+/*
+
+ 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 <http://www.gnu.org/licenses/>.
+ * 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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff