Changeset 4814 for palm/trunk/SCRIPTS/.palm.config.default
- Timestamp:
- Dec 9, 2020 1:08:08 PM (4 years ago)
- File:
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- 1 edited
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palm/trunk/SCRIPTS/.palm.config.default (modified) (5 diffs)
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palm/trunk/SCRIPTS/.palm.config.default
r4484 r4814 4 4 #----------------------------------------------------------------------------- 5 5 # working directory from where palmrun or palmbuild are called 6 %base_directory $HOME/palm/current_version6 %base_directory $HOME/palm/current_version 7 7 8 8 # directory where PALM I/O is stored (used in .palm.iofiles) 9 %base_data ~/palm/current_version/JOBS9 %base_data ~/palm/current_version/JOBS 10 10 11 11 # path to PALM's FORTRAN sources (installation folder) 12 %source_path $HOME/palm/current_version/trunk/SOURCE12 %source_path $base_directory/trunk/SOURCE 13 13 14 14 # path to user interface routines 15 %user_source_path $base_directory/JOBS/$run_identifier/USER_CODE15 %user_source_path $base_data/$run_identifier/USER_CODE 16 16 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 22 34 23 35 # folder for job protocols 24 #%local_jobcatalog $HOME/job_logfiles 36 %local_jobcatalog $base_data/$run_identifier/LOG_FILES 25 37 26 38 # 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 28 40 29 41 # local ip of your computer. Use 127.0.0.0 if you are running PALM … … 49 61 #%defaultqueue <queue> 50 62 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 51 68 # command to submit batch jobs 52 69 #%submit_command /opt/moab/default/bin/msub -E … … 65 82 66 83 # 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 -lnetcdff84 %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 68 85 69 86 # 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 -lnetcdff87 %linker_options -L/path/to/fftw/lib -lfftw3 -L/path/to/netcdf/lib -lnetcdf -lnetcdff 71 88 72 # name of hostfile to be used 73 %hostfile auto89 # name of hostfile to be used (see online documentation for more details) 90 #%hostfile auto 74 91 75 92 # command to start the PALM executable 76 %execute_command mpi exec -machinefile hostfile -n {{mpi_tasks}}palm93 %execute_command mpirun -n {{mpi_tasks}} ./palm 77 94 78 95 # memory request per core … … 80 97 81 98 # module commands to load required libraries 82 #%module_commands module switch craype-ivybridge craype-haswell; module load fftw cray-hdf5-parallel cray-netcdf-hdf5parallel99 #%module_commands module switch env-ivybridge env-haswell && module load fftw netcdf 83 100 84 101 # special commands to be carried out at login and start of batch jobs on the remote host 85 102 #%login_init_cmd .execute_special_profile 86 103 104 #------------------------------------------------------------------------------- 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 # Example using PBS: 110 BD:#!/bin/bash 111 #BD:#PBS -A {{project_account}} 112 BD:#PBS -N {{run_id}} 113 BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}} 114 BD:#PBS -l nodes={{nodes}}:ppn={{tasks_per_node}} 115 BD:#PBS -o {{job_protocol_file}} 116 BD:#PBS -j oe 117 BD:#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: 140 BDT:#!/bin/bash 141 #BDT:#PBS -A {{project_account}} 142 BDT:#PBS -N job_protocol_transfer 143 BDT:#PBS -l walltime=00:30:00 144 BDT:#PBS -l nodes=1:ppn=1 145 BDT:#PBS -o {{job_transfer_protocol_file}} 146 BDT:#PBS -j oe 147 BDT:#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}} 87 160 88 161 #---------------------------------------------------------------------------- 89 # INPUT-commands, executed before running PALM - lines must start with "IC:" 162 # INPUT-commands, executed before running PALM - lines must start with "IC:" 90 163 #---------------------------------------------------------------------------- 91 164 #IC:ulimit -s unlimited … … 100 173 #---------------------------------------------------------------------------- 101 174 #OC:echo \\\"PALM job finished\\\" | mailx user@somewhere 102 103 104 #-------------------------------------------------------------------------------105 # Directives to be used for batch jobs106 # 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/bash110 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 oe115 BD:#PBS -q {{queue}}116 117 118 #-------------------------------------------------------------------------------119 # Directives for batch jobs used to send back the jobfiles from a remote to a local host120 # Lines must start with "BDT:". If $-characters are required, excape them with triple backslash121 # Internal variables can be used as {{variable_name}}. Please see documentation.122 #-------------------------------------------------------------------------------123 BDT:#!/bin/bash124 BDT:#PBS -N job_protocol_transfer125 BDT:#PBS -l walltime=00:30:00126 BDT:#PBS -l nodes=1:ppn=1127 BDT:#PBS -o {{job_transfer_protocol_file}}128 BDT:#PBS -j oe129 BDT:#PBS -q dataq
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