I can confirm that the first program fails (bcast a single int).
I'm trying to understand how the implementation works, but this may take some
time (due to the holidays, etc.).
On Dec 22, 2012, at 2:53 AM, Siegmar Gross wrote:
> Hi
>
>> Interesting. My best guess is that the OMPI libraries aren't being
>> found, though I'm a little surprised because the error message
>> indicates an inability to malloc - but it's possible the message
>> isn't accurate.
>>
>> One thing stands out - I see you compiled your program with "javac".
>> I suspect that is the source of the trouble - you really need to use
>> the Java wrapper compiler "mpijavac" so all the libs get absorbed
>> and/or linked correctly.
>
> No, I only compiled the first two programs (which don't use any MPI
> methods) with javac. The MPI program "InitFinalizeMain.java" was
> compiled with "mpijavac" (I use a script file and GNUmakefile).
>
> linpc1 java 102 make_classfiles
> ...
> === linpc1 ===
> Warning: untrusted X11 forwarding setup failed: xauth key data not generated
> Warning: No xauth data; using fake authentication data for X11 forwarding.
> mpijavac -d /home/fd1026/Linux/x86_64/mpi_classfiles InitFinalizeMain.java
> ...
>
>
> The other programs work also if I compile them with "mpijavac"
>
> linpc1 prog 107 mpijavac MemAllocMain.java
> linpc1 prog 108 mpiexec java -cp `pwd` MemAllocMain
> Type something ("quit" terminates program): dgdas
> Received input: dgdas
> Converted to upper case: DGDAS
> Type something ("quit" terminates program): quit
> Received input: quit
> Converted to upper case: QUIT
> linpc1 prog 109
>
>
> My environment should be valid as well. LD_LIBRARY_PATH contains
> first the directories for 32 bit libraries and then the directories
> for 64 bit libraries. I have split the long lines for the PATH
> variables so that they are easier to read.
>
> linpc1 java 111 mpiexec java EnvironVarMain
>
> Operating system: LinuxProcessor architecture: x86_64
>
> CLASSPATH:
> /usr/local/junit4.10:
> /usr/local/junit4.10/junit-4.10.jar:
> //usr/local/jdk1.7.0_07-64/j3d/lib/ext/j3dcore.jar:
> //usr/local/jdk1.7.0_07-64/j3d/lib/ext/j3dutils.jar:
> //usr/local/jdk1.7.0_07-64/j3d/lib/ext/vecmath.jar:
> /usr/local/javacc-5.0/javacc.jar:
> .:
> /home/fd1026/Linux/x86_64/mpi_classfiles
>
> LD_LIBRARY_PATH:
> /usr/lib:
> ...
> /usr/lib64:
> /usr/local/jdk1.7.0_07-64/jre/lib/amd64:
> /usr/local/gcc-4.7.1/lib64:
> /usr/local/gcc-4.7.1/libexec/gcc/x86_64-unknown-linux-gnu/4.7.1:
> /usr/local/gcc-4.7.1/lib/gcc/x86_64-unknown-linux-gnu/4.7.1:
> /usr/local/lib64:
> /usr/local/ssl/lib64:
> /usr/lib64:
> /usr/X11R6/lib64:
> /usr/local/openmpi-1.9_64_cc/lib64:
> /home/fd1026/Linux/x86_64/lib64
> linpc1 java 112
>
> Can I provide any other information to solve this problem?
>
>
> Kind regards
>
> Siegmar
>
>
>> On Dec 21, 2012, at 9:46 AM, Siegmar Gross
>> wrote:
>>
>>> Hi
>>>
Hmmm...weird. Well, it looks like OMPI itself is okay, so the issue
appears to be in the Java side of things. For whatever reason, your
Java VM is refusing to allow a malloc to succeed. I suspect it has
something to do with its setup, but I'm not enough of a Java person
to point you to the problem.
Is it possible that the program was compiled against a different
(perhaps incompatible) version of Java?
>>>
>>> No, I don't think so. A small Java program without MPI methods works.
>>>
>>> linpc1 bin 122 which mpicc
>>> /usr/local/openmpi-1.9_64_cc/bin/mpicc
>>> linpc1 bin 123 pwd
>>> /usr/local/openmpi-1.9_64_cc/bin
>>> linpc1 bin 124 grep jdk *
>>> mpijavac:my $my_compiler = "/usr/local/jdk1.7.0_07-64/bin/javac";
>>> mpijavac.pl:my $my_compiler = "/usr/local/jdk1.7.0_07-64/bin/javac";
>>> linpc1 bin 125 which java
>>> /usr/local/jdk1.7.0_07-64/bin/java
>>> linpc1 bin 126
>>>
>>>
>>> linpc1 prog 110 javac MiniProgMain.java
>>> linpc1 prog 111 java MiniProgMain
>>> Message 0
>>> Message 1
>>> Message 2
>>> Message 3
>>> Message 4
>>> linpc1 prog 112 mpiexec java MiniProgMain
>>> Message 0
>>> Message 1
>>> Message 2
>>> Message 3
>>> Message 4
>>> linpc1 prog 113 mpiexec -np 2 java MiniProgMain
>>> Message 0
>>> Message 1
>>> Message 2
>>> Message 3
>>> Message 4
>>> Message 0
>>> Message 1
>>> Message 2
>>> Message 3
>>> Message 4
>>>
>>>
>>> A small program which allocates buffer for a new string.
>>> ...
>>> stringBUFLEN = new String (string.substring (0, len));
>>> ...
>>>
>>> linpc1 prog 115 javac MemAllocMain.java
>>> linpc1 prog 116 java MemAllocMain
>>> Type something ("quit" terminates program): ffghhfhh
>>> Received input: ffghhfhh
>>> Converted to upper case: FFGHHFHH
>>> Type something ("quit" terminates program): quit
>>> Received input: quit
>>> Converted to upper case: QUIT
>>>
>>> linpc1 prog 117 mpiexec java MemAllocMain
>>> Type something ("quit" terminates program): fbhshnhjs
>>> Received input: fbhshnhjs
>>> Converted t
