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====== Singularity ====== The pulsar group servers (dogmatix0/1 and miraculix/miraculix2) used to have Docker installed. Since Docker needs root permissions to execute, and therefore a security hazard, the service was discontinued on the group servers. Instead, we have decided to use the Singularity container, which can be also be used to run previously built Docker containers without the need for root privileges. Here is a short how-to on getting access to PSRCHIVE/DSPSR based on a previously build Docker container. * If you are in a hurry and have to use psrchive/dspsr, use a prebuilt Singularity container: ''singularity shell -B /fpra/timing/01 /homes/ramesh/dspsr_fits_mt.sif'' * In the above ''-B /fpra/timing/01'' is the directory that needs to visible inside singularity. * Access all other commands/utilities as you normally do: ramesh@dogmatix0 ~ $ singularity shell -B /fpra/timing/01 /homes/ramesh/dspsr_fits_mt.sif bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) Singularity dspsr_fits_mt.sif:~> pwd /homes/ramesh Singularity dspsr_fits_mt.sif:~> cd /fpra/timing/01/MAGNETARS/ Singularity dspsr_fits_mt.sif:/fpra/timing/01/MAGNETARS> cd J1818-1607/PSRIX0/20200314/search/ Singularity dspsr_fits_mt.sif:/fpra/timing/01/MAGNETARS/J1818-1607/PSRIX0/20200314/search> vap -c "freq bw" 2020-03-14-06:37:20.ar filename freq bw 2020-03-14-06:37:20.ar 1358.926 -250.000 Singularity dspsr_fits_mt.sif:/fpra/timing/01/MAGNETARS/J1818-1607/PSRIX0/20200314/search> Note that the container above has only tempo2. ====== Using a docker container under Singularity ====== * Make sure that a prebuilt Docker container exists on Dockerhub * Build a singularity image by: '''singularity pull docker:/ /mpifrpsr/dspsr:fits_mt'''. (**NOTE**: no extra space between the forward slashes - unable to find the escape sequence in this Wiki). * The above will create a singularity image ''dspsr_fits_mt.sif'' in the current directory. ====== Vivek's docker/singularity containers ====== The instructions to use Vivek's container are given here: https://github.com/vivekvenkris/pulsar_docker ====== Henning's Notes ====== A while back Henning gave a tutorial on using singularity. The PDF document is {{:computing:docksing.pdf| here}} ====== Using PRESTO ====== The following is based on a docker container built with the Dockerfile contained in the PRESTO package. git clone https://github.com/scottransom/presto.git cd presto docker build . --tag presto:r4.0 The above image was pushed to bhcpsr's Dockerhub and this can be readily accessed within Singularity: paf0:~> setenv SINGULARITY_TMPDIR /media/titan0/sing paf0:~> singularity shell -e -B /media/titan0/ docker://bhcpsr/presto:r4.0 If you have trouble getting your display to work, try setting the DISPLAY environment variable (as set before firing up the container) and copy $HOME/.Xauthority file to the home directory within the Singularity container.