Changes between Version 2 and Version 3 of doc/app/palm_iofiles

Timestamp:

Aug 27, 2018 3:26:17 PM (6 years ago)

Author:

raasch

Comment:

--

doc/app/palm_iofiles

@@ -28 +28 @@
 
 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
-* {{{tr}}}
-* {{{tra}}}
-* {{{pe}}}
-* {{{lnpe}}}
-* {{{trpe}}}
+* {{{tr}}} \\
+  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.
+
+* {{{tra}}} \\
+  Can only be used for ASCII output files. Same as {{{tr}}}, but the local file from the remote host will be appended, if a respective file already exists in the user's folder on the local host. In such a case, no new file cycle will be created.
+
+* {{{pe}}} \\
+  The filename is interpreted as a directory name, and it is assumed that the respective folder contains multiple files, one from each MPI process. Filenames are expected as {{{_######}}}, where {{{######}}} is the six-digit MPI-id number. If you are running PALM on 4 cores (4 MPI processes), files will be {{{_000000}}}, {{{_000001}}}, {{{_000002}}}, and {{{_000003}}}. {{{palmrun}}} will copy the complete folders.
+
+* {{{lnpe}}} \\
+  Same as {{{pe}}}, but {{{palmrun}}} tries to move the files using {{{ln}}} instead of {{{cp}}}, which reduces the time to copy the file drastically, but only if both folders (the local temporary folder and the user's folder) reside on the same file system. This attribute is given for restart files in the default file configuration file, because they may have huge sizes.
+
+* {{{trpe}}} \\
+  Same as {{{pe}}}, but the folders are transferred between the local and the remote host via {{{scp}}}.
 
 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, {{{-d "d3#"}}} causes {{{palmrun}}} to provide the input files {{{PARIN}}} and {{{TOPOGRAPHY_DATA}}}. Option {{{-d "d3# restart"}}} additional copies/saves the output file {{{BINOUT}}}. Note that activation strings need to be separated by blanks when given with the option {{{-d}}} 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 {{{-d}}}. Wildcards in the third column are not allowed for input files.