Changes between Version 6 and Version 7 of doc/app/palm_iofiles
- Timestamp:
- Nov 21, 2018 5:49:51 PM (6 years ago)
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doc/app/palm_iofiles
v6 v7 13 13 # List of input-files 14 14 #--------------------------------------------------------------------------------------------- 15 PARIN in:tr d3# $base_data/$ jobname/INPUT _p3d*16 PARIN in:tr d3r $base_data/$ jobname/INPUT _p3dr*17 TOPOGRAPHY_DATA inopt:tr d3#:d3r $base_data/$ jobname/INPUT _topo*18 DATA_1D_PR_NETCDF inopt prr $base_data/$ jobname/OUTPUT _pr* nc15 PARIN in:tr d3# $base_data/$run_identifier/INPUT _p3d* 16 PARIN in:tr d3r $base_data/$run_identifier/INPUT _p3dr* 17 TOPOGRAPHY_DATA inopt:tr d3#:d3r $base_data/$run_identifier/INPUT _topo* 18 DATA_1D_PR_NETCDF inopt prr $base_data/$run_identifier/OUTPUT _pr* nc 19 19 # 20 20 #--------------------------------------------------------------------------------------------- 21 21 # List of output-files 22 22 #--------------------------------------------------------------------------------------------- 23 BINOUT* out:lnpe restart $fast_io_catalog/$ jobname/RESTART _d3d24 DATA_3D_NETCDF* out:tr * $base_data/$ jobname/OUTPUT _3d nc23 BINOUT* out:lnpe restart $fast_io_catalog/$run_identifier/RESTART _d3d 24 DATA_3D_NETCDF* out:tr * $base_data/$run_identifier/OUTPUT _3d nc 25 25 }}} 26 26 … … 29 29 The '''second column''' gives the file attributes, which need to be separated by a colon (":"). Two attributes are allowed. The '''first attribute''' says, whether the file is an input ({{{in}}}) or an output file ({{{out}}}). {{{palmrun}}} immediately terminates, if it cannot find the user's input file, because it assumes that PALM cannot run without files with attribute {{{in}}}. If you do not want {{{palmrun}}} to terminate, you may give the attribute {{{inopt}}}, which says that this file is optional. The '''second attribute''' can be 30 30 * {{{tr}}} \\ 31 In case of running jobs on remote hosts, transfer the file between the remote and local host via {{{scp}}}. \\\\Input files will be transferred from the user's folder on the local host to palmrun's temporary working directory on the remote host, before PALM is executed. This transfer is actually done before the batch job to the remote host is submitted. Files will be stored on the remote host in folder {{{$fast_io_catalog/SOURCES_FOR_RUN_$ jobname}}}. As soon as the batch job executes, files are copied from the SOURCES_FOR_RUN-folder to the temporary working directory. \\\\Output files will be transferred from the temporary working directory on the remote host to the user's folder on the local host, after PALM has finished execution.31 In case of running jobs on remote hosts, transfer the file between the remote and local host via {{{scp}}}. \\\\Input files will be transferred from the user's folder on the local host to palmrun's temporary working directory on the remote host, before PALM is executed. This transfer is actually done before the batch job to the remote host is submitted. Files will be stored on the remote host in folder {{{$fast_io_catalog/SOURCES_FOR_RUN_$run_identifier}}}. As soon as the batch job executes, files are copied from the SOURCES_FOR_RUN-folder to the temporary working directory. \\\\Output files will be transferred from the temporary working directory on the remote host to the user's folder on the local host, after PALM has finished execution. 32 32 33 33 * {{{tra}}} \\ … … 45 45 The '''third column''' gives the so-called activation strings. Two or more strings need to be separated by colons (":"). Activation strings are those given in the {{{palmrun}}} option {{{-a}}}. The respective file connection statement is only processed (i.e. the file is copied), if at least one of its activation strings is set with option {{{-a}}}. In case of the above example, {{{-r "d3#"}}} causes {{{palmrun}}} to provide the input files {{{PARIN}}} and {{{TOPOGRAPHY_DATA}}}. Option {{{-r "d3# restart"}}} additional copies/saves the output file {{{BINOUT}}}. Note that activation strings need to be separated by blanks when given with the option {{{-r}}} and that they need to be embraced by {{{"}}}, even if only one string is given (otherwise, a {{{#}}} would cause the shell to interpret the remaining part of the command as a comment). For output files, a wildcard may be given in the third column. Respective local files will then always be copied, in case they exist, independently from the activation strings given with option {{{-r}}}. No warning will be issued if no file exists. Wildcards in the third column are not allowed for input files. 46 46 47 The path to the user's permanent file is given in the '''fourth column'''. It may contain environment variables that have been defined in the file connection file. {{{$ jobname}}} will be replaced with the argument of {{{palmrun}}} option {{{-r}}}.47 The path to the user's permanent file is given in the '''fourth column'''. It may contain environment variables that have been defined in the file connection file. {{{$run_identifier}}} will be replaced with the argument of {{{palmrun}}} option {{{-r}}}. 48 48 49 49 The '''fifth column''' gives the appendix of the user's permanent file. … … 60 60 As an example, the file connection statement 61 61 {{{ 62 DATA_3D_NETCDF* out:tr * $base_data/$ jobname/OUTPUT _3d nc62 DATA_3D_NETCDF* out:tr * $base_data/$run_identifier/OUTPUT _3d nc 63 63 }}} 64 64 plus entry … … 76 76 In case of nested runs, masked 3d-output and wind turbine model output, PALM expects or creates multiple input/output files with additional suffixes. As an example, a nested run with a parent and one child requires two parameter files for steering the simulation, where the second file is expected to have the suffix {{{_N02}}}. Each additional nest would require another parameter file with suffixes {{{_N03}}}, {{{_N04}}}, etc. In order to simplify the file connection file, only one file connection statement 77 77 {{{ 78 PARIN in:tr d3# $base_data/$ jobname/INPUT _p3d*78 PARIN in:tr d3# $base_data/$run_identifier/INPUT _p3d* 79 79 }}} 80 80 is required for this, where the wildcard in {{{_p3d*}}} causes {{{palmrun}}} to copy files with these suffixes too. Assuming an INPUT folder with files … … 92 92 The same holds for output files. Here the wildcard must be given as part of the local filename (first column). The example given below assumes one nest (root domain plus one child domain), two output masks for the root domain, and three masks for the child. Assuming a file connection statement for an output file 93 93 {{{ 94 DATA_MASK_NETCDF* out:tr * $base_data/$ jobname/OUTPUT _masked nc94 DATA_MASK_NETCDF* out:tr * $base_data/$run_identifier/OUTPUT _masked nc 95 95 }}} 96 96 and following local files that have been created by PALM
