[GE users] Something Wrong with drmaa

templedf dan.templeton at sun.com
Fri Aug 7 21:04:56 BST 2009


qmon requires Motif, which isn't included with all Linux distros.  See 
the following:

http://wikis.sun.com/display/gridengine62u3/How+to+Verify+and+Install+Linux+Motif+Libraries

Daniel

TianJing wrote:
> i am sorry that this bring some new problems,
> the qmon doesn't work
>
> qmon:error while loading share libraries:libXm.so.3:can't open shared 
> object file:no such file or directory
>
> 2009/8/7 TianJing <tianjing at genomics.org.cn 
> <mailto:tianjing at genomics.org.cn>>
>
>     Hi,
>
>     i think there might be problem with the files in $SGE_ROOT/lib in
>     sge6.2u2_1 in rocks 5.2,
>
>     i downoad the sge62u2_1_linux24-x64_targz.zip from the website and
>     replace the lib files above,then it works.
>
>     thanks.
>
>     2009/8/7 Daniel Templeton <Dan.Templeton at sun.com
>     <mailto:Dan.Templeton at sun.com>>
>
>         Then try to get a simple C program to compile and run.  Try
>         compiling and running this one:
>
>         #include <stdio.h>
>         #include "drmaa.h"
>
>         int main (int argc, char **argv) {
>          char error[DRMAA_ERROR_STRING_BUFFER];
>          int errnum = 0;
>
>          errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
>
>          if (errnum != DRMAA_ERRNO_SUCCESS) {
>             fprintf (stderr, "Could not initialize the DRMAA library:
>         %s\n", error);
>             return 1;
>          }
>
>          printf ("DRMAA library was started successfully\n");
>
>          return 0;
>         }
>
>         If that works, then there's no excuse for your Java app not to
>         work.  The Java binding is just a wrapper around the C binding.
>
>         Daniel
>
>
>
>         Guangxia Yang wrote:
>
>             Yes,it is /opt/gridengine/lib/lx26-amd64/ and the kernel is
>             2.6.9-55.0.2.ELsmp
>
>
>             On 8/7/09 2:00 PM, "Daniel Templeton"
>             <Dan.Templeton at Sun.COM> wrote:
>
>              
>
>                 There have been no reported issues of that sort with
>                 DRMAA in any
>                 version of SGE.  When these problems show up, it is
>                 always an issue with
>                 the setup or configuration.  Did you check that you
>                 actually have an
>                 /opt/gridengine/lib/lx26-amd64 directory?  I believe
>                 the installer only
>                 creates /opt/gridengine/lib/lx24-amd64, even on a 2.6
>                 kernel machine.
>
>                 Daniel
>
>
>                 TianJing wrote:
>                    
>
>                     hi,
>
>                     i have check the LD_LIBRARY_PATH,but it still
>                     doesn't work,
>
>                     we use linux x86_64,the sge is 6.2u2_1 in Rocks 5.2.
>
>                     i do this test in another platform also with sge
>                     6.2u2_1,the same
>                     error occured!
>
>                     does this mean there is something wrong with the
>                     release of DRMAA(we
>                     use version 0.5)?
>
>                     thanks.
>
>                     2009/8/7 Guangxia Yang <yanggx at genomics.org.cn
>                     <mailto:yanggx at genomics.org.cn>
>                     <mailto:yanggx at genomics.org.cn
>                     <mailto:yanggx at genomics.org.cn>>>
>
>
>                        ------ Forwarded Message
>                        From: templedf <dan.templeton at sun.com
>                     <mailto:dan.templeton at sun.com>
>                     <mailto:dan.templeton at sun.com
>                     <mailto:dan.templeton at sun.com>>>
>                        Reply-To: users <users at gridengine.sunsource.net
>                     <mailto:users at gridengine.sunsource.net>
>                        <mailto:users at gridengine.sunsource.net
>                     <mailto:users at gridengine.sunsource.net>>>
>                        Date: Thu, 06 Aug 2009 21:02:44 -0700
>                        To: <users at gridengine.sunsource.net
>                     <mailto:users at gridengine.sunsource.net>
>                        <mailto:users at gridengine.sunsource.net
>                     <mailto:users at gridengine.sunsource.net>>>
>                        Subject: Re: [GE users] Something Wrong with drmaa
>
>                        That exception only happens when the JRE has a
>                     problem finding or
>                        using
>                        the libdrmaa shared library.  The possible
>                     reasons include that the
>                        LD_LIBRARY_PATH isn't set to include the
>                     libdrmaa shared library, the
>                        libdrmaa shared library isn't where it's
>                     supposed to be, the libdrmaa
>                        shared library is somehow damaged, or there's
>                     an architecture
>                        mismatch.
>                        Check the file size of the libdrmaa shared
>                     library.  Check that it's
>                        readable by your platform.  Double-check the
>                     LD_LIBRARY_PATH.  BTW,
>                        what's the platform?  Not HP-UX per chance?
>
>                        Daniel
>
>
>                        yvonne_young wrote:
>                          
>
>                         i am sure that i hava set the LD_LIBRARY_PATH,
>
>                         $LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64
>
>                         /opt/gridengine is my $SGE_ROOT,
>
>                         but it still has the some error.
>
>
>                         On 8/6/09 10:05 PM, "dagru" <d.gruber at sun.com
>                         <mailto:d.gruber at sun.com>
>                                
>
>                        <mailto:d.gruber at sun.com
>                     <mailto:d.gruber at sun.com>>> wrote:
>                          
>
>                            Did you ensure that you have set the
>                         LD_LIBRARY_PATH environment
>                            variable correctly to the library directory
>                         shipped with
>                            6.2u2? The native library is in
>                         $SGE_ROOT/lib/$ARCH where
>                                
>
>                        $ARCH is
>                          
>
>                            your architecture.
>
>                            Daniel
>
>                            On 08/06/09 12:05, yvonne_young wrote:
>
>                                Something Wrong with drmaa Hello everyone,
>
>                                 my SGE engeine was update from 6.1 to
>                         6.2u2.and when I qsub
>                                the tasks used java program it prompt
>                         the following errors:
>
>                                Exception in thread "main"
>                         java.lang.UnsatisfiedLinkError:
>                                      
>
>                      
>                      com.sun.grid.drmaa.SessionImpl.nativeInit(Ljava/lang/String;)V
>                          
>
>                                        at
>                         com.sun.grid.drmaa.SessionImpl.nativeInit(Native
>                                Method)
>                                        at
>                              
>                          com.sun.grid.drmaa.SessionImpl.init(SessionImpl.java:277)
>                                        at Test1.main(Test1.java:36)
>
>
>                                Thanks!
>
>
>
>                                
>
>                      
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>                        11303
>
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>                        ------ End of Forwarded Message
>
>
>
>
>
>                     -- 
>                     Tianjing
>
>                          
>
>
>
>              
>
>
>
>
>
>     -- 
>     Tianjing
>
>     Bioinformatics Center,
>     Beijing Genomics Institute,Shenzhen
>     Tel:+86-755-25273851
>     MSN:tianjing217 at hotmail.com <mailto:MSN%3Atianjing217 at hotmail.com>
>
>
>
>
> -- 
> Tianjing
>
> Bioinformatics Center,
> Beijing Genomics Institute,Shenzhen
> Tel:+86-755-25273851
> MSN:tianjing217 at hotmail.com <mailto:MSN%3Atianjing217 at hotmail.com>

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