Changeset 3043
- Timestamp:
- May 25, 2018 10:47:54 AM (7 years ago)
- Location:
- palm/trunk/SCRIPTS
- Files:
-
- 2 edited
Legend:
- Unmodified
- Added
- Removed
-
palm/trunk/SCRIPTS/.palm.config.default
r2834 r3043 1 1 #$Id$ 2 2 #column 1 column 2 3 #name of variable value of variable (~ must not be used) 4 #---------------------------------------------------------------------------- 3 #name of variable value of variable (~ must not be used except for base_data) 4 #----------------------------------------------------------------------------- 5 # working directory from where palmrun or palmbuild are called 5 6 %base_directory $HOME/palm/current_version 7 8 # directory where PALM I/O is stored (used in .palm.iofiles) 6 9 %base_data ~/palm/current_version/JOBS 10 11 # path to PALM's FORTRAN sources (installation folder) 7 12 %source_path $HOME/palm/current_version/trunk/SOURCE 13 14 # path to user interface routines 8 15 %user_source_path $base_directory/JOBS/$jobname/USER_CODE 9 # 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> 22 23 # folder for job protocols 24 #%local_jobcatalog $HOME/job_queue 25 26 # folder for job protocols to be used on the remote host 27 #%remote_jobcatalog <path/to/directory on remote host> 28 29 # local ip of your computer. Use 127.0.0.0 if you are running PALM 30 # in interactive mode on your local computer 10 31 %local_ip <replace by your computers IP address> 32 33 # your local UNIX username 11 34 %local_username <replace by your unix username> 12 %fast_io_catalog <replace by a folder name which allows for fast I/O> 35 36 # ip address of the remote host 37 #%remote_ip <ip> 38 39 # username on the remote host 40 #%remote_username <username> 41 42 # ssh-key to be used for ssh/scp calls to the remote host 43 #%ssh_key ~/.ssh/id_rsa 44 45 # name of login-node on the remote machine 46 #%remote_loginnode <loginnode> 47 48 # default queue to be used if palmrun-option -q is omitted 49 #%defaultqueue <queue> 50 51 # command to submit batch jobs 52 #%submit_command /opt/moab/default/bin/msub -E 53 54 # compilername to generate MPI executables 13 55 %compiler_name mpif90 56 57 # compilername to generate non-MPI executables running on one core 14 58 %compiler_name_ser ifort 59 60 # preprocessor directives to be used for compiling the PALM code 15 61 %cpp_options -cpp -D__parallel -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__fftw -D__netcdf 62 63 # used for parallel compilation 16 64 %make_options -j 4 65 66 # options to be used to compile PALM 17 67 %compiler_options -openmp -fpe0 -O3 -xHost -fp-model source -ftz -fno-alias -no-prec-div -no-prec-sqrt -ip -nbs -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 68 69 # options to be used to link the PALM executable 18 70 %linker_options -openmp -fpe0 -O3 -xHost -fp-model source -ftz -fno-alias -no-prec-div -no-prec-sqrt -ip -nbs -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 71 72 # name of hostfile to be used 19 73 %hostfile auto 74 75 # command to start the PALM executable 20 76 %execute_command mpiexec -machinefile hostfile -n {{mpi_tasks}} palm 21 # 77 78 # memory request per core 79 #%memory 2300 80 81 # module commands to load required libraries 82 #%module_commands module load fftw cray-hdf5-parallel cray-netcdf-hdf5parallel 83 84 # special commands to be carried out at login and start of batch jobs on the remote host 85 #%login_init_cmd module switch craype-ivybridge craype-haswell 86 87 22 88 #---------------------------------------------------------------------------- 23 89 # INPUT-commands, executed before running PALM - lines must start with "IC:" 24 90 #---------------------------------------------------------------------------- 25 #IC: 91 #IC:ulimit -s unlimited 26 92 # 27 93 #---------------------------------------------------------------------------- 28 94 # ERROR-commands - executed when program terminates abnormally 29 95 #---------------------------------------------------------------------------- 30 EC:[[ \$locat = execution ]] && cat RUN_CONTROL 31 EC:[[ \$locat = execution ]] && cat PARTICLE_INFOS/* 96 #EC:[[ \$locat = execution ]] && cat RUN_CONTROL 32 97 # 33 98 #---------------------------------------------------------------------------- 34 99 # OUTPUT-commands - executed when program terminates normally 35 100 #---------------------------------------------------------------------------- 36 # 37 # Combine 1D- and 3D-profile output (these files are not usable for plotting) 38 OC:[[ -f LIST_PROFIL_1D ]] && cat LIST_PROFIL_1D >> LIST_PROFILE 39 OC:[[ -f LIST_PROFIL ]] && cat LIST_PROFIL >> LIST_PROFILE 40 # 41 # Combine all particle information files 42 OC:[[ -f PARTICLE_INFOS/_0000 ]] && cat PARTICLE_INFOS/* >> PARTICLE_INFO 101 #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 {{job_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 -
palm/trunk/SCRIPTS/palmrun
r3033 r3043 27 27 # ----------------- 28 28 # $Id$ 29 # check for setting of fast_io_catalog 30 # 31 # 3033 2018-05-23 15:26:19Z raasch 29 32 # -T option not required for interactive runs (tasks per node = 30 33 # total number of cores is assumed as default, if option is not given), … … 527 530 528 531 # CHECK SETTING OF REQUIRED PARAMETERS 532 if [[ "$fast_io_catalog" = "" ]] 533 then 534 printf "\n +++ no fast_io_catalog found in $config_file" 535 printf "\n Please add line \"fast_io_catalog ...\" to that file." 536 locat=config_file; exit 537 fi 529 538 if [[ "$compiler_name" = "" ]] 530 539 then … … 563 572 then 564 573 printf "\n +++ no hostfile \"$hostfile\" found" 565 printf "\n Please check line \" hostfile ...\" in $config_file"574 printf "\n Please check line \"%hostfile ...\" in $config_file" 566 575 locat=config_file; exit 567 576 fi
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