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Ticket Resolution Summary Owner Reporter
#1507 fixed qmake crash with buffer overflow Dave Love <d.love@…> tourist
Description

Hi from jon.stahl@…:

I was seeing a qmake crash with a buffer overflow segfault on CentOS 6.5 x86_64.

I was able to resolve it by the following patch:

3rd_party/qmake/remote-sge.c

if(gethostname(hostbuffer, 1023) != 0) {

to

if(gethostname(hostbuffer, sizeof hostbuffer) != 0) {

#1420 fixed qmake 8.1.0 puts "\n" in multiline commands, causing the commands to fail. sbridgett sbridgett
Description

When there are multi-line commands (with the "\" continuation character at end of each line) in a "Makefile", qmake 8.0 and latest 8.1.0 replace the "\newline" with "\n", causing the command to fail. (where "newline" means an actual newline character, and "n" means the character "n").

Whereas the earlier Grid engine GE 6.1u6 replaced the "\newline" with a space so the command succeeded.

For example:

The "Makefile" contains:

all:
[Tab]echo Hello \
        how \
        are \
        you?; \
        ls \
        -al  

where "[Tab]" is a Horizontal Tab character, and the lines below it start with spaces rather than tabs.

The "runqmake.sh" contains:

#!/bin/bash

# Print the version of Grid engine:
qsub -help | grep GE

qmake -cwd -v PATH -- -j 2

Then submitting with qsub using:

  qsub -cwd -v PATH -sync yes runqmake.sh

In the resulting "runqmake.sh.o281786" the earlier grid engine GE 6.1 outputs:

GE 6.1u6
echo Hello \
        how \
        are \
        you?; \
        ls \
        -al
dynamic mode
Hello how are you?
total 64
drwxrwxr-x  2 sbridget biology  4096 Jun 14 17:24 .
drwxrwxr-x 33 root     biology 16384 Jun 14 17:05 ..
-rw-rw-r--  1 sbridget biology    89 Jun 14 17:23 Makefile
-rwxrwxr-x  1 sbridget biology    98 Jun 14 17:19 runqmake.sh

Whereas the latest SGE 8.1.0 outputs:

SGE 8.1.0
echo Hello \
        how \
        are \
        you?; \
        ls \
        -al
dynamic mode
Hello \n how \n are \n you?

NOTE: The "\n" embedded within the "Hello \n how \ are \n you?"

And the "ls -al" command fails, outputting a file "runqmake.sh.e9188" containing:

/bin/sh: \n: command not found
qmake: *** [all] Error 127

Which I think is because the ls command is being output as "ls \n -al" rather than the "ls -al", so the error message "\n: command not found" is given.

I've looked into the qmake source code, including the read.c and misc.c files, but am not just sure why this is occurring.

Perhaps there is something I have set incorrectly in the sge configuration?

We are running SGE 8.1.0 on Centos 6 (whereas the GE 6.1u is running in Centos 5)

Thank you for help with this.

If I just use "make" on the Centos 6 cluster (where SGE 8.1.0 is installed), I get the correct output:

make

echo Hello \
        how \
        are \
        you?; \
        ls \
        -al
Hello  how are you?
total 259K
drwxrwxr-x  2 sbridget biology  545 Jun 14 17:23 .
drwxrwxr-x 25 sbridget biology 2414 Jun 14 11:37 ..
-rw-rw-r--  1 sbridget biology   91 Jun 14 17:23 Makefile
-rw-rw-r--  1 sbridget biology   98 Jun 14 17:20 runqmake.sh

Several of the perl scripts that we use to run processes have long multiline commands with many command-line options, so these programs fail on SGE 8.1.0.

#1576 fixed qconf - not an admin host Dave Love <d.love@…> christopher.webb@…
Description

Hi,

I think a recent update to qconf has broken previous functionality. You used to be able to run the "show" commands on non-admin hosts, they now return a "not an admin host" error:

[spimcmw@nanlnx4 ~]1% qconf -sh denied: host "nanlnx4.iop.kcl.ac.uk" is not an admin host [spimcmw@nanlnx4 ~]1%

This information can be still be obtained from qmon on non-admin hosts so I assume this is not deliberate. I wonder if it was due to the fix for #1547?

This is causing problems with the FSL package (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) as their programs use the qconf to check queues before submitting jobs.

[spimcmw@nanlnx4 bin]0% grep QCONF fsl_sub

QCONF=which qconf if [ "x$QCONF" = "x" ]; then QCONF=echo

$QCONF -sq $queue >/dev/null 2>&1

$QCONF -sp $peName >/dev/null 2>&1

[spimcmw@nanlnx4 bin]0% grep qconf bedpostx

qconf -sq $FSLGECUDAQ 2>&1 >/dev/null

[spimcmw@nanlnx4 bin]0%

[spimcmw@nanlnx4 ~]1% qconf | & head -n1 SGE 8.1.9 [spimcmw@nanlnx4 ~]1%

Chris

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