[GE users] Something Wrong with drmaa

templedf dan.templeton at sun.com
Tue Aug 11 17:45:22 BST 2009


DRMAA assumes all jobs are binary by default.  If you want to get the
same behavior as qsub, add "-b n" to the native specification, the job
category, or a sge_request file.

Daniel

TianJing wrote:
> i use java API to qsub the scripts in submit server,but the work can
> not be qsub,the .o and .e files are empty.
>
> in the /opt/gridengine/default/spool/www-0-1/message file, it says:
> 08/11/2009 13:50:38|  main|www-0-1|E|shepherd of job 155.1 exited with
> exit status = 27
> 08/11/2009 13:50:38|  main|www-0-1|E|can't open usage file
> "active_jobs/155.1/usage" for job 155.1: No such file or directory
> 08/11/2009 13:50:38|  main|www-0-1|E|08/11/2009 13:50:37 [0:24253]:
> execvp(/share/bccdata/Cloud/tmp/test.sh, "/share/bccdata/
> Cloud/tmp/test.sh") failed: Permission denied
>
> the script is without x permission,  if i chmod +x to the scripts,it
> works,but can we do the something by modify the sge configure file?
>
>
>
>
> 2009/8/8 Daniel Templeton <Dan.Templeton at sun.com
> <mailto:Dan.Templeton at sun.com>>
>
>     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>
>         <mailto: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>
>            <mailto: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>>
>                            <mailto: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>>
>                            <mailto: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>>
>                               <mailto: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>>
>                               <mailto: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>>
>
>                               <mailto: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>
>         <mailto:MSN%3Atianjing217 at hotmail.com
>         <mailto:MSN%253Atianjing217 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>
>         <mailto:MSN%3Atianjing217 at hotmail.com
>         <mailto:MSN%253Atianjing217 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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