SW:cctools

cctools

The Cooperative Computing Tools (cctools) is a software package for enabling large scale distributed computing on clusters, clouds, and grids. It is used primarily for attacking large scale problems in science and engineering. "parrot_run" can be used to access CVMFS.

Parrot

Parrot is a tool for attaching existing programs to remote I/O systems through the filesystem interface. Parrot "speaks" a variety of remote I/O services include HTTP, FTP, GridFTP, iRODS, CVMFS, and Chirp on behalf of ordinary programs.

Parrot cache dir is set to /scratch/user/YourNetID/parrot_cache. User can change it's location by updating environment variable PARROT_CVMFS_ALIEN_CACHE prior running "parrot_run" command

export PARROT_CVMFS_ALIEN_CACHE=/scratch/user/YourNetID/my_favorite_cache_dir

Access Parrot

Parrot is available on Terra cluster and it's working on both login nodes and compute nodes. HPRC compute nodes do not have access to internet, thus a proxy server is used when running on the compute nodes.

To access parrot, user can load cctools module

module load cctools/7.0.22-Python-2.7

Alternatively, user can load cctools with Python 3.6 toolchain via

module load cctools/7.0.22-Python-3.7

Parrot examples

In the following examples, the commands are listed in bold face.

User can list CVMFS file system using "parrot_run"

[user@terra1 ~]$ parrot_run ls -lad /cvmfs/cms.cern.ch/slc6_amd64_gcc530
LibCvmfs version 2.4, revision 25
drwxr-xr-x 1 root root 44 Dec 19 05:10 /cvmfs/cms.cern.ch/slc6_amd64_gcc530

User can get a shell with "parrot_run". Please ignore the error of "bash: /usr/bin/mount: Permission denied"

[user@terra1 ~]$ parrot_run bash
2020/02/19 15:03:46.07 parrot_run[17105] <child:17149> notice: warning: system call 316 (renameat2) not supported for program /usr/bin/mv
2020/02/19 15:03:46.38 parrot_run[17105] <child:17178> notice: cannot execute the program /usr/bin/mount because it is setuid.
bash: /usr/bin/mount: Permission denied
[user@terra1 ~]$ ls -l /cvmfs/atlas.cern.ch
LibCvmfs version 2.4, revision 25
total 1
drwxr-xr-x 1 root root 3 Dec  5 08:41 repo

User will get a warning message when running "parrot_run" inside "parrot_run bash"

[user@terra1 ~]$ parrot_run bash
sorry, parrot_run cannot be run inside of itself.
version already running is 7.0.22 FINAL.

User can check if "parrot_run" is running via "parrot_run --is-running" command. If "parrot_run" is not running, no output will be given, otherwise version number will be printed.

[user@terra1 ~]$ parrot_run --is-running
7.0.22 FINAL

User can change prompt for parrot_run to indicate that you are inside a parrot_run shell.

[user@terra1 ~]$ PS1="(Parrot) [\u@terra1 \W]\$ " parrot_run bash --login --noprofile
(Parrot) [user@terra1 ~]$ ls -l /cvmfs/atlas.cern.ch
LibCvmfs version 2.4, revision 25
total 1
drwxr-xr-x 1 root root 3 Dec  5 08:41 repo
(Parrot) [user@terra1 ~]$ exit
logout

Show which filesystems are supported by parrot_run

[user@terra1 ~]$ parrot_run --help | grep Enabled
Enabled filesystems are: chirp ftp cvmfs multi http hdfs grow anonftp

Sample job script for Terra

The sample job script below shows two methods to run parrot_run with list of commands. The first method uses commands listed in an external script and the second methods uses pipe and heredoc (Here document).

#!/bin/bash

##NECESSARY JOB SPECIFICATIONS
#SBATCH --job-name=parrot_test       #Set the job name to "parrot_test"
#SBATCH --time=00:10:00              #Set the wall clock limit to 10min
#SBATCH --ntasks=1                   #Request 1 task
#SBATCH --mem=2560M                  #Request 2560MB (2.5GB) per node
#SBATCH --output=parrot_test.%j      #Send stdout/err to "parrot_test.[jobID]"

echo "start testing..."

# load module
module load cctools

# execute commands listed in "mycommands.sh"
parrot_run $SHELL mycommands.sh

# pipe commands using heredoc (Here document); "EOF" is the delimiting identifier
parrot_run $SHELL << EOF
echo "# test: 'ls /cvmfs/geant4.cern.ch' ..."
ls /cvmfs/geant4.cern.ch
EOF

echo "end of testing..."

References

• CCL software page: https://ccl.cse.nd.edu/software/
• Parrot User Manual: https://cctools.readthedocs.io/en/latest/parrot/