cleaning modules
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/a82e34ec Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/a82e34ec Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/a82e34ec Branch: refs/heads/develop Commit: a82e34ec016dd85caebad0192f46ff9bee7bd925 Parents: cdce06d Author: scnakandala <[email protected]> Authored: Fri Nov 4 11:35:49 2016 -0400 Committer: scnakandala <[email protected]> Committed: Fri Nov 4 11:35:49 2016 -0400 ---------------------------------------------------------------------- modules/amqpwstunnel/python/amqpwstunnel.py | 583 -------- modules/amqpwstunnel/python/config.json | 10 - modules/amqpwstunnel/wstest.html | 157 --- modules/simstream/README.md | 18 - modules/simstream/example/README.md | 9 - .../simstream/example/logfile_checker/README.md | 23 - .../example/logfile_checker/generate_logs.sh | 22 - .../example/logfile_checker/log_consumer.py | 43 - .../example/logfile_checker/log_streamer.py | 111 -- .../example/logfile_checker/remote_log.slurm | 21 - .../simstream/example/logfile_checker/test.txt | 657 --------- .../simstream/example/mem_streamer/README.md | 17 - .../example/mem_streamer/memory_consumption.py | 83 -- .../example/mem_streamer/memory_streamer.py | 46 - .../simstream/example/openmm_example/README.md | 33 - .../application/alanine_dipeptide.py | 55 - .../openmm_example/application/input.pdb | 24 - .../openmm_example/application/trajectory.dcd | 0 .../example/openmm_example/openmm_consumer.py | 8 - .../openmm_example/openmm_log_consumer.py | 32 - .../openmm_example/openmm_rmsd_consumer.py | 36 - .../example/openmm_example/openmm_stream.slurm | 19 - .../example/openmm_example/openmm_streamer.py | 130 -- .../simstream/example/openmm_example/test.txt | 0 modules/simstream/example/settings.json | 6 - modules/simstream/setup.py | 19 - modules/simstream/simstream/__init__.py | 11 - modules/simstream/simstream/datacollector.py | 110 -- modules/simstream/simstream/datareporter.py | 169 --- modules/simstream/simstream/eventhandler.py | 17 - modules/simstream/simstream/eventmonitor.py | 46 - .../simstream/simstream/pikaasyncconsumer.py | 203 --- modules/simstream/simstream/pikaproducer.py | 202 --- modules/simstream/simstream/simstream.py | 167 --- modules/xbaya/pom.xml | 329 ----- .../src/main/java/org/airavata/xbaya/App.java | 32 - .../org/airavata/xbaya/ui/home/HomeWindow.java | 42 - .../src/main/resources/images/airavata-2.png | Bin 5582 -> 0 bytes .../main/resources/images/airavata-config.png | Bin 1297 -> 0 bytes .../src/main/resources/images/airavata-icon.png | Bin 584 -> 0 bytes .../main/resources/images/airavata-icon2.png | Bin 981 -> 0 bytes .../src/main/resources/images/airavata-name.png | Bin 8261 -> 0 bytes .../resources/images/airavata-title-text.png | Bin 16438 -> 0 bytes .../src/main/resources/images/airavata.png | Bin 17280 -> 0 bytes .../src/main/resources/images/application.png | Bin 894 -> 0 bytes .../src/main/resources/images/applications.png | Bin 657 -> 0 bytes .../xbaya/src/main/resources/images/closed.gif | Bin 923 -> 0 bytes .../xbaya/src/main/resources/images/cloud.png | Bin 573 -> 0 bytes .../src/main/resources/images/experiment.png | Bin 543 -> 0 bytes .../src/main/resources/images/experiments.png | Bin 1142 -> 0 bytes .../src/main/resources/images/gfac_url.png | Bin 739 -> 0 bytes .../src/main/resources/images/gfac_urls.png | Bin 816 -> 0 bytes .../xbaya/src/main/resources/images/host.png | Bin 652 -> 0 bytes .../xbaya/src/main/resources/images/hosts.png | Bin 671 -> 0 bytes .../src/main/resources/images/input_para.png | Bin 428 -> 0 bytes .../src/main/resources/images/jcr-repo.png | Bin 1010 -> 0 bytes .../xbaya/src/main/resources/images/leaf.gif | Bin 906 -> 0 bytes .../src/main/resources/images/menu/jcr.png | Bin 1158 -> 0 bytes .../src/main/resources/images/menu/new2.png | Bin 1175 -> 0 bytes .../src/main/resources/images/menu/open1.png | Bin 925 -> 0 bytes .../src/main/resources/images/menu/open2.png | Bin 964 -> 0 bytes .../src/main/resources/images/menu/open_dir.png | Bin 749 -> 0 bytes .../src/main/resources/images/menu/pause1.png | Bin 1101 -> 0 bytes .../resources/images/menu/pause_monitor1.png | Bin 873 -> 0 bytes .../src/main/resources/images/menu/play3.png | Bin 1192 -> 0 bytes .../src/main/resources/images/menu/play4.png | Bin 765 -> 0 bytes .../images/menu/resume_monitoring1.png | Bin 957 -> 0 bytes .../src/main/resources/images/menu/save1.png | Bin 1200 -> 0 bytes .../src/main/resources/images/menu/stop.png | Bin 316 -> 0 bytes .../xbaya/src/main/resources/images/opened.gif | Bin 917 -> 0 bytes .../src/main/resources/images/output_para.png | Bin 490 -> 0 bytes .../src/main/resources/images/parameter.png | Bin 544 -> 0 bytes .../xbaya/src/main/resources/images/pause.jpeg | Bin 458 -> 0 bytes .../xbaya/src/main/resources/images/play.jpeg | Bin 471 -> 0 bytes .../src/main/resources/images/registry.png | Bin 3419 -> 0 bytes .../xbaya/src/main/resources/images/service.png | Bin 871 -> 0 bytes .../src/main/resources/images/services.png | Bin 899 -> 0 bytes .../xbaya/src/main/resources/images/step.gif | Bin 211 -> 0 bytes .../xbaya/src/main/resources/images/stop.jpeg | Bin 497 -> 0 bytes .../src/main/resources/images/workflow.png | Bin 601 -> 0 bytes .../resources/images/workflow_templates.png | Bin 710 -> 0 bytes .../src/main/resources/images/workflows.png | Bin 778 -> 0 bytes .../xbaya/src/main/resources/views/home.fxml | 587 -------- .../test/java/org/airavata/xbaya/AppTest.java | 58 - pom.xml | 1301 +++++++++--------- sandbox/amqpwstunnel/python/amqpwstunnel.py | 583 ++++++++ sandbox/amqpwstunnel/python/config.json | 10 + sandbox/amqpwstunnel/wstest.html | 157 +++ sandbox/simstream/README.md | 18 + sandbox/simstream/example/README.md | 9 + .../simstream/example/logfile_checker/README.md | 23 + .../example/logfile_checker/generate_logs.sh | 22 + .../example/logfile_checker/log_consumer.py | 43 + .../example/logfile_checker/log_streamer.py | 111 ++ .../example/logfile_checker/remote_log.slurm | 21 + .../simstream/example/logfile_checker/test.txt | 657 +++++++++ .../simstream/example/mem_streamer/README.md | 17 + .../example/mem_streamer/memory_consumption.py | 83 ++ .../example/mem_streamer/memory_streamer.py | 46 + .../simstream/example/openmm_example/README.md | 33 + .../application/alanine_dipeptide.py | 55 + .../openmm_example/application/input.pdb | 24 + .../openmm_example/application/trajectory.dcd | 0 .../example/openmm_example/openmm_consumer.py | 8 + .../openmm_example/openmm_log_consumer.py | 32 + .../openmm_example/openmm_rmsd_consumer.py | 36 + .../example/openmm_example/openmm_stream.slurm | 19 + .../example/openmm_example/openmm_streamer.py | 130 ++ .../simstream/example/openmm_example/test.txt | 0 sandbox/simstream/example/settings.json | 6 + sandbox/simstream/setup.py | 19 + sandbox/simstream/simstream/__init__.py | 11 + sandbox/simstream/simstream/datacollector.py | 110 ++ sandbox/simstream/simstream/datareporter.py | 169 +++ sandbox/simstream/simstream/eventhandler.py | 17 + sandbox/simstream/simstream/eventmonitor.py | 46 + .../simstream/simstream/pikaasyncconsumer.py | 203 +++ sandbox/simstream/simstream/pikaproducer.py | 202 +++ sandbox/simstream/simstream/simstream.py | 167 +++ 119 files changed, 3738 insertions(+), 4785 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/amqpwstunnel/python/amqpwstunnel.py ---------------------------------------------------------------------- diff --git a/modules/amqpwstunnel/python/amqpwstunnel.py b/modules/amqpwstunnel/python/amqpwstunnel.py deleted file mode 100644 index af5d68a..0000000 --- a/modules/amqpwstunnel/python/amqpwstunnel.py +++ /dev/null @@ -1,583 +0,0 @@ -import argparse -import base64 -import functools -import json -import sys -import uuid -import weakref - -from threading import Thread, Lock - -try: - from urllib.parse import urlencode -except ImportError: - from urllib import urlencode - -import pika -import tornado.websocket -import tornado.ioloop -import tornado.auth -import tornado.escape -import tornado.concurrent - - -SETTINGS = {} - - -class Error(Exception): - """Base error class for exceptions in this module""" - pass - -class ConsumerConfigError(Error): - """Raised when an issue with consumer configuration occurs""" - def __init__(self, message): - self.message = message - -class ConsumerKeyError(Error): - def __init__(self, message, key): - self.message = message - self.key = key - -class AuthError(Error): - """Raised when something went wrong during authentication""" - def __init__(self, error, code): - self.message = error - self.code = code - - - -class PikaAsyncConsumer(Thread): - - """ - The primary entry point for routing incoming messages to the proper handler. - - """ - - def __init__(self, rabbitmq_url, exchange_name, queue_name, - exchange_type="direct", routing_key="#"): - """ - Create a new instance of Streamer. - - Arguments: - rabbitmq_url -- URL to RabbitMQ server - exchange_name -- name of RabbitMQ exchange to join - queue_name -- name of RabbitMQ queue to join - - Keyword Arguments: - exchange_type -- one of 'direct', 'topic', 'fanout', 'headers' - (default 'direct') - routing_keys -- the routing key that this consumer listens for - (default '#', receives all messages) - - """ - print("Creating new consumer") - super(PikaAsyncConsumer, self).__init__(daemon=True) - self._connection = None - self._channel = None - self._shut_down = False - self._consumer_tag = None - self._url = rabbitmq_url - self._client_list = [] - self._lock = Lock() - - # The following are necessary to guarantee that both the RabbitMQ - # server and Streamer know where to look for messages. These names will - # be decided before dispatch and should be recorded in a config file or - # else on a per-job basis. - self._exchange = exchange_name - self._exchange_type = exchange_type - self._queue = queue_name - self._routing_key = routing_key - - def add_client(self, client): - """Add a new client to the recipient list. - - Arguments: - client -- a reference to the client object to add - """ - self._lock.acquire() - # Create a weakref to ensure that cyclic references to WebSocketHandler - # objects do not cause problems for garbage collection - self._client_list.append(weakref.ref(client)) - self._lock.release() - - def remove_client(self, client): - """Remove a client from the recipient list. - - Arguments: - client -- a reference to the client object to remove - """ - self._lock.acquire() - for i in range(0, len(self._client_list)): - # Parentheses after _client_list[i] to deference the weakref to its - # strong reference - if self._client_list[i]() is client: - self._client_list.pop(i) - break - self._lock.release() - - - def connect(self): - """ - Create an asynchronous connection to the RabbitMQ server at URL. - - """ - return pika.SelectConnection(pika.URLParameters(self._url), - on_open_callback=self.on_connection_open, - on_close_callback=self.on_connection_close, - stop_ioloop_on_close=False) - - def on_connection_open(self, unused_connection): - """ - Actions to perform when the connection opens. This may not happen - immediately, so defer action to this callback. - - Arguments: - unused_connection -- the created connection (by this point already - available as self._connection) - - """ - self._connection.channel(on_open_callback=self.on_channel_open) - - def on_connection_close(self, connection, code, text): - """ - Actions to perform when the connection is unexpectedly closed by the - RabbitMQ server. - - Arguments: - connection -- the connection that was closed (same as self._connection) - code -- response code from the RabbitMQ server - text -- response body from the RabbitMQ server - - """ - self._channel = None - if self._shut_down: - self._connection.ioloop.stop() - else: - self._connection.add_timeout(5, self.reconnect) - - def reconnect(self): - """ - Attempt to reestablish a connection with the RabbitMQ server. - """ - self._connection.ioloop.stop() # Stop the ioloop to completely close - - if not self._shut_down: # Connect and restart the ioloop - self._connection = self.connect() - self._connection.ioloop.start() - - def on_channel_open(self, channel): - """ - Store the opened channel for future use and set up the exchange and - queue to be used. - - Arguments: - channel -- the Channel instance opened by the Channel.Open RPC - """ - self._channel = channel - self._channel.add_on_close_callback(self.on_channel_close) - self.declare_exchange() - - - def on_channel_close(self, channel, code, text): - """ - Actions to perform when the channel is unexpectedly closed by the - RabbitMQ server. - - Arguments: - connection -- the connection that was closed (same as self._connection) - code -- response code from the RabbitMQ server - text -- response body from the RabbitMQ server - """ - self._connection.close() - - def declare_exchange(self): - """ - Set up the exchange that will route messages to this consumer. Each - RabbitMQ exchange is uniquely identified by its name, so it does not - matter if the exchange has already been declared. - """ - self._channel.exchange_declare(self.declare_exchange_success, - self._exchange, - self._exchange_type) - - def declare_exchange_success(self, unused_connection): - """ - Actions to perform on successful exchange declaration. - """ - self.declare_queue() - - def declare_queue(self): - """ - Set up the queue that will route messages to this consumer. Each - RabbitMQ queue can be defined with routing keys to use only one - queue for multiple jobs. - """ - self._channel.queue_declare(self.declare_queue_success, - self._queue) - - def declare_queue_success(self, method_frame): - """ - Actions to perform on successful queue declaration. - """ - self._channel.queue_bind(self.munch, - self._queue, - self._exchange, - self._routing_key - ) - - def munch(self, unused): - """ - Begin consuming messages from the Airavata API server. - """ - self._channel.add_on_cancel_callback(self.cancel_channel) - self._consumer_tag = self._channel.basic_consume(self._process_message) - - def cancel_channel(self, method_frame): - if self._channel is not None: - self._channel._close() - - def _process_message(self, ch, method, properties, body): - """ - Receive and verify a message, then pass it to the router. - - Arguments: - ch -- the channel that routed the message - method -- delivery information - properties -- message properties - body -- the message - """ - print("Received Message: %s" % body) - self._lock.acquire() - for client in self._client_list: - # Parentheses after client to deference the weakref to its - # strong reference - client().write_message(body) - self._lock.release() - self._channel.basic_ack(delivery_tag=method.delivery_tag) - - def stop_consuming(self): - """ - Stop the consumer if active. - """ - if self._channel: - self._channel.basic_cancel(self.close_channel, self._consumer_tag) - - def close_channel(self, unused): - """ - Close the channel to shut down the consumer and connection. - """ - self._channel.queue_delete(queue=self._queue) - self._channel.close() - - def run(self): - """ - Start a connection with the RabbitMQ server. - """ - self._connection = self.connect() - self._connection.ioloop.start() - - def stop(self): - """ - Stop an active connection with the RabbitMQ server. - """ - self._closing = True - self.stop_consuming() - - -class Wso2OAuth2Mixin(tornado.auth.OAuth2Mixin): - _OAUTH_AUTHORIZE_URL = "https://idp.scigap.org:9443/oauth2/authorize"; - _OAUTH_ACCESS_TOKEN_URL = "https://idp.scigap.org:9443/oauth2/token"; - - @tornado.auth._auth_return_future - def get_authenticated_user(self, username, password, callback=None): - print("Authenticating user %s" % (username)) - http = self.get_auth_http_client() - body = urlencode({ - "client_id": SETTINGS["oauth_client_key"], - "client_secret": SETTINGS["oauth_client_secret"], - "grant_type": SETTINGS["oauth_grant_type"], - "username": username, - "password": password - }) - http.fetch(self._OAUTH_ACCESS_TOKEN_URL, functools.partial(self._on_access_token, callback), method="POST", body=body) - - def _on_access_token(self, future, response): - if response.error: - print(str(response)) - print(response.body) - print(response.error) - future.set_exception(AuthError(response.error, response.code)) - return - - print(response.body) - future.set_result(tornado.escape.json_decode(response.body)) - -class AuthHandler(tornado.web.RequestHandler, Wso2OAuth2Mixin): - def get_current_user(self): - expires_in = self.get_secure_cookie("expires-in", max_age_days=SETTINGS['maximum_cookie_age']) - print(expires_in) - if expires_in: - return self.get_secure_cookie("ws-auth-token", max_age_days=float(expires_in)) - return None - - def set_default_headers(self): - self.set_header("Content-Type", "text/plain") - self.set_header("Access-Control-Allow-Origin", "*") - self.set_header("Access-Control-Allow-Headers", "x-requested-with") - self.set_header('Access-Control-Allow-Methods', 'POST, GET, OPTIONS') - - def get(self): - if self.get_current_user(): - self.set_status(200) - print("Authenticated") - self.write("Authenticated") - - else: - self.set_status(403) - print("Not Authenticated") - self.write("Not Authenticated") - - @tornado.gen.coroutine - def post(self): - try: - username = self.get_body_argument("username") - password = self.get_body_argument("password") - redirect = self.get_body_argument("redirect") - if username == "" or password == "": - raise tornado.web.MissingArgumentError - - access = yield self.get_authenticated_user(username, password) - days = (access["expires_in"] / 3600) / 24 # Convert to days - print(days) - self.set_secure_cookie("ws-auth-token", - access["access_token"], - expires_days=days) - self.set_secure_cookie("expires-in", - str(1), - expires_days=SETTINGS['maximum_cookie_age']) - self.write("Success") - except tornado.web.MissingArgumentError: - print("Missing an argument") - self.set_status(400) - self.write("Authentication information missing") - except AuthError as e: - print("The future freaks me out") - self.set_status(access.code) - self.set_header("Content-Type", "text/html") - self.write(access.message) - - success_code = """<p>Redirecting to <a href="%(url)s">%(url)s</a></p> -<script type="text/javascript"> -window.location = %(url)s; -</script> - """ % { 'url': redirect} - self.set_status(200) - self.redirect(redirect) - #return self.render_string(success_code) - - - -class AMQPWSHandler(tornado.websocket.WebSocketHandler):#, Wso2OAuth2Mixin): - - """ - Pass messages to a connected WebSockets client. - - A subclass of the Tornado WebSocketHandler class, this class takes no - action when receiving a message from the client. Instead, it is associated - with an AMQP consumer and writes a message to the client each time one is - consumed in the queue. - """ - - # def set_default_headers(self): - # self.set_header("Access-Control-Allow-Origin", "*") - # self.set_header("Access-Control-Allow-Headers", "x-requested-with") - # self.set_header('Access-Control-Allow-Methods', 'POST, GET, OPTIONS') - - def check_origin(self, origin): - """Check the domain origin of the connection request. - - This can be made more robust to ensure that connections are only - accepted from verified PGAs. - - Arguments: - origin -- the value of the Origin HTTP header - """ - return True - - def open(self, resource_type, resource_id): - """Associate a new connection with a consumer. - - When a new connection is opened, it is a request to retrieve data - from an AMQP queue. The open operation should also do some kind of - authentication. - - Arguments: - resource_type -- "experiment" or "project" or "data" - resource_id -- the Airavata id for the resource - """ - self.stream.set_nodelay(True) - self.resource_id = resource_id - self.write_message("Opened the connection") - - self.add_to_consumer() - - # expires_in = self.get_secure_cookie("expires_in", max_age_days=SETTINGS["maximum_cookie_age"]) - # if expires_in is not None and self.get_secure_cookie("ws-auth-token", max_age_days=float(expires_in)): - # print("Found secure cookie") - # self.write_message("Authenticated") - # self.add_to_consumer() - # else: - # print("Closing connection") - # self.close() - - def on_message(self, message): - """Handle incoming messages from the client. - - Tornado requires subclasses to override this method, however in this - case we do not wish to take any action when receiving a message from - the client. The purpose of this class is only to push messages to the - client. - """ - print(message) - message = tornado.escape.json_decode(message) - access = yield self.get_authenticated_user(message["username"], message["password"]) - access = access - days = (access["expires_in"] / 3600) / 24 # Convert to days - print(days) - self.set_secure_cookie("ws-auth-token", - access["access_token"], - expires_days=days) - self.set_secure_cookie("expires_in", - str(days), - expires_days=SETTINGS['maximum_cookie_age']) - - - def on_close(self): - try: - print("Closing connection") - self.application.remove_client_from_consumer(self.resource_id, self) - except KeyError: - print("Error: resource %s does not exist" % self.resource_id) - finally: - self.close() - - def add_to_consumer(self): - try: - self.application.add_client_to_consumer(self.resource_id, self) - except AttributeError as e: - print("Error: tornado.web.Application object is not AMQPWSTunnel") - print(e) - - -class AMQPWSTunnel(tornado.web.Application): - - """ - Send messages from an AMQP queue to WebSockets clients. - - In addition to the standard Tornado Application class functionality, this - class maintains a list of active AMQP consumers and maps WebSocketHandlers - to the correct consumers. - """ - - def __init__(self, consumer_list=None, consumer_config=None, handlers=None, - default_host='', transforms=None, **settings): - print("Starting AMQP-WS-Tunnel application") - super(AMQPWSTunnel, self).__init__(handlers=handlers, - default_host=default_host, - transforms=transforms, - **settings) - - self.consumer_list = {} if consumer_list is None else consumer_list - if consumer_config is None: - raise ConsumerConfigError("No consumer configuration provided") - self.consumer_config = consumer_config - - def consumer_exists(self, resource_id): - """Determine if a consumer exists for a particular resource. - - Arguments: - resource_id -- the consumer to find - """ - return resource_id in self.consumer_list - - def add_client_to_consumer(self, resource_id, client): - """Add a new client to a consumer's messaging list. - - Arguments: - resource_id -- the consumer to add to - client -- the client to add - """ - if not self.consumer_exists(resource_id): - print("Creating new consumer") - print(self.consumer_config) - consumer = PikaAsyncConsumer(self.consumer_config["rabbitmq_url"], - self.consumer_config["exchange_name"], - self.consumer_config["queue_name"], - exchange_type=self.consumer_config["exchange_type"], - routing_key=resource_id) - print("Adding to consumer list") - self.consumer_list[resource_id] = consumer - print("Starting consumer") - consumer.start() - - print("Adding new client to %s" % (resource_id)) - consumer = self.consumer_list[resource_id] - consumer.add_client(client) - - def remove_client_from_consumer(self, resource_id, client): - """Remove a client from a consumer's messaging list. - - Arguments: - resource_id -- the consumer to remove from - client -- the client to remove - """ - if self.consumer_exists(resource_id): - print("Removing client from %s" % (resource_id)) - self.consumer_list[resource_id].remove_client(client) - #else: - # raise ConsumerKeyError("Trying to remove client from nonexistent consumer", resource_id) - - def shutdown(self): - """Shut down the application and release all resources. - - - """ - for name, consumer in self.consumer_list.items(): - consumer.stop() - #consumer.join() - #self.consumer_list[name] = None - - #self.consumer_list = {} - - - -if __name__ == "__main__": - i = open(sys.argv[1]) - config = json.load(i) - i.close() - - SETTINGS["oauth_client_key"] = config["oauth_client_key"] - SETTINGS["oauth_client_secret"] = config["oauth_client_secret"] - SETTINGS["oauth_grant_type"] = config["oauth_grant_type"] - SETTINGS["maximum_cookie_age"] = config["maximum_cookie_age"] - - settings = { - "cookie_secret": base64.b64encode(uuid.uuid4().bytes + uuid.uuid4().bytes), - #"xsrf_cookies": True - } - - application = AMQPWSTunnel(handlers=[ - (r"/auth", AuthHandler), - (r"/(experiment)/(.+)", AMQPWSHandler) - ], - consumer_config=config, - debug=True, - **settings) - - application.listen(8888) - - try: - tornado.ioloop.IOLoop.current().start() - except KeyboardInterrupt: - application.shutdown() http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/amqpwstunnel/python/config.json ---------------------------------------------------------------------- diff --git a/modules/amqpwstunnel/python/config.json b/modules/amqpwstunnel/python/config.json deleted file mode 100644 index b092001..0000000 --- a/modules/amqpwstunnel/python/config.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "rabbitmq_url": "amqp://airavata:[email protected]:5672/messaging", - "exchange_name": "simstream", - "queue_name": "test", - "exchange_type": "direct", - "oauth_client_key": "y7xgdnNUx6ifOswJTPcqtzw4aOEa", - "oauth_client_secret": "CgfbuupAPhaOBSBPSScZUWHNANwa", - "oauth_grant_type": "password", - "maximum_cookie_age": 1 -} http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/amqpwstunnel/wstest.html ---------------------------------------------------------------------- diff --git a/modules/amqpwstunnel/wstest.html b/modules/amqpwstunnel/wstest.html deleted file mode 100644 index eedbf78..0000000 --- a/modules/amqpwstunnel/wstest.html +++ /dev/null @@ -1,157 +0,0 @@ -<!DOCTYPE html> - -<html lang="en"> - -<head> - <meta charset="utf-8" /> - <title>AMQP Websockets Test</title> - - <style> - #content { - width: 100%; - min-height: 250px; - } - - #ws-url-label, #ws-url-input, #ws-connect-button { - display: inline; - float: left; - margin-right: 10px; - } - - #logs { - background-color: #888888; - width: 50%; - overflow-y: auto; - list-style: none; - padding: 3px; - margin-left: auto; - margin-right: auto; - text-align: center; - } - - .log { - background-color: #cccccc; - display: inline-block; - min-height: 30px; - width: 90%; - border: 1px solid #000000; - padding: 3px; - margin-left: auto; - margin-right: auto; - margin-bottom: 5px; - text-align: left; - } - </style> -</head> - -<body> - -<div id="content"> - <div id="ws-url"> - <label id="ws-url-label" for="ws-url-input">WebSockets URL</label> - <input type="text" name="ws-url-input" id="ws-url-input" /> - <input type="text" name="username" id="username" placeholder="Username" /> - <input type="password" name="password" id="password" placeholder="Password" /> - <button id="ws-connect-button" class="open">Connect</button> - <button id="ws-send-credentials">Send</button><br /> - <frame> - <form action="http://localhost:8888/auth"; method="post"> - <input type="text" name="username" id="username" placeholder="Username" /> - <input type="password" name="password" id="password" placeholder="Password" /> - <input type="hidden" name="redirect" id="redirect" value="file:///Users/jeffkinnison/development/amqp-ws-tunnel/wstest.html" /> - <input type="submit" value="Auth" /> - </form> - </frame> - </div> - - <ul id="logs"><p>Logs</p></ul> -</div> - -<script src="https://code.jquery.com/jquery-3.1.0.min.js"; - integrity="sha256-cCueBR6CsyA4/9szpPfrX3s49M9vUU5BgtiJj06wt/s=" - crossorigin="anonymous"></script> -<script type="text/javascript"> - var ws, open_handler, message_handler, error_handler, close_handler; - - console.log(document.cookie); - - $("#ws-connect-button").on("click", function() { - ws = new WebSocket("ws://localhost:8888/experiment/test"); - - ws.onopen = function() { - var username, password; - $("#ws-connect-button").toggleClass("open close").text("Disconnect"); - $("#ws-url-input").prop("disabled", true); - ws.send("hi"); - // username = $("#username").val(); - // password = $("#password").val(); - // ws.send(JSON.stringify({username: username, password: password})); - } - - ws.onmessage = function(e) { - var msg; - - console.log(e.data); - - //msg = JSON.parse(e.data); - // if (msg.hasOwnProperty("logs")) { - // for (log in msg.logs) { - // if (msg.logs.hasOwnProperty(log)) { - // $("#logs").append($('<li class="log">' + log + '</li>')); - // } - // } - // } - } - - ws.onclose = function(e) { - $("#ws-connect-button").toggleClass("open close").text("Connect"); - $("#ws-url-input").prop("disabled", false); - } - }); - - $("#ws-send-credentials").on("click", function(e) { - uname = $("#username").val(); - pass = $("#password").val(); - console.log("Sending credentials"); - //ws.send("moop"); - //ws.send(JSON.stringify({username: uname, password: pass})); - $.ajax({ - url: "http://localhost:8888/auth";, - method: "post", - data: {username: uname, password: pass}, - crossDomain: true, - success: function(data) { - console.log("Success"); - console.log(document.cookie); - }, - error: function(e) { - console.log(e); - }, - complete: function() { - $.ajax({ - url: "http://localhost:8888/auth";, - method: "get", - crossDomain: true, - xhrHeaders: { - - }, - success: function(data) { - console.log(data); - }, - error: function(xhr) { - console.log(xhr); - } - }); - } - }); - }); - - // $("form").on("submit", function(e) { - // e.preventDefault(); - // }); - -</script> - -</body> - -</html> http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/README.md ---------------------------------------------------------------------- diff --git a/modules/simstream/README.md b/modules/simstream/README.md deleted file mode 100755 index 9ab1379..0000000 --- a/modules/simstream/README.md +++ /dev/null @@ -1,18 +0,0 @@ -# simstream -A utility for user-defined remote system and simulation data monitoring. - -## Dependencies -* pika >= 0.10.0 (`pip install pika`) -* A running, accessible instance of RabbitMQ server - -## Installation -1. Clone this repository -2. `python setup.py install` - -## Running the Example -The example runs a simple collector that records the maximum memory used by the server (MB) and a timestamp. It also generates a plot of the results. - -1. Edit `example/memory_consumption.py` and `example/memory_streamer.py` with the correct RabbitMQ settings -2. From the repository root, run `python example/memory_consumption.py` -3. Open a new terminal session and run `python example/memory_streamer.py` -4. Memory usage information should now be collected in the current terminal and received in the original terminal http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/README.md ---------------------------------------------------------------------- diff --git a/modules/simstream/example/README.md b/modules/simstream/example/README.md deleted file mode 100755 index 23f36d5..0000000 --- a/modules/simstream/example/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# SimStream Examples - -This directory contains several examples showcasing the functionality of SimStream. To run them, download and install Python 2.7/3.5, install SimStream using setup.py, and modify the settings.json file to match your RabbitMQ server settings. - -## The Examples - -* mem_streamer: Stream max RSS memory consumed by a basic SimStream utility -* logfile_checker: Collect, filter, and stream tagged log file entries -* openmm_example: Run a molecular dynamics simulation and return log information and system state measured by root mean squared deviation \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/logfile_checker/README.md ---------------------------------------------------------------------- diff --git a/modules/simstream/example/logfile_checker/README.md b/modules/simstream/example/logfile_checker/README.md deleted file mode 100755 index 30ed071..0000000 --- a/modules/simstream/example/logfile_checker/README.md +++ /dev/null @@ -1,23 +0,0 @@ -# SimStream Example: Logfile Streaming - -This example filters log file entries by starting tag and sends them to a remote listener. The listener prints the logs it receives to terminal. - -## Instructions - -### Start the Publisher -1. Open a terminal -2. `cd path/to/simstream/examples/logfile_checker` -3. `python log_streamer.py` - -### Start the Consumer -1. Open a terminal -2. `cd path/to/simstream/examples/logfile_checker` -3. `python log_consumer.py` - -### Write Some Logs -1. Open a terminal -2. `cd path/to/simstream/examples/logfile_checker` -3. `chmod 700 generate_logs.sh` -4. `./generate_logs.sh` - -This will write logs to `test.txt`. The Publisher will continuously check for new logs, filter based on the [STATUS] and [ERROR] tags, and send the filtered results to the RabbitMQ server. The Consumer will receive the filtered log entries and print them to the terminal. http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/logfile_checker/generate_logs.sh ---------------------------------------------------------------------- diff --git a/modules/simstream/example/logfile_checker/generate_logs.sh b/modules/simstream/example/logfile_checker/generate_logs.sh deleted file mode 100755 index 5fb7aa0..0000000 --- a/modules/simstream/example/logfile_checker/generate_logs.sh +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env bash - -outfile="test.txt" - -echo "[STATUS] Starting logfile generator" >> $outfile - -sleep 2 - -echo "[STATUS] Doing stuff" >> $outfile -echo "Stuff that doesn't need to be reported" >> $outfile -echo "Stuff that also doesn't need to be reported" >> $outfile -echo "[DATA] 7.267" >> $outfile - -sleep 2 - -echo "[STATUS] Doing more stuff" >> $outfile -echo "Yet more stuff that doesn't need to be reported" >> $outfile -echo "[ERROR] Some non-fatal error that the user should know about" >> $outfile - -sleep 2 - -echo "[STATUS] Finished generating logs" >> $outfile \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/logfile_checker/log_consumer.py ---------------------------------------------------------------------- diff --git a/modules/simstream/example/logfile_checker/log_consumer.py b/modules/simstream/example/logfile_checker/log_consumer.py deleted file mode 100755 index bf3beac..0000000 --- a/modules/simstream/example/logfile_checker/log_consumer.py +++ /dev/null @@ -1,43 +0,0 @@ -import json -from simstream import PikaAsyncConsumer - -#settings = { -# "url": "amqp://guest:guest@localhost:5672", -# "exchange": "simstream", -# "queue": "test", -# "routing_key": "logfile", -# "exchange_type": "topic" -#} - -settings = {} - -with open("../settings.json", 'r') as f: - settings = json.load(f) - settings["routing_key"] = "memory" - -def print_log_line(body): - try: - lines = json.loads(body.decode()) - if lines is not None: - for line in lines: - print(line) - except json.decoder.JSONDecodeError as e: - print("[Error]: Could not decode %s" % (body)) - except UnicodeError as e: - print("[Error]: Could not decode from bytes to string: %s" % (e.reason)) - - -consumer = PikaAsyncConsumer( - settings["url"], - settings["exchange"], - settings["queue"], - print_log_line, - exchange_type=settings["exchange_type"], - routing_key=settings["routing_key"] - ) - -if __name__ == "__main__": - try: - consumer.start() - except KeyboardInterrupt: - consumer.stop() http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/logfile_checker/log_streamer.py ---------------------------------------------------------------------- diff --git a/modules/simstream/example/logfile_checker/log_streamer.py b/modules/simstream/example/logfile_checker/log_streamer.py deleted file mode 100755 index 65f84f0..0000000 --- a/modules/simstream/example/logfile_checker/log_streamer.py +++ /dev/null @@ -1,111 +0,0 @@ -from simstream import SimStream, DataReporter - -import sys, json - -class LogMonitor(object): - """ - A callable class that returns unprocessed lines in an open logfile. - - Instance Variables: - logfile -- the path to the logfile to monitor - """ - - def __init__(self, logfile): - """ - Set up a monitor for a logfile. - - Arguments: - logfile -- the path to the logfile to monitor - """ - self.logfile = logfile - self._generator = None - self._version = sys.version_info[0] - - def __call__(self): - """ - Get the next line from the logfile. - """ - if not self._generator: - self._generator = self._monitor_logfile() - - lines = [] - - line = self._next() - while line is not None: - lines.append(line) - line = self._next() - - return lines - - def _monitor_logfile(self): - """ - Yield the next set of lines from the logfile. - """ - try: - # Make the file persistent for the lifetime of the generator - with open(self.logfile) as f: - f.seek(0,2) # Move to the end of the file - while True: - # Get the next line or indicate the end of the file - line = f.readline() - if line: - yield line.strip() - else: - yield None - - except EnvironmentError as e: - # Handle I/O exceptions in an OS-agnostic way - print("Error: Could not open file %s: %s" % (self.logfile, e)) - - def _next(self): - """ - Python 2/3 agnostic retrieval of generator values. - """ - return self._generator.__next__() if self._version == 3 else self._generator.next() - - -def get_relevant_log_lines(log_lines): - import re - relevant_lines = [] - pattern = r'^\[(STATUS|ERROR)\]' - for line in log_lines: - if re.match(pattern, line) is not None: - relevant_lines.append(line) - return relevant_lines - - -#settings = { -# "url": "amqp://guest:guest@localhost:5672", -# "exchange": "simstream", -# "queue": "test", -# "routing_key": "logfile", -# "exchange_type": "topic" -#} - -settings = {} - -with open("../settings.json", 'r') as f: - settings = json.load(f) - settings["routing_key"] = "memory" - -if __name__ == "__main__": - logfile = sys.argv[1] - log_reporter = DataReporter() - log_reporter.add_collector("logger", - LogMonitor(logfile), - settings["url"], - settings["exchange"], - limit=10, - interval=2, - exchange_type=settings["exchange_type"], - postprocessor=get_relevant_log_lines) - - log_reporter.start_streaming("logger", settings["routing_key"]) - - streamer = SimStream(config=settings, reporters={"log_reporter": log_reporter}) - streamer.setup() - - try: - streamer.start() - except KeyboardInterrupt: - streamer.stop() http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/logfile_checker/remote_log.slurm ---------------------------------------------------------------------- diff --git a/modules/simstream/example/logfile_checker/remote_log.slurm b/modules/simstream/example/logfile_checker/remote_log.slurm deleted file mode 100644 index 55834e9..0000000 --- a/modules/simstream/example/logfile_checker/remote_log.slurm +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env bash - -#SBATCH -J remote_logger # Job name -#SBATCH -o remote_logger.o%j # Name of stdout output file(%j expands to jobId) -#SBATCH -e remote_logger.o%j # Name of stderr output file(%j expands to jobId) -#SBATCH -p development # large queue for jobs > 256 nodes -#SBATCH -t 00:10:00 # Run time (hh:mm:ss) - 1.5 hours -#SBATCH -n 1 # Nodes to use - -module use "/home1/03947/tg832463/modulefiles" -module load openmm - -touch test.txt - -python log_streamer.py test.txt & - -while true; do - bash generate_logs.sh - sleep 5 -done - http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/logfile_checker/test.txt ---------------------------------------------------------------------- diff --git a/modules/simstream/example/logfile_checker/test.txt b/modules/simstream/example/logfile_checker/test.txt deleted file mode 100755 index 2ffb48c..0000000 --- a/modules/simstream/example/logfile_checker/test.txt +++ /dev/null @@ -1,657 +0,0 @@ -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs -[STATUS] Starting logfile generator -[STATUS] Doing stuff -Stuff that doesn't need to be reported -Stuff that also doesn't need to be reported -[DATA] 7.267 -[STATUS] Doing more stuff -Yet more stuff that doesn't need to be reported -[ERROR] Some non-fatal error that the user should know about -[STATUS] Finished generating logs http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/mem_streamer/README.md ---------------------------------------------------------------------- diff --git a/modules/simstream/example/mem_streamer/README.md b/modules/simstream/example/mem_streamer/README.md deleted file mode 100755 index 897b77a..0000000 --- a/modules/simstream/example/mem_streamer/README.md +++ /dev/null @@ -1,17 +0,0 @@ -# SimStream Example: Memory Usage Streamer - -This example collects data on the memory used by the Publisher and sends that data to the Consumer. - -## Instructions - -### Start the Consumer -1. Open a terminal -2. `cd path/to/simstream/examples/logfile_checker` -3. `python log_consumer.py` - -### Starting the Consumer -1. Open a new terminal -2. `cd path/to/simstream/examples/mem_streamer` -3. `python memory_consumer.py - -The Consumer should receive the memory used by the Publisher (KB) and the time that the data was collected (s since UNIX epoch) at a 2-second interval. http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/mem_streamer/memory_consumption.py ---------------------------------------------------------------------- diff --git a/modules/simstream/example/mem_streamer/memory_consumption.py b/modules/simstream/example/mem_streamer/memory_consumption.py deleted file mode 100755 index b67e975..0000000 --- a/modules/simstream/example/mem_streamer/memory_consumption.py +++ /dev/null @@ -1,83 +0,0 @@ -import tornado.ioloop -import tornado.web -import tornado.websocket - -import json - -from simstream import PikaAsyncConsumer, PikaProducer - -#settings = { -# "url": "amqp://localhost:5672", -# "exchange": "simstream", -# "queue": "remote_node", -# "routing_key": "test", -# "exchange_type": "topic" -#} - -settings = {} - -with open("../settings.json", 'r') as f: - settings = json.load(f) - settings["routing_key"] = "memory" - - -def print_result(body): - try: - data = json.loads(body.decode()) - print("%s: %s" % (data["x"], data["y"])) - except json.decoder.JSONDecodeError as e: - print("[ERROR] Could not decode JSON %s: %s", (body, e)) - except UnicodeError as e: - print("[ERROR] Could not decode message %s: %s" % (body, e.reason)) - -consumer = PikaAsyncConsumer(settings['url'], - settings['exchange'], - settings['queue'], - print_result, - exchange_type=settings['exchange_type'], - routing_key=settings['routing_key']) - -consumer.start() - -# class PlotHandler(tornado.web.RequestHandler): - -# def get(self): -# pass - - -# class StreamingHandler(tornado.websocket.WebSocketHandler): - -# def open(self): -# self.consumer = PikaAsyncConsumer(settings.url, -# settings.exchange, -# settings.queue, -# self.send_data, -# routing_keys=settings.routing_key, -# exchange_type=settings.exchange_type -# ) -# self.producer = PikaProducer("", -# remote_settings.url, -# remote_settings.exchange, -# remote_settings.queue, -# remote_settings.routing_key) - -# def on_message(self, message): -# if hasattr(self, producer) and producer is not None: -# self.producer.send_data(message) - -# def on_close(self): -# self.consumer.stop() -# self.producer.shutdown() -# self.consumer = None -# self.producer = None - -# def send_data(self, ch, method, properties, body): -# self.write_message(body) - -# if __name__ == "__main__": -# app = tornado.web.Application([ -# (r"/plot/(.*)", ) -# (r"/stream/(.*)", StreamingHandler) -# ]) -# app.listen(8888) -# tornado.ioloop.IOLoop.current().start() http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/mem_streamer/memory_streamer.py ---------------------------------------------------------------------- diff --git a/modules/simstream/example/mem_streamer/memory_streamer.py b/modules/simstream/example/mem_streamer/memory_streamer.py deleted file mode 100755 index 88f0d9a..0000000 --- a/modules/simstream/example/mem_streamer/memory_streamer.py +++ /dev/null @@ -1,46 +0,0 @@ -import resource -import time -import json - -from simstream import SimStream, DataReporter, DataCollector - -#settings = { -# "url": "amqp://localhost:5672", -# "exchange": "simstream", -# "queue": "remote_node", -# "routing_key": "stream_sender", -# "exchange_type": "topic" -#} - -settings = {} - -with open("../settings.json", 'r') as f: - settings = json.load(f) - settings["routing_key"] = "memory" - -def mem_callback(): - return {'x': time.time() * 1000, - 'y': resource.getrusage(resource.RUSAGE_SELF).ru_maxrss} - - -def mem_postprocessor(rss): - rss.y = rss.y / 1000000 - return rss - -mem_reporter = DataReporter() -mem_reporter.add_collector("rss", - mem_callback, - settings["url"], - settings["exchange"], - limit=100, - interval=2, - postprocessor=mem_postprocessor, - ) - -mem_reporter.start_streaming("rss", "test") - -if __name__ == "__main__": - resource_streamer = SimStream(reporters={"memory": mem_reporter}, - config=settings) - resource_streamer.setup() - resource_streamer.start() http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/openmm_example/README.md ---------------------------------------------------------------------- diff --git a/modules/simstream/example/openmm_example/README.md b/modules/simstream/example/openmm_example/README.md deleted file mode 100644 index 59a0588..0000000 --- a/modules/simstream/example/openmm_example/README.md +++ /dev/null @@ -1,33 +0,0 @@ -# SimStream Example: Simulating Alanine Dipeptide - -This example runs a simulation of the small molecule Alanine Dipeptide and streams logs and RMSD. RMSD is a metric for judging how similar two molecular states are for the same model. - -## Instructions - -### Installing OpenMM -The easiest way to install OpenMM is to use the Anaconda distribution of Python and run -`conda install -c https://conda.anaconda.org/omnia openmm` - -If you do not wish to use Anaconda, install OpenMM from source by following the instructions in the [OpenMM docs](http://docs.openmm.org/7.0.0/userguide/application.html#installing-openmm "OpenMM documentation") - -### Start the Logfile Consumer -1. Open a terminal -2. `cd path/to/simstream/examples/openmm_example` -3. `python openmm_log_consumer.py` - -### Start the RMSD Consumer -1. Open a terminal -2. `cd path/to/simstream/examples/openmm_example` -3. `python openmm_rmsd_consumer.py` - -### Starting the Producer -1. Open a new terminal -2. `cd path/to/simstream/examples/openmm_example` -3. `python openmm_streamer.py application/sim.out application/trajectory.dcd application/input.pdb application/input.pdb` - -### Starting the Simulation -1. Open a new terminal -2. `cd path/to/simstream/examples/openmm_example/application` -3. `python alanine_dipeptide.py > sim.out` - -The Logfile Consumer should now be printing tagged log entries to the screen; the RMSD Consumer should be printing the calculated RMSD each time the trajectory file is written. http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/openmm_example/application/alanine_dipeptide.py ---------------------------------------------------------------------- diff --git a/modules/simstream/example/openmm_example/application/alanine_dipeptide.py b/modules/simstream/example/openmm_example/application/alanine_dipeptide.py deleted file mode 100644 index 8b22b16..0000000 --- a/modules/simstream/example/openmm_example/application/alanine_dipeptide.py +++ /dev/null @@ -1,55 +0,0 @@ -########################################################################## -# this script was generated by openmm-builder. to customize it further, -# you can save the file to disk and edit it with your favorite editor. -########################################################################## - -from __future__ import print_function -from simtk.openmm import app -import simtk.openmm as mm -from simtk import unit -from sys import stdout - -print("[START] Application is now running") - -pdb = app.PDBFile('input.pdb') -print("[STATUS] Loaded model") -forcefield = app.ForceField('amber03.xml', 'amber03_obc.xml') -print("[STATUS] Loaded force field") - -system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, - constraints=None, rigidWater=False) -print("[STATUS] Created system") -integrator = mm.LangevinIntegrator(300*unit.kelvin, 91/unit.picoseconds, - 1.0*unit.femtoseconds) -print("[STATUS] Created integrator") - -try: - platform = mm.Platform.getPlatformByName('CPU') -except Exception as e: - print("[ERROR] Could not load platform CPU. Running Reference") - platform = mm.Platform.getPlatformByName("Reference") - -simulation = app.Simulation(pdb.topology, system, integrator, platform) -print("[STATUS] Set up compute platform") -simulation.context.setPositions(pdb.positions) -print("[STATUS] Set atomic positions") - -print('[STATUS] Minimizing...') -simulation.minimizeEnergy() -print('[STATUS] Equilibrating...') -simulation.step(100) - -simulation.reporters.append(app.DCDReporter('trajectory.dcd', 1000)) -simulation.reporters.append(app.StateDataReporter(stdout, 1000, step=True, - potentialEnergy=True, totalEnergy=True, temperature=True, separator='\t')) -print("[STATUS] Set up reporters") - -print('[STATUS] Running Production...') - -increment = 1000 - -for i in range(0,100000,increment): - print("[STATUS] Step %s" % (i)) - simulation.step(increment) - -print('[END] Done!') http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/openmm_example/application/input.pdb ---------------------------------------------------------------------- diff --git a/modules/simstream/example/openmm_example/application/input.pdb b/modules/simstream/example/openmm_example/application/input.pdb deleted file mode 100644 index a47f196..0000000 --- a/modules/simstream/example/openmm_example/application/input.pdb +++ /dev/null @@ -1,24 +0,0 @@ -ATOM 1 1HH3 ACE 1 4.300 13.100 8.600 1.00 0.00 -ATOM 2 CH3 ACE 1 5.200 13.600 8.800 1.00 0.00 -ATOM 3 2HH3 ACE 1 4.900 14.300 9.600 1.00 0.00 -ATOM 4 3HH3 ACE 1 5.600 14.200 7.900 1.00 0.00 -ATOM 5 C ACE 1 6.100 12.500 9.400 1.00 0.00 -ATOM 6 O ACE 1 6.400 12.500 10.600 1.00 0.00 -ATOM 7 N ALA 2 6.600 11.600 8.500 1.00 0.00 -ATOM 8 H ALA 2 6.500 11.600 7.500 1.00 0.00 -ATOM 9 CA ALA 2 7.300 10.400 9.100 1.00 0.00 -ATOM 10 HA ALA 2 7.900 10.700 10.000 1.00 0.00 -ATOM 11 CB ALA 2 6.200 9.500 9.600 1.00 0.00 -ATOM 12 HB1 ALA 2 5.700 9.100 8.800 1.00 0.00 -ATOM 13 HB2 ALA 2 6.600 8.700 10.200 1.00 0.00 -ATOM 14 HB3 ALA 2 5.400 10.000 10.200 1.00 0.00 -ATOM 15 C ALA 2 8.400 9.800 8.200 1.00 0.00 -ATOM 16 O ALA 2 8.400 9.900 7.000 1.00 0.00 -ATOM 17 N NME 3 9.300 9.000 8.800 1.00 0.00 -ATOM 18 H NME 3 9.100 9.000 9.800 1.00 0.00 -ATOM 19 CH3 NME 3 10.500 8.400 8.300 1.00 0.00 -ATOM 20 1HH3 NME 3 10.700 7.700 9.100 1.00 0.00 -ATOM 21 2HH3 NME 3 10.400 8.000 7.300 1.00 0.00 -ATOM 22 3HH3 NME 3 11.300 9.100 8.300 1.00 0.00 -TER -ENDMDL http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/openmm_example/application/trajectory.dcd ---------------------------------------------------------------------- diff --git a/modules/simstream/example/openmm_example/application/trajectory.dcd b/modules/simstream/example/openmm_example/application/trajectory.dcd deleted file mode 100644 index e69de29..0000000 http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/openmm_example/openmm_consumer.py ---------------------------------------------------------------------- diff --git a/modules/simstream/example/openmm_example/openmm_consumer.py b/modules/simstream/example/openmm_example/openmm_consumer.py deleted file mode 100644 index 4ba2763..0000000 --- a/modules/simstream/example/openmm_example/openmm_consumer.py +++ /dev/null @@ -1,8 +0,0 @@ -import json -from simstream import PikaAsyncConsumer - -def recv_log(body): - try: - logs = json.loads(body.decode()) - for log in logs: - print(log) \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/openmm_example/openmm_log_consumer.py ---------------------------------------------------------------------- diff --git a/modules/simstream/example/openmm_example/openmm_log_consumer.py b/modules/simstream/example/openmm_example/openmm_log_consumer.py deleted file mode 100644 index e28043f..0000000 --- a/modules/simstream/example/openmm_example/openmm_log_consumer.py +++ /dev/null @@ -1,32 +0,0 @@ -import json -from simstream import PikaAsyncConsumer - -settings = {} - -with open("../settings.json", 'r') as f: - settings = json.load(f) -settings["routing_key"] = "openmm.log" - -def print_log_line(body): - try: - lines = json.loads(body.decode()) - if lines is not None: - for line in lines: - print(line) - except json.decoder.JSONDecodeError as e: - print("[Error]: Could not decode %s" % (body)) - except UnicodeError as e: - print("[Error]: Could not decode from bytes to string: %s" % (e.reason)) - -consumer = PikaAsyncConsumer(settings["url"], - settings["exchange"], - "openmm.log", # settings["queue"], - message_handler=print_log_line, - routing_key=settings["routing_key"], - exchange_type=settings["exchange_type"]) - -if __name__ == "__main__": - try: - consumer.start() - except KeyboardInterrupt: - consumer.stop() http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/openmm_example/openmm_rmsd_consumer.py ---------------------------------------------------------------------- diff --git a/modules/simstream/example/openmm_example/openmm_rmsd_consumer.py b/modules/simstream/example/openmm_example/openmm_rmsd_consumer.py deleted file mode 100644 index f5d87c6..0000000 --- a/modules/simstream/example/openmm_example/openmm_rmsd_consumer.py +++ /dev/null @@ -1,36 +0,0 @@ -import json -from simstream import PikaAsyncConsumer - -settings = {} - -with open("../settings.json", 'r') as f: - settings = json.load(f) -settings["routing_key"] = "openmm.rmsd" - -def print_rmsd(body): - try: - lines = json.loads(body.decode()) - if lines is not None: - for line in lines: - print(line[0]) - except json.decoder.JSONDecodeError as e: - print("[Error]: Could not decode %s" % (body)) - except UnicodeError as e: - print("[Error]: Could not decode from bytes to string: %s" % (e.reason)) - except IndexError as e: - print("[Error]: List is empty") - except KeyError: - print(lines) - -consumer = PikaAsyncConsumer(settings["url"], - settings["exchange"], - "openmm.rmsd", # settings["queue"], - message_handler=print_rmsd, - routing_key=settings["routing_key"], - exchange_type=settings["exchange_type"]) - -if __name__ == "__main__": - try: - consumer.start() - except KeyboardInterrupt: - consumer.stop() http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/openmm_example/openmm_stream.slurm ---------------------------------------------------------------------- diff --git a/modules/simstream/example/openmm_example/openmm_stream.slurm b/modules/simstream/example/openmm_example/openmm_stream.slurm deleted file mode 100644 index 837e4d4..0000000 --- a/modules/simstream/example/openmm_example/openmm_stream.slurm +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env bash - -#SBATCH -J remote_logger # Job name -#SBATCH -o remote_logger.o%j # Name of stdout output file(%j expands to jobId) -#SBATCH -e remote_logger.o%j # Name of stderr output file(%j expands to jobId) -#SBATCH -p development # large queue for jobs > 256 nodes -#SBATCH -t 00:10:00 # Run time (hh:mm:ss) - 1.5 hours -#SBATCH -n 1 # Nodes to use - -#module use "/home1/03947/tg832463/modulefiles" -#module load openmm - -touch test.txt - -python openmm_streamer.py ./application/sim.out ./application/trajectory.dcd ./application/input.pdb ./application/input.pdb & - -cd application -python alanine_dipeptide.py > sim.out -sleep 5
