Usage¶
If running on Cori, it is preferable to run from $CSCRATCH rather than
/global/homes. Running from the latter may result in a
‘Resource temporarily unavailable’ error.
Note
If you have not logged into HSI before, you will have to do so before running zstash with HPSS.
On NERSC machines, just run hsi on the command line and enter your credentials.
Note that hsi is only available on the log-in nodes, not the compute nodes.
Note
If you set --hpss=none, there is no need to set --keep, as the former option includes the effects of the latter.
Warning
When specifying files, wildcards should be enclosed in double quotes (e.g., "a*").
Warning
Specifying a high number for --workers will result in slow downloads for each of the tars since your bandwidth
is limited. User discretion is advised.
Create¶
To create a new zstash archive:
$ zstash create --hpss=<path to HPSS> <local path>
where
--hpss=<path to HPSS>specifies the destination path on the HPSS file system where the archive files will be stored. This directory should be unique for each zstash archive. If--hpss=none, then files will be archived locally instead of being transferred to HPSS. Thenoneoption should be used when running Zstash on a machine without HPSS. The option also accepts a Globus URL,globus://<Globus endpoint UUID/<path to archive>. Then zstash will use Globus to store a new zstash archive on a Globus endpoint. Namesalcfandnerscare recognized as referring to the ALCF HPSS and NERSC HPSS endpoints, e.g.globus://nersc/~/my_archive.<local path>specifies the path to the local directory that should be archived.
Additional optional arguments:
--cacheto use a cache other than the default ofzstash. If hpss is--hpss=none, then this will be the archive.--excludecomma separated list of file patterns to exclude--keepto keep a copy of the tar files on the local file system after they have been transferred to HPSS. Normally, they are deleted after successful transfer.--maxsize MAXSIZEspecifies the maximum size (in GB) for tar files. The default is 256 GB. Zstash will create tar files that are smaller than MAXSIZE except when individual input files exceed MAXSIZE (as individual files are never split up between different tar files).-vincreases output verbosity.
Local tar files as well as the sqlite3 index database (index.db) will be stored
under <local path>/zstash.
After you run zstash create it’s highly recommended that you
run zstash check, detailed in the section below.
Basic example¶
To archive output from an E3SM simulation located under $CSCRATCH/ACME_simulations/20170731.F20TR.ne30_ne30.edison:
$ cd $CSCRATCH/ACME_simulations/20170731.F20TR.ne30_ne30.edison
$ zstash create --hpss=test/E3SM_simulations/20170731.F20TR.ne30_ne30.edison .
Once done, you should see the archive files on hsi:
$ hsi
> cd test/E3SM_simulations/20170731.F20TR.ne30_ne30.edison
> ls
000000.tar index.db
The data from this test simulation is small, so in this case there is only a single tar file (000000.tar) and the index database (index.db).
Examples excluding some files¶
You may decide that certain files do not need to be archived. For example, if you want to exclude *.o and *.mod files under the build subdirectory:
$ cd $CSCRATCH/ACME_simulations/20170731.F20TR.ne30_ne30.edison
$ zstash create --hpss=test/ACME_simulations/20170731.F20TR.ne30_ne30.edison \
--exclude="build/*/*.o","build/*/*.mod" .
Or you may decide that you only want to archive restart files every 5 years to conserve storage space:
$ cd $CSCRATCH/ACME_simulations/20170731.F20TR.ne30_ne30.edison
$ zstash create --hpss=test/ACME_simulations/20170731.F20TR.ne30_ne30.edison \
--exclude="archive/rest/???[!05]-*/" .
This exclude pattern will skip all restart subdirectories under the short-term archive, except for those with years ending in ‘0’ or ‘5’.
Example with Globus¶
If you run zstash on the system without the HPSS file system, but has a Globus endpoint set up, you can use a Globus URL:
$ cd $CSCRATCH/ACME_simulations/20170731.F20TR.ne30_ne30.anvil
$ zstash create --hpss=globus://9cd89cfd-6d04-11e5-ba46-22000b92c6ec/~/test/E3SM_simulations/20170731.F20TR.ne30_ne30.anvil .
9cd89cfd-6d04-11e5-ba46-22000b92c6ec is the NERSC HPSS Globus endpoint UUID. Two names nersc and alcf
are recognized by zstash and substituted internally with a corresponding Globus UUID
for the NERSC HPSS Globus endpoint (9cd89cfd-6d04-11e5-ba46-22000b92c6ec) and
the ALCF HPSS Globus endpoint (de463ec4-6d04-11e5-ba46-22000b92c6ec) endpoint.
If you want to store zstash archive on these two remote HPSS file systems, you can use the names instead of UUIDs:
$ zstash create --hpss=globus://nersc/~/test/E3SM_simulations/20170731.F20TR.ne30_ne30.anvil .
Note
If you are a new Globus user, you should first do a small transfer to test functionality.
Note
Always activate Globus endpoints via the Globus web interface before running zstash.
Check¶
Note: Most of the commands for this are the same for zstash extract and zstash ls.
To verify that your files were uploaded on HPSS successfully, go to a new, empty directory and run:
$ zstash check --hpss=<path to HPSS> [--workers=<num of processes>] [--cache=<cache>] [--keep] [-v] [files]
where
--hpss=<path to HPSS>specifies the destination path on the HPSS file system. If--hpss=none, thenzstash checkwill check the cache.--workers=<num of processes>an optional argument which specifies the number of processes to use, resulting in checking being done in parallel. Using a high number will result in slow downloads for each of the tars since your bandwidth is limited. User discretion is advised.--cacheto use a cache other than the default ofzstash.--keepto keep a copy of the tar files on the local file system after they have been extracted from the archive. Normally, they are deleted after successful transfer.--tarsto specify specific tars to check. See below for example usage.-vincreases output verbosity.[files]is a list of files to check (standard wildcards supported).Leave empty to check all the files.
List of files with support for wildcards. Please note that any expression containing wildcards should be enclosed in double quotes (“…”) to avoid shell substitution.
Names of specific tar archives to check all files within these tar archives.
zstash check will download the tar archives to the local disk cache (under
the zstash/ subdirectory) and verify the md5 checksum against the checksum
stored in the index database (index.db).
After the check is complete, a list of all corrupted files in the HPSS archive, along with the tar archive they belong is listed. Below is an example:
INFO: Opening tar archive zstash/000000.tar
INFO: Checking archive/atm/hist/20180129.DECKv1b_piControl.ne30_oEC.edison.cam.h0.0001-01.nc
DEBUG: Valid md5: cfb388d9c4ffe3bf45985fa470855801 archive/atm/hist/20180129.DECKv1b_piControl.ne30_oEC.edison.cam.h0.0001-01.nc
INFO: Checking archive/atm/hist/20180129.DECKv1b_piControl.ne30_oEC.edison.cam.h0.0001-02.nc
DEBUG: Valid md5: ce9bb79fb60fdef2ca4c2c29afc54776 archive/atm/hist/20180129.DECKv1b_piControl.ne30_oEC.edison.cam.h0.0001-02.nc
...
ERROR: Encountered an error for files:
ERROR: archive/atm/hist/20180129.DECKv1b_piControl.ne30_oEC.edison.cam.h0.0214-06.nc in 00000a.tar
ERROR: archive/atm/hist/20180129.DECKv1b_piControl.ne30_oEC.edison.cam.h0.0214-07.nc in 00000a.tar
ERROR: archive/atm/hist/20180129.DECKv1b_piControl.ne30_oEC.edison.cam.h0.0214-08.nc in 00000a.tar
...
ERROR: archive/ocn/hist/mpaso.hist.am.timeSeriesStatsMonthly.0085-08-01.nc in 000029.tar
ERROR: archive/ocn/hist/mpaso.hist.am.timeSeriesStatsMonthly.0085-09-01.nc in 000029.tar
ERROR: The following tar archives had errors:
ERROR: 00000a.tar
ERROR: 000029.tar
If you encounter an error, save your original data.
You may need to reupload it via zstash create.
Please contact the zstash development team, we’re working on
identifying what causes these issues.
Example using --hpss=none:
$ mkdir zstash_demo
$ echo 'file0 stuff' > zstash_demo/file0.txt
$ zstash create --hpss=none zstash_demo
$ ls zstash_demo/
file0.txt zstash
$ ls zstash_demo/zstash/
000000.tar index.db
$ cd zstash_demo
$ zstash check --hpss=none
INFO: Opening tar archive zstash/000000.tar
INFO: Checking file0.txt
INFO: No failures detected when checking the files. If you have a log file, run "grep -i Exception <log-file>" to double check.
Example usage of --tars:
# Starting at 00005a until the end
zstash check --tars=00005a-
# Starting from the beginning to 00005a (included)
zstash check --tars=-00005a
# Specific range
zstash check --tars=00005a-00005c
# Selected tar files
zstash check --tars=00003e,00004e,000059
# Mix and match
zstash check --tars=000030-00003e,00004e,00005a-
Update¶
An existing zstash archive can be updated to add new or modified files:
$ cd <mydir>
$ zstash update --hpss=<path to HPSS> [--cache=<cache>] [--dry-run] [--exclude] [--keep] [-v]
where
--hpss=<path to HPSS>specifies the destination path on the HPSS file system,--cacheto use a cache other than the default ofzstash.--dry-runan optional argument to specify a dry run, only lists files to be updated in archive.--excludean optional argument of comma separated list of file patterns to exclude--keepto keep a copy of the tar files on the local file system after they have been extracted from the archive. Normally, they are deleted after successful transfer.-vincreases output verbosity.
Note: in the event that an update includes revisions to files previously archived, zstash update
will archive the new revisions. zstah extract will only extract the latest revision, but all
file versions will still be listed with the zstash ls and zstash ls -l commands.
Starting with zstash v1.1.0 the md5 hash for the tars will be computed on zstash create.
If you’re using an existing database, then zstash update will begin keeping track
of the tars automatically.
Example¶
Following the ‘zstash create’ example above, we now run zstash again with the ‘update’ functionality:
$ cd $CSCRATCH/ACME_simulations/20170731.F20TR.ne30_ne30.edison
$ zstash update --hpss=test/ACME_simulations/20170731.F20TR.ne30_ne30.edison
Since nothing has changed, zstash simply returns
INFO: Nothing to update
Now, let’s add a new file
$ mkdir new
$ echo "This is a new file..." > new/file.txt
and rerun zstash update
$ zstash update --hpss=test/ACME_simulations/20170731.F20TR.ne30_ne30.edison
Zstash recognizes the presence of a new file and adds it to the archive:
INFO: Gathering list of files to archive
INFO: Creating new tar archive 000001.tar
INFO: Archiving new/file.txt
DEBUG: Closing tar archive 000001.tar
INFO: Transferring file to HPSS: zstash/000001.tar
INFO: Transferring file to HPSS: zstash/index.db
Note that the new file is added into a new archive tar file (000001.tar) even though the first archive tar file (000000.tar) is smaller than the target size and therefore could potentially hold more data. This is a design choice that was made out of caution to avoid the risk of damaging an existing tar file by appending to it.
Extract¶
Note: Most of the commands for this are the same for zstash check and zstash ls.
To extract files from an existing zstash archive into current <mydir>:
$ cd <mydir>
$ zstash extract --hpss=<path to HPSS> [--workers=<num of processes>] [--cache=<cache>] [--keep] [-v] [files]
where
--hpss=<path to HPSS>specifies the destination path on the HPSS file system. Note that if--hpss=none, then--keepis automatically set toTrue. The option also accepts a Globus URL,globus://<Globus endpoint UUID/<path to archive>. Then zstash will use Globus to extract from a zstash archive on a Globus endpoint. Namesalcfandnerscare recognized as referring to the ALCF HPSS and NERSC HPSS endpoints, e.g.globus://nersc/~/my_archive.--workers=<num of processes>an optional argument which specifies the number of processes to use, resulting in extracting being done in parallel. Using a high number will result in slow downloads for each of the tars since your bandwidth is limited. User discretion is advised.--cacheto use a cache other than the default ofzstash.--keepto keep a copy of the tar files on the local file system after they have been extracted from the archive. Normally, they are deleted after successful transfer.--tarsto specify specific tars to extract. See “Check” above for example usage.-vincreases output verbosity.[files]is a list of files to be extracted (standard wildcards supported).Leave empty to extract all the files.
List of files with support for wildcards. Please note that any expression containing wildcards should be enclosed in double quotes (“…”) to avoid shell substitution.
Names of specific tar archives to extract all files within these tar archives.
You must pass in the path relative to the top level for the file(s). For help
finding path names, you can use zstash ls as documented below.
A few words about performance. All of the files are grouped into 256GB tar archives by default.
(See the --maxsize argument for zstash create for more information).
If the tar file is not already present in the local disk cache (under
the zstash/ sub-directory), it must first be downloaded from HPSS before
the desired file can be extracted.
Downloading a 256GB file on Cori/Edison takes about 30 mins (or more depending on load).
Using NERSC data transfer nodes (DTN) may be about 3x faster, according to some users.
Again, to see which of your files are in what tar archives, use
zstash ls -l.
Note the
-largument.The sixth column is the tar archive that the file is in.
Please see the List documentation below for more information.
Examples¶
Extracting a single file by its full path archive/logs/atm.log.8229335.180130-143234.gz
$ zstash extract --hpss=/home/g/golaz/2018/E3SM_simulations/20180129.DECKv1b_piControl.ne30_oEC.edison archive/logs/atm.log.8229335.180130-143234.gz
DEBUG: Opening index database
DEBUG: Running zstash extract
DEBUG: Local path : /global/cscratch1/sd/golaz/ACME_simulations/20180129.DECKv1b_piControl.ne30_oEC.edison
DEBUG: HPSS path : /home/g/golaz/2018/E3SM_simulations/20180129.DECKv1b_piControl.ne30_oEC.edison
DEBUG: Max size : 274877906944
DEBUG: Keep local tar files : False
INFO: Opening tar archive zstash/000018.tar
INFO: Extracting archive/logs/atm.log.8229335.180130-143234.gz
DEBUG: Valid md5: e8161bba53500848dc917258d1d8f56a archive/logs/atm.log.8229335.180130-143234.gz
DEBUG: Closing tar archive zstash/000018.tar
DEBUG: Closing index database
If the index database is already in the local disk cache (zstash/index.db), you can leave out the --hpss
path. For example:
$ zstash extract archive/logs/atm.log.8229335.180130-143234.gz
However, recall that wildcards are supported, so this full path isn’t needed when using them.
Instead, you could download files matching "*atm.log.8229335.180130-143234.gz*". Note
the use of double quotes (“) to avoid shell level substitution.
$ zstash extract --hpss=/home/g/golaz/2018/E3SM_simulations/20180129.DECKv1b_piControl.ne30_oEC.edison "*atm.log.8229335.180130-143234.gz*"
DEBUG: Opening index database
DEBUG: Running zstash extract
DEBUG: Local path : /global/cscratch1/sd/golaz/ACME_simulations/20180129.DECKv1b_piControl.ne30_oEC.edison
DEBUG: HPSS path : /home/g/golaz/2018/E3SM_simulations/20180129.DECKv1b_piControl.ne30_oEC.edison
DEBUG: Max size : 274877906944
DEBUG: Keep local tar files : False
INFO: Opening tar archive zstash/000018.tar
INFO: Extracting archive/logs/atm.log.8229335.180130-143234.gz
DEBUG: Valid md5: e8161bba53500848dc917258d1d8f56a archive/logs/atm.log.8229335.180130-143234.gz
DEBUG: Closing tar archive zstash/000018.tar
INFO: Opening tar archive zstash/000047.tar
INFO: Extracting case_scripts/logs/atm.log.8229335.180130-143234.gz
DEBUG: Valid md5: e8161bba53500848dc917258d1d8f56a case_scripts/logs/atm.log.8229335.180130-143234.gz
DEBUG: Closing tar archive zstash/000047.tar
DEBUG: Closing index database
In this particular example, the pattern matches two specific files, one under archive/logs/ and another one under case_scripts/logs/. If you didn’t intend to retrieve both of them, a more efficient approach would have been to first identify the desired files with ‘zstash ls’.
Another example of wildcards would be to retrieve all cam.h0 (monthly atmosphere output files) between years 0030 and 0069 for the DECKv1 piControl simulation. The zstash command would be:
$ zstash extract --hpss=/home/g/golaz/2018/E3SM_simulations/20180129.DECKv1b_piControl.ne30_oEC.edison \
"*.cam.h0.00[3-6]?-??.nc"
You may specify the cache with the --cache option. Notice that there is no need to include
--keep when not using HPSS.
$ zstash extract --hpss=none \
--cache=/p/user_pub/e3sm/archive/1_1/BGC-v1/20181217.BCRC_CNPCTC20TR_OIBGC.ne30_oECv3.edison \
"*cam.h3.1906-01-*-*.nc"
Example with Globus¶
To extract from the archive created with Globus in the zstash create example, you would run:
$ zstash extract --hpss=globus://9cd89cfd-6d04-11e5-ba46-22000b92c6ec/~/test/E3SM_simulations/20170731.F20TR.ne30_ne30.anvil
List¶
Note: Most of the commands for this are the same for zstash extract and zstash check.
You can view the files in an existing zstash archive:
$ zstash ls --hpss=<path to HPSS> [-l] [--cache=<cache>] [--tars] [-v] [files]
where
--hpss=<path to HPSS>specifies the destination path on the HPSS file system,-lan optional argument to display more information.--cacheto use a cache other than the default ofzstash.--tarsto list the tars in addition to the files.-vincreases output verbosity.[files]is a list of files to be listed (standard wildcards supported).Leave empty to list all the files.
List of files with support for wildcards. Please note that any expression containing wildcards should be enclosed in double quotes (“…”) to avoid shell substitution.
Names of specific tar archives to list all files within these tar archives.
Below is an example. Note the names of the columns:
$ zstash ls -l --hpss=/home/g/golaz/2018/E3SM_simulations/20180129.DECKv1b_piControl.ne30_oEC.edison "*atm.log.8229335.180130-143234.gz*"
DEBUG: Opening index database
DEBUG: Running zstash ls
DEBUG: HPSS path : /home/g/golaz/2018/E3SM_simulations/20180129.DECKv1b_piControl.ne30_oEC.edison
id name size mtime md5 tar offset
30482 archive/logs/atm.log.8229335.180130-143234.gz 20156521 2018-02-01 10:02:35 e8161bba53500848dc917258d1d8f56a 000018.tar 131697281536
51608 case_scripts/logs/atm.log.8229335.180130-143234.gz 20156521 2018-02-01 10:02:52 e8161bba53500848dc917258d1d8f56a 000047.tar 202381473280
Below is an example of using ls to look at the tars in addition to the files:
$ mkdir source_directory
$ touch source_directory/file0.txt
$ zstash create --hpss=hpss_archive source_directory
INFO: Gathering list of files to archive
INFO: Creating new tar archive 000000.tar
INFO: Archiving file0.txt
INFO: tar name=000000.tar, tar size=10240, tar md5=97d3e0ffaff4880251c77699d7438fe2
INFO: Transferring file to HPSS: zstash/000000.tar
INFO: Transferring file to HPSS: zstash/index.db
$ zstash ls --hpss=hpss_archive --tars
INFO: Transferring file from HPSS: zstash/index.db
file0.txt
Tars:
000000.tar
Warning
Running zstash ls outside the source directory (the directory you’re archiving)
is not advised. zstash will only retrieve index.db from the HPSS archive
if a local archive (cache) is not present.
Example 1 – changing the HPSS archive:
$ zstash create --hpss=hpss_archive source_directory # Creates an HPSS archive named `hpss_archive` and a local archive (cache) `source_directory/zstash`.
$ zstash ls --hpss=hpss_archive # List the contents of `hpss_archive` and creates a cache `zstash` at the same level of `source_directory`.
# Add `source_directory/new_file.txt`
$ zstash create --hpss=different_hpss_archive source_directory # Create a different HPSS archive of the source directory. This overwrites the local archive (cache) `source_directory/zstash`.
$ zstash ls --hpss=different_hpss_archive # `new_file.txt` will NOT be shown. The existing cache `zstash` (same level as `source_directory`) is being used.
$ rm -rf zstash # Delete the cache. (You could instead change to another directory).
$ zstash ls --hpss=different_hpss_archive # `new_file.txt` will be shown.
Example 2 – updating the HPSS archive:
$ zstash create --hpss=hpss_archive source_directory # Creates an HPSS archive named `hpss_archive` and a local archive (cache) `source_directory/zstash`.
$ zstash ls --hpss=hpss_archive # List the contents of `hpss_archive` and creates a cache `zstash` at the same level of `source_directory`.
# Add `source_directory/new_file.txt`
$ cd source_directory
$ zstash update --hpss=hpss_archive # Add `new_file.txt` to the HPSS archive. This updates the cache `zstash` (in `source_directory`).
$ cd ..
$ zstash ls --hpss=hpss_archive # `new_file.txt` will NOT be shown. The existing cache `zstash` (same level as `source_directory`) is being used.
$ rm -rf zstash # Delete the cache. (You could instead change to another directory).
$ zstash ls --hpss=hpss_archive # `new_file.txt` will be shown.
Example 3 – changing the HPSS archive, running zstash_ls from the source directory:
$ zstash create --hpss=hpss_archive source_directory # Creates an HPSS archive named `hpss_archive` and a local archive (cache) `source_directory/zstash`.
$ cd source_directory # This is the directory we are archiving.
$ zstash ls --hpss=hpss_archive # List the contents of `hpss_archive` and uses the existing cache `zstash` (in `source_directory`).
# Add `new_file.txt`
$ cd ..
$ zstash create --hpss=different_hpss_archive source_directory # Create a different HPSS archive of the source directory. This overwrites the local archive (cache) `source_directory/zstash`.
$ cd source_directory
$ zstash ls --hpss=different_archive # `new_file.txt` will be shown.
Example 4 – updating the HPSS archive, running zstash_ls from the source directory:
$ zstash create --hpss=hpss_archive source_directory # Creates an HPSS archive named `hpss_archive` and a local archive (cache) `source_directory/zstash`.
$ cd source_directory # This is the directory we are archiving.
$ zstash ls --hpss=hpss_archive # List the contents of `hpss_archive` and uses the existing cache `zstash` (in `source_directory`).
# Add new_file.txt
$ zstash update --hpss=hpss_archive # Add `new_file.txt` to the HPSS archive. This updates the cache `zstash` (in `source_directory`).
$ zstash ls --hpss=hpss_archive # `new_file.txt` will be shown.
Version¶
Starting with version 0.3, you can check the version of zstash from the command line:
$ zstash version
v0.3.0