Class JobTemplateImpl

  • All Implemented Interfaces:
    JobTemplate

    public class JobTemplateImpl
    extends java.lang.Object
    implements JobTemplate
    This class represents a remote job and its attributes. It is used to set up the environment for a job to be submitted.

    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 Attributes
    DRMAA Attributeqsub Option
    remoteCommandscript file
    argsscript file arguments
    jobSubmissionState = HOLD_STATE-h
    jobEnvironment-v
    workingDirectory = $PWD-cwd
    jobCategory(qtsch qtask)*
    nativeSpecificationALL*
    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.

    Since:
    0.5
    Version:
    1.0
    See Also:
    JobTemplate, Session, SessionImpl, sge_request(5), qsub(1), qtask(5)
    • Method Detail

      • setRemoteCommand

        public void setRemoteCommand​(java.lang.String remoteCommand)
                              throws DrmaaException
        Specifies the remote command to execute. The remoteCommand must be the path of an executable that is available at the job's execution host. If the path is relative, it is assumed to be relative to the working directory, usually set through the workingDirectory property. If workingDirectory is not set, the path is assumed to be relative to the user's home directory.

        The file pointed to by remoteCommand may either be an executable binary or an executable script. If a script, it must include the path to the shell in a #! line at the beginning of the script. By default, the remote command will be executed directly, as by exec. (See the exec(2) man page.) To have the remote command executed in a shell, such as to preserve environment settings, use the nativeSpecification property to include the "-shell yes" option. Jobs which are executed by a wrapper shell fail differently from jobs which are executed directly. When a job which contains a user error, such as an invalid path to the executable, is executed by a wrapper shell, the job will execute successfully, but exit with a return code of 1. When a job which contains such an error is executed directly, it will enter the DRMAA_PS_FAILED state upon execution.

        No binary file management is done.

        Specified by:
        setRemoteCommand in interface JobTemplate
        Parameters:
        remoteCommand - the command to execute as the job
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
      • getRemoteCommand

        public java.lang.String getRemoteCommand()
                                          throws DrmaaException
        Get the command string to execute as the job.
        Specified by:
        getRemoteCommand in interface JobTemplate
        Returns:
        the command to execute as the job or null if it has not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setRemoteCommand(String)
      • setArgs

        public void setArgs​(java.util.List args)
                     throws DrmaaException
        Specifies the arguments to the job.
        Specified by:
        setArgs in interface JobTemplate
        Parameters:
        args - the parameters passed as arguments to the job
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
      • getArgs

        public java.util.List getArgs()
                               throws DrmaaException
        Get the arguments to the job.
        Specified by:
        getArgs in interface JobTemplate
        Returns:
        the parameters passed as arguments to the job or null if they have not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setArgs(List)
      • setJobSubmissionState

        public void setJobSubmissionState​(int state)
                                   throws DrmaaException
        Specifies the job state at submission. The possible values are HOLD_STATE and ACTIVE_STATE:
        • ACTIVE means the job is submitted in a runnable state.
        • HOLD means the job is submitted in user hold state (either Session.USER_ON_HOLD or Session.USER_SYSTEM_ON_HOLD).

        This parameter is largely equivalent to the qsub submit option "-h".

        Specified by:
        setJobSubmissionState in interface JobTemplate
        Parameters:
        state - the job state at submission
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        qsub(1)
      • getJobSubmissionState

        public int getJobSubmissionState()
                                  throws DrmaaException
        Get the job state at submission.
        Specified by:
        getJobSubmissionState in interface JobTemplate
        Returns:
        the job state at submission
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setJobSubmissionState(int)
      • setJobEnvironment

        public void setJobEnvironment​(java.util.Map env)
                               throws DrmaaException
        Sets the environment values that define the remote environment. The values override the remote environment values if there is a collision.
        Specified by:
        setJobEnvironment in interface JobTemplate
        Parameters:
        env - the environment values that define the remote environment
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
      • getJobEnvironment

        public java.util.Map getJobEnvironment()
                                        throws DrmaaException
        Get the environment values that define the remote environment.
        Specified by:
        getJobEnvironment in interface JobTemplate
        Returns:
        the environment values that define the remote environment or null if it has not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setJobEnvironment(Map)
      • setWorkingDirectory

        public void setWorkingDirectory​(java.lang.String wd)
                                 throws DrmaaException
        Specifies the directory name where the job will be executed. A HOME_DIRECTORY placeholder at the beginning of the directory name denotes that the remaining portion of the directory name is to be resolved relative to the job submiter's home directory on the execution host.

        When the DRMAA job template is used for bulk job submission (see also Session.runBulkJobs(org.ggf.drmaa.JobTemplate,int,int,int) the PARAMETRIC_INDEX placeholder can be used at any position within the directory name to cause a substitution with the parametric job's index. The directory name must be specified in a syntax that is common at the host where the job will be executed. If no placeholder is used, an absolute directory specification is recommended. If set to a relative path and no placeholder is used, a path relative to the user's home directory is assumed. If not set, the working directory will default to the user's home directory. If set, and the directory does not exist, the job will enter the state FAILED when the job is run.

        Specified by:
        setWorkingDirectory in interface JobTemplate
        Parameters:
        wd - the directory where the job is executed
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        JobTemplate.HOME_DIRECTORY, JobTemplate.PARAMETRIC_INDEX, Session.FAILED
      • getWorkingDirectory

        public java.lang.String getWorkingDirectory()
                                             throws DrmaaException
        Get the directory where the job is executed.
        Specified by:
        getWorkingDirectory in interface JobTemplate
        Returns:
        the directory where the job is executed or null if it has not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setWorkingDirectory(String)
      • setJobCategory

        public void setJobCategory​(java.lang.String category)
                            throws DrmaaException
        Specifies the DRMAA job category. The category string is used by Grid Engine as reference into the qtask file. Certain qsub options used in the referenced qtask file line are applied to the job template before submission to allow site-specific resolving of resources and/or policies. The cluster qtask file, the local qtask file, and the user qtask file are searched. Job settings resulting from job template category are overridden by settings resulting from the job template nativeSpecification property as well as by explict DRMAA job template property settings.

        The options -help, -sync, -t, -verify, and -w w|v are ignored. The -cwd option is ignored unless the $SGE_DRMAA_ALLOW_CWD environment variable is set.

        Specified by:
        setJobCategory in interface JobTemplate
        Parameters:
        category - an opaque string specifying how to resolve site-specific resources and/or policies.
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        qtask(5), qsub(1)
      • getJobCategory

        public java.lang.String getJobCategory()
                                        throws DrmaaException
        Get the opaque string specifying how to resolve site-specific resources and/or policies.
        Specified by:
        getJobCategory in interface JobTemplate
        Returns:
        the opaque string specifying how to resolve site-specific resources and/or policies or null if it has not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setJobCategory(String)
      • setNativeSpecification

        public void setNativeSpecification​(java.lang.String spec)
                                    throws DrmaaException
        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 in the nativeSpecification, 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. Options set in the nativeSpecification will be overridden by the corresponding DRMAA properties. See the qsub(1) man page for more information on qsub command line options.
        Specified by:
        setNativeSpecification in interface JobTemplate
        Parameters:
        spec - an opaque string that is passed by the end user to DRMAA to specify site-specific resources and/or policies
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        qsub(1)
      • getNativeSpecification

        public java.lang.String getNativeSpecification()
                                                throws DrmaaException
        Get the opaque string that is passed by the end user to DRMAA to specify site-specific resources and/or policies.
        Specified by:
        getNativeSpecification in interface JobTemplate
        Returns:
        the opaque string that is passed by the end user to DRMAA to specify site-specific resources and/or policies or null if it has not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setNativeSpecification(String)
      • setEmail

        public void setEmail​(java.util.Set email)
                      throws DrmaaException
        Set the list of email addresses used to report the job completion and status.
        Specified by:
        setEmail in interface JobTemplate
        Parameters:
        email - the list of email addresses used to report the job completion and status.
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
      • getEmail

        public java.util.Set getEmail()
                               throws DrmaaException
        Get the list of email addresses used to report the job completion and status.
        Specified by:
        getEmail in interface JobTemplate
        Returns:
        the list of email addresses used to report the job completion and status or null if they have not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setEmail(java.util.Set)
      • setBlockEmail

        public void setBlockEmail​(boolean blockEmail)
                           throws DrmaaException
        Specifies whether e-mail sending shall blocked or not. By default email is not sent. If, however, a setting in a cluster or user settings file or the nativeSpecification or jobCategory property enables sending email in association with job events, the blockEmail property will override that setting, causing no email to be sent.
        Specified by:
        setBlockEmail in interface JobTemplate
        Parameters:
        blockEmail - whether to block sending e-mail by default
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
      • getBlockEmail

        public boolean getBlockEmail()
                              throws DrmaaException
        Get whether to block sending e-mail by default, regardless of the DRMS settings.
        Specified by:
        getBlockEmail in interface JobTemplate
        Returns:
        whether to block sending e-mail by default
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setBlockEmail(boolean)
      • setStartTime

        public void setStartTime​(PartialTimestamp startTime)
                          throws DrmaaException
        Set the earliest time when the job may be eligible to be run.
        Specified by:
        setStartTime in interface JobTemplate
        Parameters:
        startTime - the earliest time when the job may be eligible to be run
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        PartialTimestamp
      • getStartTime

        public PartialTimestamp getStartTime()
                                      throws DrmaaException
        Get the earliest time when the job may be eligible to be run.
        Specified by:
        getStartTime in interface JobTemplate
        Returns:
        the earliest time when the job may be eligible to be run or null if it has not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setStartTime(org.ggf.drmaa.PartialTimestamp)
      • setJobName

        public void setJobName​(java.lang.String name)
                        throws DrmaaException
        Set the name of the job. A job name will be comprised of alpha-numeric and _ characters. Setting the job name is equivalent to use of the qsub submit option "-N" with name as option argument and has the same restrictions. See the qsub(1) man page.
        Specified by:
        setJobName in interface JobTemplate
        Parameters:
        name - the name of the job
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        qsub(1)
      • getJobName

        public java.lang.String getJobName()
                                    throws DrmaaException
        Get the name of the job.
        Specified by:
        getJobName in interface JobTemplate
        Returns:
        the name of the job or null if it has not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setJobName(String)
      • setInputPath

        public void setInputPath​(java.lang.String inputPath)
                          throws DrmaaException
        Set the job's standard input path. Unless set elsewhere, if not explicitly set in the job template, the job is started with an empty input stream. If the standard input is set, it specifies the network path of the job's input stream file in the form of [hostname]:file_path

        When the transferFiles property is supported and the set TranferFileMode instance's inputStream property is set to true, the input file will be fetched by Grid Engine from the specified host or from the submit host if no hostname is specified. When the transferFiles property is unsupported or the set TranferFileMode instance's inputStream property is not set or is set to false, the input file is always expected to be at the host where the job is executed, regardless of any hostname specified.

        When the DRMAA job template is used for bulk job submission (see also Session.runBulkJobs(org.ggf.drmaa.JobTemplate,int,int,int) the PARAMETRIC_INDEX placeholder can be used at any position within the file name to cause a substitution with the parametric job's index. A HOME_DIRECTORY placeholder at the beginning of the file path denotes the remaining portion of the file path as a relative file specification to be resolved relative to the job user's home directory at the host where the file is located. A WORKING_DIRECTORY placeholder at the beginning of file path denotes the remaining portion of the file path as a relative file specification to be resolved relative to the job's working directory at the host where the file is located. The file name must be specified in a syntax that is common at the host where the job will be executed. If no home or working directory placeholder is used, an absolute file specification is recommended. If set to a relative file path and no home or working directory placeholder is used, a path relative to the user's home directory is assumed.

        When the job is run, if this attribute is set, and the file can't be read, the job will enter the state FAILED.

        Specified by:
        setInputPath in interface JobTemplate
        Parameters:
        inputPath - the job's standard input path
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        JobTemplate.HOME_DIRECTORY, JobTemplate.WORKING_DIRECTORY, JobTemplate.PARAMETRIC_INDEX, Session.FAILED
      • getInputPath

        public java.lang.String getInputPath()
                                      throws DrmaaException
        Get the job's standard input path.
        Specified by:
        getInputPath in interface JobTemplate
        Returns:
        the job's standard input path or null if it has not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setInputPath(String)
      • setOutputPath

        public void setOutputPath​(java.lang.String outputPath)
                           throws DrmaaException
        Sets how to direct the job's standard output. Unless set elsewhere, if not explicitly set in the job template, the whereabouts of the job's output stream is not defined. If the standard output is set, it specifies the network path of the job's output stream file in the form of [hostname]:file_path

        When the transferFiles property is supported and the set TranferFileMode instance's outputStream property is set to true, the output file will be transferred by Grid Engine to the specified host or to the submit host if no hostname is specified. When the transferFiles property is unsupported or the set TranferFileMode instance's outputStream property is not set or is set to false, the output file is always kept at the host where the job is executed, regardless of any hostname specified.

        When the DRMAA job template is used for bulk job submission (see also Session.runBulkJobs(org.ggf.drmaa.JobTemplate,int,int,int) the PARAMETRIC_INDEX placeholder can be used at any position within the file name to cause a substitution with the parametric job's index. A HOME_DIRECTORY placeholder at the beginning of the file path denotes the remaining portion of the file path as a relative file specification to be resolved relative to the job user's home directory at the host where the file is located. A WORKING_DIRECTORY placeholder at the beginning of file path denotes the remaining portion of the file path as a relative file specification to be resolved relative to the job's working directory at the host where the file is located. The file name must be specified in a syntax that is common at the host where the job will be executed. If no home or working directory placeholder is used, an absolute file specification is recommended. If set to a relative file path and no home or working directory placeholder is used, a path relative to the user's home directory is assumed.

        When the job is run, if this attribute is set, and the file can't be read, the job will enter the state FAILED.

        Specified by:
        setOutputPath in interface JobTemplate
        Parameters:
        outputPath - how to direct the job's standard output
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        JobTemplate.HOME_DIRECTORY, JobTemplate.WORKING_DIRECTORY, JobTemplate.PARAMETRIC_INDEX, Session.FAILED
      • getOutputPath

        public java.lang.String getOutputPath()
                                       throws DrmaaException
        Gets how to direct the job's standard output.
        Specified by:
        getOutputPath in interface JobTemplate
        Returns:
        how to direct the job's standard output or null if it has not been set
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setOutputPath(String)
      • setErrorPath

        public void setErrorPath​(java.lang.String errorPath)
                          throws DrmaaException
        Sets how to direct the job's standard error. Unless set elsewhere, if not explicitly set in the job template, the whereabouts of the job's error stream is not defined. If the standard error is set, it specifies the network path of the job's error stream file in the form of [hostname]:file_path

        When the transferFiles property is supported and the set TranferFileMode instance's errorStream property is set to true, the error file will be transferred by Grid Engine to the specified host or to the submit host if no hostname is specified. When the transferFiles property is unsupported or the set TranferFileMode instance's errorStream property is not set or is set to false, the error file is always kept at the host where the job is executed, regardless of any hostname specified.

        When the DRMAA job template is used for bulk job submission (see also Session.runBulkJobs(org.ggf.drmaa.JobTemplate,int,int,int) the PARAMETRIC_INDEX placeholder can be used at any position within the file name to cause a substitution with the parametric job's index. A HOME_DIRECTORY placeholder at the beginning of the file path denotes the remaining portion of the file path as a relative file specification to be resolved relative to the job user's home directory at the host where the file is located. A WORKING_DIRECTORY placeholder at the beginning of file path denotes the remaining portion of the file path as a relative file specification to be resolved relative to the job's working directory at the host where the file is located. The file name must be specified in a syntax that is common at the host where the job will be executed. If no home or working directory placeholder is used, an absolute file specification is recommended. If set to a relative file path and no home or working directory placeholder is used, a path relative to the user's home directory is assumed.

        When the job is run, if this attribute is set, and the file can't be read, the job will enter the state FAILED.

        Specified by:
        setErrorPath in interface JobTemplate
        Parameters:
        errorPath - how to direct the job's standard error
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        JobTemplate.HOME_DIRECTORY, JobTemplate.WORKING_DIRECTORY, JobTemplate.PARAMETRIC_INDEX, Session.FAILED
      • getErrorPath

        public java.lang.String getErrorPath()
                                      throws DrmaaException
        Gets how to direct the job's standard error.
        Specified by:
        getErrorPath in interface JobTemplate
        Returns:
        how to direct the job's standard error
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setErrorPath(String)
      • setJoinFiles

        public void setJoinFiles​(boolean join)
                          throws DrmaaException
        Sets whether the error stream should be intermixed with the output stream. If not explicitly set in the job template the attribute defaults to false. If true, the underlying DRM system will ignore the value of the errorPath property and intermix the standard error stream with the standard output stream as specified with outputPath.
        Specified by:
        setJoinFiles in interface JobTemplate
        Parameters:
        join - whether the error stream should be intermixed with the output stream
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
      • getJoinFiles

        public boolean getJoinFiles()
                             throws DrmaaException
        Gets whether the error stream should be intermixed with the output stream.
        Specified by:
        getJoinFiles in interface JobTemplate
        Returns:
        Whether the error stream should be intermixed with the output stream
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setJoinFiles(boolean)
      • setTransferFiles

        public void setTransferFiles​(FileTransferMode mode)
                              throws DrmaaException

        Set Transfer Files

        Specifies, which of the standard I/O files (stdin, stdout and stderr) are to be transferred to/from the execution host. If not set, defaults to the equivalent of a FileTransferMode instance with all properties set to false. See inputPath, outputPath and errorPath setters for information about how to specify the standard input file, standard output file, and standard error file.

        If the FileTransferMode instance's errorStream property is set to true, the errorPath property is taken to specify the location to which error files should be transfered after the job finishes.

        If the FileTransferMode instance's inputStream property is set to true, the inputPath property is taken to specify the location from which input files should be transfered before the job starts.

        If the FileTransferMode instance's outputStream property is set to true, the outputPath property is taken to specify the location to which output files should be transfered after the job finishes.

        The file transfer mechanism itself must be configured by the administrator. (See the sge_conf(5) man page.) When it is configured, the administrator has to enable the transferFiles property by setting the execd param, delegated_file_staging, to true. If it is not configured, transferFiles is not supported and accessing this property will result in an UnsupportedAttributeException being thrown.

        Specified by:
        setTransferFiles in interface JobTemplate
        Parameters:
        mode - how to transfer files between hosts.
        Throws:
        DrmaaException - May be one of the following:
        • InvalidAttributeFormatException -- the format of the argument is invalid
        • InvalidAttributeValueException -- the value of the argument is invalid
        • ConflictingAttributeValuesException -- the value of the argument conflicts with the value of another job template property
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • IllegalArgumentException -- an argument is invalid
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setInputPath(String), setOutputPath(String), setErrorPath(String), sge_conf(5)
      • getTransferFiles

        public FileTransferMode getTransferFiles()
                                          throws DrmaaException
        Gets how to transfer files between hosts.
        Specified by:
        getTransferFiles in interface JobTemplate
        Returns:
        how to transfer files between hosts.
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
        See Also:
        setTransferFiles(org.ggf.drmaa.FileTransferMode)
      • setSoftRunDurationLimit

        public void setSoftRunDurationLimit​(long softRunLimit)
                                     throws UnsupportedAttributeException
        Unsupported property. Will throw an UnsupportedAttributeException if called.
        Specified by:
        setSoftRunDurationLimit in interface JobTemplate
        Parameters:
        softRunLimit - an estimate as to how long the job will need to remain in a running state to complete. Specified in seconds
        Throws:
        UnsupportedAttributeException - unsupported property
      • getAttributeNames

        public java.util.Set getAttributeNames()
                                        throws DrmaaException
        Returns the list of supported properties names. With the execd param, delegated_file_staging, set to false, this list includes only the list of DRMAA required properties. With delegated_file_staging set to true, the list also includes the transferFiles property.
        Specified by:
        getAttributeNames in interface JobTemplate
        Returns:
        the list of supported property names
        Throws:
        DrmaaException - May be one of the following:
        • NoActiveSessionException -- the session has not yet been initialized or has already been exited
        • DrmCommunicationException -- the DRMAA implementation was unable to contact the DRM
        • AuthorizationException -- the executing user does not have sufficient permissions to execute the desired action
        • InternalException -- an error has occured in the DRMAA implementation
      • equals

        public boolean equals​(java.lang.Object obj)
        Tests whether this JobTemplateImpl represents the same native job template as the given object. This implementation means that even if two JobTemplateImpl instance's have all the same settings, they are not equal, because they are associated with different native job templates.
        Overrides:
        equals in class java.lang.Object
        Parameters:
        obj - the object against which to compare
        Returns:
        whether the the given object is the same as this object
      • hashCode

        public int hashCode()
        Returns a hash code based on the associated native job template's table index.
        Overrides:
        hashCode in class java.lang.Object
        Returns:
        the hash code