[2481] | 1 | #$Id: .palm.config.default 3455 2018-10-30 14:12:31Z schwenkel $ |
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| 2 | #column 1 column 2 |
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[3043] | 3 | #name of variable value of variable (~ must not be used except for base_data) |
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| 4 | #----------------------------------------------------------------------------- |
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| 5 | # working directory from where palmrun or palmbuild are called |
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[2481] | 6 | %base_directory $HOME/palm/current_version |
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[3043] | 7 | |
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| 8 | # directory where PALM I/O is stored (used in .palm.iofiles) |
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[2481] | 9 | %base_data ~/palm/current_version/JOBS |
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[3043] | 10 | |
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| 11 | # path to PALM's FORTRAN sources (installation folder) |
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[2481] | 12 | %source_path $HOME/palm/current_version/trunk/SOURCE |
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[3043] | 13 | |
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| 14 | # path to user interface routines |
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[3236] | 15 | %user_source_path $base_directory/JOBS/$run_identifier/USER_CODE |
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[3043] | 16 | |
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| 17 | # path to file system with fast discs (if available). This folder |
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| 18 | # is used for temporary catalogs generated by palmrun and to store large |
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| 19 | # I/O files (used in .palm.iofiles). This folder must be accessible from |
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| 20 | # all compute nodes, i.e. it must reside in a global file system |
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| 21 | %fast_io_catalog <replace by a folder name which allows for fast I/O> |
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| 22 | |
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| 23 | # folder for job protocols |
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[3455] | 24 | #%local_jobcatalog $HOME/job_logfiles |
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[3043] | 25 | |
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| 26 | # folder for job protocols to be used on the remote host |
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| 27 | #%remote_jobcatalog <path/to/directory on remote host> |
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| 28 | |
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| 29 | # local ip of your computer. Use 127.0.0.0 if you are running PALM |
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| 30 | # in interactive mode on your local computer |
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[2481] | 31 | %local_ip <replace by your computers IP address> |
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[3043] | 32 | |
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| 33 | # your local UNIX username |
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[2481] | 34 | %local_username <replace by your unix username> |
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[3043] | 35 | |
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| 36 | # ip address of the remote host |
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| 37 | #%remote_ip <ip> |
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| 38 | |
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| 39 | # username on the remote host |
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| 40 | #%remote_username <username> |
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| 41 | |
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| 42 | # ssh-key to be used for ssh/scp calls to the remote host |
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| 43 | #%ssh_key ~/.ssh/id_rsa |
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| 44 | |
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| 45 | # name of login-node on the remote machine |
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| 46 | #%remote_loginnode <loginnode> |
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| 47 | |
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| 48 | # default queue to be used if palmrun-option -q is omitted |
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| 49 | #%defaultqueue <queue> |
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| 50 | |
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| 51 | # command to submit batch jobs |
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| 52 | #%submit_command /opt/moab/default/bin/msub -E |
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| 53 | |
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| 54 | # compilername to generate MPI executables |
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[2481] | 55 | %compiler_name mpif90 |
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[3043] | 56 | |
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| 57 | # compilername to generate non-MPI executables running on one core |
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[2481] | 58 | %compiler_name_ser ifort |
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[3043] | 59 | |
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| 60 | # preprocessor directives to be used for compiling the PALM code |
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[2481] | 61 | %cpp_options -cpp -D__parallel -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__fftw -D__netcdf |
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[3043] | 62 | |
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| 63 | # used for parallel compilation |
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[2481] | 64 | %make_options -j 4 |
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[3043] | 65 | |
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| 66 | # options to be used to compile PALM |
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[3205] | 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 |
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[3043] | 68 | |
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| 69 | # options to be used to link the PALM executable |
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[3205] | 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 |
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[3043] | 71 | |
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| 72 | # name of hostfile to be used |
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[2481] | 73 | %hostfile auto |
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[3043] | 74 | |
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| 75 | # command to start the PALM executable |
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[2693] | 76 | %execute_command mpiexec -machinefile hostfile -n {{mpi_tasks}} palm |
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[3043] | 77 | |
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| 78 | # memory request per core |
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| 79 | #%memory 2300 |
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| 80 | |
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| 81 | # module commands to load required libraries |
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[3199] | 82 | #%module_commands module switch craype-ivybridge craype-haswell; module load fftw cray-hdf5-parallel cray-netcdf-hdf5parallel |
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[3043] | 83 | |
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| 84 | # special commands to be carried out at login and start of batch jobs on the remote host |
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[3199] | 85 | #%login_init_cmd .execute_special_profile |
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[3043] | 86 | |
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| 87 | |
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[2481] | 88 | #---------------------------------------------------------------------------- |
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| 89 | # INPUT-commands, executed before running PALM - lines must start with "IC:" |
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| 90 | #---------------------------------------------------------------------------- |
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[3043] | 91 | #IC:ulimit -s unlimited |
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[2481] | 92 | # |
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| 93 | #---------------------------------------------------------------------------- |
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| 94 | # ERROR-commands - executed when program terminates abnormally |
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| 95 | #---------------------------------------------------------------------------- |
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[3043] | 96 | #EC:[[ \$locat = execution ]] && cat RUN_CONTROL |
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[2481] | 97 | # |
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| 98 | #---------------------------------------------------------------------------- |
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| 99 | # OUTPUT-commands - executed when program terminates normally |
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| 100 | #---------------------------------------------------------------------------- |
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[3151] | 101 | #OC:echo \\\"PALM job finished\\\" | mailx user@somewhere |
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[3043] | 102 | |
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| 103 | |
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| 104 | #------------------------------------------------------------------------------- |
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| 105 | # Directives to be used for batch jobs |
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| 106 | # Lines must start with "BD:". If $-characters are required, hide them with \ |
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| 107 | # Internal variables can be used as {{variable_name}}. Please see documentation. |
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| 108 | #------------------------------------------------------------------------------- |
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| 109 | BD:#!/bin/bash |
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| 110 | BD:#PBS -N {{job_id}} |
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| 111 | BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}} |
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| 112 | BD:#PBS -l nodes={{nodes}}:ppn={{tasks_per_node}} |
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| 113 | BD:#PBS -o {{job_protocol_file}} |
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| 114 | BD:#PBS -j oe |
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| 115 | BD:#PBS -q {{queue}} |
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| 116 | |
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| 117 | |
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| 118 | #------------------------------------------------------------------------------- |
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| 119 | # Directives for batch jobs used to send back the jobfiles from a remote to a local host |
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| 120 | # Lines must start with "BDT:". If $-characters are required, excape them with triple backslash |
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| 121 | # Internal variables can be used as {{variable_name}}. Please see documentation. |
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| 122 | #------------------------------------------------------------------------------- |
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| 123 | BDT:#!/bin/bash |
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| 124 | BDT:#PBS -N job_protocol_transfer |
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| 125 | BDT:#PBS -l walltime=00:30:00 |
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| 126 | BDT:#PBS -l nodes=1:ppn=1 |
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| 127 | BDT:#PBS -o {{job_transfer_protocol_file}} |
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| 128 | BDT:#PBS -j oe |
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| 129 | BDT:#PBS -q dataq |
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