1 // ****************************************************************************** 2 // 3 // Title: Force Field X. 4 // Description: Force Field X - Software for Molecular Biophysics. 5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2024. 6 // 7 // This file is part of Force Field X. 8 // 9 // Force Field X is free software; you can redistribute it and/or modify it 10 // under the terms of the GNU General Public License version 3 as published by 11 // the Free Software Foundation. 12 // 13 // Force Field X is distributed in the hope that it will be useful, but WITHOUT 14 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 15 // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more 16 // details. 17 // 18 // You should have received a copy of the GNU General Public License along with 19 // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple 20 // Place, Suite 330, Boston, MA 02111-1307 USA 21 // 22 // Linking this library statically or dynamically with other modules is making a 23 // combined work based on this library. Thus, the terms and conditions of the 24 // GNU General Public License cover the whole combination. 25 // 26 // As a special exception, the copyright holders of this library give you 27 // permission to link this library with independent modules to produce an 28 // executable, regardless of the license terms of these independent modules, and 29 // to copy and distribute the resulting executable under terms of your choice, 30 // provided that you also meet, for each linked independent module, the terms 31 // and conditions of the license of that module. An independent module is a 32 // module which is not derived from or based on this library. If you modify this 33 // library, you may extend this exception to your version of the library, but 34 // you are not obligated to do so. If you do not wish to do so, delete this 35 // exception statement from your version. 36 // 37 // ****************************************************************************** 38 package ffx.ui; 39 40 import java.io.File; 41 import java.util.logging.Logger; 42 import org.apache.commons.lang3.SystemUtils; 43 import org.apache.commons.lang3.builder.ToStringBuilder; 44 45 /** 46 * FFXExec encapsulates a native replacement for the JDK System.exec() method. TINKER programs are 47 * executed in their own thread through a call to a Native method called "FFXExec" which in turn 48 * calls the function "system()". The reason we are not using the System.exec() methods is that some 49 * TINKER routines execute indefinitely. Users may want to exit Force Field X and shut down the JVM 50 * after launching a dynamics run, for example. In this case the thread should not be dependent on a 51 * JVM instance. 52 * 53 * @author Michael J. Schnieders 54 */ 55 public class FFXExec implements Runnable { 56 57 private static final Logger logger = Logger.getLogger(FFXExec.class.getName()); 58 private static String path; 59 private static String ld_library_path; 60 private static String classpath; 61 private FFXSystem system; 62 private String name; 63 private String args; 64 private String dir; 65 private MainPanel mainPanel; 66 private File newFile; 67 private boolean alive = true; 68 private boolean openOnto; 69 private int returnValue = 0; 70 /** 71 * Constructor 72 * 73 * @param s FFXSystem the Native command will execute on 74 * @param n Name of the log file 75 * @param a Command to execute 76 * @param d Directory to launch the command in 77 * @param m MainPanel 78 * @param file File to open 79 * @param o Load the resulting version file onto the passed FFXSystem 80 */ 81 public FFXExec(FFXSystem s, String n, String a, String d, MainPanel m, File file, boolean o) { 82 system = s; 83 name = n; 84 args = a; 85 dir = d; 86 mainPanel = m; 87 newFile = file; 88 openOnto = o; 89 logger.info(toString()); 90 } 91 92 /** 93 * Getter for the field <code>returnValue</code>. 94 * 95 * @return a int. 96 */ 97 public int getReturnValue() { 98 return returnValue; 99 } 100 101 /** 102 * isAlive 103 * 104 * @return a boolean. 105 */ 106 public boolean isAlive() { 107 return alive; 108 } 109 110 /** 111 * Executes the native call to "System()" and notifies the ResultPanel upon completion. This 112 * should only be called indirectly by Thread.Start() 113 */ 114 public void run() { 115 setEnv(); 116 if (args == null 117 || dir == null 118 || path == null 119 || classpath == null 120 || ld_library_path == null) { 121 Logger.getLogger("ffx") 122 .severe( 123 "Native executable could not be executed." 124 + "\nCommand: " 125 + args 126 + "\nDIR: " 127 + dir 128 + "\nPATH: " 129 + path 130 + "\nCLASSPATH: " 131 + classpath 132 + "\nLD_LIBRARY_PATH: " 133 + ld_library_path); 134 return; 135 } 136 Logger.getLogger("ffx") 137 .info( 138 "Native command invoked." 139 + "\nCommand: " 140 + args 141 + "\nDIR: " 142 + dir 143 + "\nFFXExec - PATH: " 144 + path 145 + "\nCLASSPATH: " 146 + classpath 147 + "\nLD_LIBRARY_PATH: " 148 + ld_library_path); 149 returnValue = nativeExec(args, dir, path, classpath, ld_library_path); 150 // Check for a bad return value 151 if (returnValue < 0) { 152 Logger.getLogger("ffx") 153 .warning("The following job exited with a failure status: " + returnValue + "\n" + args); 154 } 155 // Open any created file and display the log. 156 if (mainPanel != null) { 157 if (newFile != null) { 158 String[] labels = args.split(" +"); 159 String command = labels[0].toUpperCase() + " on " + system.getFile().getName(); 160 if (openOnto) { 161 mainPanel.openOn(newFile, system, command); 162 } else { 163 mainPanel.open(newFile, command); 164 } 165 } 166 // mainPanel.getLogPanel().setDone(name); 167 } 168 alive = false; 169 } 170 171 /** 172 * {@inheritDoc} 173 * 174 * <p>Commons.Lang Style toString. 175 */ 176 @Override 177 public String toString() { 178 ToStringBuilder toStringBuilder = 179 new ToStringBuilder(this).append(path).append(classpath).append(ld_library_path); 180 return toStringBuilder.toString(); 181 } 182 183 // Set up the PATH (to TINKER/bin), CLASSPATH and LD_LIBRARY_PATH 184 private void setEnv() { 185 path = MainPanel.ffxDir.getAbsolutePath(); 186 classpath = MainPanel.classpath; 187 // java.home should be the jre directory. 188 ld_library_path = System.getProperty("java.home", "."); 189 if (!SystemUtils.IS_OS_WINDOWS) { 190 ld_library_path = 191 ld_library_path 192 + "/lib/i386/client:" 193 + ld_library_path 194 + "/lib/i386:" 195 + ld_library_path 196 + "/lib/i386/native_threads"; 197 } else { 198 ld_library_path = ld_library_path + "\\bin\\client"; 199 path = path + File.pathSeparator + ld_library_path; 200 } 201 } 202 203 /** 204 * nativeExec method for launching native executables 205 * 206 * @param argv String 207 * @param dir String 208 * @param path String 209 * @param classpath String 210 * @param jre String 211 * @return int 212 */ 213 private native int nativeExec(String argv, String dir, String path, String classpath, String jre); 214 }