Virtual Repository (VR) Version 1.0 Operation Manual

Transcription

1 UCB-NE-4230 Virtual Repository (VR) Version 1.0 Operation Manual K. Tsujimoto, D. Kawasaki, J. Ahn, and P. L. Chambré Department of Nuclear Engineering University of California Berkeley, California December, 2000

2 The authors invite comments and would appreciate being notified of any errors in the report. Joonhong Ahn Department of Nuclear Engineering University of California Berkeley, CA USA Windows NT, Visual Basic, Visual C++, and Access are trademarks of Microsoft Corporation. All other trademarks contained in this report are the property of their respective holders. The Regents of the University of California hold the copyright of the computer programs, Virtual Repository (VR), developed in the work described in this report. Redistribution of the VR code in any form is prohibited without written consent. Disclaimer: This document was prepared as an account of work sponsored by the Japan Nuclear Cycle Development Institute (JNC). Neither JNC nor any agency thereof, nor the Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability of responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial products process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by JNC or any agency thereof, or the Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of JNC or any agency thereof or the Regents of the University of California and shall not be used for advertising or product endorsement purposes. ii

3 Table of contents 1 Introduction VR System Overview General Description System Features Multi-compartment Model Object-oriented Simulation Parallel and Distributed Computation How to Set up VR System Summary Making a New Windows NT Account on Local Machines Installing Visual Basic 6.0 and Access Installing Visual C Installing Remote Shell Daemon Acquiring the Software Installation Registering a User in Trusted User Database Verifying the Behavior of Remote Shell Daemon Installing PVM Acquiring the Software Installation Setting Environment Variables Verifying the Behavior of PVM Installing VR slave software Installing the Slave Simulation Engine Installing the Source Codes Installing VR master software Installing the Master Simulation Engine Installing the Source Codes Installing HCI and Database Setup for Multiple Users Operating VR Overview Constructing PVM System Constructing PVM system manually Constructing PVM System Using a Hostfile Operating VR with HCI Starting HCI Making an Input File Calculation Database Query Window Browsing Plots of the Calculation Results iii

4 5.3.6 Terminating HCI Terminating PVM Input File Output Files ot5.txt Inventory Files mass_dis.txt Release Rate Files glassinv_zero.txt distrib.txt Other Output Files Operating VR without HCI Modifying VR Modifying win32visual.def Compiling PVM simulation program Copying Slave Program of VR Simulation Engine Known Bugs References Appendix 1: VR Structure Appendix 2: The Contents of Files Relating VR TM compiling List of Win32visual.def List of makepro.bat (vrmaster) List of ex3m01.mak (vrmaster) List of makepro.bat (slave) List of ex3s01.mak (slave) iv

5 1 INTRODUCTION VR (Virtual Repository) is a computer code for simulating radionuclide transport in a high-level radioactive waste (HLW) repository that consists of thousands of waste canisters surrounded by the bentonite buffer and the rock. A repository is divided into compartments, each of which includes the waste canister, the buffer and the rock. The VR code consists of objects, which define functionality and behavior of actual physical objects included in the repository. Modification of the code for different repository configuration can be done more flexibly than the ordinary simulation using procedure-oriented language. Another important characteristic of VR is that it applies parallel and distributed computing. VR is able to run on several Windows NT machines connected via Local Area Network (LAN). Calculation can be finished in a shorter time with multiple machines than with a single machine. In this manual, a brief overview of the VR system, how to install and configure the VR system in computers, and how to perform calculation are described. All descriptions are based on version 1.0 of the VR system, completed August Executable files of this version of VR system and their source codes can be found in the CD-ROM attached to this manual. 1

6 2 VR SYSTEM OVERVIEW 2.1 General Description VR is a computer simulation code, developed for the safety assessment of a HLW geologic repository. The main features of VR are summarized as follows: Multi-compartment model: The HLW repository is divided into multiple finite, closed regions of identical size and structure, which are called compartments. Radionuclide release from glass waste, diffusion in the bentonite buffer and concentrations of radionuclides in near-field rock are calculated within each compartment, and advection of the radionuclides is calculated through the near-field rock region of all the compartments. Object-oriented coding Parallel and distributed computation: More than one computer can be used simultaneously in order to perform a calculation task. Parallel computation can make calculation faster. 2.2 System Features VR is composed of three main components, i.e., the simulation engine, Human Computer Interface (HCI), and the database. The simulation engine executes calculation for the radionuclide transport in the repository. The simulation engines are located at the host and slave computers. HCI is a tool to make an input file that contains all the necessary parameter values for calculation (See 5.3.2). The calculation results can be browsed with HCI. HCI module uses Microsoft Visual Basic as a programming tool. It also can show the summary of calculation result and display numerical results in two-dimensional graph format ( 5.3.5). The database stores the simulation results. It uses ACCESS as the database management software. Numerical results at time points specified by the user in a logarithmic time scale are stored in the database module. From the viewpoint of hardware, VR is executed by a host (master) machine and by multiple slave machines. VR adopts PC with Windows NT as platform. The simulation engine, HCI, and the database are installed in the host machine. In the slave machines, only a necessary part of the simulation engine is installed. (See Fig ) HCI Simulation Engine Simulation Engine Slave Machine Database Host Machine Simulation Engine Slave Machine Figure VR System. The hardware required for VR is as follows: Windows NT machines connected to each other via LAN ( 64 MB RAM is recommended for the host machine.) The softwares required for VR are as follows: Windows NT 4.0 Workstation operating system 2

7 VisualC or 6.0 for the simulation engine PVM 3.4 for the parallel computation tool ( 2.5 and 3.6) Visual BASIC 6.0 for HCI ACCESS 97 for Database The configuration of machines is shown on Fig WindowsNT machines Host (Master) LAN Slave Slave Slave 2.3 Multi-compartment Model WindowsNT machines Figure Hardware structure of VR. The repository is divided into many imaginary compartments of the same size which is composed of glass waste, overpack, buffer and near-field rock. The simulation engine uses a one-dimensional repository model composed of multiple compartments and a far-field region. In the present model, the area inside the repository is called the near-field. The area outside the repository is called the far-field. The far-field region is attached to the last compartment in the row. The groundwater flows in the direction of the compartment array. In the current version of VR, the overpack region is neglected. However, a class for overpack is prepared in the source code so that adding the overpack region to the model can be done without changing the structure of the code. An object-oriented model is suitable for modeling the repository, since the waste repository is composed of canisters of the same size and similar composition. The detail of the waste repository model including mathematical formulation is given by Ahn et al. [1]. See Appendix 1 also. Groundwater Flow H Near Field Rock Buffer Overpack Vitrified Waste Groundwater Flow Near Field Rock Buffer Overpack Vitrified Waste Overpack Buffer Near Field Rock Compartment Configuration Groundwater Flow Compartment Groundwater Flow Compartment Model (One-dimensional Plate Model) Compartme nt Far Field Far Field No. N No. N-1 No.2 No.1 Figure Multi-compartment model. Repository Model 3

8 2.4 Object-oriented Simulation The simulation engine is written in VisualC++ language and utilizes object-oriented simulation (OOS) technologies. The repository model is made of objects, and property and function of each object is designed to achieve simulation calculation. In the object-oriented approach, an object is designed to simulate physical entity. An object includes the input and output ports, which are used to receive the input data from another object and pass the output data to another. The organization of the system is shown in Figure The lower layer consists of the data communication library for parallel computing. The upper layer consists of the classes that compose the application. The classes are divided into the master and slave classes. There are two kinds of classes in the system. The classes of one kind are related to the simulation engine, and are included in the slave part. The classes of the other kind handle system management (such as I/O, data summary and data printing), and are included in the master part. Master Slave Simulation Engine master read_ input iteration slave_ trans nuclide glass overpack Class datasum open _file trans buffer near_ field far_field repository print mesh Data Communication PVM PVM Figure Structure of VR simulation engine. 2.5 Parallel and Distributed Computation PVM (Parallel Virtual machine) [2] enables a collection of heterogeneous computer systems to be viewed as a single parallel virtual machine. PVM handles all message passing, data conversion, and task scheduling across networked computers. The features of PVM are summarized as follow: 1) User-configured host pool: The application's computational tasks execute on a set of machines (i.e., host pool ) that are selected by the user for a given run of the PVM program such as VR. The host pool may be altered by adding and deleting machines during operation by a user. 2) Explicit message-passing model: Collections of computational tasks, each performing a part of an application s workload using data-, functional-, or hybrid decomposition, cooperate by explicitly sending and receiving messages to one another. 3) Heterogeneity support: The PVM system supports heterogeneity in terms of machines, networks, and applications. With regard to message passing, PVM permits messages containing more than one data type to be exchanged between machines having different data representations. 4) Software structure: The main components of PVM are daemon, library, console, sample programs, and makefile. PVM daemon is the core program of PVM, which oversees communication between machines and controls tasks in parallel calculation. PVM library offers commands or functions that are used in a user application and have the basic functions of parallel calculation. VR utilizes PVM as a portable message-passing tool. Master-and-Slave model is applied as parallel computation model. (See Figure 2.5-1) In each time step, the host machine sends values of the isotope ratio to slaves. Then slaves execute transport calculation and return the calculation results to the master. In the current VR system, the unit of calculation assigned to each slave is transport calculation for one radioactive-decay chain. To achieve parallel and distributed computing on Windows-NT with PVM, Remote Shell Daemon (RSHD) is 4

9 needed to make remote Windows NT machines accessible to each other. With RSHD running, a user can access to, and execute commands on, that machine from a remote machine. A local host means the machine that a user is logging on. A remote host means a machine that is connected by network to the local host. As Windows NT does not support RSHD officially, the user must install RSHD made by a vendor other than Microsoft. From the viewpoint of security, RSHD must have the trusted database that is used to judge whether a remote user has access privilege. If a user logging in a distant remote host accesses to the local host in Figure 2.5-2, RSHD refers to the trusted database, and check whether the user name and password stored in the trusted database math those typed in by the user. If the user name and password typed in match those in the database, the user is allowed to access the local host. Generally, a user can access to the remote host with a user name and password that is different from his user name and password. The software structure for parallel computation is shown in Figure Each machine has host or slave application. Every machine must have PVM, RSHD and the trusted database. An application communicates with each other using RSHD via LAN. To make communication possible between machines, the trusted database belonging to each machine must have the user name and password. Krypton Plutonium Host machine Isotope Ratio data Inventory, mass, concentration and accumulation data Boron Uranium Neptunium Slave machine Figure Data flow for parallel calculation. Configuration available at UCBNE Nuclear Waste Research Laboratory as of August User: A Password: AA User: B Password: BB Trust ed Da tabase -User B -Password BB Log on user A Remot e Host Remo te Log on Local Host LAN Figure Remote access and security using trusted database. Master Program Slave Program Slave Program Log on USER PVM USERNAME PASSWORD PVM USERNAME PASSWORD PVM USERNAME PASSWORD Remote Shell Daemon Trusted Database Remote Shell Daemon Trusted Database Remote Shell Daemon Trusted Database LAN Figure Software structure for parallel and distributed computation. 5

10 3 HOW TO SET UP VR SYSTEM All the procedures necessary for installing and configuring software in both host and slave machines are described in this chapter. These procedures are only required when VR-system software is installed in the machine for the first time. Once it is installed, only a few procedures are necessary for another user to set up a new account. The procedures for another user to set up in a machine in which VR is already installed are described in Chapter 4. Since some packages of the software required by VR system can be updated and changed by their developers, there might be differences between the behavior of the software described in this manual and that of the version you are going to use. 3.1 Summary In this section, a brief overview of installation and configuration of VR system is described. The detailed procedures of each step are described in later sections. Listed below are the procedures necessary for setting up VR-system software in the host machine: 1. Make a new Windows NT account on the local machine. 2. Install Visual Basic ver Install ACCESS Install Visual C++ ver 5.0 or Install Remote Shell Daemon (RSHD). 6. Install PVM. 7. Install VR slave software. 8. Install VR master software. Installation of VR slave software in the host machine is necessary because the VR slave simulation engine is executed not only on the slave machines but also on the host machine. Steps necessary for slave machines are fewer than those for the host machine. Installation of Visual Basic ver 6.0, ACCESS 97, and VR master software in slave machines is not necessary. The following are the steps necessary for setting up the software in slave machines: 1. Make a new Windows NT account on the local machine. 2. Install VisualC++ ver 5.0 or Install Remote Shell Daemon. 4. Install PVM. 5. Install VR slave software. Since all the software and setup procedures necessary for a slave machine are included in those necessary for a host machine, the host machine in one configuration of a PVM system can also be used as a slave machine in another configuration of virtual machine system, provided that there is another machine that can be a host machine. For example, suppose there are two Windows NT machines, A and B, connected to each other via LAN, and the software necessary for a host machine is installed in both machines. Because both machines A and B can either be a host machine or a slave machine, there are two ways of configuration of virtual machine system: the one is to have machine A as the host machine, and machine B as the slave machine; the other is to have machine B as the host machine, and machine A as the slave machine. 3.2 Making a New Windows NT Account on Local Machines Before installing software, you need to make a Windows NT local user account on each machine that consists of the VR system. The user account is necessary for all the slave machines and the host machine. The local user account must have the administrator privilege. The administrator privilege is required when you install and run the VR. The following are the procedures to make a new local user account on a Windows NT machine. 1. Log on machine as administrator (put domain name in domain box) (Figure 3.2-1) 2. Click Start button 3. Click Programs in the menu 4. Click Administrative Tools in the menu 5. Click User Manager in the menu (Figure 3.2-2) 6. Select User at the menu bar 7. Select New User (Figure 3.2-3) 6

11 8. Type the new username in Username field, and a password for the user in Password and Confirm Password fields. (Figure 3.2-4) 9. Click on Groups button in the bottom-left corner of the window to open Group Memberships window. 10. Select Administrator in Not member of: list, and click on <- Add button, in order to have the new user a member of administrator. This step can be skipped if Administrator is already shown in Member of: list. (Figure 3.2-5) 11. Select Users in Not member of: list, and click on <- Add button, in order to have the new user a member of users. This step can be skipped if Users is already shown in Member of: list. 12. Click on OK button in the Group Memberships window. 13. Click on OK button in the User Properties window. 14. Click Exit in the User menu of the User Manager window. (Figure 3.2-6) 15. Log off the machine 16. Log on the machine with the newly made account Figure Logging on the machine. (Step 1) Figure Opening User Manager. (Steps 2 5) 7

12 Figure Selecting New User. (Step 7) Figure New User window. (Step 8) Figure Making the new user a member of Administrators and Users. (Steps 10 12) 8

13 Figure Closing User Manager window. (Step 14) 3.3 Installing Visual Basic 6.0 and Access 97 Microsoft Visual Basic 6.0 and Microsoft Access 97 are necessary in order to run HCI (Human-Computer Interface). Since HCI is used only on the host machine, Visual Basic 6.0 and Access 97 are also required only on the host machine. It is not necessary to install Microsoft Visual Basic 6.0 or Microsoft Access 97 in slave machines. Since Visual Basic and Access are the products of Microsoft Corporation, the installation procedures of these products should be done as is described in official documents provided by Microsoft Corporation. The installation procedures are not shown in this manual. Note that Visual Basic 6.0, not earlier versions of Visual Basic, must be used since version 6 significantly differs from the earlier versions. The current version of HCI does not work with Visual Basic earlier than version 6. There is only one important requirement on Access that must be noted. Since the current version of HCI assumes that the executable file of Access is located at C:\Program Files\Microsoft Office\Office\Msaccess.EXE, HCI will not work correctly if the executable file of Access is not located there. 3.4 Installing Visual C++ Microsoft Visual C++ version 5.0 or version 6.0 is necessary in order to compile the VR simulation engine. Visual C++ is the product of Microsoft Corporation, and the installation procedures of it should be done as is described in official documents provided by Microsoft Corporation. The installation procedures for this software are not shown in this manual. 3.5 Installing Remote Shell Daemon Remote Shell Daemon (RSHD) enables communication between two machines, and is required by PVM. It is necessary to install RSHD both in the host machine and in the slave machines. There are several packages of RSHD developed and distributed by different vendors. The current version of VR works with RSHD developed by Dr. Markus Fischer ( Acquiring the Software RSHD Service for Microsoft WIN32 (Remote Shell Daemon for Windows NT developed by Mr. Markus Fischer) can be purchased at his web site. As of this writing, the official distribution site of Remote Shell Daemon for Windows NT is 9

14 3.5.2 Installation The package of RSHD developed by Dr. Markus Fischer contains self-extracting setup wizard and uninstalling program. Information on RSHD made by Dr. Markus Fischer is available from the following web site: Installation of RSHD is necessary for all machines in the VR system. The list of the detailed procedures of installation is as follows: 1. Click NT-RSH-DAEMON.exe downloaded from the above web site. (Figure 3.5-1) 2. Click Yes button in the initial window of installation wizard. (Figure 3.5-2) 3. Click Next button of the second window of installation wizard. (Figure 3.5-3) 4. Type Password in the password box, then click Next button. The password should be obtained by communication with Dr. Markus Fisher by . (Figure 3.5-4) 5. License agreement panel appears. Read the license agreement document and click Next button. (Figure 3.5-5) 6. Indicate the directory in which RSHD is installed as c:\program files\, then click Finish button. (Figure 3.5-6) 7. Welcome panel appears. Then click Next button (Install Shield Wizard started.) (Figure 3.5-7) 8. License agreement panel appears. Read the documents carefully and click Yes button. (Figure 3.5-8) 9. Destination location panel appears. Verify that the destination folder is correct and click Next button. (Figure 3.5-9) 10. Select components panel appears. Verify that the both components are selected and click Next button. (Figure ) 11. Setup complete panel appears. Click the two check boxes and click Finish button. (Figure ) 12. Remote shell daemon help panel appears. Read the help panel carefully and close the panel. (Figure ) 13. Restart the computer in order to start the daemon. (Figure ) The directory named NT-RSH-DAEMON is made under the directory c:\program files\ and RSHD is automatically installed in the directory of c:\program files\nt-rsh-daemon\. Figure Opening NT-RSH-DAEMON.exe in Explorer window. (Step 1) 10

15 Figure Initial widow of the installation wizard. (Step 2) Figure The second window of the installation wizard. (Step 3) Figure Typing the password. (Step 4) 11

16 Figure License agreement window. (Step 5) Figure Setting the directory in which the wizard files are unpacked. (Step 6) Figure Welcome panel. (Step 7) 12

17 Figure License agreement panel. (Step 8) Figure Setting the directory in which the software is installed. (Step 9) Figure Selecting both components to be installed. (Step 10) 13

18 Figure Setup Complete window. (Step 11) Figure Remote Shell Daemon HELP window. (Step 12) Figure Restarting the computer. (Step 13) 14

19 3.5.3 Registering a User in Trusted User Database Every user of RSHD needs to have his/her user information stored in a so-called trusted user database on each machine. Each time a user tries to access a remote machine using RSHD, RSHD verifies whether the user is authorized to access the remote machine, checking the username and the password against the trusted user database. All users need to have their usernames, passwords, and remote IP addresses registered before they can utilize RSHD. This procedure is also required when making a new user account on a machine in which VR-system software is already installed by another user. The procedures listed below should be followed in order to register new user information. 1. Open command prompt console window. (Figure ) 2. Type c: and press Enter to change the hard disk drive. (Figure ) 3. Type cd c:\program files\nt-rsh-daemon and press Enter to move to the directory where RSHD is located. (Figure ) 4. Type configure add <remote user name> <local user name> <IP list> and press Enter. (Figure ) In step 4, the first argument to the configure command, <remote user name>, is the username with which the user is going to access remote machines. The second argument <local user name> is the username with which the user has logged on the local machine. Although there are two kinds of usernames to be typed in, both must be the same due to the restriction of the function of RSHD. The third argument <IP list> is a list of IP addresses of the machines that the user is allowed to access with RSHD, i.e., a list of IP addresses of all the machines to be included in the VR system. The wildcard character * can be used in <IP list>. For example, when a username berkeley is to be registered and the IP address of a remote machine is , you can type in the command prompt console window as follows: configure add berkeley berkeley or you can also type as follows: configure add berkeley berkeley * The latter form is especially convenient when there are more than one machine to be specified as remote machines. When * is typed as <IP list>, the newly registered user will be allowed to access all the machines whose IP addresses begin with Following the message printed in the console window, type local user s password and press Enter. (Figure ) 6. Type exactly the same password again and press Enter, to ensure. (Figure ) 7. Type configure list and press Enter to see a list of information about all the users registered. (Figure ) 8. Make sure that the new user name and IP list are correctly shown in the list. (Figure ) 9. Type exit and press Enter to close the console window. Figure Opening Command Prompt window. (Step 1) 15

20 Figure Changing directory. (Steps 2, 3) Figure Typing the command configure. (Step 4) Figure Typing a password. (Step 5) Figure Re-typing the same password. (Step 6) Figure Checking the list of registered users. (Steps 7, 8) Verifying the Behavior of Remote Shell Daemon Properly running RSHD is indispensable for VR calculation. Hence, before you start using VR, it is highly recommended to check if RSHD is correctly installed. Whether RSHD is correctly installed or not can be checked issuing the rsh command. RSHD is properly installed and is working correctly if you can access a remote machine using rsh command and if any command (e.g., dir ) can be executed on the remote machine. It should be noted that RSHD also needs to have been installed in the remote machine that you are trying to access by rsh command. Obviously, RSHD has to be installed at least in two machines in the VR system before verification can be done. 16

21 The verification procedures are as follows: 1. Open command prompt console window. (Figure ) 2. Type rsh <remote host> -l <user name> cmd /c dir c: and press Enter in the console window. (Figure ) 3. Check if the file list of the remote machine is shown in the console window. If the file list appears, the communication between two machines is properly done and installation of RSHD is verified. (Figure ) In step 2, <remote host> is the host name (or IP address) of the remote machine, and <user name> is the username which has been registered in the trusted user database (see 3.5.3). For example, one can type rsh uranium l berkeley cmd /c dir c:, in which case uranium is the remote host name and berkeley is the username. If a list of files in the remote machine is shown in the console window after step 2, RSHD on the two machines has been successfully installed. The set-up procedures for RSHD are complete. In case an error message is displayed instead of the expected list of files, RSHD is not working correctly. Whole procedures for installation and configuration must be checked again. If the error message says: <remote host>: unknown host rsh: can t establish connection the host name you have specified as <remote host> is not found in the network, or the host name is not recognized. Check the machines, and make sure that they are correctly connected to the network and that the host name is recognized in the network. If IP addresses can be recognized instead of host names, you can verify installation of RSHD replacing <remote host> with the corresponding IP address. In Nuclear Waste Research Laboratory in UCBNE, host names of the machines, which are currently connected to the intra-net, are not automatically recognized by each machine. IP addresses and corresponding host names of all the machines in the intra-net can be designated in a certain text file in each machine. The file is usually located at C:\WINNT\system32\drivers\etc\Hosts. Open the file with a text editor, add pairs of an IP address and a host name for all machines in the intra-net in the bottom of the text, and save the file exactly with the same name at the same location as it was. Doing so will make the machine recognize the host names of the machines in the intra-net. If the error message says: -> <remote host>:connection refused rsh: can t establish connection the machine you have specified as <remote host> may be probably busy on other tasks. Try the verification procedures later again, and if you still receive the same error message, RSHD might not be correctly installed in <remote host>. Make sure that RSHD is also installed in <remote host>. Note that both of the machines, i.e., the one you locally logged in and the one you want to access remotely using rsh command, must have RSHD installed in them. Figure Opening Command Prompt window. (Step 1) 17

22 Figure Typing the command rsh. (Step 2) 3.6 Installing PVM Figure File list in the remote machine is displayed. (Step 3) PVM enables parallel and distributed computation using multiple computers. It is necessary to have PVM installed both in a host machine and in slave machines. Since PVM works together with Remote Shell Daemon, Remote Shell Daemon has to be installed in the machines in advance Acquiring the Software The official distribution site of PVM for Windows NT is The self-extracting setup wizard can be obtained directly from The package of PVM software currently used is also kept in the CD-ROM attached to this manual Installation Make sure that Microsoft Visual C++ and Remote Shell Daemon are already installed in the machine before installing PVM. The current version of PVM is The package of PVM for Windows NT ver contains self-extracting setup wizard. Information of PVM for Windows NT is available from the following web site: Installation of PVM is necessary for all machines in VR system. The list of the detailed procedures of installation is as follows: 1. Double-click pvm3.4.3.exe obtained from the web site. (Figure 3.6-1) 2. File extraction starts. Check PVM version number, then click Continue button. (Figure 3.6-2) 3. The install wizard starts. (Figure 3.6-3) 4. Read the notice for exiting all the windows programs, then click Next button. (Figure 3.6-4) 5. Read the software license agreement, then click Yes button. (Figure 3.6-5) 6. Read the notice on PVM, then click Next button. (Figure 3.6-6) 18

23 7. Select Server as installation type, then click Next button. (Figure 3.6-7) 8. The installation destination selection window appears. Select c:\program Files\PVM3.4 as destination by using Browse button (or c:\program Files\PVM3.4 may be default directory), then click Next button. (Figure 3.6-8) 9. The temporary directory for installation selection windows appears. Confirm the temporary directory, then click Next button. (Figure 3.6-9) 10. The setup type selection window appears. Select the typical, then click Next button. (Figure ) 11. The C compiler selection window appears. Select the version of Microsoft Visual C++ which you have installed, then click Next button. (Figure ) 12. The C compiler directory selection window appears. Select the directory in which C compiler is installed, then click Next button. (Figure ) 13. The FORTRAN compiler selection window appears. Select the version of the FORTRAN compiler if any has been installed, then click Next button. (Figure ) 14. The PVM icon name selection window appears. Select PVM3.4 (Default), then click Next button. (Figure ) 15. The Setup information window appears. Confirm the set up information, then click Next button. (Figure ) 16. PVM is being installed by wizard. (Figure ) 17. Finishing installation, the notice to change the registry appears. Confirm the notice, then click OK button. (Figure ) 18. The setup completion windows appears. Select both box, then click Finish button. (Figure ) 19. PVM start window, readme file, and help file appear. (Figure ) 20. You should restart the machine to complete the installation process of PVM. Select Restart my computer, then click Finish button. (Figure ) Figure Opening the self-extracting file in Explorer window. (Step 1) Figure The initial window. (Step 2) 19

24 Figure Starting the setup program. (Step 3) Figure Welcome window. (Step 4) Figure License agreement window. (Step 5) 20

25 Figure Information window. (Step 6) Figure Selecting Server option. (Step 7) Figure Specifying the install destination. (Step 8) 21

26 Figure Setting the temporary directory. (Step 9) Figure Selecting Typical. (Step 10) Figure Selecting the version of Visual C++. (Step 11) 22

27 Figure Locating the C compiler directory. (Step 12) Figure Selecting the version of Digital Fortran. (Step 13) Figure Selection of a program folder. (Step 14) 23

28 Figure Confirming the settings. (Step 15) Figure Installing. (Step 16) Figure Adding the registry values. (Step 17) 24

29 Figure Finishing the setup wizard. (Step 18) Figure PVM start window, readme file and help file. (Step 19) Figure Restarting the computer. (Step 20) 25

30 3.6.3 Setting Environment Variables Most of the environment variables necessary for PVM to run properly are automatically set by the installation wizard. However, there is one necessary environment variable which is not set by the wizard. An additional procedure is necessary for this reason: setting the environment variable PVM_ROOT to be pathname to the directory where PVM software has been installed, i.e., c:\progra~1\pvm3.4. Procedures for setting the environment variable are as follows: 1. Click Settings in the Start menu. (Figure ) 2. Click Control Panel. (Figure ) 3. Double-click system icon in Control Panel window. (Figure ) 4. Click Environment tab in System Properties window. (Figure ) 5. Scroll the System Variables list (upper part of the dialog box) down to the bottom, and click on the blank part of the list. (Figure ) 6. Type PVM_ROOT in Variable box. (Figure ) 7. Type c:\progra~1\pvm3.4 in Value box. (Figure ) 8. Click Set button. (Figure ) Figure Opening Control Panel. (Steps 1, 2) Figure Opening System. (Step 3) Figure Environment panel. (Step 4) Figure Scrolling down the System Variables list. (Step 5) 26

31 9. Click Apply button. (Figure ) 10. Check that the following variables are set correctly: variables set by Visual C++: Bin, include, Lib, variables set by PVM: PVM_ARCH, PVM_CBIN, PVM_CINCLUDE, PVM_CINCLUDE, PVM_ROOT, PVM_TEMP, PVM_VERSION. 11. Click OK button to close system Properties window. (Figure ) 12. Restart the computer to activate environment variable. (Figure ) Figure Adding variable PVM_ROOT (Steps 6 9). Figure Restarting the computer. (Step 12) Verifying the Behavior of PVM Before you start using VR, it is highly recommended to check if PVM is correctly installed. Since PVM does not work without Remote Shell Daemon running, installation of Remote Shell Daemon must be verified beforehand. Whether PVM is correctly installed or not can be checked by constructing a virtual machine system, which can be done by adding each of the remote machines with add command in PVM Console window. Open PVM Console window on the host machine. The rest of the machines that are added with add command will be slave machines. Note that PVM has to be installed in all the machines in PVM system before its behavior can be checked. It should be verified that each machine can be set as a host machine (i.e., PVM console window can be opened on each machine), and that all the remote machines can be added to the virtual machine system in each case. The verification procedures are as follows: 1. Log on a local machine. The machine you log on here will be the host machine in the system. 2. Click Programs in Start menu. (Figure ) 3. Click PVM 3.4 in the submenu. (Figure ) 4. Click PVM Console in the menu to open the PVM Console window. (Figure ) 5. PVM Console window opens. Wait until a prompt text pvm> appears. (Figure ) 6. Type add <remote host>, and press Enter to add a machine to the system. (Figure ) In step 6, <remote host> is the name of the remote machine to be added to the system. For example, typing add krypton will add machine krypton. 7. Repeat step 4 for other remote machines until every remote machine which will be used as a slave machine in VR system is added to PVM system. (Figure ) 8. Type conf and press Enter to see the list of remote machines which have been added to PVM system. Check that all remote machines are in the list. (Figure ) 9. Type halt and press Enter in order to disconnect all the machines which have been added to PVM system, and close PVM Console window. (Figure ) PVM console must always be closed by halt command. Otherwise, additional procedures have to be done 27

32 before PVM console can be used again. Those additional procedures are described in Section 5.4. Figure Selecting PVM Console in the menu. (Steps 2 4) Figure PVM Console window. Waiting to get ready. (Step 5) Figure Adding and confirming remote machines. (Steps 6 8) Figure Exiting PVM Console window with halt command. (Step 9) 28

33 3.7 Installing VR slave software VR slave software consists of two parts: the executable file of the slave simulation engine vrslave.exe, and the source codes from which the executable file was built. The executable file vrslave.exe needs to be installed in all the machines that compose VR system. On the other hand, the source codes are not necessary when you operate VR calculation. The source codes are only necessary when you re-compile and rebuild the executable file Installing the Slave Simulation Engine The executable file vrslave.exe must be installed in all the machines in the VR system. It has to be installed not only in slave machines but also in the host machine. The installation of the executable file is done simply by copying the file vrslave.exe into the directory PVM_ROOT\bin\PVM_ARCH where PVM_ROOT and PVM_ARCH are the environment variables which were set during installation of PVM (see Section 3.6.3). If you have followed the instruction described in Section 3.6.3, the environment variable PVM_ROOT is set to c:\progra~1\pvm3.4. The other variable PVM_ARCH is set to win32 by default. Therefore, the above expression for the directory into which the file vrslave.exe should be copied indicates the following directory: c:\progra~1\pvm3.4\bin\win32. The executable file of slave simulation engine, i.e., vrslave.exe, is to be placed in the above directory of each machine Installing the Source Codes While the executable file vrslave.exe always has to be installed in all the machines, the source codes are not necessarily to be installed in all the machines. The source codes are only required when a user wants to modify VR simulation engine and rebuild the executable file. The installation of the source codes can be done by copying the folder ex3s into the following directory: c:\progra~1\pvm3.4\ The folder ex3s contains all the source codes necessary for building the executable file vrslave.exe. 3.8 Installing VR master software While it is necessary to have VR slave simulation engine installed both in the host machine and in the slave machines, it is only necessary to install VR master software in the host machine. VR master software consists of four parts: the executable file of the master simulation engine vrmaster.exe, the source codes from which the master simulation engine was built, HCI (Human-Computer Interface) the file name of which is vr01.exe, and the database file Db2.mdb Installing the Master Simulation Engine The executable file vrmaster.exe must be copied into a certain directory in the host machine. The directory path of the location of vrmaster.exe is fixed to d:\vrengine\vr\. This is due to the behavior of the current version of HCI, i.e., vr01.exe. If the file vrmaster.exe is not placed in the above directory, HCI cannot locate vrmaster.exe, and hence computation cannot be started. Changing the location of vrmaster.exe will require modification and recompiling of HCI. To install the master simulation engine in the host machine, follow the procedures listed below. 1. Double-click on My Computer icon on the desktop of the host machine. 2. Double-click on the icon of D: drive in the window. 3. Click File menu and select Folder in New submenu. A new folder is created in drive D:. 4. Rename the new folder as vrengine. 5. Double-click on the new folder icon named vrengine. 6. Click File menu and select Folder in New submenu again to make another new folder in the directory D:\vrengine. 29

34 7. Rename the new folder as vr. 8. Copy the executable file of VR master engine vrmaster.exe into the new folder vr Installing the Source Codes As well as the source codes for VR slave simulation engine, the source codes for VR master simulation engine are not necessarily installed in the host machine. The source codes are only required when a user wants to modify behavior of VR simulation engine and rebuild the executable file. The installation of the source codes can be done by copying the folder ex3m into the following directory: c:\progra~1\pvm3.4\ The folder ex3m contains all the source codes necessary for building the executable file vrmaster.exe. PVM3.4 :directory bin conf WIN32 xxx:classes which compose of simulation engine vrmaster.exe vrslave.exe win32visual. def ex3m WIN32 xxx.cpp, makefile.mak, makepro.bat (master part) xxx.obj (master part) ex3s WIN32 xxx.cpp, makefile.mak, makepro.bat (slave part) xxx.obj (slave part) Figure Directory structure for PVM Installing HCI and Database VR simulation engine is fully functional without HCI and can be operated manually with Command Prompt console. However, it is more convenient to use HCI to operate VR simulation engine. In order for HCI to work properly, Visual Basic 6.0 and Access 97 is required. The database Db2.mdb is also required for HCI. Installation of HCI and the database can be done by copying the files vr01.exe and Db2.mdb into the directory d:\vrengine\vr\ into which vrmaster.exe has also been copied. The locations for these files are also fixed due to the behavior of HCI. 30

35 4 SETUP FOR MULTIPLE USERS Since all the software necessary for VR is already installed in Chapter 3, it is not necessary for another new user to install the software again as long as the users are using the same machines and the same VR simulation engine. More than one user can set up their VR system configuration, sharing the same software installed in machines. Hence, most of the steps of software installation described in Chapter 3 are omitted when setup for the second user is attempted. The procedures necessary for a new user to become able to use VR system are described in this chapter. After the whole installation steps described in Chapter 3 are finished, the one who installed the entire software already has a user account in VR system, since he/she was required to make a user account in order to install and configure the software. The procedures described in this chapter are not necessary for the user who has installed the software. Listed below are the sections necessary to be followed when setup for a new user in VR system is done: Registering a User Verifying the Behavior of Remote Shell Daemon Verifying the Behavior of PVM The details of the procedures are exactly the same as described in the above sections, and those sections should be referred to. 31

36 5 OPERATING VR 5.1 Overview How to operate VR with and without HCI is described in this chapter. In order to perform calculation of VR, the parallel virtual machine system (PVM system) has to be constructed each time before VR simulation engine is executed. When the VR master simulation engine is executed on a host machine, it distributes calculation tasks to the slave machines by means of PVM and Remote Shell Daemon. The details about constructing the PVM system are described in Section 5.2. Every time the VR master simulation engine is executed, an input file has to be passed to the master engine. The input file is a text file in which all the parameters necessary for the calculation are listed in a certain format. The details about the format of the input file are described in Section 5.5. When calculation is done, the master engine creates several output files that contain calculation results. All the output files are text files and can be opened with any text-editor software. The details about the output files are described in Section 5.6. The input file for the VR master engine can easily be created with help of HCI, and the master simulation engine can be executed within HCI window. HCI also reads the output files created by the master engine and can plot the result in its own window. Although the input file can be created and output file can be browsed with any editor software, that can be done more easily with HCI. When using HCI, it is also less probable to make an input file with a wrong format of parameters in it which causes unexpected calculation or which cannot be even read by the master engine. The details about the operation of HCI are described in Section 5.3. In order to perform a calculation of VR using HCI, the steps listed below should be followed. 1. Log on the local machine that will be the host machine in the VR system. 2. Construct PVM system. 3. Launch HCI. 4. Make an input file with HCI. 5. Execute VR master engine from within HCI. 6. See the result of calculation using HCI. 7. Terminate HCI. 8. Terminate PVM system. The master engine can also be executed manually (i.e., without HCI) from command prompt console window. Such operation of VR master engine is described in Section Constructing PVM System The parallel virtual machine system (PVM system) must always be constructed before VR simulation engine is executed, and must always be terminated after VR simulation engine terminates by itself. Otherwise, calculation cannot be done properly by the simulation engine. There are two ways to construct a PVM system: one is to add each machine manually, the other is to use a hostfile, where names of remote machines are contained Constructing PVM system manually Constructing a PVM system can be done manually by procedures similar to verification of the behavior of PVM described in Section All the procedures of constructing a PVM system are done with the PVM Console window on the host machine. A PVM system is constructed by adding remote machines as slave machines in PVM Console window. The machine on which you open PVM Console window will be the host machine of PVM system, and hence the host machine of VR system. The other machines added to PVM system will be slave machines. The procedures for constructing PVM system is as follows: 1. Click Programs in Start menu of the machine which will be the host machine of PVM system. (Figure 5.2-1) 2. Click PVM 3.4 in the submenu. (Figure 5.2-1) 3. Click PVM Console in the submenu to open the PVM Console window. (Figure 5.2-1) 4. PVM Console window appears. Wait until the prompt text pvm> appears. (Figure 5.2-2) 5. Type add <remote host>, and press Enter to add a slave machine to virtual machine system. (Figure 5.2-3) In step 5, <remote host> is the host name of the remote machine to be added to PVM system. For example, typing add krypton will add a machine whose host name is krypton. 32

37 6. Repeat step 4 for other remote machines until every remote machine which will be used as a slave machine in VR system is added to PVM system. (Figure 5.2-3) 7. Type conf and press Enter to see the list of remote machines which have been added to PVM system. Check that all remote machines are in the list. (Figure 5.2-4) If some error occurs in the above steps, you should go back to Section and check the set-up procedures. Figure Selecting PVM Console in the menu. (Steps 1 3) Figure Waiting until the prompt text pvm> appears. (Step 4) Figure Adding remote machines. (Steps 5, 6) Figure Check the list of the machines in virtual machine system. (Step 7) 33

38 5.2.2 Constructing PVM System Using a Hostfile There is another way to construct a PVM system. With the names of all the remote machines specified in a socalled hostfile, you can have all the remote machines added to the PVM system automatically when PVM Console (i.e., pvm.exe ) is opened. This is a convenient way if you use PVM system always with the same remote machines. The procedures for constructing PVM system using a hostfile is as follows: 1. Make a hostfile that specifies all the remote machines in PVM system if you do not have one already. 2. Open Command Prompt Console window. 3. Type cd c:\program files\pvm3.4\lib\win32 in Command Prompt Console window and press Enter to change the current directory. 4. Type pvm <hostfile name> and press Enter to execute pvm.exe. The Command Prompt Console window will work as a PVM Console window. <hostfile name> is the full pathname of the hostfile you have created in step 1. (Figure 5.2-5) 5. The machines specified in the hostfile are automatically added to PVM system. Type conf and press Enter to check machines are added correctly. (Figure 5.2-7) Figure Executing pvm.exe with a hostfile. (Step 4) Figure PVM window. Figure Checking the machines added to virtual machine system. (Step 5) 5.3 Operating VR with HCI HCI (Human-Computer Interface) helps a user create an input file for the simulation engine, execute the simulation engine, and browse calculation results. HCI cannot be executed without Microsoft Visual Basic 6.0 installed in the host machine. HCI does not work correctly if it is not installed as is described in Section 3.8. If VR master software is not properly installed, VR master simulation engine cannot be executed by HCI. It is also necessary that Microsoft Access 97 be installed as is described in Section 3.3, in order to use database query window of HCI described later in Section 3. Throughout this section, procedures are described in the order that you can follow step by step and run a calculation. 34

39 5.3.1 Starting HCI Make sure that you have logged on the host machine with your local user account. And make sure that PVM system is already constructed. When you have constructed PVM system of Windows NT machines, it is time to launch HCI. 1. Open Windows NT Explorer. (Figure 5.3-2) 2. Change directory to d:\vrengine\vr\. (Figure 5.3-2) 3. Double-click vr01.exe icon to launch HCI. (Figure 5.3-2) The main window of HCI opens. The main window has five buttons. There are four buttons in the center of the main window, each of which opens a new window (Figure 5.3-3). The top button, MAKE INPUT, helps you make an input file. The second button, EXECUTE CALCULATION, invokes the VR simulation engine and start calculation. The third button, DATABASE QUERY, will show you numerical result. The fourth button in the bottom, DISPLAY RESULTS, shows the plots of the calculation results. The button END in the bottom-right corner of the main window lets you exit HCI program. You can operate VR basically by proceeding from the top button to the bottom button. Element Data Input Window Chain Data Input Window Make input Execute calculation Database Query Display Results Initial Window Input Window for Input data file name DB Register DB Query DB Listing DB Query Menu Calculation Progress Display DB Query Result Display DB Listing Dispaly Calculation Results Display Figure Hierarchical relations of HCI windows. Figure Opening HCI. (Steps 1 3) 35

40 Figure The main window of HCI Making an Input File The first thing to be done with HCI is to prepare an input file. All the parameters necessary for VR calculation are to be input in the windows of HCI. HCI will create a new input file following the parameters in the windows Making an Input File from the Scratch Procedures to create a completely new input file are described in this section. 1. Click on MAKE INPUT button in the main window. (Figure 5.3-3) 2. A new window appears, and you can choose whether to make a totally new input file or to modify an existing input file. Click on MAKE NEW INPUT button in order to make a new one. (Figure 5.3-4) A data input window appears. It is necessary to input all the parameters required in this window. 3. Before you start typing parameters, click on INPUT ELEMENT DATA button in the top-right corner of the window. (Figure 5.3-5) 4. Another window appears and you are asked to input the number of elements in all the decay chains in your calculation. Type the number of elements in the field, and click on OK button in the window. (Figure 5.3-6) After step 4, HCI adjusts number of the element data fields in the bottom of the data input window, and some of the fields are disabled if the number of the elements is less than Input all the parameters into the corresponding fields. Explanation of each field is given in the end of this section. (Figure 5.3-7) 6. After you have filled all the parameter fields necessary in the window, click on GO TO CHAIN DATA PANEL button. (Figure 5.3-8) 7. Decay chain data window appears. (Figure 5.3-9) 8. Click on INPUT CHAIN DATA button in the chain data window. (Figure 5.3-9) 9. A new window appears, and you are asked to input the number of decay chains that is considered in calculation. Type the number of decay chains in the field, and click on OK button. 10. Now you are asked to input the number of radionuclide members in each decay chain, one after another. Type the number of members and click on OK button until you input the numbers of the members for all the decay chains. (Figure ) 11. The chain data window comes to the front with numbers automatically set in Chain and Member fields according to the numbers you have typed in steps 9 & 10. (Figure ) 12. Fill all the fields in the chain data window with a mass number, half-life, initial mass, the element index number of each radionuclide. Explanation of these parameters is given in the end of this section. (Figure ) 13. After filling all the fields in the chain data window, click on BACK button to return to the data input window. (Figure ) 36

41 14. By this time, all the parameters necessary for your calculation is supposed to be input in appropriate fields. Check the parameters, and click on DATA INPUT FINISHED button to create an input file. 15. A small new window appears and you are asked to input the pathname of the new input file. In current version of HCI, the default pathname already appears as d:\vrengine\vr\imp001.txt. It is convenient not to change the pathname because calculation can be done only with an input file in the directory d:\vrengien\vr\. Click on OK button to save the input file. (Figure ) 16. Click on BACK button in the data input window to go back to the main window of HCI. Figure Clicking on MAKE NEW INPUT button in order to make a new input file from the scratch. (Step 2) Figure The data input window before typing parameters. (Step 3) Figure Inputting total number of elements. (Step 4) 37

42 Figure Data input window with the element data fields adjusted. Figure Data input window with parameters typed in. (Step 6) 38

43 Figure Chain data window. (Step 7) Figure Inputting the number of decay chains. (Step 9) Figure Inputting the number of radionuclide members in a chain. (Step 10) Figure Chain data window. (Step 11) 39

44 Figure Chain data window with parameters typed in. (Step 12) Figure Specifying the location where the new input file is saved. (Step 15) No of Canisters: Number of canisters per row not the number of canisters in whole repository. Length of Repository (m): The length of total compartments arranged in one row. Distance between Canisters (m): The distance between two adjacent canisters in the direction parallel to the canister row, or longitudinal length of one compartment. This parameter seems to be redundant because a relation, (Distance between Canisters) = (Length of Repository) / (No of Canisters), must always be satisfied. However, current version of VR simulation engine requires all these three parameters to be input correctly. Surface (m 2 ): A half of the side-surface area of one glass log. The half comes from the symmetric geometry in the model. Buffer Thickness (m): Thickness of the bentonite buffer region. Buffer Porosity (-): Porosity in the bentonite buffer region. Rock Porosity (-): Porosity in the near-field rock region. Groundwater Velocity (m/y): Pore velocity of ground water in the repository. This value is assumed to be constant in space and in time. Weight for Numerical: Parameter used in numerical scheme for diffusion equation in the buffer region. This parameter can take decimal number usually Especially, setting this parameter to 0, 0.5, 1 corresponds to explicit method, Crank-Nicolson method, implicit method, respectively. Time Increment (y): Time step width for calculation. 40

45 Cut off Time (y): The time until which the radionuclide transportation should be calculated. Print Interval: This parameter has no effect on calculation in the current version of VR simulation engine. Type a dummy number in this field. No of Compart. to print: Because printing the information about every compartment can create an extremely large file, only the information for a certain number of specified compartment is printed. The number of compartments is to be input in this field. The number of compartments to be printed must be larger or equal to 0, and smaller or equal to 5. In the five fields just below this, you can specify the compartment to print. Element No of U: The element index number for uranium. Element index numbers are shown on the left of element data fields in the data input window. Set this to zero if there is no uranium in the decay chains. Task No: Input up to four task numbers to assign a slave machine to each decay chain. You can specify with these parameters how the calculation of decay chains is distributed to slave machines. Task numbers must be larger or equal to 0, and smaller than the total number of machines in VR system. Leach Time (y): The time when the glass matrix in canisters completely dissolves. Element: Symbols of the elements that appear in the decay chains. Retardation Factor in Buffer: Retardation factor for the element in the bentonite buffer region. Retardation factor K e for an element e is defined as Ke = ε ρ Kde, where ρ [kg/m 3 ] and ε are the density and the ε porosity of the buffer, respectively. Kd e [m 3 /kg] is the sorption distribution coefficient of element e for the bentonite buffer. Diffusion Co. in Buffer (m 2 /y): Diffusion coefficient of the element in the bentonite buffer. Solubility (mol/m 3 ): Solubility of the element in groundwater. Retardation Factor in Rock: Retardation factor for the element in the near-field rock region. Retardation factor R e p e for an element e is defined as Re = ε ρ pkdp, where ρ p [kg/m 3 ] and ε p are the density and the ε p e porosity of the near-field rock, respectively. K dp [m 3 /kg] is the sorption distribution coefficient of element e for the near-field rock. Data range set yes/no=1/0: This parameter has no effect on calculation in the current version of VR simulation engine. The parameter field is kept for future improvement. Start time: This parameter has no effect on calculation in the current version of VR simulation engine. The parameter field is kept for future improvement. Time step: This parameter has no effect on calculation in the current version of VR simulation engine. The parameter field is kept for future improvement. Mass Number: The mass number of each radionuclide. Half-life (y): The half-life of each radionuclide. Initial Mass (mol): A half of the mass of each radionuclide initially contained in one canister. The half comes from the symmetric geometry in the model. Nuclide Number: The index number for each radionuclide which indicates the element input in data input window. This number corresponds to the number that appears on the left of element data fields Modifying an Existing Input File Although you can always create an input file from the scratch as is described in the previous section, it is somewhat inefficient to do so when you already have an input file and you are going to make a new input file in which only a few parameters are different from the existing input file. If you are going to make an input file which is slightly different from an existing input file, modifying the existing input file may be preferred. HCI can retrieve the parameters from an existing input file into the data input windows. You can modify some or all of the parameters and save a new input file. 1. Copy an existing input file to the directory d:\vrengine\vr\. 2. Click on MAKE INPUT button in the main window of HCI. (Figure ) 41

46 3. A new window appears. Type the name of the input file you have copied in the text field. The filename here must not contain the name of the directory. (Figure ) 4. Click on RETRIEVE INPUT button to read the file. (Figure ) 5. A data input window appears with all the parameter fields filled with the data according to the existing input file. (Figure ) 6. Modify the parameters. (Figure ) 7. After modification, click on DATA INPUT FINISHED button to create a new one. (Figure ) 8. A small new window appears and you are asked to input the pathname of the new input file. In current version of HCI, the default pathname already appears as d:\vrengine\vr\imp001.txt. It is convenient not to change the pathname because calculation can be done only with an input file in the directory d:\vrengien\vr\. Click on OK button to save the input file. 9. Click on BACK button in the data input window to go back to the main window of HCI. Figure Main window of HCI. (Step 2) Figure Setting the name of the retrieved file. (Step 3, 4) 42

47 Figure Data input window. (Steps 5 7) Calculation With the new input file in the directory d:\vrengine\vr\, you are ready to execute calculation. Procedures to execute calculation are as follows: 1. Click on EXECUTE CALCULATION button in the main window of HCI. (Figure ) 2. An input panel appears, and you are asked to type the pathname of the input file. Assuming that you have followed the pathname described in Section 5.3.2, type d:\vrengine\vr\inp001.txt, and click on OK button. (Figure ) Figure Clicking on EXECUTE CALCULATION button in the main window of HCI, and specifying the input-file path. (Steps 1, 2) 43

48 Figure Displayed output text during VR calculation. (Step 3) 3. VR simulation engine launches calculation. A DOS Prompt window named d:\vrengine\vr\vrmaster.exe appears and output text from vrmaster.exe is printed in the window. When the calculation is done, the window closes by itself, and the main window of HCI comes to the front again. (Figure ) 4. After the calculation is done, you may go on to the next step and explore the results. During the calculation, several output files are created in the directory, d:\vrengine\vr\, by VR master simulation engine. Details about these output files are described in Section Database Query Window If you click DATABASE QUERY button in the initial window, you can register the calculation results of VR or retrieve the data from database. A DATABASE QUERY MENU window appears (Figure ) if you click DATABASE QUERY button in the initial window. If you click DATA REGISTRATION button in the DATABASE QUERY MENU window, the calculation results are stored in the database in VR. If you choose DATA QUERY, the query condition input box appears in the desktop. If you specify retrieve condition (time, chain number, member number, and compartment number), calculation results that match the condition will be retrieved and displayed in the DATABASE QUERY RESULT window. If you click DATA LISTING in the DATABASE QUERY MENU, DATABASE LISTING window appears in the desktop. By using scroll bar, you can show the inventory and mass data in each time step. Figure DATABASE QUERY window. Figure Database query result window in a window of Access. 44

49 Figure DATABASE LISTING window Browsing Plots of the Calculation Results Masses of the radionuclides in each component of the system can be plotted by HCI as a function of time. It is convenient to use the HCI when you want to check the calculation result quickly. You can make a choice to plot the masses in the glass, the bentonite buffer region, near-field rock region, near-field (whole repository), far-field, or total system. When this function is used, HCI always reads the output file: d:\vrengine\vr\mass_data2. Although this is the only output file necessary for plotting, the location of the file and its name have to be exactly the same as the above. 1. Click on DISPLAY RESULTS button in the main window of HCI. 2. The result window appears. (Figure ) 3. Click on one of the six radio buttons to select the region, and click on DRAW GRAPH button to display the plot. 4. Repeat Step 3 as many times as you want. 5. Click on BACK button to go back to the main window of HCI. Figure Result window. (Steps 2, 3) 45

50 5.3.6 Terminating HCI To terminate and exit HCI, all that required is to click on END button in the corner of the main window of HCI. All the windows of HCI will be deleted and HCI will terminate. Terminating HCI does not change any file, and leaves all files as they are, i.e., the input file and all the output files created by the calculation are still left in the directory d:\vrengien\vr\. You can re-launch HCI and still browse the results as long as the file mass_data2 exists in the directory d:\vrengine\vr\. Figure The HCI main window. Click on END button to terminate HCI. 5.4 Terminating PVM To disconnect all the slave machines in the PVM system and terminate PVM, follow the procedures below. 1. Bring PVM Console window to the front. 2. Type halt in PVM Console window and press Enter. All the remote machines are freed from PVM system, and PVM Console window is closed. Figure Terminating PVM with halt command. (Step 2) It should be noted that PVM Console window must always be closed by halt command. Otherwise (e.g., the upper right button of the PVM Console window is clicked to close the window), PVM daemon does not terminate properly, and as a result, you will not be able to open PVM Console window again until the following procedures are done. 1. Check if a file named pvmd.<username> exists in the directory specified with the environment variable PVM_TMP. PVM daemon is running if the file exists. (Figure 5.4-2, Figure 5.4-3) In step 1, <username> is the local username with which you log on the local Windows NT machine. For example, the file name will be pvmd.berkeley for username berkeley. The environment variable PVM_TMP can be checked in System control panel (See Section 3.6.3). PVM_TMP is set to C:\TEMP\ by default. 2. Click Start menu. 3. Click Programs in the menu. (Figure 5.4-4) 46

51 4. Click PVM 3.4 in the submenu. (Figure 5.4-4) 5. Click PVM Daemon in the submenu. PVM Daemon is executed and quickly terminates by itself. 6. Delete the file pvmd.<username> which is mentioned in step 1. (Figure 5.4-5) Figure Checking if the file pvmd.*** exists. (Step 1) Figure Contents of the file pvmd.***. Figure Executing PVM Daemon. (Steps 3,4) 47

52 5.5 Input File Figure Deleting file pvmd.***. (Step 6) Shown below is an example of input file created by the current version of HCI. Description of each parameter is also printed in the file by HCI, so that checking the parameters and editing the input file can be done easily. 200 ; =No_of_canisters================ 2000 ; =Length_of_repository(m)======== 10 ; =Distance_bet_canisters(m)====== ; =Surface(m2)==================== 0.98 ; =Buffer_thickness(m)============ 0.3 ; =Buffer_porosity(-)============= 0.5 ; =Rock_porosity(-)=============== 1 ; =Groundwaster_velosity(m)======= 2 ; =No_of_elements=================== //=1=element_name================== //=2=Retardation_factor_of_buffer== //=3=Diffusion_coef._of_buffer====== //=4=Solubility_in_glass============ //=5=Retardation_factor_of_rock===== //=6=Diffusion_coef._of_rock======== //================================ //================================ //================================ //================================ //=cahin_no======================= //=member_no====================== //=1=mass_number================== //=2=half_life(y)================ //=3=initial_mass(mol)=========== //=4=element_no=================== //================================ //================================ //================================ //================================ //================================ //================================ //================================ Pu, U, ; =No_of_Chain================== 48

53 1 ; =No_of_member============= //================================ ; =No_of_member============= //================================ E ; =No_of_member============= //================================ E ; =weight_for_numerical_scheme===== 5 ; =time_increment================== 1E+07 ; =cut_off_time==================== 1000 ; =leach_time====================== 1 ; =print_interval================== 4 ; =no_of_compt_for_print============ 1 ; ==compt_no_for_print====== 10 ; ==compt_no_for_print====== 100 ; ==compt_no_for_print====== 200 ; ==compt_no_for_print====== 2 ; =element_no_of_u================= 0 ; =task_no_for_parallel_calc==== 0 ; =task_no_for_parallel_calc==== 0 ; =task_no_for_parallel_calc==== 0 ; =task_no_for_parallel_calc==== 1 ; =printing_to_db_option==== ; =printing_to_db_option=st=del=== 5.6 Output Files Contents of the output files are described in this section. Several output files are created when VR simulation engine is executed. All of them are created in the directory d:\vrengine\vr\ Òot5.txtÓ Almost all the information related to the calculation can be found in the file ot5.txt. Input parameters which have been obtained from an input file are first listed in the beginning of the file ot5.txt. Then the correspondence of decay chains and slave machines are printed. For example, the following text is a part of the file. chain no:1 task no:0 chain no:2 task no:1 chain no:3 task no:2 ioptprt 0 Repository : number_of_compartment : 50 length_of_repository : 5.000e+002 height_of_repository : 5.000e+000 width_of_compartment : 9.050e-002 length_of_compartment : 1.000e+001 area_of_compartment_bottom : 9.050e-001 area_of_compartment_cross_section : 4.525e-001 ******************************************************************** < time_increment,cut_off_time > : 5.000e e+004 ******************************************************************** SLAVE no:0 TID: SLAVE no:1 TID: SLAVE no:2 TID: host name plutonium task ID for the host host name neptunium task ID for the host host name uranium task ID for the host With the first three lines in above example, calculation of decay chain 1 is set to task 0, that of chain 2 is set to task 1, and that of chain 3 is set to task 2. The later three lines after skipping the following 13 lines show that task 0 49

54 corresponds to the task ID , and so on. The last three lines show that the slave machine ID corresponds to the host name of the slave machine, plutonium, and so on. Since the slave machine IDs are similar to task IDs only the last two or three figures are different it can be easily told that task ID corresponds to slave machine ID After all, we know that calculation for decay chain 1 was done by the machine whose host name was plutonium. After the correspondence information, the calculation result, i.e., the list of the masses of radionuclides in components of the system at each time, is printed. Time is printed in the unit of years. And the masses are printed in the unit of mol. Because of symmetric geometry of the model, the mass is in fact the mass per half of the compartment row. In the very last line of the file, the time spent for the calculation is printed in the unit of seconds Inventory Files Execution of VR simulation engine also creates six inventory files, in which the masses of radionuclides in a certain component at each time are tabulated. The file names are as follows: inv_buffer.txt (inventory in bentonite buffer region), inv_ff_rock.txt (inventory in far-field rock region), inv_glass.txt (inventory in glass logs), inv_nf.txt (inventory in near-field, i.e., whole repository), inv_nf_rock.txt (inventory in near-field rock region), inv_total_system.txt (inventory in the total system). Inventory in the near-field is sum of the inventories in glass logs, bentonite buffer region and near-field rock region. Inventory in the total system is sum of the inventories in glass logs, bentonite buffer region, near-field rock region and far-field rock region. For example, the first six lines of the file inv_buffer.txt created through a certain calculation are shown below: Total inventory in buffer time Pu239 U235 U e e e e e e e e e e e e-004 This calculation has been done for three radionuclides Pu-239, U-235 and U-238, and the mass [mol] of each radionuclide in the bentonite buffer region is tabulated in the file. This mass is again the mass per half of compartment row because of the symmetric geometry of the model. The time [y] is shown in the leftmost column Òmass_dis.txtÓ The normalized radionuclide masses [-] at each time [y] in the total system, in the whole near-field region, and in the far-field region are tabulated in the file mass_dis.txt. The masses are normalized to the initial mass in glass logs. For example, the first six lines of mass_dis.txt are shown below. Mass distribution in system time Pu239TOTAL Pu239IN Pu239OUT U235TOTAL U235IN e e e e e e e e e e e e e e e e e e Release Rate Files Files gtob_release.txt, bton_release.txt, ntof_release.txt, and fractional_rr.txt are created during calculation. However, the current version of VR does not print actual data into these files Òglassinv_zero.txtÓ The time [y] when each radionuclide disappears in the glass log in each compartment is tabulated in the file glassinv_zero.txt. An example of this file is shown below. Inventory zero time 50

55 1:Pu239 2:Pu239 3:Pu239 4:Pu e e e e : U235 2: U235 3: U235 4: U e e e e Pairs of a compartment number and the name of radionuclide are listed first. The number just below each pair indicates the time [y] when the radionuclide completely depletes from the glass log in the compartment Òdistrib.txtÓ The profiles of mass and concentration for each radionuclide in each compartment at each time step [y] is stored in the file "distrib.txt". The following data for a radionuclide in the compt-th compartment are listed in the file: the masses [mol] in the glass log (glass_mass), in the buffer region (buf_mass) and in the near-field rock region (nfr_mass), the total mass [mol] in the compartment (compt_mass), the concentration [mol/m 3 ] in the pore water at the inner boundary of the buffer region (bibconc), the concentration [mol/m 3 ] in the pore water in the near-field rock region, the release rates [mol/y] from the glass log into the buffer (gtob), from the buffer into the near-field rock (bton) and from the near-field rock region into the next compartment (nfrr). For example, the first four lines of mass_dis.txt are shown below. time, chain, member, compt, glass_mass, buf_mass, nfr_mass, compt_mass, e+000, 1, 1, 1, 1.964e+000, 9.579e-005, 0.000e+000, 1.964e+000, e+000, 1, 1, 2, 1.964e+000, 9.579e-005, 0.000e+000, 1.964e+000, e+000, 1, 1, 3, 1.964e+000, 9.579e-005, 0.000e+000, 1.964e+000, Other Output Files There are other output files created by VR master simulation engine. Some of those are created for code debugging, and some are to be read by HCI. The details about those output files are not described in this manual. Names of the output files are listed below: data_com debug_output.txt mass_data mass_data2 nuc_data 5.7 Operating VR without HCI Execution of VR simulation engine using HCI is already described in Section However, VR simulation engine can also be executed without help of HCI. The way to execute VR simulation engine without HCI is described in this section. The procedures described in Section can be replaced with the ones described in this section. It is assumed that an input file in correct format has already been prepared in the directory d:\vrengine\vr, and that PVM system has been constructed. Without using HCI, VR simulation engine can be executed in Command Prompt console window. The procedures are listed below. 1. Open Command Prompt console window. (Figure 5.7-1) 2. Type d: and press Enter to change the hard disk drive. ( Figure 5.7-2) 3. Type cd d:\vrengine\vr and press Enter to change current directory to the place where vrmaster.exe is located. ( Figure 5.7-2) 4. Type vrmaster <input file name> <output file name> and press Enter to start calculation. ( Figure 5.7-3) In step 4, <input file name> is the name of the input file, and <output file name> is the name of output file. For example, type vrmaster inp001.txt ot5.txt if your input file is named inp001.txt and you want to have the output file named ot5.txt. <output file name> is automatically set to ot5.txt when HCI is used to execute VR simulation engine. 51

56 Figure Opening Command Prompt window. (Step 1) Figure Changing directory. (Steps 2, 3) Figure Execute vrmaster.exe. (Step 4) Figure Output text during the calculation. 52

57 6 MODIFYING VR When the mathematical model of VR calculation is changed, modification of source codes for VR simulation engine and re-compilation are required. Re-compilation is explained in this chapter. There are several files and software that are necessary for modification and re-compilation of VR software but are not necessary when calculation is done without modification of VR. Make sure that all the software described in Chapter 3 is installed in the machine with which you are going to modify VR software. 6.1 Modifying win32visual.def The file win32visual.def has to be modified before compilation in order to set the environment parameter for compiler correctly. Then you should compile master and slave programs of PVM simulation program. You should modify the file win32visual.def. All you have to do is to replace the existing file with the one shown in appendix 6. The full path name of win32visual.def to be modified is as follows: c:\program files\pvm3.4\conf\ win32visual.def 6.2 Compiling PVM simulation program You should compile PVM simulation program by using makefile. The makefile is kicked by makepro.bat file. The directory structure of relevant files are shown in Fig.3-2 The source list of all the file related to compiling is shown in Appendix.6. The detailed procedure to compile VR simulation program is as follows: (a)compiling of master program of VR simulation engine 1. Open command prompt console (Figure 6.2-1) 2. Change directory to c:\program files\pvm3.4\ex3m (Figure 6.2-2) 3. Input makepro, then push enter key. 4. Compiling starts. (Figure 6.2-3) (b)compiling of slave program of VR simulation engine 5. Change directory to c:\program files\pvm3.4\ex3s 6. Input makepro, then push enter key. (Figure 6.2-4) 7. Compiling starts. (Figure 6.2-5) Figure Opening Command Prompt window. (Step 1) 53

58 Figure Change directory. (Step 2) Figure Compiling. (Step 4) Figure Typing the command makepro. (Step 6) Figure Compiling. (Step 7) 54