Installing Vagrant Mac: bus errors and SSH command responding with a non-zero status

[edwinvanrijn1]

Hello readers,

As I am installing vagrant on my Macbook Pro 2011 (2,4 GHz Intel Core i5, 4GB 1333 MHz DDR3) with OSX High Sierra 10.13.3. Nearly 70 GB storage left on a 160 SATA disk.

Even after following the instructions on the page and in other issues, I do not get it working.
For these instructions I edited the Vagrantfile with

 vbox.memory = 2048
 vbox.gui = true

I included the log from where it went wrong: 'default: installing: libffi-3.0.13-0 ...' went okay but after that errors occur.

Thank you in advance!

default: installing: jpeg-8d-0 ...
default: installing: jsonschema-2.4.0-py27_0 ...
default: installing: libdynd-0.6.5-0 ...
default: installing: libffi-3.0.13-0 ...
default: /home/vagrant/Anaconda-2.3.0-Linux-x86_64.sh: line 240: 10731 Bus error tar xjf ${DIST}.tar.bz2 -C $DIST --no-same-owner
default: /tmp/vagrant-shell: line 37: 10739 Segmentation fault grep -q -i anaconda .bashrc
default: /tmp/vagrant-shell: line 36: /home/vagrant/.bashrc: Read-only file system
default: /tmp/vagrant-shell: line 41: 10740 Bus error wget -q http://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip
default: /tmp/vagrant-shell: line 42: 10742 Bus error unzip -q MCR_R2017b_glnxa64_installer.zip
default: /tmp/vagrant-shell: line 43: ./install: No such file or directory
default: /tmp/vagrant-shell: line 45: /home/vagrant/.bashrc: Read-only file system
default: rm: 
default: cannot remove ‘/tmp/MCR_R2017b_glnxa64_installer.zip’
default: : No such file or directory
default: Installing OpenSMILE
default: /tmp/vagrant-shell: line 51: 10746 Bus error wget -q http://audeering.com/download/1131/ -O OpenSMILE-2.1.tar.gz
default: tar (child): 
default: OpenSMILE-2.1.tar.gz: Cannot open
default: : No such file or directory
default: tar (child): 
default: Error is not recoverable: exiting now
default: tar: 
default: Child returned status 2
default: tar: 
default: Error is not recoverable: exiting now
default: rm: 
default: cannot remove ‘OpenSMILE-2.1.tar.gz’
default: : No such file or directory
default: /tmp/vagrant-shell: line 72: 10751 Bus error git clone http://github.com/riebling/OpenSAT
default: /tmp/vagrant-shell: line 73: 10753 Bus error git clone http://github.com/riebling/ib_diarization_toolkit
default: /tmp/vagrant-shell: line 75: 10755 Bus error git clone http://github.com/riebling/dscore
default: /tmp/vagrant-shell: line 76: 10757 Bus error git clone https://github.com/rajatkuls/lena-clean
default: /tmp/vagrant-shell: line 77: 10759 Bus error git clone https://github.com/ACLEW/TOcomboSAD
default: /tmp/vagrant-shell: line 81: 10761 Bus error git clone https://github.com/aclew/tools.git
default: /tmp/vagrant-shell: line 82: 10763 Bus error git clone https://github.com/aclew/varia.git
default: /tmp/vagrant-shell: line 85: /usr/bin/wget: No such file or directory
default: /tmp/vagrant-shell: line 86: /bin/tar: No such file or directory
default: /tmp/vagrant-shell: line 87: cd: speech_tools: No such file or directory
default: /tmp/vagrant-shell: line 88: ./configure: No such file or directory
default: /tmp/vagrant-shell: line 89: 10768 Bus error make
default: /tmp/vagrant-shell: line 93: /usr/bin/wget: No such file or directory
default: /tmp/vagrant-shell: line 94: /bin/tar: No such file or directory
default: /tmp/vagrant-shell: line 95: cd: festvox: No such file or directory
default: /tmp/vagrant-shell: line 96: ./configure: No such file or directory
default: /tmp/vagrant-shell: line 97: 10773 Bus error make -j 4
default: /tmp/vagrant-shell: line 101: /usr/bin/wget: No such file or directory
default: /tmp/vagrant-shell: line 102: /bin/tar: No such file or directory
default: /tmp/vagrant-shell: line 103: /usr/bin/wget: No such file or directory
default: /tmp/vagrant-shell: line 104: /bin/tar: No such file or directory
default: /tmp/vagrant-shell: line 105: /usr/bin/wget: No such file or directory
default: /tmp/vagrant-shell: line 106: /bin/tar: No such file or directory
default: /tmp/vagrant-shell: line 107: /usr/bin/wget: No such file or directory
default: /tmp/vagrant-shell: line 108: /bin/tar: No such file or directory
default: /tmp/vagrant-shell: line 109: /usr/bin/wget: No such file or directory
default: /tmp/vagrant-shell: line 110: /bin/tar: No such file or directory
default: /tmp/vagrant-shell: line 111: cd: festival: No such file or directory
default: /tmp/vagrant-shell: line 112: ./configure: No such file or directory
default: /tmp/vagrant-shell: line 113: 10786 Bus error make
default: /tmp/vagrant-shell: line 117: 10788 Bus error mkdir LIUM
default: /tmp/vagrant-shell: line 118: cd: LIUM: No such file or directory
default: /tmp/vagrant-shell: line 119: /usr/bin/wget: No such file or directory
default: /tmp/vagrant-shell: line 120: 10791 Bus error gunzip lium_spkdiarization-8.4.1.jar.gz
default: /tmp/vagrant-shell: line 121: 10793 Bus error cp /vagrant/diarization.sh .
default: /tmp/vagrant-shell: line 122: 10795 Bus error ln -s /home/vagrant/tools/eesen-offline-transcriber/models .
default: /tmp/vagrant-shell: line 126: 10797 Bus error mkdir G
default: /tmp/vagrant-shell: line 127: cd: G: No such file or directory
default: /tmp/vagrant-shell: line 128: 10799 Bus error git clone http://github.com/yajiemiao/pdnn
default: /tmp/vagrant-shell: line 129: 10801 Bus error git clone http://github.com/riebling/coconut
default: /tmp/vagrant-shell: line 132: 10803 Bus error cp /vagrant/.theanorc /home/${user}/
default: /tmp/vagrant-shell: line 137: 10805 Segmentation fault sudo -i -u ${user} /home/${user}/anaconda/bin/conda install -y theano=0.8.2
default: /tmp/vagrant-shell: line 141: 10806 Segmentation fault sudo -i -u ${user} /home/${user}/anaconda/bin/pip install pympi-ling tgt intervaltree
default: /tmp/vagrant-shell: line 144: 10807 Segmentation fault sudo -i -u ${user} /home/${user}/anaconda/bin/conda install numpy scipy mkl dill tabulate joblib
default: /tmp/vagrant-shell: line 147: 10808 Bus error mkdir -p /home/${user}/tools
default: /tmp/vagrant-shell: line 148: cd: /home/vagrant/tools: No such file or directory
default: /tmp/vagrant-shell: line 149: 10810 Bus error git clone https://github.com/srvk/srvk-eesen-offline-transcriber
default: /tmp/vagrant-shell: line 150: 10812 Bus error mv srvk-eesen-offline-transcriber eesen-offline-transcriber
default: /tmp/vagrant-shell: line 152: cd: eesen-offline-transcriber: No such file or directory
default: /tmp/vagrant-shell: line 153: 10814 Bus error ln -s /home/${user}/eesen/asr_egs/tedlium/v2-30ms/steps .
default: /tmp/vagrant-shell: line 154: 10816 Bus error ln -s /home/${user}/eesen/asr_egs/tedlium/v2-30ms/utils .
default: /tmp/vagrant-shell: line 157: 10818 Bus error mkdir -p /vagrant/{build,log,transcribe_me,src-audio}
default: /tmp/vagrant-shell: line 159: 10820 Bus error ln -s /vagrant/build /home/${user}/tools/eesen-offline-transcriber/build
default: /tmp/vagrant-shell: line 160: 10822 Bus error ln -s /vagrant/src-audio /home/${user}/tools/eesen-offline-transcriber/src-audio
default: /tmp/vagrant-shell: line 167: 10824 Bus error ln -s /home/${user}/tools/eesen-offline-transcriber /home/${user}/bin
default: /tmp/vagrant-shell: line 170: /usr/bin/yes: No such file or directory
default: /tmp/vagrant-shell: line 171: /usr/sbin/create-munge-key: No such file or directory
default: /tmp/vagrant-shell: line 172: 10828 Bus error mkdir -p /var/run/munge /var/run/slurm-llnl
default: /tmp/vagrant-shell: line 173: 10830 Bus error chown munge:root /var/run/munge
default: /tmp/vagrant-shell: line 174: 10832 Bus error chown slurm:slurm /var/run/slurm-llnl
default: /tmp/vagrant-shell: line 175: /etc/default/munge: No such file or directory
default: /tmp/vagrant-shell: line 176: 10834 Bus error cp /vagrant/conf/slurm.conf /etc/slurm-llnl/slurm.conf
default: /tmp/vagrant-shell: line 177: 10836 Bus error cp /vagrant/conf/reconf-slurm.sh /root/
default: /tmp/vagrant-shell: line 181: 10838 Bus error cp /vagrant/conf/supervisor.conf /etc/supervisor.conf
default: /tmp/vagrant-shell: line 182: 10840 Bus error mkdir -p /etc/supervisor/conf.d
default: /tmp/vagrant-shell: line 183: 10842 Bus error cp /vagrant/conf/slurm.sv.conf /etc/supervisor/conf.d/
default: /tmp/vagrant-shell: line 185: 10844 Bus error apt-get install -y supervisor
default: /tmp/vagrant-shell: line 188: 10846 Bus error sed -i s/Prompt=lts/Prompt=never/ /etc/update-manager/release-upgrades
default: /tmp/vagrant-shell: line 190: /usr/lib/ubuntu-release-upgrader/release-upgrade-motd: No such file or directory
default: /tmp/vagrant-shell: line 193: 10850 Bus error touch /home/${user}/.Xauthority
default: /tmp/vagrant-shell: line 196: 10852 Bus error chown -R ${user}:${user} /home/${user}
The SSH command responded with a non-zero exit status. Vagrant
assumes that this means the command failed. The output for this command
should be in the log above. Please read the output to determine what
went wrong.

[riebling]

The bus error is a pretty serious problem with the virtual machine itself. I would first suggest trying 'vagrant destroy' and running 'vagrant up' again, but also wonder if it's something fundamental about the amount of RAM the VM is requesting, or disk space.

The subsequent errors seem to happen with file writes which also makes me suspect the virtual disk created by VirtualBox has something fundamental wrong, so would also check disk space to make sure there was enough room for it to be created. I looked at my VM and it's virtual disk seems to be 30 GB (that's rather big!) but not only that, there is no provision in the Vagrantfile for setting or limiting the virtual disk size, it seems to come from the base VM image ubuntu/trusty64. Maybe we should warn people the system requires at least this much free space to store the virtual disk!

Lastly (this is just a tiny issue) the latest/greatest version of the VM should be coming from the srvk/DiarizationVM repository, not this one (aclew/DiViMe) though it has no changes that would have resulted in the errors we see here.

Where the error 'read only file system' first appears, that happened because there was a file I/O error and so the filesystem was remounted read-only. Everything after that is noise because of no longer being able to write files :-/