[gridengine users] Java DRMAA options
"Hung-Sheng Tsao (Lao Tsao 老曹) Ph. D."
laotsao at gmail.com
Tue Mar 1 13:25:18 UTC 2011
this is from DT
http://blogs.sun.com/templedf/entry/hierarchy_of_command_line_switches
*Hierarchy of QSub Command Line Switches*
Since there has been a recent flurry of conversation on the Grid Engine
mailing lists
<http://gridengine.sunsource.net/servlets/ProjectMailingListList> about
assembling a useful Grid Engine knowledge base, I felt compelled to
contribute. So, I present you the hierarchy of command line switches
used by qsub.
The following list is in order of precedence, with 1 having the highest
precedence. A higher precedence option will overwrite a lower precedence
option.
1. Options passed directly to qsub via the command line. Options
contained in the file referenced by -@ in the qsub command line
are inlined into the command line switches.
2. Options embedded in the script file (if no -b y|yes|Y|YES is
included in any of the other option sources.)
3. Options contained in the sge_request file in the current directory
4. Options contained in the sge_request file in the user's home directory
5. Options contained in the sge_request file in the
$SGE_ROOT/$SGE_CELL/common directory
In DRMAA, the option list is similar, except that there are four
additional sources for switches, and there is no command line. Here's
the DRMAA switch hierarchy:
1. Options resulting directly from DRMAA attribute settings. See the
drmaa_attributes man page
<http://gridengine.sunsource.net/nonav/source/browse/%7Echeckout%7E/gridengine/doc/htmlman/htmlman3/drmaa_attributes.html>
for a table.
2. Options contained in the native specification attribute
3. Options referenced by the job category attribute. Options
contained in the file referenced by -@ in the job category
attribute are inlined into the job category's switches.
4. Options embedded in the script file (if no -b y|yes|Y|YES is
included in any of the other option sources.)
5. Options contained in the sge_request file in the current directory
6. Options contained in the sge_request file in the user's home directory
7. Options contained in the sge_request file in the
$SGE_ROOT/$SGE_CELL/common directory
8. DRMAA default options:
* -p 0
* -b y
* -shell n
* -w e
On 3/1/2011 7:11 AM, Dave Love wrote:
> [I should have said before, that I assume Prentice has already tried
> getting support from Wolfram and found the fees you pay get as much help
> as they typically do in such cases.]
>
> "Hung-Sheng Tsao (Lao Tsao 老曹) Ph. D."<laotsao at gmail.com> writes:
>
>> FYI
>> In JobTemplateImpl.java/
>>> By default DRMAA sets four options for all jobs. They are
>> * -p 0 -b yes -shell no, and -w e. This means that by default, all jobs will
>> have priority 0, all jobs will be treated as binary, i.e. no scripts args will
>> be parsed, all jobs will be executed without a wrapper shell, and jobs which
>> are unschedulable will cause a submit error.
>>
>> Specifies native qsub options which will be interpreted as part of the
>> * DRMAA job template. All options available to the qsub command may be
>> * used except for -help, -sync, -t, -verify, and -w w|v. -cwd may only be
>> used if the $SGE_DRMAA_ALLOW_CWD enviroment variable is set.
> I've appended the relevant javadoc text about the means of setting the
> options for Java DRMAA, in the hope that it appears on searches. I
> should try to get it online somehow, but there are problems at least
> with broken links to sunsource. I assume using sge_request is
> appropriate, per Reuti's suggestion.
>
>> On 2/28/2011 5:29 PM, Prentice Bisbal wrote:
>>
>> Dave Love wrote:
>>
>> Reuti<reuti at staff.uni-marburg.de> writes:
>>
>>
>> This doesn't look like a DRMAA error per se - the job requests something which can't be satisfied.
>>
>> I.e. DRMAA has a default implicit `-w e' if I recall correctly.
>>
>> I did some googling before posting here for help, and on eof my hits
>> mentioend the same thing and recommend adding '-w n' to my job
>> submission script, to override the default validation behavior of the
>> DRMAA. Didn't help.
>>
>> Of course I added that to my submission script, which starts the first
>> Mathematica job. I really need to find a way to add it to the
>> Mathematica script so I can debug why the DRMAA calls are failing. If I
>> could do that, '-w p' or '-w v' should identify the problem right away.
>>
>> Is there anyway to force '-w p' or '-w v' for all DRMAA jobs?
> DRMMA Attributes
>
> DRMAA job template attributes can be set from six different
> sources. In order of precedence, from lowest to highest, there are:
> options set by DRMAA automatically by default, options set in the
> sge_request file(s), options set in the script file, options set by
> the jobCategory property, options set by the nativeSpecification
> property, and options set through other DRMAA properties.
>
> By default DRMAA sets four options for all jobs. They are "-p 0", "-b
> yes", "-shell no", and "-w e". This means that by default, all jobs
> will have priority 0, all jobs will be treated as binary, i.e. no
> scripts args will be parsed, all jobs will be executed without a
> wrapper shell, and jobs which are unschedulable will cause a submit
> error.
>
> The sge_request file, found in the $SGE_ROOT/$SGE_CELL/common
> directory, may contain options to be applied to all jobs. The
> .sge_request file found in the user's home directory or the current
> working directory may also contain options to be applied to certain
> jobs. See the sge_request(5) man page for more information.
>
> If the sge_request file contains "-b no" or if the nativeSpecification
> property is set and contains "-b no", the script file will be parsed
> for in-line arguments. Otherwise, no script's args will be
> interpreted. See the qsub(1) man page for more information.
>
> If the jobCategory property is set, and the category it points to
> exists in one of the qtask files, the options associated with that
> category will be applied to the job template. See the qtask(5) man
> page and setJobCategory(String) below for more information.
>
> If the nativeSpecification property is set, all options contained
> therein will be applied to the job template. See
> setNativeSpecification(String) below for more information.
>
> Other DRMAA attributes will override any previous settings. For
> example, if the sge_request file contains "-j y", but the joinFiles
> property is set to false, the ultimate result is that the input and
> output files will remain separate.
>
> For various reasons, some options are silently ignored by
> DRMAA. Setting any of these options will have no effect. The ignored
> options are: "-cwd", "-help", "-sync", "-t", "-verify", "-w w", and
> "-w v". The "-cwd" option can be reenabled by setting the environment
> variable, SGE_DRMAA_ALLOW_CWD. However, the "-cwd" option is not
> thread safe and should not be used in a multi-threaded context.
>
> Attribute Correlations
>
> The following DRMAA attributes correspond to the following qsub options:
> DRMAA Attribute qsub Option
> remoteCommand script file
> args script file arguments
> jobSubmissionState = HOLD_STATE -h
> jobEnvironment -v
> workingDirectory = $PWD -cwd
> jobCategory (qtsch qtask)*
> nativeSpecification ALL*
> emailAddresses -M
> blockEmail = true -m n
> startTime -a
> jobName -N
> inputPath -i
> outputPath -o
> errorPath -e
> joinFiles -j
> transferFiles (prolog and epilog)*
>
> * See the individual attribute setter description below
>
> The following attributes are unsupported by Grid Engine:
>
> * deadlineTime
> * hardWallclockTimeLimit
> * softWallclockTimeLimit
> * hardRunDurationTimeLimit
> * softRunDurationTimeLimit
>
> Using the accessors for any of these attributes will result in an
> UnsupportedAttributeException being thrown.
>
> _______________________________________________
> users mailing list
> users at gridengine.org
> https://gridengine.org/mailman/listinfo/users
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