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Ticket Resolution Summary Owner Reporter
#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.

#1413 fixed qalter -w reports "job is already running" for held job Dave Love <d.love@…> dlove
Description

$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID


147 0.00000 true dlove hqw 02/27/2012 16:43:41 1

$ qalter -w p 147 verification: job is already running

#1412 fixed check in rc script that the shepherd, at least, will load Dave Love <d.love@…> dlove
Description

The failure is obscure if shared libraries are missing when the shepherd tries to run (see http://arc.liv.ac.uk/pipermail/sge-discuss/2012-March/000235.html).

The script could check, say, sge_shepherd -help after setting at least LD_LIBRARY_PATH consistent with execd's.

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