X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FMemorySetting.java;h=bb545cbd54305e8a173f43a6646dd59bb53a6c2a;hb=353cb52722490edcba2c13b18836b6d37c5455de;hp=c8bc222890808346c967420c8aafa093960d1d47;hpb=50050bb6537154a1e74a706a002f1a4a33195449;p=jalview.git diff --git a/src/jalview/bin/MemorySetting.java b/src/jalview/bin/MemorySetting.java index c8bc222..bb545cb 100644 --- a/src/jalview/bin/MemorySetting.java +++ b/src/jalview/bin/MemorySetting.java @@ -1,51 +1,412 @@ +/* + + private static String ADJUSTMENT_MESSAGE = null; + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.bin; -import java.lang.management.ManagementFactory; -import java.lang.management.OperatingSystemMXBean; +import java.util.Locale; +/** + * Methods to decide on appropriate memory setting for Jalview based on two + * optionally provided values: jvmmempc - the maximum percentage of total + * physical memory to allocate, and jvmmemmax - the maximum absolute amount of + * physical memory to allocate. These can be provided as arguments or system + * properties. Other considerations such as minimum application requirements and + * leaving space for OS are used too. + * + * @author bsoares + * + */ public class MemorySetting { - public static final long leaveFreeMinMemory = 536870912; // 0.5 GB + public static final String MAX_HEAPSIZE_PERCENT_PROPERTY_NAME = "jvmmempc"; + + public static final String MAX_HEAPSIZE_PROPERTY_NAME = "jvmmemmax"; + + private static final int MAX_HEAPSIZE_PERCENT_DEFAULT = 90; // 90% + + private static final long GIGABYTE = 1073741824; // 1GB + + public static final long LEAVE_FREE_MIN_MEMORY = GIGABYTE / 2; + + public static final long APPLICATION_MIN_MEMORY = GIGABYTE / 2; + + private static final long MAX_HEAPSIZE_GB_DEFAULT = 32; + + private static final long NOMEM_MAX_HEAPSIZE_GB_DEFAULT = 8; + + public static final String NS = "MEMORY"; + + public static final String CUSTOMISED_SETTINGS = NS + + "_CUSTOMISED_SETTINGS"; + + public static final String MEMORY_JVMMEMPC = NS + "_" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME.toUpperCase(Locale.ROOT); + + public static final String MEMORY_JVMMEMMAX = NS + "_" + + MAX_HEAPSIZE_PROPERTY_NAME.toUpperCase(Locale.ROOT); + + protected static boolean logToClassChecked = false; - public static final long applicationMinMemory = 536870912; // 0.5 GB + public static String memorySuffixes = "bkmgt"; // order of the suffixes is + // important! - protected static long getPhysicalMemory() + public static long getMemorySetting() { - final OperatingSystemMXBean o = ManagementFactory - .getOperatingSystemMXBean(); + return getMemorySetting(null, null); + } + + public static long getMemorySetting(String jvmmemmaxarg, + String jvmmempcarg) + { + return getMemorySetting(jvmmemmaxarg, jvmmempcarg, true, false); + } + + /** + * Decide on appropriate memory setting for Jalview based on the two arguments + * values: jvmmempc - the maximum percentage of total physical memory to + * allocate, and jvmmemmax - the maximum absolute amount of physical memory to + * allocate. These can be provided as arguments. If not provided as arguments + * (or set as null) system properties will be used instead (if set). The + * memory setting returned will be the lower of the two values. If either of + * the values are not provided then defaults will be used (jvmmempc=90, + * jvmmemmax=32GB). If total physical memory can't be ascertained when + * jvmmempc was set or neither jvmmempc nor jvmmemmax were set, then jvmmemmax + * defaults to a much safer 8GB. In this case explicitly setting jvmmemmax and + * not setting jvmmempc can set a higher memory for Jalview. The calculation + * also tries to ensure 0.5GB memory for the OS, but also tries to ensure at + * least 0.5GB memory for Jalview (which takes priority over the OS) If there + * is less then 0.5GB of physical memory then the total physical memory is + * used for Jalview. + * + * @param jvmmemmaxarg + * Maximum value of memory to set. This can be a numeric string + * optionally followed by "b", "k", "m", "g", "t" (case insensitive) + * to indicate bytes, kilobytes, megabytes, gigabytes, terabytes + * respectively. If null a default value of 32G will be used. If null + * and either physical memory can't be determined then the default is + * 8GB. + * @param jvmmempcarg + * Max percentage of physical memory to use. Defaults to "90". + * + * @param useProps + * boolean to decide whether to look at System properties. + * + * @return The amount of memory (in bytes) to allocate to Jalview + */ + public static long getMemorySetting(String jvmmemmaxarg, + String jvmmempcarg, boolean useProps, boolean quiet) + { + // actual Xmx value-to-be + long maxMemLong = -1; + clearAdjustmentMessage(); + + // (absolute) jvmmaxmem setting, start with default + long memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE; + if (jvmmemmaxarg == null && useProps) + { + jvmmemmaxarg = System.getProperty(MAX_HEAPSIZE_PROPERTY_NAME); + } + String jvmmemmax = jvmmemmaxarg; + if (jvmmemmax != null && jvmmemmax.length() > 0) + { + // parse the arg + try + { + memmax = memoryStringToLong(jvmmemmax); + if (memmax == 0) + { + throw (new NumberFormatException("Not allowing 0")); + } + } catch (NumberFormatException e) + { + memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE; + setAdjustmentMessage("MemorySetting Property '" + + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg + + "') badly formatted or 0, using default (" + + MAX_HEAPSIZE_GB_DEFAULT + "g).", quiet); + } + + // check at least minimum value (this accounts for negatives too) + if (memmax < APPLICATION_MIN_MEMORY) + { + memmax = APPLICATION_MIN_MEMORY; + setAdjustmentMessage("MemorySetting Property '" + + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg + + ") too small, using minimum (" + APPLICATION_MIN_MEMORY + + ").", quiet); + } + } + else + { + // no need to warn if no setting + // adjustmentMessage("MemorySetting Property '" + maxHeapSizeProperty + // + "' not + // set."); + } + + // get max percent of physical memory, starting with default + float percent = MAX_HEAPSIZE_PERCENT_DEFAULT; + if (jvmmempcarg == null && useProps) + { + jvmmempcarg = System.getProperty(MAX_HEAPSIZE_PERCENT_PROPERTY_NAME); + } + String jvmmempc = jvmmempcarg; + long mempc = -1; try { - if (o instanceof com.sun.management.OperatingSystemMXBean) + if (jvmmempc != null) { - final com.sun.management.OperatingSystemMXBean osb = (com.sun.management.OperatingSystemMXBean) o; - return osb.getTotalPhysicalMemorySize(); + int trypercent = Integer.parseInt(jvmmempc); + if (0 <= trypercent && trypercent <= 100) + { + percent = trypercent; + } + else + { + setAdjustmentMessage("MemorySetting Property '" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + + "' should be in range 0..100. Using default " + percent + + "%", quiet); + } } - } catch (NoClassDefFoundError e) + } catch (NumberFormatException e) { - // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM - Cache.log.error("No com.sun.management.OperatingSystemMXBean"); + setAdjustmentMessage("MemorySetting property '" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg + + ") badly formatted", quiet); } - // We didn't get a com.sun.management.OperatingSystemMXBean. - return -1; + // catch everything in case of no com.sun.management.OperatingSystemMXBean + boolean memoryPercentError = false; + try + { + long physicalMem = GetMemory.getPhysicalMemory(); + if (physicalMem > APPLICATION_MIN_MEMORY) + { + // try and set at least applicationMinMemory and thereafter ensure + // leaveFreeMinMemory is left for the OS + + mempc = (long) ((physicalMem / 100F) * percent); + + // check for memory left for OS + boolean reducedmempc = false; + if (physicalMem - mempc < LEAVE_FREE_MIN_MEMORY) + { + mempc = physicalMem - LEAVE_FREE_MIN_MEMORY; + reducedmempc = true; + setAdjustmentMessage("MemorySetting Property '" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg + + ") too large. Leaving free space for OS and reducing to (" + + mempc + ").", quiet); + } + + // check for minimum application memsize + if (mempc < APPLICATION_MIN_MEMORY) + { + if (reducedmempc) + { + setAdjustmentMessage("Reduced MemorySetting (" + mempc + + ") too small. Increasing to application minimum (" + + APPLICATION_MIN_MEMORY + ").", quiet); + } + else + { + setAdjustmentMessage("MemorySetting Property '" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + + jvmmempcarg + ") too small. Using minimum (" + + APPLICATION_MIN_MEMORY + ").", quiet); + } + mempc = APPLICATION_MIN_MEMORY; + } + } + else + { + // not enough memory for application, just try and grab what we can! + mempc = physicalMem; + setAdjustmentMessage( + "Not enough physical memory for application. Ignoring MemorySetting Property '" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + + jvmmempcarg + + "). Using maximum memory available (" + + physicalMem + ").", + quiet); + } + + } catch (Throwable t) + { + memoryPercentError = true; + setAdjustmentMessage( + "Problem calling GetMemory.getPhysicalMemory(). Likely to be problem with com.sun.management.OperatingSystemMXBean", + quiet); + t.printStackTrace(); + } + + // In the case of an error reading the percentage of physical memory (when + // jvmmempc was set OR neither jvmmempc nor jvmmemmax were set), let's cap + // maxMemLong to 8GB + if (memoryPercentError && mempc == -1 + && !(jvmmempcarg == null && jvmmemmaxarg != null) // the same as + // (jvmmempcarg != + // null || + // (jvmmempcarg == + // null && + // jvmmemmaxarg + // == null)) + && memmax > NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE) + { + setAdjustmentMessage( + "Capping maximum memory to " + NOMEM_MAX_HEAPSIZE_GB_DEFAULT + + "g due to failure to read physical memory size.", + quiet); + memmax = NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE; + } + + if (mempc == -1) // percentage memory not set + { + maxMemLong = memmax; + } + else + { + maxMemLong = Math.min(mempc, memmax); + } + + return maxMemLong; } - public static long memPercent(int percent) + public static boolean isValidMemoryString(String text) { - long memPercent = -1; + if (text.length() > 0) + { + char lastChar = text.charAt(text.length() - 1); + char[] otherChars = text.substring(0, text.length() - 1) + .toCharArray(); + for (char c : otherChars) + { + if (c < '0' || c > '9') + { + return false; + } + } + if ((lastChar < '0' || lastChar > '9') && memorySuffixes + .indexOf(Character.toLowerCase(lastChar)) == -1) + { + return false; + } + } + return true; + } - long physicalMem = getPhysicalMemory(); - if (physicalMem > applicationMinMemory) + public static long memoryStringToLong(String memString) + throws NumberFormatException + { + if (!isValidMemoryString(memString)) // not valid + { + throw (new NumberFormatException("Not a valid memory string")); + } + char suffix = Character + .toLowerCase(memString.charAt(memString.length() - 1)); + if ('0' <= suffix && suffix <= '9') // no suffix + { + return Long.valueOf(memString); + } + if (memorySuffixes.indexOf(suffix) == -1) // suffix is unknown + { + return -1; + } + + long multiplier = (long) Math.pow(2, + memorySuffixes.indexOf(suffix) * 10); // note order of suffixes in + // memorySuffixes important + // here! + // parse the arg. NumberFormatExceptions passed on to calling method + long mem = Long + .parseLong(memString.substring(0, memString.length() - 1)); + if (mem == 0) { - // try and set at least applicationMinMemory and thereafter ensure - // leaveFreeMinMemory is left for the OS - memPercent = Math.max(applicationMinMemory, - physicalMem - Math.max(physicalMem * (100 - percent) / 100, - leaveFreeMinMemory)); + return 0; } - return memPercent; + // apply multiplier only if result is not too big (i.e. bigger than a long) + if (Long.MAX_VALUE / mem > multiplier) + { + return multiplier * mem; + } + else + { + // number too big for a Long. Limit to Long.MAX_VALUE + System.out.println("Memory parsing of '" + memString + + "' produces number too big. Limiting to Long.MAX_VALUE=" + + Long.MAX_VALUE); + return Long.MAX_VALUE; + } + } + + public static String memoryLongToString(long mem) + { + return memoryLongToString(mem, "%.3f"); + } + + public static String memoryLongToString(long mem, String format) + { + int exponent = 0; + float num = mem; + char suffix = 'b'; + + for (int i = 0; i < memorySuffixes.length(); i++) + { + char s = Character.toUpperCase(memorySuffixes.charAt(i)); + if (mem < (long) Math.pow(2, exponent + 10) + || i == memorySuffixes.length() - 1) // last suffix + { + suffix = s; + num = (float) (mem / Math.pow(2, exponent)); + break; + } + exponent += 10; + } + + return String.format(format, num) + suffix; + } + + private static String ADJUSTMENT_MESSAGE = null; + + private static void setAdjustmentMessage(String reason, boolean quiet) + { + ADJUSTMENT_MESSAGE = reason; + if (!quiet) + { + System.out.println(reason); + } + } + + public static void clearAdjustmentMessage() + { + ADJUSTMENT_MESSAGE = null; + } + + public static String getAdjustmentMessage() + { + return ADJUSTMENT_MESSAGE; } }