New Statistical Algorithms for the Analysis of Mass - FU Berlin, FB MI ...

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128 CHAPTER 5. COMPUTER SCIENCE GRID STRATEGIES 5.3.4 Monitoring One of the central features of the QAD Grid platform are the monitoring functions and reactions on events such as worker failure. The next sections describe what is monitored in the system, what events can occur and what actions are taken if particular events occur. Worker Monitoring The worker monitoring comprises two things: Alive check: if a worker does not send a status message at least every 300 seconds to the QAD platform server (see section 5.4.3) a worker is considered lost. In this case the platform server will update the database and mark this node as down. If the node that was lost was controlled by the QAD Grid server the platform will try to re-connect to the client machine and restart the worker (client software) as described in section 5.3.3. Workload check: If the local load of a worker exceeds a certain threshold the worker is considered overloaded (see section 5.4.3). If so, this worker is set into paused state in which a worker will not request new tasks and sleep until the workload gets again to a level below the threshold. If the worker computes a task at the moment it was set into the sleep state it will mark this task as suspended and create a dump file of the current task state. This file contains all variables necessary to restart this task on another worker / machine at exactly this position (see section 5.4.4). This file is then copied to the QAD platform server which will distribute it to another client machine that will resume from this state. Offline Machine Monitoring In addition to active workers the system can also monitor client machines that are registered at the QAD Grid system as possible computing nodes and allow the QAD Grid server to login but are not running a worker. This is done by periodically logging into the target machine and running a quick status check. The resulting values and machine details such as CPU speed and available memory are then inserted into the Grid server’s database. Task Execution Monitoring This monitoring checks whether the execution of a tasks was interrupted or terminated because of a worker failure. The former condition can fail if a node is lost during task execution (see previous section). In this case the state of this task (at the QAD’s platform server) will be set to new, that is, another worker can request and compute this task. Result Check/Verification In some cases an explicit result verification is necessary. To achieve this a task will be computed by two different workers and the results compared prior to insertion into the database. This is done by setting the draft flag of the two (identical) task and inserting the ID of the opposite task into the linked task
5.4. QAD GRID WORKER 129 field. A worker that computes a task with a draft flag will not directly insert the result into the database or copy into a target repository but will send it into a to be verified zone on the QAD platform server. If the results from the different workers have arrived the platform server compares and either stores or rejects them. In the latter case two new tasks are created until the two results are identical. 5.4 QAD Grid Worker The QAD Grid worker is a program that runs on a client machine and can perform exactly one particular kind of analysis / computation (such as peak picking) or service (e.g. convert a file). As described in section 5.3.1 communication within the Grid (that is between servers and workers) is entirely done via database entries. The most striking feature of a QAD Grid worker is that � it can be written in any programming language � runs on (almost) any hardware / operating system platform � can contain arbitrarily complex algorithms � can perform system calls (e.g. OS dependent copy functions) � can enable non-Grid enabled executable programs (binaries or scripts) A worker can be tailored to specific needs and written in any programming language that supports (T-)SQL database access. The following sections describe the basic functions a worker needs to support and an extended standard reference implementation. Further, details of worker integration into the QAD Grid are given. 5.4.1 Functionality Base As described above a worker essentially runs on some client machine and computes available jobs. Therefore, a worker needs to have these base features: � Connect to and register at the Grid’s Platform Server. Registration includes the announcement of what kind of job it can compute (see section 5.3.1). � Request a job and respective parameters to compute � Load needed data (see section 5.3.2). � Compute job � Transfer results back into the Grid (see section 5.3.1). � Send alive and status messages (e.g. local workload) to the Grid
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New Statistical Algorithms for the
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Contents Acknowledgments . . . . .
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New Statistical Algorithms for the
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Extended Abstract English Version M
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German Version Das Gebiet der Prote
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Chapter 1 Introduction and Survey 1
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1.2. GOALS, OBJECTIVES AND TASKS 7
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1.2. GOALS, OBJECTIVES AND TASKS 9
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Chapter 2 Preliminaries 2.1 Topic O
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2.1. TOPIC OVERVIEW 13 Figure 2.1.1
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2.1. TOPIC OVERVIEW 15 completeness
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2.2. AN EXAMPLE 17 (a) Opera A (b)
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2.2. AN EXAMPLE 19 Figure 2.2.6: Tw
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2.2. AN EXAMPLE 21 successes. We ca
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Chapter 3 Mathematical Modeling and
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3.2. INTRODUCTION TO MALDI TOF MS 2
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3.3. PREPROCESSING 31 mix (external
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3.3. PREPROCESSING 33 Figure 3.3.5:
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3.3. PREPROCESSING 35 Figure 3.3.7:
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3.4. HIGHLY SENSITIVE PEAK DETECTIO
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3.5. PEAK DETECTION IN 2D MAPS 43
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3.6. PEAK REGISTRATION (ALIGNMENT)
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3.7. IDENTIFYING POTENTIAL FEATURES
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3.8. EXTRACTING FINGERPRINTS 57 Fig
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3.8. EXTRACTING FINGERPRINTS 59 FID
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3.8. EXTRACTING FINGERPRINTS 61 Dim
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3.9. COMPLEXITY ANALYSIS 63 3.9 Com
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Chapter 4 (Bio-)Medical Application
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4.1. DATA USED 67 4.1.2 Serum Data
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4.2. STATISTICAL REMARKS 69 1. Vali
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4.2. STATISTICAL REMARKS 71 Molar v
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4.2. STATISTICAL REMARKS 73 � Fir
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4.2. STATISTICAL REMARKS 75 Let ˆ
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Page 89 and 90: 4.3. STUDY RESULTS 83 � kNN (gen.
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Page 183 and 184: References Aebersold, R. and Mann,
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REFERENCES 179 Breiman, L. (2001).
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REFERENCES 181 Downard, K. M. and M
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REFERENCES 183 Gillette, M. A., Man
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REFERENCES 185 Huyghe, E., Muller,
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REFERENCES 187 Kuijpens, J. L. P.,
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REFERENCES 189 McLachlan, S. M. and
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REFERENCES 191 Platt, J. C. (1999).
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REFERENCES 193 Stone, M. (1974). Cr
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REFERENCES 195 Washburn, M. P., Wol
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