484d3e_1000 conda-forge six 1.14.0 py36_0 conda-forge sklearn-contrib-lightning 0.5.0 py36_0 conda-forge snappy 1.1.7 he1b5a44_1003 conda-forge sqlite 3.30.1 hcee41ef_0 conda-forge statsmodels 0.10.2 py36hc1659b7_0 conda-forge terminado 0.8.3 py36_0 conda-forge testpath 0.4.4 py_0 conda-forge thrift-cpp 0.12.0 hf3afdfd_1004 conda-forge tk 8.6.10 hed695b0_0 conda-forge tornado 6.0.3 py36h516909a_0 conda-forge tqdm 4.41.1 py_0 conda-forge traitlets 4.3.3 py36_0 conda-forge trawler 2.0 3 bioconda ucsc-bedtogenepred 377 h35c10e6_0 bioconda ucsc-bigbedtobed 357 1 bioconda ucsc-genepredtobed 377 h35c10e6_2 bioconda ucsc-genepredtogtf 377 h35c10e6_2 bioconda ucsc-gff3togenepred 357 1 bioconda ucsc-gtftogenepred 377 h35c10e6_2 bioconda uriparser 0.9.3 he1b5a44_1 conda-forge urllib3 1.25.7 py36_0 conda-forge wcwidth 0.1.8 py_0 conda-forge webencodings 0.5.1 py_1 conda-forge weeder 2.0 h6bb024c_3 bioconda wheel 0.33.6 py36_0 conda-forge widgetsnbextension 3.5.1 py36_0 conda-forge xdg 4.0.1 py_1 conda-forge xgboost 0.90 py36he1b5a44_4 conda-forge xmltodict 0.12.0 py_0 conda-forge xorg-fixesproto 5.0 h14c3975_1002 conda-forge xorg-inputproto 2.3.2 h14c3975_1002 conda-forge xorg-kbproto 1.0.7 h14c3975_1002 conda-forge xorg-libx11 1.6.9 h516909a_0 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.3 h516909a_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxfixes 5.0.3 h516909a_1004 conda-forge xorg-libxi 1.7.10 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-libxtst 1.2.3 h516909a_1002 conda-forge xorg-recordproto 1.14.2 h516909a_1002 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h14c3975_1007 conda-forge xxmotif 1.6 h2d50403_2 bioconda xz 5.2.4 h14c3975_1001 conda-forge yaml 0.1.7 h14c3975_1001 conda-forge zeromq 4.3.2 he1b5a44_2 conda-forge zipp 1.0.0 py_0 conda-forge zlib 1.2.11 h516909a_1006 conda-forge zstd 1.4.4 h3b9ef0a_1 conda-forge

Additional context Add any other context about the problem here.

[simonvh]

I think it is this issue: pytorch/pytorch#2575 (comment)

The Ubuntu version on mbscourse is indeed Trusty, which is not supported anymore by Ubuntu. @Maarten-vd-Sande @mkolmus can you try if this command solves it:

LD_PRELOAD=~/anaconda3/lib/libgomp.sov

(replace /anaconda3/ with your anaconda install directory)

[Maarten-vd-Sande]

This seems to fix it for me on mbscourse :tada:

[simonvh]

Great. I'll add it to the FAQ.