Changeset 4814 for palm/trunk/SCRIPTS/.palm.config.default_trace

Timestamp:

Dec 9, 2020 1:08:08 PM (3 years ago)

Author:

gronemeier

Message:

add additional output paths to palm.iofiles and update configuration files accordingly

File:

• palm/trunk/SCRIPTS/.palm.config.default_trace (modified) (5 diffs)

palm/trunk/SCRIPTS/.palm.config.default_trace

@@ -4 +4 @@
 #-----------------------------------------------------------------------------
 # working directory from where palmrun or palmbuild are called
-%base_directory    $HOME/palm/current_version
+%base_directory      $HOME/palm/current_version
 
 # directory where PALM I/O is stored (used in .palm.iofiles)
-%base_data         ~/palm/current_version/JOBS
+%base_data           ~/palm/current_version/JOBS
 
 # path to PALM's FORTRAN sources (installation folder)
-%source_path       $HOME/palm/current_version/trunk/SOURCE
+%source_path         $base_directory/trunk/SOURCE
 
 # path to user interface routines
-%user_source_path  $base_directory/JOBS/$run_identifier/USER_CODE
+%user_source_path    $base_data/$run_identifier/USER_CODE
 
-# path to file system with fast discs (if available). This folder
-# is used for temporary catalogs generated by palmrun and to store large
-# I/O files (used in .palm.iofiles). This folder must be accessible from
-# all compute nodes, i.e. it must reside in a global file system
-%fast_io_catalog   <replace by a folder name which allows for fast I/O>
+# path to temporary working directory. This folder contains the files
+# temporarily created by PALM during execution.
+# WARNING:
+# Large I/O files are generated during execution! It is recommended to direct
+# this path to a file system with fast discs (if available). This folder must
+# be accessible from all compute nodes, i.e. it must reside in a global file
+# system.
+%fast_io_catalog     $base_directory/tmp
+
+# directory where PALM restart files are stored. It is recommended to set this
+# path to the same file system as the temporary directory (fast_io_catalog) to
+# allow internal linking of the restart files instead of copying (increases
+# post-processing performance of palmrun).
+%restart_data_path   $fast_io_catalog
+
+# directory where PALM output files are stored (see also .palm.iofiles)
+%output_data_path    $base_data
 
 # folder for job protocols
-#%local_jobcatalog    $HOME/job_logfiles
+%local_jobcatalog    $base_data/$run_identifier/LOG_FILES
 
 # folder for job protocols to be used on the remote host
-#%remote_jobcatalog   <path/to/directory on remote host>
+#%remote_jobcatalog   $local_jobcatalog
 
 # local ip of your computer. Use 127.0.0.0 if you are running PALM
@@ -49 +61 @@
 #%defaultqueue        <queue>
 
+# default project account to be used if palmrun-option -A is omitted. For this
+# setting to be active, the batch directive must also be activated (see BD and
+# BDT settings below).
+#%project_account     <project-account>
+
 # command to submit batch jobs
 #%submit_command      /opt/moab/default/bin/msub -E
@@ -64 +81 @@
 %make_options        -j 4
 
-# options to be used to compile PALM in debug mode
-%compiler_options    -fpe0 -O0 -check -check nooutput_conversion-ffree-line-length-none  -traceback -g -I /muksoft/packages/fftw/3.3.4/include -L/muksoft/packages/fftw/3.3.4/lib64 -lfftw3 -I /muksoft/packages/netcdf/4_intel/include -L/muksoft/packages/netcdf/4_intel/lib -lnetcdf -lnetcdff
+# options to be used to compile PALM
+%compiler_options    -fpe0 -O0 -check -check nooutput_conversion-ffree-line-length-none  -traceback -g -I /path/to/fftw/include -I /path/to/netcdf/include
 
 # options to be used to link the PALM executable
-%linker_options      -fpe0 -O0 -check -check nooutput_conversion -ffree-line-length-none -traceback -g -I /muksoft/packages/fftw/3.3.4/include -L/muksoft/packages/fftw/3.3.4/lib64 -lfftw3 -I /muksoft/packages/netcdf/4_intel/include -L/muksoft/packages/netcdf/4_intel/lib -lnetcdf -lnetcdff
+%linker_options      -L/path/to/fftw/lib -lfftw3 -L/path/to/netcdf/lib -lnetcdf -lnetcdff
 
-# name of hostfile to be used
-%hostfile            auto
+# name of hostfile to be used (see online documentation for more details)
+#%hostfile            auto
 
 # command to start the PALM executable
-%execute_command     mpiexec  -machinefile hostfile  -n {{mpi_tasks}}  palm
+%execute_command     mpirun -n {{mpi_tasks}}  ./palm
 
 # memory request per core
@@ -80 +97 @@
 
 # module commands to load required libraries
-#%module_commands     module switch craype-ivybridge craype-haswell; module load fftw cray-hdf5-parallel cray-netcdf-hdf5parallel
+#%module_commands     module switch env-ivybridge env-haswell && module load fftw netcdf
 
 # special commands to be carried out at login and start of batch jobs on the remote host
 #%login_init_cmd      .execute_special_profile
 
+#-------------------------------------------------------------------------------
+# Directives to be used for batch jobs
+# Lines must start with "BD:". If $-characters are required, hide them with \
+# Internal variables can be used as {{variable_name}}. Please see documentation.
+#-------------------------------------------------------------------------------
+# Example using PBS:
+BD:#!/bin/bash
+#BD:#PBS -A {{project_account}}
+BD:#PBS -N {{run_id}}
+BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}}
+BD:#PBS -l nodes={{nodes}}:ppn={{tasks_per_node}}
+BD:#PBS -o {{job_protocol_file}}
+BD:#PBS -j oe
+BD:#PBS -q {{queue}}
+#
+# Example using SLURM:
+#BD:#!/bin/bash
+##BD:#SBATCH --dependency=afterany:{{previous_job}}
+#BD:#SBATCH -A {{project_account}}
+#BD:#SBATCH --job-name={{run_id}}
+#BD:#SBATCH --time={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}}
+#BD:#SBATCH --ntasks={{mpi_tasks}}
+#BD:#SBATCH --nodes={{nodes}}
+#BD:#SBATCH --ntasks-per-node={{tasks_per_node}}
+#BD:#SBATCH --partition={{queue}}
+#BD:#SBATCH --output={{job_protocol_file}}
+#BD:#SBATCH --error={{job_protocol_file}}
+#BD:#SBATCH --mail-type=ALL
+#BD:#SBATCH --mail-user=user@somewhere
+
+#-------------------------------------------------------------------------------
+# Directives for batch jobs used to send back the jobfiles from a remote to a local host
+# Lines must start with "BDT:". If $-characters are required, excape them with triple backslash
+# Internal variables can be used as {{variable_name}}. Please see documentation.
+#-------------------------------------------------------------------------------
+# Example using PBS:
+BDT:#!/bin/bash
+#BDT:#PBS -A {{project_account}}
+BDT:#PBS -N job_protocol_transfer
+BDT:#PBS -l walltime=00:30:00
+BDT:#PBS -l nodes=1:ppn=1
+BDT:#PBS -o {{job_transfer_protocol_file}}
+BDT:#PBS -j oe
+BDT:#PBS -q dataq
+#
+# Example using SLURM:
+#BDT:#!/bin/bash
+#BDT:#SBATCH -A {{project_account}}
+#BDT:#SBATCH --job-name=job_transfer
+#BDT:#SBATCH --time=00:30:00
+#BDT:#SBATCH --ntasks=1
+#BDT:#SBATCH --nodes=1
+#BDT:#SBATCH --ntasks-per-node=1
+#BDT:#SBATCH --partition={{queue}}
+#BDT:#SBATCH --output={{job_transfer_protocol_file}}
+#BDT:#SBATCH --error={{job_transfer_protocol_file}}
 
 #----------------------------------------------------------------------------
-# INPUT-commands, executed before running PALM - lines must start with "IC:" 
+# INPUT-commands, executed before running PALM - lines must start with "IC:"
 #----------------------------------------------------------------------------
 #IC:ulimit -s unlimited
@@ -100 +173 @@
 #----------------------------------------------------------------------------
 #OC:echo \\\"PALM job finished\\\" | mailx user@somewhere
-
-
-#-------------------------------------------------------------------------------
-# Directives to be used for batch jobs
-# Lines must start with "BD:". If $-characters are required, hide them with \
-# Internal variables can be used as {{variable_name}}. Please see documentation.
-#-------------------------------------------------------------------------------
-BD:#!/bin/bash
-BD:#PBS -N {{run_id}}
-BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}}
-BD:#PBS -l nodes={{nodes}}:ppn={{tasks_per_node}}
-BD:#PBS -o {{job_protocol_file}}
-BD:#PBS -j oe
-BD:#PBS -q {{queue}}
-
-
-#-------------------------------------------------------------------------------
-# Directives for batch jobs used to send back the jobfiles from a remote to a local host
-# Lines must start with "BDT:". If $-characters are required, excape them with triple backslash
-# Internal variables can be used as {{variable_name}}. Please see documentation.
-#-------------------------------------------------------------------------------
-BDT:#!/bin/bash
-BDT:#PBS -N job_protocol_transfer
-BDT:#PBS -l walltime=00:30:00
-BDT:#PBS -l nodes=1:ppn=1
-BDT:#PBS -o {{job_transfer_protocol_file}}
-BDT:#PBS -j oe
-BDT:#PBS -q dataq