[GE users] 6.2u3 qsub Segmentation fault when using -V and -jsv ?

stephendennis sdennis at univaud.com
Fri Sep 25 18:01:45 BST 2009


Hello Mark

I encountered the same problem.  Fix is in the head as of 9/09/09.

Work around for this is to comment out jsv_send_env(); in jsv_on_start().

http://gridengine.sunsource.net/issues/show_bug.cgi?id=3088

In detail, if you have a "%." in your environment it can trigger a segfault
in the jsv protocol decoder.  There is an fprintf that passes the protocol
buffer straight through....oops.

It is notable that in the sample jsv.sh, jsv_send_env is commented out....

Until the binary fix is available, I supposed if you want to use -V then you
will need to filter the environment for any %. that will be processed
by the fprintf.

Thanks
Stephen

________________________________________
From: ccaamad [m.c.dixon at leeds.ac.uk]
Sent: Friday, September 25, 2009 11:31 AM
To: users at gridengine.sunsource.net
Subject: Re: [GE users] 6.2u3 qsub Segmentation fault when using -V and -jsv ?

On Thu, 24 Sep 2009, ccaamad wrote:
...
> That's really good news - I'll try and 6.2u3 installed on a lx24-amd64 box
> for further testing. I hope -V works with -jsv... it's really nice to
> have!
...

On the off-chance that anyone else is interested in this...

I installed the lx24-amd64 version of GE 6.2u3 on a 64-bit system, but
also installed the lx24-x86 (courtesy) binaries. I only get a segfault
when using the 32-bit client - let's hope the bug isn't doing other harm
on 64-bit...

I'll open a bug report.

* 64-bit seems to work:

$ /scratch/ge6.2u3/bin/lx24-amd64/qsub -V test.sh
Your job 10 ("test.sh") has been submitted
$ /scratch/ge6.2u3/bin/lx24-amd64/qsub -jsv ./test_pl.jsv test.sh
Your job 11 ("test.sh") has been submitted
$ /scratch/ge6.2u3/bin/lx24-amd64/qsub -V -jsv ./test_pl.jsv test.sh
Your job 12 ("test.sh") has been submitted

* 32-bit doesn't:

$ /scratch/ge6.2u3/bin/lx24-x86/qsub -V test.sh
Your job 13 ("test.sh") has been submitted
$ /scratch/ge6.2u3/bin/lx24-x86/qsub -jsv ./test_pl.jsv test.sh
Your job 14 ("test.sh") has been submitted
$ /scratch/ge6.2u3/bin/lx24-x86/qsub -V -jsv ./test_pl.jsv test.sh
Segmentation fault (core dumped)
$ gdb /scratch/ge6.2u3/bin/lx24-x86/qsub core.14770
GNU gdb Fedora (6.8-27.el5)
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu"...

warning: Can't read pathname for load map: Input/output error.
Reading symbols from /lib/libdl.so.2...done.
Loaded symbols for /lib/libdl.so.2
Reading symbols from /lib/libm.so.6...done.
Loaded symbols for /lib/libm.so.6
Reading symbols from /lib/libpthread.so.0...done.
Loaded symbols for /lib/libpthread.so.0
Reading symbols from /lib/libc.so.6...done.
Loaded symbols for /lib/libc.so.6
Reading symbols from /lib/ld-linux.so.2...done.
Loaded symbols for /lib/ld-linux.so.2
Core was generated by `/scratch/ge6.2u3/bin/lx24-x86/qsub -V -jsv ./test_pl.jsv test.sh'.
Program terminated with signal 11, Segmentation fault.
[New process 14770]
#0  0x0072b96b in strlen () from /lib/libc.so.6
(gdb) bt
#0  0x0072b96b in strlen () from /lib/libc.so.6
#1  0x006fbbce in vfprintf () from /lib/libc.so.6
#2  0x00701e02 in fprintf () from /lib/libc.so.6
#3  0x080c73dd in jsv_send_data ()
#4  0x080c56da in jsv_send_command ()
#5  0x080ccfa3 in jsv_handle_started_command ()
#6  0x080c80da in jsv_do_communication ()
#7  0x080c6a85 in jsv_do_verify ()
#8  0x0809b6c5 in sge_gdi_packet_execute_external ()
#9  0x08093f54 in sge_gdi2_multi ()
#10 0x08093cf6 in sge_gdi2 ()
#11 0x08083c4d in japi_send_job ()
#12 0x0807bf70 in japi_run_job ()
#13 0x080648d0 in main ()
(gdb)

Cheers,

Mark
--
-----------------------------------------------------------------
Mark Dixon                       Email    : m.c.dixon at leeds.ac.uk
HPC/Grid Systems Support         Tel (int): 35429
Information Systems Services     Tel (ext): +44(0)113 343 5429
University of Leeds, LS2 9JT, UK
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