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palm_config

Timestamp:: Oct 30, 2018 2:22:55 PM (6 years ago)
Author:: raasch
Comment:: --

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doc/app/palm_config

-                      v21
+                      v22
 %subfolder1  $default_folder/efgh
 }}}
   which means that {{{subfolder1}}} has the value {{{/work/abcd/efgh}}}. You can also use any variables that are already defined within the {{{palmrun}}}/{{{palmbuild}}} scripts. The most important one is {{{jobname}}}, which value is given with {{{palmrun}}} option {{{-d}}}, and which defines the so-called ''jobname''. This variable is mentioned here because it is used in the default configuration files for naming I/O files and to better sort I/O files from different PALM runs in an organized folder structure. Beside the value replacement using the UNIX shell syntax (i.e. {{{$abcd}}} gives the value of variable {{{abcd}}}), another way to insert values of environment variables is to write them in double curly brackets, i.e. {{{ {{abcd}} }}} will be replaced by the value of {{{abce}}}. This way of variable replacement is required for some special variables and in the job directives.
+  which means that {{{subfolder1}}} has the value {{{/work/abcd/efgh}}}. You can also use any variables that are already defined within the {{{palmrun}}}/{{{palmbuild}}} scripts. The most important one is {{{jobname}}}, which value is given with {{{palmrun}}} option {{{-r}}}, and which defines the so-called ''jobname''. This variable is mentioned here because it is used in the default configuration files for naming I/O files and to better sort I/O files from different PALM runs in an organized folder structure. Beside the value replacement using the UNIX shell syntax (i.e. {{{$abcd}}} gives the value of variable {{{abcd}}}), another way to insert values of environment variables is to write them in double curly brackets, i.e. {{{ {{abcd}} }}} will be replaced by the value of {{{abce}}}. This way of variable replacement is required for some special variables and in the job directives.
 * lines starting with {{{IC:}}} define any unix commands that are executed by {{{palmrun}}} just before the PALM code is started. A typical input command might be
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 ||base_data         ||Directory where the PALM I/O-files are stored. This variable is used in the file configuration file (see [source:palm/trunk/SCRIPTS/.palm.iofiles .palm.iofiles], and the [wiki:doc/app/palm_iofiles description] of this file). Since this variable is also used to determine file locations on remote hosts, it must use the {{{~}}} instead of {{{$HOME}}}. ||
 ||source_path       ||Path to PALM's FORTRAN source files. This is the place where the automatic installer has put the download, or which has been defined in the user's {{{svn checkout}}} command. ||
 ||user_source_path  ||Path to the [wiki:doc/app/userint user interface routines]. The variable {{{jobname}}} that may be used in the default path is replaced by the argument given with {{{palmrun}}}-option {{{-d}}}. ||
+||user_source_path  ||Path to the [wiki:doc/app/userint user interface routines]. The variable {{{jobname}}} that may be used in the default path is replaced by the argument given with {{{palmrun}}}-option {{{-r}}}. ||
 ||fast_io_catalog   ||Path to a file system with fast discs (if available). This folder is used so store the temporary catalog generated by {{{palmrun}}} during each run. It should also be used to store large I/O files (e.g. restart data or 3D-output) in order to reduce I/O time. This variable is used in the default {{{.palm.iofiles}}} for the restart data files. The folder must be accessible from all compute nodes, i.e. it must reside in a global file system. WARNING: {{{/tmp}}} will only work on single node systems! In case of batch jobs on remote hosts, the variable refers to a folder on the remote host. The variable has no default value and must be set by the user. ||
 ||local_jobcatalog  ||Folder on the local host to store the batch job protocols. In case of batch jobs running on remote hosts, the job protocol will be created on the {{{remote_jobcatalog}}} and then be transferred via scp to the {{{local_jobcatalog}}}. ||
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 ||project_account    ||Account number under which the batch job shall run.  ||argument of {{{palmrun}}} option {{-A}}}  ||
 ||job_id             ||Job name under which you can find the job in the respective job queue  ||argument of {{{palmrun}}} option {{{-d}}} plus a 5-digit random number, separated by a dot, e.g. {{{palmrun -d abcde ...}}} may generate {{{abcde.12345}}}  ||
+||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}}}  ||
 ||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}}}  ||
 ||timestring         ||Requested CPU time in format hh:mm:ss  ||calculated from {{{palmrun}}} option {{{-t}}}  ||
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 ||nodes              ||Number of compute nodes requested by the job  ||calculated from {{{palmrun}}} options {{{-X}}} (total number of cores to be used), {{{-T}}} (number of MPI tasks to be started on each node), and {{{-O}}} (number of OpenMP threads to be started by each MPI task). {{{nodes}}} is calculated as {{{cores / ( tasks_per_node * threads_per_task)}}}. {{{threads_per_task}}} is one in pure MPI applications. If {{{tasks_per_node * threads_per_task}}} is not an integral divisor of the total number of cores, less tasks/threads will run on the last node.  ||
 ||mpi_tasks          ||Total number of MPI tasks to be started  ||calculated as {{{cores / threads_per_task}}}  ||
 ||job_protocol_file  ||Name of the file (including path) to which the job protocol is written   ||generated from {{{palmrun}}} options {{{-h}}} and {{{-d}}} and the path set by environment variable {{{local_jobcatalog}}}. As an example, if {{{local_jobcatalog = /home/user/job_queue}}}, the call of {{{palmrun -d testrun -h mycluster ....}}} gives a job protocol file {{{home/user/job_queue/mycluster_testrun}}}.  ||
+||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}}}.  ||
 ||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.  ||
 ||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.  ||