Ignore:
Timestamp:
Dec 9, 2020 1:08:08 PM (11 months ago)
Author:
gronemeier
Message:

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

File:
1 edited

Legend:

Unmodified
Added
Removed
  • palm/trunk/SCRIPTS/.palm.config.default

    r4484 r4814  
    44#-----------------------------------------------------------------------------
    55# working directory from where palmrun or palmbuild are called
    6 %base_directory    $HOME/palm/current_version
     6%base_directory      $HOME/palm/current_version
    77
    88# directory where PALM I/O is stored (used in .palm.iofiles)
    9 %base_data         ~/palm/current_version/JOBS
     9%base_data           ~/palm/current_version/JOBS
    1010
    1111# path to PALM's FORTRAN sources (installation folder)
    12 %source_path       $HOME/palm/current_version/trunk/SOURCE
     12%source_path         $base_directory/trunk/SOURCE
    1313
    1414# path to user interface routines
    15 %user_source_path  $base_directory/JOBS/$run_identifier/USER_CODE
     15%user_source_path    $base_data/$run_identifier/USER_CODE
    1616
    17 # path to file system with fast discs (if available). This folder
    18 # is used for temporary catalogs generated by palmrun and to store large
    19 # I/O files (used in .palm.iofiles). This folder must be accessible from
    20 # all compute nodes, i.e. it must reside in a global file system
    21 %fast_io_catalog   <replace by a folder name which allows for fast I/O>
     17# path to temporary working directory. This folder contains the files
     18# temporarily created by PALM during execution.
     19# WARNING:
     20# Large I/O files are generated during execution! It is recommended to direct
     21# this path to a file system with fast discs (if available). This folder must
     22# be accessible from all compute nodes, i.e. it must reside in a global file
     23# system.
     24%fast_io_catalog     $base_directory/tmp
     25
     26# directory where PALM restart files are stored. It is recommended to set this
     27# path to the same file system as the temporary directory (fast_io_catalog) to
     28# allow internal linking of the restart files instead of copying (increases
     29# post-processing performance of palmrun).
     30%restart_data_path   $fast_io_catalog
     31
     32# directory where PALM output files are stored (see also .palm.iofiles)
     33%output_data_path    $base_data
    2234
    2335# folder for job protocols
    24 #%local_jobcatalog    $HOME/job_logfiles
     36%local_jobcatalog    $base_data/$run_identifier/LOG_FILES
    2537
    2638# folder for job protocols to be used on the remote host
    27 #%remote_jobcatalog   <path/to/directory on remote host>
     39#%remote_jobcatalog   $local_jobcatalog
    2840
    2941# local ip of your computer. Use 127.0.0.0 if you are running PALM
     
    4961#%defaultqueue        <queue>
    5062
     63# default project account to be used if palmrun-option -A is omitted. For this
     64# setting to be active, the batch directive must also be activated (see BD and
     65# BDT settings below).
     66#%project_account     <project-account>
     67
    5168# command to submit batch jobs
    5269#%submit_command      /opt/moab/default/bin/msub -E
     
    6582
    6683# options to be used to compile PALM
    67 %compiler_options    -fpe0 -O3 -xHost -fp-model source -ftz -no-prec-div -no-prec-sqrt -ip -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
     84%compiler_options    -fpe0 -O3 -xHost -fp-model source -ftz -no-prec-div -no-prec-sqrt -ip -I /path/to/fftw/include -I /path/to/netcdf/include
    6885
    6986# options to be used to link the PALM executable
    70 %linker_options      -fpe0 -O3 -xHost -fp-model source -ftz -no-prec-div -no-prec-sqrt -ip -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
     87%linker_options      -L/path/to/fftw/lib -lfftw3 -L/path/to/netcdf/lib -lnetcdf -lnetcdff
    7188
    72 # name of hostfile to be used
    73 %hostfile            auto
     89# name of hostfile to be used (see online documentation for more details)
     90#%hostfile            auto
    7491
    7592# command to start the PALM executable
    76 %execute_command     mpiexec  -machinefile hostfile  -n {{mpi_tasks}}  palm
     93%execute_command     mpirun -n {{mpi_tasks}}  ./palm
    7794
    7895# memory request per core
     
    8097
    8198# module commands to load required libraries
    82 #%module_commands     module switch craype-ivybridge craype-haswell; module load fftw cray-hdf5-parallel cray-netcdf-hdf5parallel
     99#%module_commands     module switch env-ivybridge env-haswell && module load fftw netcdf
    83100
    84101# special commands to be carried out at login and start of batch jobs on the remote host
    85102#%login_init_cmd      .execute_special_profile
    86103
     104#-------------------------------------------------------------------------------
     105# Directives to be used for batch jobs
     106# Lines must start with "BD:". If $-characters are required, hide them with \
     107# Internal variables can be used as {{variable_name}}. Please see documentation.
     108#-------------------------------------------------------------------------------
     109# Example using PBS:
     110BD:#!/bin/bash
     111#BD:#PBS -A {{project_account}}
     112BD:#PBS -N {{run_id}}
     113BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}}
     114BD:#PBS -l nodes={{nodes}}:ppn={{tasks_per_node}}
     115BD:#PBS -o {{job_protocol_file}}
     116BD:#PBS -j oe
     117BD:#PBS -q {{queue}}
     118#
     119# Example using SLURM:
     120#BD:#!/bin/bash
     121##BD:#SBATCH --dependency=afterany:{{previous_job}}
     122#BD:#SBATCH -A {{project_account}}
     123#BD:#SBATCH --job-name={{run_id}}
     124#BD:#SBATCH --time={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}}
     125#BD:#SBATCH --ntasks={{mpi_tasks}}
     126#BD:#SBATCH --nodes={{nodes}}
     127#BD:#SBATCH --ntasks-per-node={{tasks_per_node}}
     128#BD:#SBATCH --partition={{queue}}
     129#BD:#SBATCH --output={{job_protocol_file}}
     130#BD:#SBATCH --error={{job_protocol_file}}
     131#BD:#SBATCH --mail-type=ALL
     132#BD:#SBATCH --mail-user=user@somewhere
     133
     134#-------------------------------------------------------------------------------
     135# Directives for batch jobs used to send back the jobfiles from a remote to a local host
     136# Lines must start with "BDT:". If $-characters are required, excape them with triple backslash
     137# Internal variables can be used as {{variable_name}}. Please see documentation.
     138#-------------------------------------------------------------------------------
     139# Example using PBS:
     140BDT:#!/bin/bash
     141#BDT:#PBS -A {{project_account}}
     142BDT:#PBS -N job_protocol_transfer
     143BDT:#PBS -l walltime=00:30:00
     144BDT:#PBS -l nodes=1:ppn=1
     145BDT:#PBS -o {{job_transfer_protocol_file}}
     146BDT:#PBS -j oe
     147BDT:#PBS -q dataq
     148#
     149# Example using SLURM:
     150#BDT:#!/bin/bash
     151#BDT:#SBATCH -A {{project_account}}
     152#BDT:#SBATCH --job-name=job_transfer
     153#BDT:#SBATCH --time=00:30:00
     154#BDT:#SBATCH --ntasks=1
     155#BDT:#SBATCH --nodes=1
     156#BDT:#SBATCH --ntasks-per-node=1
     157#BDT:#SBATCH --partition={{queue}}
     158#BDT:#SBATCH --output={{job_transfer_protocol_file}}
     159#BDT:#SBATCH --error={{job_transfer_protocol_file}}
    87160
    88161#----------------------------------------------------------------------------
    89 # INPUT-commands, executed before running PALM - lines must start with "IC:" 
     162# INPUT-commands, executed before running PALM - lines must start with "IC:"
    90163#----------------------------------------------------------------------------
    91164#IC:ulimit -s unlimited
     
    100173#----------------------------------------------------------------------------
    101174#OC:echo \\\"PALM job finished\\\" | mailx user@somewhere
    102 
    103 
    104 #-------------------------------------------------------------------------------
    105 # Directives to be used for batch jobs
    106 # Lines must start with "BD:". If $-characters are required, hide them with \
    107 # Internal variables can be used as {{variable_name}}. Please see documentation.
    108 #-------------------------------------------------------------------------------
    109 BD:#!/bin/bash
    110 BD:#PBS -N {{run_id}}
    111 BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}}
    112 BD:#PBS -l nodes={{nodes}}:ppn={{tasks_per_node}}
    113 BD:#PBS -o {{job_protocol_file}}
    114 BD:#PBS -j oe
    115 BD:#PBS -q {{queue}}
    116 
    117 
    118 #-------------------------------------------------------------------------------
    119 # Directives for batch jobs used to send back the jobfiles from a remote to a local host
    120 # Lines must start with "BDT:". If $-characters are required, excape them with triple backslash
    121 # Internal variables can be used as {{variable_name}}. Please see documentation.
    122 #-------------------------------------------------------------------------------
    123 BDT:#!/bin/bash
    124 BDT:#PBS -N job_protocol_transfer
    125 BDT:#PBS -l walltime=00:30:00
    126 BDT:#PBS -l nodes=1:ppn=1
    127 BDT:#PBS -o {{job_transfer_protocol_file}}
    128 BDT:#PBS -j oe
    129 BDT:#PBS -q dataq
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