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Ptool

A tool to manage pools across different sites. With Ptool it is possible to take snap-shot of a pool at regular intervals and compare them to monitor the changes to the pool overtime. These snap-shots can be from the same machine or from different machines. It also provides tools to sync the state between pool on different machines.

Installation

The current approach is to clone the repository on the machine where Ptool needs to installed

git clone https://github.com/esm-tools/pool_tool.git
cd pool_tool

Create a virtual environment, either using conda or pyvenv to install the package.

Using Conda

conda env create -f environment.yml
conda activate ptool
pip install .

Usage

Ptool provides 4 commands to manage the pool.

  • checksums to create snap-shot of the pool
  • summary to get an overview by comparing 2 snap-shots
  • compare to write concrete results of comparing 2 snap-shots
  • prepare-rsync produces script to transfer files from one machine to another

checksums (snap-shot of pool)

Getting the help text to see the all the options

$ ptool checksums --help
Usage: ptool checksums [OPTIONS] PATH

  Calculates imohash checksum of file(s) at the given path. Results are
  presented as csv.

  `--ignore` and `--ignore-dirs` support *wildcards* in filtering down the
  matches.  If no *wildcards* are provided, then it performs a literal match.
  For multiple patterns, use comma separation.

Options:
  --drop-hidden-files / --no-drop-hidden-files
                                  ignore hidden files  [default: drop-hidden-
                                  files]
  --ignore TEXT                   ignore files
  --ignore-dirs TEXT              ignore directories
  -o, --outfile FILENAME          output filename
  --help                          Show this message and exit.

Lets say, Ptool is installed on Levante and the pool to take snap-shot is fesom2 project, then invoke checksum as follows:

$ ptool checksums --ignore-dirs dist_* -o levante_fesom2.csv /pool/data/AWICM/FESOM2
Gathering files...
skipping.. /pool/data/AWICM/FESOM2/FORCING/ERA5 -> /mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted
getting files Elapsed 0.22s
nfiles: 3060
Calculating hashes...
100%|██████████| 3060/3060 [00:01<00:00, 1610.56files/s]
calculating hashes Elapsed 3.21s
Writing results to levante_fesom2.csv

Remote checksums

It is also possible to get the checksums of pool on the remote site. Lets say we are on Albedo machine and want to compare snap-shot for the project fesom2 from both Albedo and Levante then we can also directly invoke checksums command on Levante from Albedo using ssh command as follows:

$ ssh [email protected] "~/miniforge3/envs/ptool/bin/ptool checksums /pool/data/AWICM/FESOM2 --ignore-dirs dist_*" > levante_fesom2.csv
Gathering files...
skipping.. /pool/data/AWICM/FESOM2/FORCING/ERA5 -> /mnt/lustre01/work/ba1138/a270099/era5/forcing/inverted
getting files Elapsed 0.22s
nfiles: 3060
Calculating hashes...
100%|██████████| 3060/3060 [00:01<00:00, 1610.56files/s]
calculating hashes Elapsed 3.21s
Writing results to <stdout>

In the above command, since there is no -o/--outfile option provided, the results are written to <stdout> which is piped to a local file on Albedo. It is also certainly possible to write the snap-shot results to a file on Levante and then copy it over to Albedo. It is up-to the user, how they want to trigger the computation but the main point here is the user is supposed to gather the snap-shots on to the machine where further analysis is carried out.

NOTE: User is free to choose any meaningful name for the csv file as they see fit. The same name is used in displaying the results in the analysis part.

Summary

Lets say we have computed the snap-shot for the project pool fesom2 on both Levante and Albedo, then invoke summary as follows to get a quick overview of the states these pool are in

$ ptool summary --compact levante_fesom2.csv albedo_fesom2.csv

Table 1: Summary with respect to LEVANTE_FESOM2

                 levante_fesom2            albedo_fesom2
---------------  ------------------------  -------------------
pool             FESOM2                    FESOM2
checksum file    levante_fesom2.csv        albedo_fesom2.csv
prefix           /pool/data/AWICM/FESOM2/  /albedo/pool/FESOM2
files            3031 (29.8 TB)            1577 (1.1 TB)
duplicate files  56 (615.2 MB)             167 (5.6 GB)
identical files  547 (44.8 GB)             547 (44.8 GB)
unique files     2458 (29.8 TB)            nan
modified files   nan                       9 (17.5 MB)
----------------------------------------------------------------------

Table 2: Common directory mapping

    rparent_levante_fesom2    rparent_albedo_fesom2
--  ------------------------  ----------------------------
 0  FORCING/CORE2             /forcing/CORE2
 1  INITIAL/phc3.0            /hydrography_dsidoren/phc3.0
 2  MESHES/CORE2              /core2_meanz_broken
 3  MESHES/CORE2/figures      /core2_meanz_broken/figures
 4  MESHES_FESOM2.1/core2     /core2
 5  MESHES_FESOM2.1/hr        /HR
 6  MESHES_FESOM2.1/mr        /mr
----------------------------------------------------------------------

Table 3: LEVANTE_FESOM2 perspective, per directory associations

                       modified      identical  unique      total
---------------------  ----------  -----------  --------  -------
MESHES_FESOM2.1/hr     1                    14  1              16
MESHES_FESOM2.1/mr     1                    14  1              16
MESHES_FESOM2.1/core2  7                    18  11             36
FORCING/CORE2          -                   479  -             479
INITIAL/phc3.0         -                     5  -               5
MESHES/CORE2/figures   -                     8  -               8
MESHES/CORE2           -                     9  -               9
----------------------------------------------------------------------

There are more options available for summary command to alter the results. Use the ptool summary --help to see and investigate other options.

comapre

To get the specifics of the per-files associations, use the compare command as follows

$ ptool compare -o lev_alb_fesom2_cmp.csv levante_fesom2.csv albedo_fesom2.csv 
Writing results as csv to file lev_alb_fesom2_cmp.csv
                                          rpath_left                         rpath_right
flag                                                                                    
identical          FORCING/CORE2/ncar_precip.1948.nc  /forcing/CORE2/ncar_precip.1948.nc
identical          FORCING/CORE2/ncar_precip.1952.nc  /forcing/CORE2/ncar_precip.1952.nc
identical          FORCING/CORE2/ncar_precip.1955.nc  /forcing/CORE2/ncar_precip.1955.nc
identical          FORCING/CORE2/ncar_precip.1953.nc  /forcing/CORE2/ncar_precip.1953.nc
identical          FORCING/CORE2/ncar_precip.1956.nc  /forcing/CORE2/ncar_precip.1956.nc
...                                              ...                                 ...
unique     FORCING/era5/forcing/inverted/t2m.1972.nc                                 NaN
unique     FORCING/era5/forcing/inverted/t2m.1940.nc                                 NaN
unique     FORCING/era5/forcing/inverted/t2m.1948.nc                                 NaN
unique     FORCING/era5/forcing/inverted/t2m.1960.nc                                 NaN
unique     FORCING/era5/forcing/inverted/t2m.1956.nc                                 NaN

[3014 rows x 2 columns]

The comparison results are written to lev_alb_fesom2_cmp.csv file. Explore the contents this file using your favorite editor or search for specific entries using the grep command. For instance, using grep to finding the occurrences of folder MESHES_FESOM2.1/hr

$ grep MESHES_FESOM2.1/hr lev_alb_fesom2_cmp.csv
identical,MESHES_FESOM2.1/hr/edgenum.out,/HR/edgenum.out
identical,MESHES_FESOM2.1/hr/elvls.out,/HR/elvls.out
identical,MESHES_FESOM2.1/hr/hr_griddes_elements.nc,/HR/hr_griddes_elements.nc
identical,MESHES_FESOM2.1/hr/hr_zaxis.txt,/HR/hr_zaxis.txt
identical,MESHES_FESOM2.1/hr/nlvls.out,/HR/nlvls.out
identical,MESHES_FESOM2.1/hr/elem2d.out,/HR/elem2d.out
identical,MESHES_FESOM2.1/hr/hr_griddes_elements_IFS.nc,/HR/hr_griddes_elements_IFS.nc
identical,MESHES_FESOM2.1/hr/nod2d.out,/HR/nod2d.out
identical,MESHES_FESOM2.1/hr/fesom.mesh.diag.nc,/HR/fesom.mesh.diag.nc
identical,MESHES_FESOM2.1/hr/aux3d.out,/HR/aux3d.out
identical,MESHES_FESOM2.1/hr/hr_griddes_nodes.nc,/HR/hr_griddes_nodes.nc
identical,MESHES_FESOM2.1/hr/hr_griddes_nodes_IFS.nc,/HR/hr_griddes_nodes_IFS.nc
identical,MESHES_FESOM2.1/hr/edge_tri.out,/HR/edge_tri.out
identical,MESHES_FESOM2.1/hr/edges.out,/HR/edges.out
modified_latest_right,MESHES_FESOM2.1/hr/README.md,/HR/README.md
unique,MESHES_FESOM2.1/hr/README,

prepare-rsync

This command produces a shell script which contains a list of rsync commands to be executed. Before running the shell script, it is recommended to check the contents of this file to see if prepare-rsync has produced the desired result. User can directly manipulate the shell script to adjust for minor artifacts in-case the options offered by the command does not yield the exact result the user is expecting. Please check out the --help command for details on the options along with few examples of invoking this command.

$ ptool prepare-rsync --help
Usage: ptool prepare-rsync [OPTIONS] LEFT RIGHT

  Prepares rsync commands for the transfer.

  Denpending on where data needs to pushed or pulled, provide either
  `--lefthost` or `--righthost` information to prefix that path.

  Note: when Albedo system is invloved, run this command on Albedo and provide
  the other host information as Albedo can not be reached from other machines.

  Examples that WORK:

  # commands executed on Albedo (i.e., we are on Albedo)

  1. sync data: Levante -> Albedo

     ptool prepare-rsync --lefthost [email protected]
     checksum_levante_fesom2.csv checksum_albedo_fesom2.csv

  2. sync data: Albedo -> Levante

     ptool prepare-rsync --righthost [email protected]
     checksum_albedo_fesom2.csv checksum_levante_fesom2.csv

  Examples that FAIL:

  # commands executed on Levante (i.e., we are on Levante)

  1. sync data: Levante -> Albedo

     ptool prepare-rsync --righthost [email protected]
     checksum_levante_fesom2.csv checksum_albedo_fesom2.csv

     will produce rsync commands as follows:

     rsync /some/path/on/levante [email protected]:/some/path/on/albedo

     Although syntactically correct command, it fails as Albedo is not
     reachable from other machines

  2. sync data: Albedo -> Levante

     ptool prepare-rsync --lefthost [email protected]
     checksum_albedo_fesom2.csv checksum_levante_fesom2.csv

Options:
  --ignore TEXT                   ignores directory and files
  --flags [unique|modified|both]  association type to include
  -t, --threshold FLOAT           minumin value to satisfy valid association
                                  [default: 0.1]
  -l, --lefthost TEXT             username@host prefix to the path for left
                                  file
  -r, --righthost TEXT            username@host prefix to the path for right
                                  file
  --help                          Show this message and exit.

Assuming we are on Albedo and want to transfer the files from Levante to Albedo, invoke the prepare-rsync command as follows:

$ ptool prepare-rsync --lefthost [email protected] levante_fesom2.csv albedo_fesom2.csv 
Created sync_cmd.sh

Verify the contents of sync_cmd.sh before executing the script. It is also possible to directly edit this file to remove selected files from the transaction.

To give a sneak-peak into the sync_cmd.sh file, looking for MESHES_FESOM2.1/hr entry as follows:

$ grep MESHES_FESOM2.1/hr sync_cmd.sh
# MESHES_FESOM2.1/hr
rsync -av --files-from=flist/95087e3b [email protected]:/pool/data/AWICM/FESOM2/MESHES_FESOM2.1/hr/ /albedo/pool/FESOM2/HR/