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Old 05-19-2011, 02:30 AM   #1
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Location: Paris

Join Date: May 2011
Posts: 3
Default Running Dindel on OS X with XGRID


I had successfully installed dindel on 5 OSX 10.6.4 computer and server. Exactly the same install for all, with exactly the same paths for all.

Dindel was successfully compiled with the same modified Makefile (add boost library file, path to samtools dir, remove static flag) and run locally on each computer but if I want to submit a dindel job trough the xgrid command :

xserver$ xgrid -job submit /opt/local/bin/dindel {
jobIdentifier = 50;
xserver$ xgrid -job results -id 50
dyld: Library not loaded: /opt/local/lib/libboost_program_options.dylib
Referenced from: /opt/local/bin/dindel
Reason: no suitable image found. Did find:
/opt/local/lib/libboost_program_options.dylib: open() failed with errno=1

if i look in /usr/include/sys/errno.h for what is errno number 1 I had a very useful : #define EPERM 1 /* Operation not permitted */

Did someone have had the same problem and find a fix for it ?

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Old 05-19-2011, 07:31 AM   #2
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Location: Paris

Join Date: May 2011
Posts: 3
Default solution

I reply to myself as I solved my problem, but it may be usefull for others.

Actually the problem was due to the sandbox access use by xgrid.

You could find explanations here :

in brief it is a permision problem. if you don't use kerberos run on xgrid will go as nobody and it don't have enought rigth to write. the good practice is to use kerberos.

The quick and dirty way is this one (on each xgrid agent) but IT'S A SECURITY HOLE!

$ sudo mv /usr/share/sandbox/xgridagentd_task_nobody{,.orig}.sb

$ sudo cp /usr/share/sandbox/xgridagentd_task_{some,no}

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