| 126 | | Strings in double curly brackets are interpreted as variables and are replaced by {{{palmrun}}} based on settings via specific {{{palmrun}}} options or settings in the environment variable section of the configurations file. From the given batch directives, {{{palmrun}}} generates a batch script (file), also called batch job, which is then submitted to the batch system using the submit command that has been defined by {{{submit_command}}} (see environment variable section above). If you like to check the generated batch script, then run {{{palmrun}}} with additional option {{{-F}}}, which will write the batch script to file {{{jobfile.#####}}} in your current working directory, where {{{#####}}} is a 5-digit random number (which is part of the so-called job-id). A batch job will not be submitted. |
| | 122 | Strings in double curly brackets are interpreted as variables and are replaced by {{{palmrun}}} based on settings via specific {{{palmrun}}} options or settings in the environment variable section of the configuration file. From the given batch directives, {{{palmrun}}} generates a batch script (file), also called batch job, which is then submitted to the batch system using the submit command that has been defined by the variable [#su_co submit_command]. If you like to check the generated batch script, then run {{{palmrun}}} with additional option {{{-F}}}, which will write the batch script to file {{{jobfile.#####}}} in your current working directory, where {{{#####}}} is a 5-digit random number (which is part of the so-called {{{run_id}}}). A batch job will not be submitted. |
| 147 | | ||project_account ||Account number under which the batch job shall run. ||argument of {{{palmrun}}} option {{-A}}} || |
| 148 | | ||job_id ||Job name under which you can find the job in the respective job queue ||argument of {{{palmrun}}} option {{{-r}}} plus a 5-digit random number, separated by a dot, e.g. {{{palmrun -r abcde ...}}} may generate {{{abcde.12345}}} || |
| 149 | | ||cpu_hours \\ cpu_minutes \\ cpu_seconds \\ cputime ||cpu time requested by the job split in hours, minutes and seconds. {{{cputime}}} is the requested time in seconds. ||Calculated from {{{palmrun}}} option {{{-t}}}, e.g. in the above example, {{{palmrun -t 3662 ...}}} will generate {{{1:1:2}}} || |
| 150 | | ||timestring ||Requested CPU time in format hh:mm:ss ||calculated from {{{palmrun}}} option {{{-t}}} || |
| 151 | | ||tasks_per_node ||Number of MPI tasks to be started on each requested node ||as given by {{{palmrun}}} option {{{-T}}} || |
| 152 | | ||threads_per_task ||Number of OpenMP threads to be started by each MPI task ||as given by {{{palmrun}}} option {{{-O}}} || |
| 153 | | ||cores ||Total number of cores requested by the job ||as given by {{{palmrun}}} option {{{-X}}} || |
| | 142 | ||cores ||Total number of cores requested by the job ||as given by {{{palmrun}}} option {{{-X}}} || |
| | 143 | ||cpu_hours \\ cpu_minutes \\ cpu_seconds \\ cputime ||cpu time requested by the job split in hours, minutes and seconds. {{{cputime}}} is the requested time in seconds. ||Calculated from {{{palmrun}}} option {{{-t}}}, e.g. in the above example, {{{palmrun -t 3662 ...}}} will generate {{{1:1:2}}} || |
| | 144 | ||job_protocol_file ||Name of the file (including path) to which the job protocol is written ||generated from {{{palmrun}}} options {{{-c}}} and {{{-r}}} and the path set by environment variable {{{local_jobcatalog}}}. As an example, if {{{local_jobcatalog = /home/user/job_queue}}}, the call of {{{palmrun -r testrun -c mycluster ....}}} gives a job protocol file {{{home/user/job_queue/mycluster_testrun}}}. || |
| | 145 | ||memory ||Requested memory in MByte ||as given by {{{palmrun}}} option {{{-m}}} or as set in the configuration file via {{{%memory}}}. Option overwrites the setting in the configuration file. || |
| | 146 | ||mpi_tasks ||Total number of MPI tasks to be started ||calculated as {{{cores / threads_per_task}}} || |
| 155 | | ||mpi_tasks ||Total number of MPI tasks to be started ||calculated as {{{cores / threads_per_task}}} || |
| 156 | | ||job_protocol_file ||Name of the file (including path) to which the job protocol is written ||generated from {{{palmrun}}} options {{{-c}}} and {{{-r}}} and the path set by environment variable {{{local_jobcatalog}}}. As an example, if {{{local_jobcatalog = /home/user/job_queue}}}, the call of {{{palmrun -r testrun -c mycluster ....}}} gives a job protocol file {{{home/user/job_queue/mycluster_testrun}}}. || |
| 157 | | ||memory ||Requested memory in MByte ||as given by {{{palmrun}}} option {{{-m}}} or as set in the configuration file via {{{%memory}}}. Option overwrites the setting in the configuration file. || |
| 158 | | ||queue ||Batch queue to which the job is submitted ||as given by {{{palmrun}}} option {{{-q}}}. If the option is omitted, a default queue defined by variable {{{default_queue}}} is used. || |
| 159 | | ||previous_job ||Job-id of a previous job ||as given with {{{palmrun}}} option {{{-W}}}. Can be used to define job dependencies. The job-id should be the one that has been assigned by the batch system to the (previous) job. || |
| | 148 | ||previous_job ||run_id of a previous job ||as given with {{{palmrun}}} option {{{-W}}}. Can be used to define job dependencies. The run_id should be the one that has been assigned by the batch system to the (previous) job. || |
| | 149 | ||project_account ||Account number under which the batch job shall run. ||argument of {{{palmrun}}} option {{{-A}}} || |
| | 150 | ||queue ||Batch queue to which the job is submitted ||as given by {{{palmrun}}} option {{{-q}}}. If the option is omitted, a default queue defined by variable {{{default_queue}}} is used. || |
| | 151 | ||run_id ||Job name under which you can find the job in the respective job queue ||argument of {{{palmrun}}} option {{{-r}}} plus a 5-digit random number, separated by a dot, e.g. {{{palmrun -r abcde ...}}} may generate {{{abcde.12345}}} || |
| | 152 | ||tasks_per_node ||Number of MPI tasks to be started on each requested node ||as given by {{{palmrun}}} option {{{-T}}} || |
| | 153 | ||threads_per_task ||Number of OpenMP threads to be started by each MPI task ||as given by {{{palmrun}}} option {{{-O}}} || |
| | 154 | ||timestring ||Requested CPU time in format hh:mm:ss ||calculated from {{{palmrun}}} option {{{-t}}} || |
| | 155 | |
| 166 | | If {{{palmrun}}} is used in remote batch mode, i.e. the batch job is submitted from your local computer to a remote computer, additional batch job directives are required to guarantee that the job protocol file is sent back to your local computer after the batch job has finished on the remote system. Since the job protocol file is often only available after the job has finished, a small additional job is started at the end of the batch job, which only purpose is to transfer the job protocol from the remote to the local system. Batch directives for this job are given in the configuration file too. Add the string {{{BDT:}}} at the beginning of each directive. As for the main job directives (that start with {{{BD:}}}), we can only give a general example here, which is again for an OpenPBS based batch system. |
| | 162 | If {{{palmrun}}} is used in remote batch mode, i.e. the batch job is submitted from your local computer to a remote computer, additional batch job directives are required to guarantee that the job protocol file is sent back to your local computer after the batch job has finished on the remote system. Since the job protocol file is often only available after the job has finished, a small additional job is started at the end of the batch job, which only purpose is to transfer the job protocol from the remote to the local system. Batch directives for this job are given in the configuration file too. Add the string {{{BDT:}}} at the beginning of each directive. As for the main job directives (that start with {{{BD:}}}), we can only give a general example here, which is again for an OpenPBS-based batch system. |
