Debuging the apps

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Profile Jack Shultz
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Message 1791 - Posted: 19 Nov 2009, 1:02:15 UTC

Ok, if your host keeps failing, take a deep breath...then exhale. You're not the only one and I'm sorry but I need you to do some testing for me.

As described in this wiki
http://boinc.berkeley.edu/trac/wiki/AppDebug
These problems can be debugged by running the client with these command-line options:

--exit_before_start
The client will exit just before running an app. At that point, look at the slot directory and make sure everything is correct. Try running the app manually in the slot directory.
--exit_after_finish
The client will exit just after an app finishes. At that point, look at the slot directory and project directories, and verify that the output files are there.

We can try it both ways if you use --exit_before_start
you will need to run the wrapper. For autodock with MGL it is called autodock_mgl
for mdrun it is called mdrun

they are linked from the slot to the project directory so if you open the file in slot/x you can see which one it is linked to. Then copy it over to the slot/x directory. Then you can execute that application from the slot.

I know its hard to describe but ask me if you have questions. Or catch me on skype john.shultz
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Profile Erkan Yilmaz
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Message 1796 - Posted: 19 Nov 2009, 22:32:21 UTC - in response to Message 1791.  
Last modified: 19 Nov 2009, 22:45:52 UTC

Not sure, if this what you are looking for.

I get this error on ubuntu64:

<core_client_version>6.10.17</core_client_version>
<![CDATA[
<message>
process exited with code 22 (0x16, -234)
</message>
<stderr_txt>
execv: No such file or directory

</stderr_txt>
]]>

It seems with ia32 package it may run
http://boincfaq.mundayweb.com/index.php?language=1&view=280

but: seems it is not contained anymore directly because "sudo aptitude install ia32-libs" doesn|t install it

Well, stopped so far, until one looks at this
On request I can provide more info


What did I do ?
1. used option --exit_before_start
2. copied the app into the slot dir and tried to run the autodock_1.410_x86_64-pc-linux-gnu as admin and normal user but get always:

ubuntu@ubuntu:~/Desktop/BOINC/slots/1$ ./autodock_1.410_x86_64-pc-linux-gnu
bash: ./autodock_1.410_x86_64-pc-linux-gnu: No such file or directory

3. also tried set chmod 755 permissions and it is on my desktop where I have access

further info:
root@ubuntu:/home/ubuntu/Desktop/BOINC/slots/1# file autodock_1.410_x86_64-pc-linux-gnu
autodock_1.410_x86_64-pc-linux-gnu: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped

root@ubuntu:/home/ubuntu/Desktop/BOINC/slots/1# ldd autodock_1.410_x86_64-pc-linux-gnu
not a dynamic executable


pc, os info: here, ubuntu 9.10 desktop amd64
above info collected with this WU
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Message 1797 - Posted: 20 Nov 2009, 2:58:08 UTC - in response to Message 1796.  
Last modified: 20 Nov 2009, 2:59:42 UTC

Great thanks for tip. Repository package ia32-libs works. Nice.
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Profile Jack Shultz
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Message 1798 - Posted: 20 Nov 2009, 15:12:36 UTC - in response to Message 1796.  

copy autodock_mgl_[VERSION}_[PLATFORM] to the slot. That is our wrapper application for autodock. It executes all the other apps.
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Message 1799 - Posted: 20 Nov 2009, 18:39:10 UTC - in response to Message 1798.  

Hi Jack,
autodoch seems to be a 32 bit binary. Therefore it fails to run on 64 bit systems if there the 32 bit compatibility libs ia32 are not installed. You can avoid such trouble, if you compile autodock on a 64 bit system (if you have the sources).

yoyo
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Message 1800 - Posted: 20 Nov 2009, 20:27:12 UTC - in response to Message 1799.  

Hi Yoyo. Nice seeing you in Barcelona!

I'm not so sure the autodock failures on 64-bit are universal. Our host is RH5 64-bit. I thought this was built on 64-bit. I've ran autodock workunits on the server and they were successful.

At which step of the job file is it failing? I got these 2 platforms
180 autodock_mgl 511 x86_64-pc-linux-gnu
183 autodock_mgl 215 i686-pc-linux-gnu

Then I got these success stats for the last 24 hours

Application OS Total
Results Pass Rate Fail Rate Failed
Downloading Failed
Downloaded Failed
Computing Failed
Uploading Failed
Uploaded Aborted
511 Linux 208 95.6731% 4.3269% 0.4808% 0.0000% 3.8462% 0.0000% 0.0000% 0.0000%

215 Linux 88 42.0455% 57.9545% 5.6818% 0.0000% 52.2727% 0.0000% 0.0000% 0.0000%
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Profile Erkan Yilmaz
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Message 1803 - Posted: 21 Nov 2009, 6:53:33 UTC - in response to Message 1800.  
Last modified: 21 Nov 2009, 6:59:31 UTC

1. scenario from above: after adding ia32-libs from repository package it worked + I could successfully calculate

2. tried again with a fresh boinc on a second ubuntu64: but again same error
see this WU please:
http://boinc.drugdiscoveryathome.com/result.php?resultid=1176440

3. the project wont send me new WUs after that :-(
so I went to the project dir to start the application from there (as root and normal user)
but still same problem, see below please


ubuntu@ubuntu:~/Desktop/BOINC/projects/boinc.drugdiscoveryathome.com$ ls -la
total 40036
drwxrwx--x 2 ubuntu ubuntu 240 2009-11-21 06:35 .
drwxrwx--x 3 ubuntu ubuntu 60 2009-11-21 06:33 ..
-rwxr-xr-x 1 ubuntu ubuntu 1060192 2009-11-21 06:34 7za_1.405_x86_64-pc-linux-gnu
-rwxr-xr-x 1 ubuntu ubuntu 10564 2009-11-21 06:34 AD4_parameters_1.401_x86_64-pc-linux-gnu
-rwxr-xr-x 1 ubuntu ubuntu 411425 2009-11-21 06:34 autodock_1.410_x86_64-pc-linux-gnu
-rwxr-xr-x 1 ubuntu ubuntu 639619 2009-11-21 06:33 autodock_mgl_1.411_x86_64-pc-linux-gnu
-rwxr-xr-x 1 ubuntu ubuntu 1312714 2009-11-21 06:33 autogrid_1.401_x86_64-pc-linux-gnu
-rwxr-xr-x 1 ubuntu ubuntu 8933 2009-11-21 06:34 LICENSES
-rwxr-xr-x 1 ubuntu ubuntu 1419 2009-11-21 06:34 make_sitecustomize_1.401_x86_64-pc-linux-gnu
-rwxr-xr-x 1 ubuntu ubuntu 37226607 2009-11-21 06:34 MGLToolsPckgs_1.401_x86_64-pc-linux-gnu.zip
-rwxr-xr-x 1 ubuntu ubuntu 124784 2009-11-21 06:34 unzip_1.401_x86_64-pc-linux-gnu
-rwxr-xr-x 1 ubuntu ubuntu 59760 2009-11-21 06:33 zip_1.401_x86_64-pc-linux-gnu

ubuntu@ubuntu:~/Desktop/BOINC/projects/boinc.drugdiscoveryathome.com$ ./autodock_mgl_1.411_x86_64-pc-linux-gnu
bash: ./autodock_mgl_1.411_x86_64-pc-linux-gnu: No such file or directory

ubuntu@ubuntu:~/Desktop/BOINC/projects/boinc.drugdiscoveryathome.com$ file autodock_mgl_1.411_x86_64-pc-linux-gnu
autodock_mgl_1.411_x86_64-pc-linux-gnu: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped

ubuntu@ubuntu:~/Desktop/BOINC/projects/boinc.drugdiscoveryathome.com$ ldd autodock_mgl_1.411_x86_64-pc-linux-gnu
not a dynamic executable


root@ubuntu:/home/ubuntu/Desktop/BOINC/projects/boinc.drugdiscoveryathome.com# ./autodock_mgl_1.411_x86_64-pc-linux-gnu
-su: ./autodock_mgl_1.411_x86_64-pc-linux-gnu: No such file or directory

root@ubuntu:/home/ubuntu/Desktop/BOINC/projects/boinc.drugdiscoveryathome.com# file autodock_mgl_1.411_x86_64-pc-linux-gnu
autodock_mgl_1.411_x86_64-pc-linux-gnu: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped

root@ubuntu:/home/ubuntu/Desktop/BOINC/projects/boinc.drugdiscoveryathome.com# ldd autodock_mgl_1.411_x86_64-pc-linux-gnu
not a dynamic executable

root@ubuntu:/home/ubuntu/Desktop/BOINC/projects/boinc.drugdiscoveryathome.com# ls -la autodock_mgl_1.411_x86_64-pc-linux-gnu
-rwxr-xr-x 1 ubuntu ubuntu 639619 2009-11-21 06:33 autodock_mgl_1.411_x86_64-pc-linux-gnu
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Message 1805 - Posted: 21 Nov 2009, 7:34:47 UTC - in response to Message 1803.  


root@ubuntu:/home/ubuntu/Desktop/BOINC/projects/boinc.drugdiscoveryathome.com# file autodock_mgl_1.411_x86_64-pc-linux-gnu
autodock_mgl_1.411_x86_64-pc-linux-gnu: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped

This is the problem. It is a ELF 32-bit executable. Not all 64 Linux systems support 32 bit executables without installing additionaly the ia32-libs. So you should compile it on a 64 bit system.
yoyo
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Message 1853 - Posted: 25 Nov 2009, 19:26:55 UTC

Everyone from my team running DD on 64bit Linux have ia32-libs installed.
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Profile Jack Shultz
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Message 1954 - Posted: 11 Dec 2009, 11:56:08 UTC - in response to Message 1853.  

Another problem I observe and may explain other issues, mdrun keeps running without terminating. You can see it in the process monitor
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