10 Replies Latest reply on Feb 1, 2018 2:36 AM by jakexxh

    libgcc_s.so.1 must be installed for pthread_cancel to work

    jakexxh

      After I go into my conda env,  when I do "conda install opencv", it crashed.

      The error is:

       

      Solving environment: failed

      libgcc_s.so.1 must be installed for pthread_cancel to work

      Aborted

       

      I have no idea to solve it, is there anyone have solutions?

        • 1. Re: libgcc_s.so.1 must be installed for pthread_cancel to work
          Intel Corporation
          This message was posted on behalf of Intel Corporation

          Hi ,
          can i know all steps you have followed from conda environment creation to "conda install opencv" and on which server your executing?

          • 2. Re: libgcc_s.so.1 must be installed for pthread_cancel to work
            jakexxh

            My server is Intel AI DevCloud, my username is u9853

             

            This is the step I followed:

             

            export LD_LIBRARY_PATH="$HOME/.chainer/lib:$HOME/.local/lib:/usr/local/lib"

            export LIBRARY_PATH="$LD_LIBRARY_PATH"

             

            wget https://nchc.dl.sourceforge.net/project/swig/swig/swig-3.0.12/swig-3.0.12.tar.gz && tar -xf swig-3.0.12.tar.gz

             

            cd swig-3.0.12

            ./configure --prefix=/home/[username]/.local

            make -j

            make install

             

            conda create -n chainer_intel intelpython3_core python=3

             

            source activate chainer_intel

             

            pip install --upgrade pip setuptools

             

            pip install wheel six h5py nose protobuf Pillow filelock

             

            git clone -b master_v3 https://github.com/intel/chainer

            cd chainer

            python setup.py install

             

            conda install opencv

            • 3. Re: libgcc_s.so.1 must be installed for pthread_cancel to work
              Intel Corporation
              This message was posted on behalf of Intel Corporation

              Hi
              Can you please append /usr/lib64 to your LD_LIBRARY_PATH & LIBRARY_PATH and then activate environment, try installing opencv with conda.
              if your still getting same error please find the path of libgcc_s.so.1 using below command
              find /usr/ -name "libgcc_s.so.*"
              and append the respective parent path where this file is present to your LD_LIBRARY_PATH & LIBRARY_PATH variables

              • 4. Re: libgcc_s.so.1 must be installed for pthread_cancel to work
                jakexxh

                Hi

                I am sorry that it does not work :-(

                 

                These are my steps:

                1. the path of libgcc_s.so.1 is /usr/lib64

                 

                (chainer_intel1) [u11153@c009 ~]$ find /usr/ -name "libgcc_s.so.*"

                find: ‘/usr/lib/firewalld’: Permission denied

                /usr/lib64/libgcc_s.so.1

                find: ‘/usr/share/polkit-1/rules.d’: Permission denied

                find: ‘/usr/libexec/initscripts/legacy-actions/auditd’: Permission denied

                 

                2. after I append it to LD_LIBRARY_PATH & LIBRARY_PATH

                 

                (chainer_intel1) [u11153@c009 ~]$ echo $LD_LIBRARY_PATH

                /home/u11153/.chainer/lib:/home/u11153/.local/lib:/usr/local/lib:/usr/lib64/

                 

                (chainer_intel1) [u11153@c009 ~]$ echo $LIBRARY_PATH

                /home/u11153/.chainer/lib:/home/u11153/.local/lib:/usr/local/lib:/usr/lib64/

                 

                3. It still crashed

                [u11153@c009 ~]$ source activate chainer_intel1

                (chainer_intel1) [u11153@c009 ~]$ conda install opencv

                Solving environment: \ libgcc_s.so.1 must be installed for pthread_cancel to work

                Aborted

                 

                :-(

                • 5. Re: libgcc_s.so.1 must be installed for pthread_cancel to work
                  Intel Corporation
                  This message was posted on behalf of Intel Corporation

                  Hi ,
                  I am able to execute with same steps.
                  the only difference i found between my steps and your steps are i am appending my environment paths i.e, LD_LIBRARY_PATH ,LIBRARY_PATH  but your setting them. This may have a chance of loosing dependent/default paths. So can you please take new session and try appending paths.

                  • 6. Re: libgcc_s.so.1 must be installed for pthread_cancel to work
                    jakexxh

                    Hi,

                     

                    Thanks for your patience

                    I applied a new server and start a new session, but it still crashed

                     

                    1.

                    [u11152@c009 ~]$ find /usr/ -name "libgcc_s.so.*"

                    find: ‘/usr/lib/firewalld’: Permission denied

                    /usr/lib64/libgcc_s.so.1

                    find: ‘/usr/share/polkit-1/rules.d’: Permission denied

                    find: ‘/usr/libexec/initscripts/legacy-actions/auditd’: Permission denied

                     

                    2.

                    [u11152@c009 ~]$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64

                    [u11152@c009 ~]$ export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib64

                     

                    [u11152@c009 ~]$ echo $LD_LIBRARY_PATH

                    /glob/development-tools/mklml/lib/:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/compiler/lib/intel64:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/compiler/lib/intel64_lin:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/mpi/intel64/lib:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/mpi/mic/lib:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/ipp/lib/intel64:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/compiler/lib/intel64_lin:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64_lin:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/tbb/lib/intel64/gcc4.7:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/tbb/lib/intel64/gcc4.7:/glob/development-tools/versions/intel-parallel-studio-2018/debugger_2018/iga/lib:/glob/development-tools/versions/intel-parallel-studio-2018/debugger_2018/libipt/intel64/lib:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/daal/lib/intel64_lin:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/daal/../tbb/lib/intel64_lin/gcc4.4:/usr/lib64

                     

                    [u11152@c009 ~]$ echo $LIBRARY_PATH

                    /glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/ipp/lib/intel64:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/compiler/lib/intel64_lin:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64_lin:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/tbb/lib/intel64/gcc4.7:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/tbb/lib/intel64/gcc4.7:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/daal/lib/intel64_lin:/glob/development-tools/versions/intel-parallel-studio-2018/compilers_and_libraries_2018.0.128/linux/daal/../tbb/lib/intel64_lin/gcc4.4:/usr/lib64

                     

                    3.

                    [u11152@c009 ~]$ conda create -n chainer_intel intelpython3_core python=3

                    Solving environment: failed

                    libgcc_s.so.1 must be installed for pthread_cancel to work

                    Aborted

                    • 7. Re: libgcc_s.so.1 must be installed for pthread_cancel to work
                      Intel Corporation
                      This message was posted on behalf of Intel Corporation

                      Hi,
                      Can i know your conda path which it is using presently by typing the command
                      which conda
                      and Can you share your .bash_profile file
                      please use new session.

                      • 8. Re: libgcc_s.so.1 must be installed for pthread_cancel to work
                        jakexxh

                        Hi,

                         

                        1. ~/.bash_profile:

                        # .bash_profile

                         

                         

                        # Get the aliases and functions

                        if [ -f ~/.bashrc ]; then

                                . ~/.bashrc

                        fi

                         

                         

                        # User specific environment and startup programs

                        export PATH=$PATH:$HOME/.local/bin:$HOME/bin

                         

                         

                        source /glob/development-tools/parallel-studio/bin/compilervars.sh intel64

                        export INTEL_LICENSE_FILE=/usr/local/licenseserver/psxe.lic

                        export PATH=/glob/intel-python/python3/bin/:/glob/intel-python/python2/bin/:${PATH}

                        export LD_LIBRARY_PATH=/glob/development-tools/mklml/lib/:${LD_LIBRARY_PATH}

                         

                        2. bashrc:

                        #~/ .bashrc

                         

                         

                        # Source global definitions

                        if [ -f /etc/bashrc ]; then

                                . /etc/bashrc

                        fi

                         

                         

                        # Uncomment the following line if you don't like systemctl's auto-paging feature:

                        # export SYSTEMD_PAGER=

                         

                         

                         

                         

                        # User specific aliases and functions

                         

                        3. conda path

                        /glob/intel-python/python3/bin/conda

                        • 9. Re: libgcc_s.so.1 must be installed for pthread_cancel to work
                          Intel Corporation
                          This message was posted on behalf of Intel Corporation

                          Hi, 
                          Please run below command for the usage of  Intel Distribution Pythons
                          conda config --add channels intel
                          And try create conda environment on compute node.
                          command:
                          qsub -I

                          1 of 1 people found this helpful
                          • 10. Re: libgcc_s.so.1 must be installed for pthread_cancel to work
                            jakexxh

                            Thank you so much!

                            It works finally!