Liviu Andronic
2009-Aug-04 11:35 UTC
[R-sig-Debian] 100% CPU when running (cran2deb) JGR on Debian
Dear all, I installed the amd64 cran2deb [1] JGR binaries on a fresh Debian testing, and JGR is missbehaving. When JGR starts up, one core of the CPU goes to 100% and stays there, even though I am keeping it idle and not performing any operation. I tried JGR with both sun-java6-jdk and openjdk-6-jdk, debian-liv:/home/liviu# update-alternatives --config java There are 4 choices for the alternative java (providing /usr/bin/java). Selection Path Priority Status ------------------------------------------------------------ 0 /usr/lib/jvm/java-6-openjdk/jre/bin/java 1061 auto mode 1 /usr/bin/gij-4.3 43 manual mode 2 /usr/lib/jvm/java-6-openjdk/jre/bin/java 1061 manual mode * 3 /usr/lib/jvm/java-6-sun/jre/bin/java 63 manual mode 4 /usr/lib/jvm/java-gcj/jre/bin/java 1043 manual mode options 3 and 0, to no avail. After changing the java alternative, I also executed debian-liv:/home/liviu# R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.6.0_14 Java home path : /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar Java library path: /usr/lib/../lib/gcj-4.3-90:/usr/lib/jni JNI linker flags : -L/usr/lib/../lib/gcj-4.3-90 -L/usr/lib/jni -ljvm JNI cpp flags : Updating Java configuration in /etc/R Done. Starting JGR via require(JGR) or the stand-alone script (/usr/local/lib/R/site-library/JGR/scripts/run) makes no difference. Neither running as user or as root. JGR will start and immediately begin using 100% of one CPU core. One thing that it complains of is: liviu at debian-liv:~$ /usr/local/lib/R/site-library/JGR/scripts/run WARNING: org.rosuda.JRI.Mutex was unlocked by other thread than locked! This may soon lead to a crash... Could anyone suggest a way to work around this issue? Thank you, Liviu [1] http://www.mail-archive.com/debian-science at lists.debian.org/msg03306.html -- Do you know how to read? http://www.alienetworks.com/srtest.cfm Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail
Liviu Andronic
2009-Aug-04 11:58 UTC
[R-sig-Debian] 100% CPU when running (cran2deb) JGR on Debian
(follow-up) After managing to get around some strange ./configure errors, I managed to build JGR and it's java-dependencies (including rJava) from source, but I still run into trouble. The warning is the same, and so is the CPU consumption: liviu at debian-liv:~$ JGR WARNING: org.rosuda.JRI.Mutex was unlocked by other thread than locked! This may soon lead to a crash... Liviu On 8/4/09, Liviu Andronic <landronimirc at gmail.com> wrote:> Dear all, > I installed the amd64 cran2deb [1] JGR binaries on a fresh Debian > testing, and JGR is missbehaving. When JGR starts up, one core of the > CPU goes to 100% and stays there, even though I am keeping it idle and > not performing any operation. > > I tried JGR with both sun-java6-jdk and openjdk-6-jdk, > debian-liv:/home/liviu# update-alternatives --config java > There are 4 choices for the alternative java (providing /usr/bin/java). > > Selection Path Priority Status > ------------------------------------------------------------ > 0 /usr/lib/jvm/java-6-openjdk/jre/bin/java 1061 auto mode > 1 /usr/bin/gij-4.3 43 manual mode > 2 /usr/lib/jvm/java-6-openjdk/jre/bin/java 1061 manual mode > * 3 /usr/lib/jvm/java-6-sun/jre/bin/java 63 manual mode > 4 /usr/lib/jvm/java-gcj/jre/bin/java 1043 manual mode > > options 3 and 0, to no avail. After changing the java alternative, I > also executed > debian-liv:/home/liviu# R CMD javareconf > Java interpreter : /usr/bin/java > Java version : 1.6.0_14 > Java home path : /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre > Java compiler : /usr/bin/javac > Java headers gen.: /usr/bin/javah > Java archive tool: /usr/bin/jar > Java library path: /usr/lib/../lib/gcj-4.3-90:/usr/lib/jni > JNI linker flags : -L/usr/lib/../lib/gcj-4.3-90 -L/usr/lib/jni -ljvm > JNI cpp flags : > > Updating Java configuration in /etc/R > Done. > > Starting JGR via require(JGR) or the stand-alone script > (/usr/local/lib/R/site-library/JGR/scripts/run) makes no difference. > Neither running as user or as root. JGR will start and immediately > begin using 100% of one CPU core. > > One thing that it complains of is: > liviu at debian-liv:~$ /usr/local/lib/R/site-library/JGR/scripts/run > WARNING: org.rosuda.JRI.Mutex was unlocked by other thread than > locked! This may soon lead to a crash... > > Could anyone suggest a way to work around this issue? Thank you, > Liviu > > [1] http://www.mail-archive.com/debian-science at lists.debian.org/msg03306.html > > > > > > > -- > Do you know how to read? > http://www.alienetworks.com/srtest.cfm > Do you know how to write? > http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail >-- Do you know how to read? http://www.alienetworks.com/srtest.cfm Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail
Liviu Andronic
2009-Aug-05 14:12 UTC
[R-sig-Debian] 100% CPU when running (cran2deb) JGR on Debian
Dear all, To follow up on my troubles, I encounter the same issues on Ubuntu. I've installed a fresh copy of Jaunty Jackalope, R 2.8.1, Sun's Java 6, and built JGR from source. On the first run, I get this message: liviu at ubuntu-liv:~$ JGR 05-Aug-2009 14:51:36 java.util.prefs.FileSystemPreferences$2 run INFO: Created user preferences directory. Subsequently, after each start JGR starts using 100% of CPU (which causes heat and makes the programme unusable) and I also get the same warning as on Ubuntu. liviu at ubuntu-liv:~$ JGR WARNING: org.rosuda.JRI.Mutex was unlocked by other thread than locked! This may soon lead to a crash... I'm currently migrating from Gentoo to Debian, and on Gentoo I had no such issues. If anyone has any ideas on what might be wrong or how to approach these issues, please let me know. Liviu ## On Ubuntu> sessionInfo()R version 2.8.1 (2008-12-22) x86_64-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] JGR_1.6-7 iplots_1.1-3 JavaGD_0.5-2 rJava_0.6-3 On Tue, Aug 4, 2009 at 12:35 PM, Liviu Andronic<landronimirc at gmail.com> wrote:> Dear all, > I installed the amd64 cran2deb [1] JGR binaries on a fresh Debian > testing, and JGR is missbehaving. When JGR starts up, one core of the > CPU goes to 100% and stays there, even though I am keeping it idle and > not performing any operation. > > I tried JGR with both sun-java6-jdk and openjdk-6-jdk, > debian-liv:/home/liviu# update-alternatives --config java > There are 4 choices for the alternative java (providing /usr/bin/java). > > ?Selection ? ?Path ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Priority ? Status > ------------------------------------------------------------ > ?0 ? ? ? ? ? ?/usr/lib/jvm/java-6-openjdk/jre/bin/java ? 1061 ? ? ?auto mode > ?1 ? ? ? ? ? ?/usr/bin/gij-4.3 ? ? ? ? ? ? ? ? ? ? ? ? ? 43 ? ? ? ?manual mode > ?2 ? ? ? ? ? ?/usr/lib/jvm/java-6-openjdk/jre/bin/java ? 1061 ? ? ?manual mode > * 3 ? ? ? ? ? ?/usr/lib/jvm/java-6-sun/jre/bin/java ? ? ? 63 ? ? ? ?manual mode > ?4 ? ? ? ? ? ?/usr/lib/jvm/java-gcj/jre/bin/java ? ? ? ? 1043 ? ? ?manual mode > > options 3 and 0, to no avail. After changing the java alternative, I > also executed > debian-liv:/home/liviu# R CMD javareconf > Java interpreter : /usr/bin/java > Java version ? ? : 1.6.0_14 > Java home path ? : /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre > Java compiler ? ?: /usr/bin/javac > Java headers gen.: /usr/bin/javah > Java archive tool: /usr/bin/jar > Java library path: /usr/lib/../lib/gcj-4.3-90:/usr/lib/jni > JNI linker flags : -L/usr/lib/../lib/gcj-4.3-90 -L/usr/lib/jni -ljvm > JNI cpp flags ? ?: > > Updating Java configuration in /etc/R > Done. > > Starting JGR via require(JGR) or the stand-alone script > (/usr/local/lib/R/site-library/JGR/scripts/run) makes no difference. > Neither running as user or as root. JGR will start and immediately > begin using 100% of one CPU core. > > One thing that it complains of is: > liviu at debian-liv:~$ /usr/local/lib/R/site-library/JGR/scripts/run > WARNING: org.rosuda.JRI.Mutex was unlocked by other thread than > locked! This may soon lead to a crash... > > Could anyone suggest a way to work around this issue? Thank you, > Liviu > > [1] http://www.mail-archive.com/debian-science at lists.debian.org/msg03306.html > > > > > > -- > Do you know how to read? > http://www.alienetworks.com/srtest.cfm > Do you know how to write? > http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail >-- Do you know how to read? http://www.alienetworks.com/srtest.cfm Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail