[GE users] SunGrid Engine & BLAST

Hrishikesh Deshmukh hdeshmuk at gmail.com
Fri Jan 28 14:45:07 GMT 2005


Hi,
I guess the libs are installed, do i have to install x-free86!!
~ sgeadmin$  otool -L qmon
otool: can't open file: qmon (No such file or directory)
emac21:~ sgeadmin$ cd /usr/local/sge/bin/darwin/
emac21:/usr/local/sge/bin/darwin sgeadmin$  otool -L qmon
qmon:
        libXltree.dylib (compatibility version 0.0.0, current version 0.0.0)
        /usr/X11R6/lib/libXm.3.dylib (compatibility version 0.0.0,
current version 0.0.0)
        /usr/X11R6/lib/libXpm.4.dylib (compatibility version 4.11.0,
current version 4.11.
0)
        /usr/X11R6/lib/libXt.6.dylib (compatibility version 6.0.0,
current version 6.0.0)
        /usr/X11R6/lib/libXext.6.dylib (compatibility version 6.4.0,
current version 6.4.0
)
        /usr/X11R6/lib/libX11.6.dylib (compatibility version 6.2.0,
current version 6.2.0)
        /usr/X11R6/lib/libSM.6.dylib (compatibility version 6.0.0,
current version 6.0.0)
        /usr/X11R6/lib/libICE.6.dylib (compatibility version 6.3.0,
current version 6.3.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0,
current version 63.0.0)

BTW, what do these error messages mean! I have a grid with 5 emacs,
each has user "blast" on it, i use the user blast on the master host
and use this blast.csh script:
http://developers.sun.com/solaris/articles/integrating_blast.html 
I can see using qstat that the job is submitted and in queue and then
transferred to one of the machines and on this machine i see these
errors:

blast$ more blast.csh.e12
[NULL_Caption] FATAL ERROR: blast: Unable to open input file
/Users/blast/Library/BLAST/queries//test1

~ blast$ more blast.csh.o12
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
 blastn 2.2.10 
 
Your help is appreaciated.
Thanks,
Hrishi


On Fri, 28 Jan 2005 10:06:05 +0100, Andre Alefeld <Andre.Alefeld at sun.com> wrote:
> Hi,
> 
> the following command shows the library paths on our MacOS machine.
> Is it possible that Motif is not installed on yours ?
> 
> pippin% otool -L qmon
> qmon:
>         libXltree.dylib (compatibility version 0.0.0, current version 0.0.0)
>         libspoolc.dylib (compatibility version 0.0.0, current version 0.0.0)
>         /usr/lib/libdl.dylib (compatibility version 1.0.0, current version 1.0.0
> )
>         /usr/X11R6/lib/libXm.3.dylib (compatibility version 0.0.0, current versi
> on 0.0.0)
>         /usr/X11R6/lib/libXpm.4.dylib (compatibility version 4.11.0, current ver
> sion 4.11.0)
>         /usr/X11R6/lib/libXt.6.dylib (compatibility version 6.0.0, current versi
> on 6.0.0)
>         /usr/X11R6/lib/libXext.6.dylib (compatibility version 6.4.0, current ver
> sion 6.4.0)
>         /usr/X11R6/lib/libX11.6.dylib (compatibility version 6.2.0, current vers
> ion 6.2.0)
>         /usr/X11R6/lib/libSM.6.dylib (compatibility version 6.0.0, current versi
> on 6.0.0)
>         /usr/X11R6/lib/libICE.6.dylib (compatibility version 6.3.0, current vers
> ion 6.3.0)
>         /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>  63.0.0)
> 
> Hrishikesh Deshmukh wrote:
> 
> > Hi All,
> > Here are the errors which i get when i try to run qmon from an x11
> > terminal. I did instal openmotif3 using fink!! The first error cannot
> > find certain library, the second one cannot find someother one!
> > ./qmon
> > dyld: ./qmon can't open library: libXltree.dylib  (No such file or
> > directory, errno = 2)
> > Trace/BPT trap
> > emac21:/usr/local/sge/bin/darwin blast$ export
> > DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/usr/l
> > ocal/sge/lib/darwin/
> > emac21:/usr/local/sge/bin/darwin blast$ ./qmon
> > dyld: ./qmon can't open library: /usr/X11R6/lib/libXm.3.dylib  (No
> > such file or directory,
> >  errno = 2)
> > Trace/BPT trap
> > emac21:/usr/local/sge/bin/darwin blast$ echo $DYLD_LIBRARY_PATH
> > :/usr/local/sge/lib/darwin/
> >
> > Thanks,
> > H
> >
> > On Thu, 27 Jan 2005 14:35:38 -0500, Hrishikesh Deshmukh
> > <hdeshmuk at gmail.com> wrote:
> >
> >>Sorry a newbie question, what is a wrapper? Also about the first
> >>suggestion what is the install_name_tool!!
> >>
> >>% install_name_tool -change libXltree.dylib <libXltree.dylib in your
> >>SGE dir> qmon
> >> % install_name_tool -change libspoolc.dylib <libspoolc.dylib in your
> >>SGE dir> qmon
> >>
> >>Thanks,
> >>H
> >>
> >>
> >>On Wed, 26 Jan 2005 20:01:42 -0800 (PST), Ron Chen
> >><ron_chen_123 at yahoo.com> wrote:
> >>
> >>>--- Paul Greidanus <paul.greidanus at ualberta.ca> wrote:
> >>>
> >>>>however, I've had it cause me lots of trouble with
> >>>>other apps
> >>>
> >>>There are 2 ways around this:
> >>>
> >>>1) use install_name_tool
> >>>If you look at the shared library dependency chain:
> >>>% otool -L qmon
> >>>qmon:
> >>>   libXltree.dylib (compatibility version 0.0.0, current version 0.0.0)
> >>>   libspoolc.dylib (compatibility version 0.0.0, current version 0.0.0)
> >>>   ...
> >>>
> >>>Only libXltree.dylib & libspoolc.dylib do not have an
> >>>absolute path, so use install_name_tool to edit the binary:
> >>>
> >>>% install_name_tool -change libXltree.dylib <libXltree.dylib in your SGE dir> qmon
> >>>% install_name_tool -change libspoolc.dylib <libspoolc.dylib in your SGE dir> qmon
> >>>(those libs are likely in $SGE_ROOT/lib/darwin/)
> >>>
> >>>2) write a wrapper, rename the qmon binary as qmon.real,
> >>>and name the wrapper as qmon, and put it in qmon's
> >>>directory:
> >>>
> >>>#!/bin/sh
> >>>
> >>>export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/usr/local/sge/lib/darwin
> >>>./qmon.real
> >>>
> >>> -Ron
> >>>
> >>>
> >>>
> >>>>, so you shouldn't do it in your .profile
> >>>>without being
> >>>>careful about how it behaves, and knowing to remove
> >>>>it if it causes trouble.
> >>>
> >>>
> >>>__________________________________
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> >>>Yahoo! Mail - Find what you need with new enhanced search.
> >>>http://info.mail.yahoo.com/mail_250
> >>>
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> >>>
> >>
> > 
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> 
> --
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Andre Alefeld                Phone: ++49 (0)941 3075-255
> Software Engineering         Fax:   ++49 (0)941 3075-222
> Sun Microsystems GmbH
> Dr.-Leo-Ritter-Str. 7        mailto: andre.alefeld at sun.com
> D-93049 Regensburg           http://www.sun.com/grid
> 
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