Merge pull request #355 from E3SM-Project/non-block-testing

Non block testing

Author: TonyB9000

tests/base.py

@@ -325,7 +325,7 @@ def add_files(self, use_hpss, zstash_path, keep=False, cache=None):
             expected_present = ["Transferring file to HPSS"]
         else:
             expected_present = ["put: HPSS is unavailable"]
-        expected_present += ["INFO: Creating new tar archive"]
+        expected_present += ["Creating new tar archive"]
         # Make sure none of the old files or directories are moved.
         expected_absent = ["ERROR", "file0", "file_empty", "empty_dir"]
         self.check_strings(cmd, output + err, expected_present, expected_absent)

tests3/README_TEST_BLOCKING

@@ -0,0 +1,103 @@
+
+This document outlines the procedures conducted to test the zstash bloclking
+and non-blocking behavior.
+
+Note: As it was intended to test blocking with regard to archive tar-creations
+vs Globus transfers, it wsa convenient to have both source snd destination be
+the same Globus endpoint.  Effectively, we are employing Globus merely to move
+tar archive files from one directory to another on the same file system.
+
+The core intent in implementing zstash blocking is to address a potential
+"low-disk" condition, where tar-files created to archive source files could
+add substantially to the disk load.  To avoid disk exhaustion, "blocking"
+("--non-blocking" is absent on the command line), tar-file creation will
+pause to wait for the previous tarfile globus transfer to complete, so that
+the local copy can be deleted before the next tar-file is created.
+
+I. File System Setup
+====================
+
+s one may want, or need to re-conduct testing under varied conditions, the
+test script:
+
+    test_zstash_blocking.sh
+
+will establish the following directory structure in the operator's current
+working directory:
+
+    [CWD]/src_data/
+
+            - contains files to be tar-archived.  One can experiment
+              with different sizes of files to trigger behaviors.
+
+    [CWD]/src_data/zstash/
+
+            - default location of tarfiles produced.  This directory is
+              created automatically by zstash unless "--cache" indicates
+              an alternate location.
+
+    [CWD]/dst_data/
+
+            - destination for Globus transfer of archives.
+    
+    [CWD]/tmp_cache/
+
+            - [Optional] alternative location for tar-file generation.
+
+Note: It may be convenient to create a "hold" directory to store files of
+various sizes that can be easily produced by running the supplied scripts.
+
+    gen_data.sh
+    gen_data_runner.sh
+
+The files to be used for a given test must be moved or copied to the src_data
+directory before a test is initiated.
+
+Note:  It never hurts to run the supplied script:
+
+    reset_test.sh
+
+before a test run.  This will delete any archives in the src_data/zstash
+cache and the receiving dst_data directories, and delete the src_data/zstash
+directory itself if it exists.  This ensures a clean restart for testing.
+The rad data files placed into src_data are not affected.
+
+II. Running the Test Script
+===========================
+
+The test script "test_zstash_blocking.sh" accepts two positional parameters:
+
+    test_zstash_blocking.sh (BLOCKING|NON_BLOCKING) [NEW_CREDS]
+
+On an initial run, or whenever Globus complains of authentication failures,
+add "NEW_CREDS" as the second parameter.  This will act to delete your
+cached Globus credentials and trigger prompts for you to paste login URLs
+to your browser (generally one per endpoint) which requires that you conduct
+a login sequence, and then paste a returned key-value at the bash command
+prompt.  After both keys are accepted, you can re-run the test script
+without "NEW_CREDS", until the credentials expire (usually 24 hours.)
+
+If "BLOCKING" is selected, zstash will run in default mode, waiting for
+each tar file to complete transfer before generating another tar file.
+
+If "NON_BLOCKING" is selected, the zstash flag "--non-blocking" is supplied
+to the zstash command line, and tar files continue to be created in parallel
+to running Globus transfers.
+
+It is suggested that you reun the test script with
+
+    test_zstash_blocking.sh (BLOCKING|NON_BLOCKING) > your_logfile 2>&1 
+
+so that your command prompt returns and you can monitor progress with
+
+    snapshot.sh
+
+which will provide a view of both the tarfile cache and the destination
+directory for delivred tar files. It is also suugested that you name your
+logfile to reflect the date, and whether BLOCKING or not.
+
+
+FINAL NOTE:  In the zstash code, the tar file "MINSIZE" parameter is taken
+to be (int) multiples of 1 GB.  During testing, this had been changed to
+"multiple of 100K" for rapid testing.  It may be useful to expose this as
+a command line parameter for debugging purposes.

tests3/gen_data.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+if [[ $# -lt 2 ]]; then
+    echo "Usage: gen_data.sh <bytes> <outputfile>"
+    exit 0
+fi
+
+len=$1
+out=$2
+
+head -c $len </dev/urandom >$out

tests3/gen_data_runner.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+i=1
+
+while [[ $i -lt 12 ]]; do
+    ./gen_data.sh 1000000 small_0${i}_1M
+    i=$((i+1))
+done

tests3/reset_test.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+rm -rf src_data/zstash/
+rm -f dst_data/*
+rm -f tmp_cache/*

tests3/snapshot.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+echo "dst_data:"
+ls -l dst_data
+
+echo ""
+echo "src_data/zstash:"
+ls -l src_data/zstash
+
+echo ""
+echo "tmp_cache:"
+ls -l tmp_cache
+
+

tests3/test_zstash_blocking.sh

@@ -0,0 +1,73 @@
+#!/bin/bash
+
+if [[ $# -lt 1 ]]; then
+    echo "Usage:  text_zstash_blocking.sh (BLOCKING|NON_BLOCKING) [NEW_CREDS]"
+    echo "  One of \"BLOCKING\" or \"NON_BLOCKING\" must be supplied as the"
+    echo "  first parameter."
+    echo "  Add \"NEW_CREDS\" if Globus credentials have expired."
+    echo "  This will cause Globus to prompt for new credentials."
+    exit 0
+fi
+
+NON_BLOCKING=1
+
+if [[ $1 == "BLOCKING" ]]; then
+    NON_BLOCKING=0
+elif [[ $1 == "NON_BLOCKING" ]]; then
+    NON_BLOCKING=1
+else
+    echo "ERROR: Must supply \"BLOCKING\" or \"NON_BLOCKING\" as 1st argument."
+    exit 0
+fi
+
+# remove old auth data, if exists, so that globus will prompt us
+# for new auth credentials in case they have expired:
+if [[ $# -gt 1 ]]; then
+    if [[ $2 == "NEW_CREDS" ]]: then
+        rm -f ~/.globus-native-apps.cfg
+    fi
+fi
+
+
+base_dir=`pwd`
+base_dir=`realpath $base_dir`
+
+
+# See if we are running the zstash we THINK we are:
+echo "CALLING zstash version"
+zstash version
+echo ""
+
+# Selectable Endpoint UUIDs
+ACME1_GCSv5_UUID=6edb802e-2083-47f7-8f1c-20950841e46a
+LCRC_IMPROV_DTN_UUID=15288284-7006-4041-ba1a-6b52501e49f1
+NERSC_HPSS_UUID=9cd89cfd-6d04-11e5-ba46-22000b92c6ec
+
+# 12 piControl ocean monthly files, 49 GB
+SRC_DATA=$base_dir/src_data
+DST_DATA=$base_dir/dst_data
+
+SRC_UUID=$LCRC_IMPROV_DTN_UUID
+DST_UUID=$LCRC_IMPROV_DTN_UUID
+
+# Optional
+TMP_CACHE=$base_dir/tmp_cache
+
+mkdir -p $SRC_DATA $DST_DATA $TMP_CACHE
+
+# Make maxsize 1 GB. This will create a new tar after every 1 GB of data.
+# (Since individual files are 4 GB, we will get 1 tarfile per datafile.)
+
+if [[ $NON_BLOCKING -eq 1 ]]; then
+    echo "TEST: NON_BLOCKING:"
+    zstash create -v --hpss=globus://$DST_UUID/$DST_DATA --maxsize 1 --non-blocking $SRC_DATA
+else
+    echo "TEST: BLOCKING:"
+    zstash create -v --hpss=globus://$DST_UUID/$DST_DATA --maxsize 1 $SRC_DATA
+    # zstash create -v --hpss=globus://$DST_UUID --maxsize 1 --non-blocking --cache $TMP_CACHE $SRC_DATA
+fi
+
+echo "Testing Completed"
+
+exit 0
+

zstash/create.py

@@ -19,6 +19,7 @@
     get_files_to_archive,
     run_command,
     tars_table_exists,
+    ts_utc,
 )
 
 
@@ -37,7 +38,7 @@ def create():
         raise TypeError("Invalid config.hpss={}".format(config.hpss))
 
     # Start doing actual work
-    logger.debug("Running zstash create")
+    logger.debug(f"{ts_utc()}: Running zstash create")
     logger.debug("Local path : {}".format(path))
     logger.debug("HPSS path  : {}".format(hpss))
     logger.debug("Max size  : {}".format(config.maxsize))
@@ -54,11 +55,13 @@ def create():
     if hpss != "none":
         url = urlparse(hpss)
         if url.scheme == "globus":
+            # identify globus endpoints
+            logger.debug(f"{ts_utc()}:Calling globus_activate(hpss)")
             globus_activate(hpss)
         else:
             # config.hpss is not "none", so we need to
             # create target HPSS directory
-            logger.debug("Creating target HPSS directory")
+            logger.debug(f"{ts_utc()}: Creating target HPSS directory {hpss}")
             mkdir_command: str = "hsi -q mkdir -p {}".format(hpss)
             mkdir_error_str: str = "Could not create HPSS directory: {}".format(hpss)
             run_command(mkdir_command, mkdir_error_str)
@@ -71,7 +74,7 @@ def create():
             run_command(ls_command, ls_error_str)
 
     # Create cache directory
-    logger.debug("Creating local cache directory")
+    logger.debug(f"{ts_utc()}: Creating local cache directory")
     os.chdir(path)
     try:
         os.makedirs(cache)
@@ -84,11 +87,14 @@ def create():
     # TODO: Verify that cache is empty
 
     # Create and set up the database
+    logger.debug(f"{ts_utc()}: Calling create_database()")
     failures: List[str] = create_database(cache, args)
 
     # Transfer to HPSS. Always keep a local copy.
+    logger.debug(f"{ts_utc()}: calling hpss_put() for {get_db_filename(cache)}")
     hpss_put(hpss, get_db_filename(cache), cache, keep=True)
 
+    logger.debug(f"{ts_utc()}: calling globus_finalize()")
     globus_finalize(non_blocking=args.non_blocking)
 
     if len(failures) > 0:
@@ -145,7 +151,7 @@ def setup_create() -> Tuple[str, argparse.Namespace]:
     optional.add_argument(
         "--non-blocking",
         action="store_true",
-        help="do not wait for each Globus transfer until it completes.",
+        help="do not wait for each Globus transfer to complete before creating additional archive files.  This option will use more intermediate disk-space, but can increase throughput.",
     )
     optional.add_argument(
         "-v", "--verbose", action="store_true", help="increase output verbosity"
@@ -185,7 +191,7 @@ def setup_create() -> Tuple[str, argparse.Namespace]:
 
 def create_database(cache: str, args: argparse.Namespace) -> List[str]:
     # Create new database
-    logger.debug("Creating index database")
+    logger.debug(f"{ts_utc()}:Creating index database")
     if os.path.exists(get_db_filename(cache)):
         # Remove old database
         os.remove(get_db_filename(cache))
@@ -254,6 +260,7 @@ def create_database(cache: str, args: argparse.Namespace) -> List[str]:
                 args.keep,
                 args.follow_symlinks,
                 skip_tars_md5=args.no_tars_md5,
+                non_blocking=args.non_blocking,
             )
         except FileNotFoundError:
             raise Exception("Archive creation failed due to broken symlink.")
@@ -268,6 +275,7 @@ def create_database(cache: str, args: argparse.Namespace) -> List[str]:
             args.keep,
             args.follow_symlinks,
             skip_tars_md5=args.no_tars_md5,
+            non_blocking=args.non_blocking,
         )
 
     # Close database