topic Re: Problems starting IDB on Ubuntu in Intel® Fortran Compiler

Problems starting IDB on Ubuntu

gdaturi — Tue, 15 Sep 2009 20:46:52 GMT

Hello -

I've been using the Fortran compiler environment for a few weeks now without any problems. Recently I have started getting problems starting the java debugger GUI, and I think it may be because of suggested synaptic updates or a java update. I have tried re-installing the debugger, made sure I am setting the JRE correctly, and even rolled back a couple updates. The debugger works in command line "idbc" mode. These are the errors I get. Any help is appreciated - I am getting no where fast!

WARNING: ASSERTION "(pdomDocument) != ((void*)0)" FAILED AT ./src/Common/Memento/XMLMemento.cpp,line 135
Stack Backtrace follows:
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libOsgJni.so [0x7f3eee16c96e]
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libGuiMgr.so((null)+0x1cc) [0x7f3eed2beafc]
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libGuiMgr.so((null)+0x2f6) [0x7f3eed53c122]
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libGuiMgr.so((null)+0x380) [0x7f3eed4fbf52]
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libGuiMgr.so((null)+0xd) [0x7f3eed4fc9fb]
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libOsgJni.so(Java_com_intel_debugger_ui_jni_NativeCallsProxy_native_1initialize+0x8b) [0x7f3eee16cca1]
[0x7f3f7a20ff50]
WARNING: ASSERTION "(m_pPersistentSettings) != ((void*)0)" FAILED AT ./src/WindowMgr/WindowMgr.cpp,line 234
Stack Backtrace follows:
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libOsgJni.so [0x7f3eee16c96e]
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libGuiMgr.so((null)+0x1fd5) [0x7f3eed53de01]
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libGuiMgr.so((null)+0x380) [0x7f3eed4fbf52]
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libGuiMgr.so((null)+0xd) [0x7f3eed4fc9fb]
/home/ocean18/intel/Compiler/11.1/046/idb/gui/intel64/libOsgJni.so(Java_com_intel_debugger_ui_jni_NativeCallsProxy_native_1initialize+0x8b) [0x7f3eee16cca1]
[0x7f3f7a20ff50]
ReactionMgr: Error in XML Structure - handler "DataChangeNtfHandler" is not supported by provider "WindowMgr"
ReactionMgr: Error in XML Structure - handler "DebuggeeEventNtfHandler" is not supported by provider "WindowMgr"
[Fatal Error] :-1:-1: Premature end of file.

Re: Problems starting IDB on Ubuntu

TimP — Wed, 16 Sep 2009 01:33:16 GMT

Does 'java -version' show the Sun 1.6 64-bit jre running? Does Ubuntu have their own version of it, in order to compensate for the non-standard paths?

Re: Problems starting IDB on Ubuntu

pacobraxe — Mon, 28 Sep 2009 18:00:23 GMT

Quoting - tim18

Does 'java -version' show the Sun 1.6 64-bit jre running? Does Ubuntu have their own version of it, in order to compensate for the non-standard paths?

I have the same problem. The result of java -version is:

java version "1.6.0_0"
OpenJDK Runtime Environment (IcedTea6 1.4.1) (6b14-1.4.1-0ubuntu11)
OpenJDK 64-Bit Server VM (build 14.0-b08, mixed mode)

I have to say that, during the installation, a compatibility check warning appeared: the program did not find java 1.5. I did not care because I thought that version 1.6 would be OK... In fact, the installation reported no errors.

Thanks,
Paco Braxe

Re: Problems starting IDB on Ubuntu

TimP — Mon, 28 Sep 2009 18:34:49 GMT

Not obvious distinctions. As Ron mentioned below, the Iced Tea designation is a warning flag.
I have installed the 11.1.056 intel64 several times, all with some version of java 1.6, which installed without complaint on the previous ifort version. Some of them gave a complaint from the installer, and require me to accept installation with missing prerequisites. In any case, only the functioning of the GUI idb would be in doubt, but I believe it is still working OK.

Re: Problems starting IDB on Ubuntu

Ron_Green — Mon, 28 Sep 2009 18:45:10 GMT

It appears Ubuntu installs a non-Sun JRE/JDK, the OpenJDK IcedTea6. Intel does not test against this nor do we support it.

I would recommend installing the Sun JRE, from here http://java.com/en/download/manual.jsp

ron

Re: Problems starting IDB on Ubuntu

TimP — Mon, 28 Sep 2009 20:39:50 GMT

Quoting - Ronald W. Green (Intel)

Before installing Sun JRE, you may have to remove OpenJDK, or at least, if /usr/bin/java is a symlink, remove that, so that the Sun JRE can install normally as the one visible to the Intel installer.

Re: Problems starting IDB on Ubuntu

pacobraxe — Tue, 29 Sep 2009 09:54:37 GMT

Quoting - tim18

Before installing Sun JRE, you may have to remove OpenJDK, or at least, if /usr/bin/java is a symlink, remove that, so that the Sun JRE can install normally as the one visible to the Intel installer.

Hi,
the problem did not disappeared install java from SUN. The problem I got was:

java.lang.UnsatisfiedLinkError: /opt/intel/Compiler/11.1/056/idb/gui/intel64/libOsgJni.so: libstdc++.so.5: shared object file cannot be opened

A smart guy told me that he had the same error and that it was related to the use of versions 32 bit or 64 bit of this library. Anyway, I could solve my problem installing:

apt-get install libstdc++5

Regards,
Paco

Re: Problems starting IDB on Ubuntu

TimP — Tue, 29 Sep 2009 13:01:41 GMT

Yes, most up to date distros make the (backward compatibility) libstdc++5 libraries separate install options (and the name for it is not uniform), as has been mentioned in several posts on this forum.

Re: Problems starting IDB on Ubuntu

gdaturi — Tue, 29 Sep 2009 17:26:06 GMT

Hi All,

Thanks so much for the help, but it still doesn't appear to be working! The IDB used to work fine, and still doesn't.

I just updated to the newest compiler and IDB - when I updated there was a warning about an incorrect JRE existing! I believe I have a compatible JRE. When I type java - version, I get the following:

java version "1.6.0_16"
Java SE Runtime Environment (build 1.6.0_16-b01)
Java HotSpot 64-Bit Server VM (build 14.2-b01, mixed mode)

I've also gone to the synaptic manager and made sure I have the latest lbstdc++5 installed.

Help! Thanks!

Re: Problems starting IDB on Ubuntu

TimP — Tue, 29 Sep 2009 18:58:14 GMT

Quoting - gdaturi

I just updated to the newest compiler and IDB - when I updated there was a warning about an incorrect JRE existing! I believe I have a compatible JRE. When I type java - version, I get the following:

java version "1.6.0_16"
Java SE Runtime Environment (build 1.6.0_16-b01)
Java HotSpot 64-Bit Server VM (build 14.2-b01, mixed mode)

I upgraded to that version of jre and re-installed ifort 11.1.056 (on RH5.2). It gave me the message about no compatible JRE, so I "accepted missing prerequisites," then checked that my test application builds and runs correctly under idb GUI. According to my tests, jre 1.6.0_13 (on RH5.3) and 1.6.0_16 (current) (on RH5.2) x86_64 versions give the ifort installer warning, but work OK. 1.6.0_14 gave no complaint with ifort installer.

Re: Problems starting IDB on Ubuntu

ohinai — Sun, 02 Oct 2011 17:45:53 GMT

This is a bit old, but I hope it might help someone else out there. I know someone who had the exact same problem. The issue was that there were temporary .idb*** files created in the home directory that were causing this error message. Check your home directory for stray files and delete them, it might fix the problem.