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Re: [ptp-dev] Remote tools now escapes all non-alphanumeric characters which causes problems for JAXB resource manager commands
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On Tue, Jan 31, 2012 at 12:43 PM, Greg Watson
<g.watson@xxxxxxxxxxxx> wrote:
I don't think Simon can use IRemoteProcessBuilder#environment() directly, since this is being specified in the JAXB
RM XML file.
Ideally, he should be able to do something like:
<submit-batch name="submit-batch" directory="${ptp_rm:directory#value}" waitForId="true" replaceEnvironment="true">
<arg>sbatch</arg>
<arg>${ptp_rm:managed_file_for_script#value}</arg>
<environment name="PATH" value="${env_var:PATH}" />
<environment name="MMCS_SERVER_IP" value="${env_var:MMCS_SERVER_IP}" />
…
However, there are a couple of problems with this. The first one is I found a bug in the JAXB environment handling code. Hopefully this is fixed now. The second is that even if ${env_var:xxx}
worked (I haven't tried it), it would only look at the local environment. There would probably need to be a special variable handler, say "remote_env_var", to look up the remote environment.
I think this would be the "correct" way to do what Simon wants, but it would take some effort to implement. Other than this, I don't see any other way of fixing Simon's problem, apart from
either providing some way to override the shell escaping, or reversing the change.
I'm strongly in favor of doing it the correct way - even if that causes a delay for Simon's contribution. Using shell character is unreliable. It is never avoidable that some string or argument contains special characters. Thus even with the suggestion of overriding the escaping, code which would use this option, would be unreliable. And I think it is much more important to be reliable than adding new features.
Roland
Greg
On Jan 31, 2012, at 1:46 AM, Roland Schulz wrote:
Simon,
we made that change on purpose to avoid unintended consequences if special shell characters are part of a directory or command argument.
E.g. the original approach wouldn't work if the
<generated batch file> would contain a dollar sign somewhere in its path.
Why don't you use org.eclipse.ptp.remote.core.IRemoteProcessBuilder.environment() to set the environment variables?
Roland
On Tue, Jan 31, 2012 at 1:10 AM, Simon Wail
<simon.wail@xxxxxxxxxxx> wrote:
Dev Team,
I've been testing my SLURM - Blue Gene JAXB resource manager in preparation for code submission and hit a major problem. My original development of the resource manager was done using PTP 5.0.1 and it was working fine. Now I've been
testing it under 5.0.4 and it doesn't work anymore. I've investigated the problem and it seems to be the way remote commands are passed to ssh using the remotetools code. The command I want to execute is "env - PATH=$PATH MMCS_SERVER_IP=$MMCS_SERVER_IP sbatch
<generated batch file>" and this is defined in the JAXB resource manager file as:
<submit-batch name="submit-batch" directory="${ptp_rm:directory#value}" waitForId="true">
<arg>env</arg>
<arg>-</arg>
<arg>PATH=$PATH</arg>
<arg>MMCS_SERVER_IP=$MMCS_SERVER_IP</arg>
<arg>sbatch</arg>
<arg>${ptp_rm:managed_file_for_script#value}</arg>
...
This all works fine under 5.0.1 and the remote shell command becomes:
tcsh -c /bin/sh -c 'echo "PID=$$ PIID=24" > /dev/pts/11; export "MESG2=World"; export "MESG=Hello World"; cd /vlsci/IBM/swail/; env - PATH=$PATH MMCS_SERVER_IP=$MMCS_SERVER_IP sbatch /vlsci/IBM/swail//3648df43-aae1-4226-ab56-2263458cb11cmanaged_file_for_script;
'
Now when moving to 5.0.4 the remote shell command becomes:
tcsh -c /bin/sh -c 'echo "PID=$$ PIID=27" > /dev/pts/17; export "MESG2=World"; export "MESG=Hello World"; cd /vlsci/IBM/swail/&& env - PATH\=\$PATH MMCS_SERVER_IP\=\$MMCS_SERVER_IP sbatch /vlsci/IBM/swail//5252c4b2-de35-47e6-ade9-de855f30904dmanaged_file_for_script'
Notice the escape "\" before the equals and dollar signs for setting PATH and MMCS_SERVER_IP. This is breaking the "env" command - the "env -" command allows you to execute a subsequent command with a cleared environment. By using
"env - PATH=$PATH sbatch ..." it allows me to clear the existing shell environment, set the PATH environment variable to the previous value (before the environment is cleared) and then execute the sbatch command. This then provides a limited environment to
the sbatch command which is required for the Blue Gene/P system.
With the escapes now in the command, the PATH environment variable is not set correctly and therefore the sbatch command is not found. This in causing the job submission to fail.
I've looked at the recent differences in the PTP code between 5.0.1 and 5.0.4 and found the following in org.eclipse.ptp.remote.remotetools.core.RemoteToolsProcessBuilder:
1) In the class constructor a set of "trusted" characters is created - this include all alphanumeric characters plus / . _ -
2) In the "start" method the remote command is built and escapes any character NOT in the trusted set - see line 130
I believe this is how the "\"s are now appearing in the remote command and this is causing my job submission to fail.
I've also tried to set the "resolve=false" attribute for each of the "arg" lines in the JAXB file but this makes no difference. I believe it might not be correct to escape all non-alphanumeric characters in the remote commands, but
if this is felt to be necessary, then maybe the "resolve" attribute in the XML could override this to enable the remote command to be sent as desired.
Regards,
| Simon Wail, Ph.D |
| HPC Specialist
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IBM Research Collaboratory for Life Sciences - Melbourne
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--
ORNL/UT Center for Molecular Biophysics
cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
--
ORNL/UT Center for Molecular Biophysics
cmb.ornl.gov865-241-1537, ORNL PO BOX 2008 MS6309
