X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FMemorySetting.java;h=56713b0acbbb94c81522e3e8c331813eba614d0f;hb=b26fefd329b60deb2025aa28cdbaae30bfb58382;hp=117be25aab7ac8f49ea880293d8c0ae9e95e9356;hpb=ab5e23473401e82bdc96056751d7a1c184b59ba6;p=jalview.git diff --git a/src/jalview/bin/MemorySetting.java b/src/jalview/bin/MemorySetting.java index 117be25..56713b0 100644 --- a/src/jalview/bin/MemorySetting.java +++ b/src/jalview/bin/MemorySetting.java @@ -1,3 +1,25 @@ +/* + + 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; /** @@ -13,152 +35,138 @@ package jalview.bin; */ 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"; - public static final long applicationMinMemory = 536870912; // 0.5 GB + private static final int MAX_HEAPSIZE_PERCENT_DEFAULT = 90; // 90% - private final static int maxHeapSizePerCentDefault = 90; + private static final long GIGABYTE = 1073741824; // 1GB - public final static String maxHeapSizePerCentPropertyName = "jvmmempc"; + public static final long LEAVE_FREE_MIN_MEMORY = GIGABYTE / 2; - private final static long maxHeapSizeDefault = 34359738368L; // 32GB + public static final long APPLICATION_MIN_MEMORY = GIGABYTE / 2; - private final static long noMemMaxHeapSizeDefault = 8589934592L; // 8GB + private static final long MAX_HEAPSIZE_GB_DEFAULT = 32; - public final static String maxHeapSizePropertyName = "jvmmemmax"; + 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(); + + public static final String MEMORY_JVMMEMMAX = NS + "_" + + MAX_HEAPSIZE_PROPERTY_NAME.toUpperCase(); 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 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. + * (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. + * 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". + * 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) + String jvmmempcarg, boolean useProps, boolean quiet) { // actual Xmx value-to-be long maxMemLong = -1; + clearAdjustmentMessage(); // (absolute) jvmmaxmem setting, start with default - long memmax = maxHeapSizeDefault; - if (jvmmemmaxarg == null) + long memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE; + if (jvmmemmaxarg == null && useProps) { - jvmmemmaxarg = System.getProperty(maxHeapSizePropertyName); + jvmmemmaxarg = System.getProperty(MAX_HEAPSIZE_PROPERTY_NAME); } 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 '" - + maxHeapSizePropertyName - + "' (" - + jvmmemmaxarg + "') 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 '" + maxHeapSizePropertyName + "' (" - + jvmmemmaxarg - + ") 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 < applicationMinMemory) + if (memmax < APPLICATION_MIN_MEMORY) { - memmax = applicationMinMemory; - System.out.println( - "MemorySetting Property '" + maxHeapSizePropertyName + "' (" - + jvmmemmaxarg - + ") too small, using minimum (" - + applicationMinMemory + ")."); + 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 + // adjustmentMessage("MemorySetting Property '" + maxHeapSizeProperty // + "' not // set."); } // get max percent of physical memory, starting with default - float percent = maxHeapSizePerCentDefault; - if (jvmmempcarg == null) + float percent = MAX_HEAPSIZE_PERCENT_DEFAULT; + if (jvmmempcarg == null && useProps) { - jvmmempcarg = System.getProperty(maxHeapSizePerCentPropertyName); + jvmmempcarg = System.getProperty(MAX_HEAPSIZE_PERCENT_PROPERTY_NAME); } String jvmmempc = jvmmempcarg; long mempc = -1; @@ -166,25 +174,24 @@ public class MemorySetting { 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 '" - + maxHeapSizePerCentPropertyName - + "' should be in range 1..100. Using default " - + percent + "%"); + 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 '" + maxHeapSizePerCentPropertyName - + "' (" + jvmmempcarg + ") badly formatted"); + setAdjustmentMessage("MemorySetting property '" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg + + ") badly formatted", quiet); } // catch everything in case of no com.sun.management.OperatingSystemMXBean @@ -192,7 +199,7 @@ public class MemorySetting try { long physicalMem = GetMemory.getPhysicalMemory(); - if (physicalMem > applicationMinMemory) + if (physicalMem > APPLICATION_MIN_MEMORY) { // try and set at least applicationMinMemory and thereafter ensure // leaveFreeMinMemory is left for the OS @@ -201,52 +208,54 @@ public class MemorySetting // check for memory left for OS boolean reducedmempc = false; - if (physicalMem - mempc < leaveFreeMinMemory) + if (physicalMem - mempc < LEAVE_FREE_MIN_MEMORY) { - mempc = physicalMem - leaveFreeMinMemory; + mempc = physicalMem - LEAVE_FREE_MIN_MEMORY; reducedmempc = true; - System.out.println("MemorySetting Property '" - + maxHeapSizePerCentPropertyName + "' (" + jvmmempcarg + setAdjustmentMessage("MemorySetting Property '" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg + ") too large. Leaving free space for OS and reducing to (" - + mempc + ")."); + + mempc + ").", quiet); } // check for minimum application memsize - if (mempc < applicationMinMemory) + if (mempc < APPLICATION_MIN_MEMORY) { if (reducedmempc) { - System.out.println("Reduced MemorySetting (" + mempc + setAdjustmentMessage("Reduced MemorySetting (" + mempc + ") too small. Increasing to application minimum (" - + applicationMinMemory + ")."); + + APPLICATION_MIN_MEMORY + ").", quiet); } else { - System.out.println("MemorySetting Property '" - + maxHeapSizePerCentPropertyName + "' (" + jvmmempcarg - + ") too small. Using minimum (" + applicationMinMemory - + ")."); + setAdjustmentMessage("MemorySetting Property '" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + + jvmmempcarg + ") too small. Using minimum (" + + APPLICATION_MIN_MEMORY + ").", quiet); } - mempc = applicationMinMemory; + mempc = APPLICATION_MIN_MEMORY; } } else { // not enough memory for application, just try and grab what we can! mempc = physicalMem; - System.out.println( + setAdjustmentMessage( "Not enough physical memory for application. Ignoring MemorySetting Property '" - + maxHeapSizePerCentPropertyName + "' (" + + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg + "). Using maximum memory available (" - + physicalMem + ")."); + + physicalMem + ").", + quiet); } } catch (Throwable t) { memoryPercentError = true; - System.out.println( - "Problem calling GetMemory.getPhysicalMemory(). 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(); } @@ -254,16 +263,20 @@ public class MemorySetting // jvmmempc was set OR neither jvmmempc nor jvmmemmax were set), let's cap // maxMemLong to 8GB if (memoryPercentError && mempc == -1 - // && (jvmmempcarg != null || (jvmmempcarg == null && jvmmemmaxarg == null)) - // the above is easier to understand but simplified to - && !(jvmmempcarg == null && jvmmemmaxarg != null) - && memmax > noMemMaxHeapSizeDefault) + && !(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 " - + (noMemMaxHeapSizeDefault + 536870912) / 1073741824 // this is the nearest integer GB for noMemMaxHeapSizeDefault - + "GB 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 (mempc == -1) // percentage memory not set @@ -278,4 +291,120 @@ public class MemorySetting return maxMemLong; } -} \ No newline at end of file + 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; + } + +}