Changes between Version 4 and Version 5 of cypress/Singularity

Timestamp:

09/28/22 16:22:40 (3 years ago)

Author:

fuji

Comment:

—

cypress/Singularity

@@ -14 +14 @@
 
 == Run Singularity Container on Cypress ==
+For example, the container built [SingularityDockerhub this page]. In an interactive session by '''idev --partition=centos7''',
+
+{{{
+[fuji@cypress01-013 SingularityTest]$ singularity exec ubuntu_14.04.sif cat /etc/os-release 
+NAME="Ubuntu"
+VERSION="14.04.6 LTS, Trusty Tahr"
+ID=ubuntu
+ID_LIKE=debian
+PRETTY_NAME="Ubuntu 14.04.6 LTS"
+VERSION_ID="14.04"
+HOME_URL="http://www.ubuntu.com/"
+SUPPORT_URL="http://help.ubuntu.com/"
+BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
+}}}
+
+The user in the container is the same as in the host machine.
+
+{{{
+[fuji@cypress01-013 SingularityTest]$ singularity exec ubuntu_14.04.sif whoami
+fuji
+}}}
+
+Singularity has a dedicated syntax to open an interactive shell prompt in a container:
+
+{{{
+[fuji@cypress01-013 SingularityTest]$ singularity shell ubuntu_14.04.sif
+Singularity> pwd
+/home/fuji
+Singularity> whoami
+fuji
+Singularity> cat /etc/os-release
+NAME="Ubuntu"
+VERSION="14.04.6 LTS, Trusty Tahr"
+ID=ubuntu
+ID_LIKE=debian
+PRETTY_NAME="Ubuntu 14.04.6 LTS"
+VERSION_ID="14.04"
+HOME_URL="http://www.ubuntu.com/"
+SUPPORT_URL="http://help.ubuntu.com/"
+BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
+Singularity> exit
+exit
+}}}
+
+=== Use host directories ===
+The container filesystem is read-only, so if you want to write output files you must do it in a bind-mounted host directory.
+'/home/userid' containing data and software are mounted by default.
+
+Following environ variable sets '/lustre/project/hpcstaff/fuji' as '/home/fuji' in the container.
+{{{
+export SINGULARITY_BINDPATH=/lustre/project/hpcstaff/fuji:/home/fuji
+}}}
+
+
+=== Run containters in a batch job ===
+For example,
+{{{
+#!/bin/bash
+#SBATCH --job-name=Singularity # Job Name
+#SBATCH --partition=centos7    # Partition
+#SBATCH --qos=normal           # Quality of Service
+#SBATCH --time=0-00:10:00      # Wall clock time limit in Days-HH:MM:SS
+#SBATCH --nodes=1              # Node count required for the job
+#SBATCH --ntasks-per-node=1    # Number of tasks to be launched per Node
+#SBATCH --cpus-per-task=1     # Number of threads per task (OMP threads)
+
+# Load Singularity module
+module load singularity/3.9.0
+
+# Set $TMPDIR in containar to /tmp, keeping $TMPDIR in host (/local/tmp/...)
+export SINGULARITYENV_TMPDIR=/tmp
+
+# Mount the lustre directory to home, $TMPDIR to /tmp
+export SINGULARITY_BINDPATH=/lustre/project/hpcstaff/fuji:/home/fuji,$TMPDIR:/tmp
+
+# Run container
+singularity exec ubuntu_14.04.sif ls
+}}}
+
 By default, the cache is stored in ~/.singularity; this location can be customized using the environment variable '''SINGULARITY_CACHEDIR'''.
 A subcommand, ''singularity cache'', can be used to manage the cache.