X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FMemorySetting.java;h=bb545cbd54305e8a173f43a6646dd59bb53a6c2a;hb=e42524a147f92c836a0a336dde394394976216d2;hp=ac1ac28067870be8e0d6a7a8ba76d5dd6f07ef53;hpb=5911188c77dae6665babf4041dc11484f4a09a0b;p=jalview.git diff --git a/src/jalview/bin/MemorySetting.java b/src/jalview/bin/MemorySetting.java index ac1ac28..bb545cb 100644 --- a/src/jalview/bin/MemorySetting.java +++ b/src/jalview/bin/MemorySetting.java @@ -1,177 +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.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; - public static final long applicationMinMemory = 536870912; // 0.5 GB + private static final long MAX_HEAPSIZE_GB_DEFAULT = 32; - private final static int maxHeapSizePerCentDefault = 90; + private static final long NOMEM_MAX_HEAPSIZE_GB_DEFAULT = 8; - public final static String maxHeapSizePerCentProperty = "jvmmempc"; + public static final String NS = "MEMORY"; - private final static long maxHeapSizeDefault = 34359738368L; // 32GB + public static final String CUSTOMISED_SETTINGS = NS + + "_CUSTOMISED_SETTINGS"; - private final static long noMemMaxHeapSizeDefault = 8589934592L; // 8GB + public static final String MEMORY_JVMMEMPC = NS + "_" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME.toUpperCase(Locale.ROOT); - public final static String maxHeapSizeProperty = "jvmmemmax"; + public static final String MEMORY_JVMMEMMAX = NS + "_" + + MAX_HEAPSIZE_PROPERTY_NAME.toUpperCase(Locale.ROOT); + + protected static boolean logToClassChecked = false; + + public static String memorySuffixes = "bkmgt"; // order of the suffixes is + // important! public static long getMemorySetting() { return getMemorySetting(null, null); } - public static long getMemorySetting(String jvmmemmaxString, - String jvmmempcString) + 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(); - // get (absolute) jvmmaxmem setting - long memmax = maxHeapSizeDefault; - String jvmmemmaxorig = jvmmemmaxString; - if (jvmmemmaxorig == null) + // (absolute) jvmmaxmem setting, start with default + long memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE; + if (jvmmemmaxarg == null && useProps) { - jvmmemmaxorig = System.getProperty(maxHeapSizeProperty); + jvmmemmaxarg = System.getProperty(MAX_HEAPSIZE_PROPERTY_NAME); } - String jvmmemmax = jvmmemmaxorig; + String jvmmemmax = jvmmemmaxarg; if (jvmmemmax != null && jvmmemmax.length() > 0) { - long multiplier = 1; - switch (jvmmemmax.toLowerCase().substring(jvmmemmax.length() - 1)) - { - case "t": - multiplier = 1099511627776L; // 2^40 - jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1); - break; - case "g": - multiplier = 1073741824; // 2^30 - jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1); - break; - case "m": - multiplier = 1048576; // 2^20 - jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1); - break; - case "k": - multiplier = 1024; // 2^10 - jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1); - break; - case "b": - multiplier = 1; // 2^0 - jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1); - break; - default: - break; - } - // parse the arg try { - memmax = Long.parseLong(jvmmemmax); + memmax = memoryStringToLong(jvmmemmax); + if (memmax == 0) + { + throw (new NumberFormatException("Not allowing 0")); + } } catch (NumberFormatException e) { - memmax = maxHeapSizeDefault; - System.out.println("MemorySetting Property '" + maxHeapSizeProperty - + "' (" - + jvmmemmaxorig + "') badly formatted, using default (" - + memmax + ")."); - } - - // apply multiplier if not too big (i.e. bigger than a long) - if (Long.MAX_VALUE / memmax < multiplier) - { - memmax = maxHeapSizeDefault; - System.out.println( - "MemorySetting Property '" + maxHeapSizeProperty + "' (" - + jvmmemmaxorig - + ") too big, using default (" + memmax + ")."); - } - else - { - memmax = multiplier * memmax; + 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 < MemorySetting.applicationMinMemory) + if (memmax < APPLICATION_MIN_MEMORY) { - memmax = MemorySetting.applicationMinMemory; - System.out.println( - "MemorySetting Property '" + maxHeapSizeProperty + "' (" - + jvmmemmaxorig - + ") too small, using minimum (" + memmax + ")."); + 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 - // System.out.println("MemorySetting Property '" + maxHeapSizeProperty + "' not + // adjustmentMessage("MemorySetting Property '" + maxHeapSizeProperty + // + "' not // set."); } - // get max percent of physical memory - float percent = maxHeapSizePerCentDefault; - String jvmmempc = jvmmempcString; - if (jvmmempc == null) + // get max percent of physical memory, starting with default + float percent = MAX_HEAPSIZE_PERCENT_DEFAULT; + if (jvmmempcarg == null && useProps) { - jvmmempc = System.getProperty(maxHeapSizePerCentProperty); + jvmmempcarg = System.getProperty(MAX_HEAPSIZE_PERCENT_PROPERTY_NAME); } - long pcmem = -1; + String jvmmempc = jvmmempcarg; + long mempc = -1; try { if (jvmmempc != null) { - float trypercent = Float.parseFloat(jvmmempc); - if (0 < trypercent && trypercent <= 100f) + int trypercent = Integer.parseInt(jvmmempc); + if (0 <= trypercent && trypercent <= 100) { percent = trypercent; } else { - System.out.println( - "MemorySetting Property '" + maxHeapSizePerCentProperty - + "' should be in range 1..100"); + setAdjustmentMessage("MemorySetting Property '" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + + "' should be in range 0..100. Using default " + percent + + "%", quiet); } } } catch (NumberFormatException e) { - System.out.println( - "MemorySetting property '" + maxHeapSizePerCentProperty - + "' (" + jvmmempc + ") badly formatted"); + setAdjustmentMessage("MemorySetting property '" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg + + ") badly formatted", quiet); } // catch everything in case of no com.sun.management.OperatingSystemMXBean boolean memoryPercentError = false; try { - pcmem = MemoryPercent.memPercent(percent); + 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; - System.out.println("Problem calling MemoryPercent.memPercent(" - + percent - + "). Likely to be problem with com.sun.management.OperatingSystemMXBean"); + 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 if physical memory, let's cap maxMemLong to 8GB - if (memoryPercentError && jvmmempc != null && pcmem == -1 - && memmax > noMemMaxHeapSizeDefault) + + // 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) { - System.out.println( - "Capping maximum memory to 8GB due to failure to read physical memory size."); - memmax = noMemMaxHeapSizeDefault; + 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 (pcmem == -1) // not set + if (mempc == -1) // percentage memory not set { maxMemLong = memmax; } else { - maxMemLong = Math.min(pcmem, memmax); + maxMemLong = Math.min(mempc, memmax); } return maxMemLong; } + public static boolean isValidMemoryString(String text) + { + 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; + } + + 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) + { + return 0; + } + + // 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; + } + }