Changes between Version 13 and Version 14 of doc/app/userint/comp

Timestamp:

Nov 22, 2018 11:39:20 AM (6 years ago)

Author:

scharf

Comment:

--

doc/app/userint/comp

@@ -2 +2 @@
 [[TracNav(doc/userint/toc)]]
 
-You can use your user-interface within a PALM-run by carrying out the following steps:\\\\
-   1. Copy the appropriate default (empty) user-interface files {{{user_***.f90}}} to the folder that has been defined in the configuration file  by variable {{{user_source_path}}}. The default for this folder is {{{$HOME/palm/current_version/JOBS/$run_identifier/USER_CODE}}}, so in case the run identifier is {{{example}}}:
+You can use your user-interface within a PALM-run by carrying out the following steps:\\
+
+   1. **Copy** the appropriate default (empty) user-interface files {{{user_***.f90}}} to the folder that has been defined in the configuration file  by variable {{{user_source_path}}}. The default for this folder is {{{$HOME/palm/current_version/JOBS/$run_identifier/USER_CODE}}}, so in case the run identifier is {{{example}}}:
 {{{
    cd ~/palm/current_version
@@ -9 +10 @@
    cp trunk/SOURCE/user_***.f90  JOBS/example/USER_CODE
 }}}
-      '''Attention: do not change the names of the user-interface files! '''
+      [[span(style=color: #FF0000, Attention: do not change the names of the user-interface files!)]]
 
-   2. Modify the interface routines according to your needs.\\
+   2. **Modify** the interface routines according to your needs.\\
 
-   3. Start a PALM run by entering
+   3. **Start** a PALM run by entering
 {{{
    palmrun -r example ...
 }}}
-      The files {{{user_***.f90}}} will be automatically compiled as part of this run, before PALM is executed, and will replace {{{PALM}}}‘s respective default user-interface routines. The compiled binaries are put into a folder named {{{SOURCES_FOR_RUN_$configuration_identifier_$run_identifier}}}, where they replace the default binaries that have been created via {{{palmbuild}}}. The {{{SOURCES_FOR_RUN}}} folder is created in the directory defined by variable {{{fast_io_catalog}}} in the configuration file. It is newly created for each manual call of {{{palmrun}}}. \\\\
 
-Since the run identifier is part of the user-interface's SOURCE path, you can use different interfaces for different runs at the same time. Just store the respective interface-files in sub-folders {{{JOB/abcd/USER_CODE}}}, {{{JOBS/cdef/USER_CODE}}}, etc. and call {{{palmrun}}} with option "{{{-r abcd}}}", "{{{-r cdef}}}", etc. \\\\
-If you like to add additional routines which are not part of the default user-interface (see the [wiki:doc/app/userint/int list of available interface routines]), you can a) append this routines to the default user-interface file {{{user_additional_routines.f90}}} or b) create new files in your user-interface folder. These files must have names different from the default {{{PALM}}} source code files. In case of b), you must also copy the default {{{Makefile}}} into the user-interface folder, e.g.:
+The files {{{user_***.f90}}} will be **automatically compiled** as part of this run, before PALM is executed, and will **replace** PALM‘s respective default user-interface routines in {{{/trunk/SOURCE/}}}. The compiled binaries are put into a folder named {{{SOURCES_FOR_RUN_$configuration_identifier_$run_identifier}}}, where they replace the default binaries that have been created via {{{palmbuild}}}. The {{{SOURCES_FOR_RUN}}} folder is created in the directory defined by variable {{{fast_io_catalog}}} in the configuration file. It is newly created for each manual call of {{{palmrun}}}. Since the run identifier is part of the user-interface's SOURCE path, you can use different interfaces for different runs at the same time. \\\\
+
+If you like to add **additional routines** which are not part of the default user-interface (see the [wiki:doc/app/userint/int list of available interface routines]), you can 
+   a) **append** this routines to the default user-interface file {{{user_additional_routines.f90}}} or \\
+
+   b) **create** new files in your user-interface folder. \\
+
+These files must have names different from the default PALM source code files. In case of b), you must also copy the default {{{Makefile}}} into the user-interface folder, e.g.:
 {{{
    cp trunk/SOURCE/Makefile  JOBS/example/USER_CODE
@@ -26 +32 @@
 Edit the {{{Makefile}}} and add your new files and possible dependencies, following the standard "make"-rules.\\\\
 
+
 == How to avoid re-compilation of user-interfaces
 
-It is important to know, that in general '''the modified user-interface files cannot be pre-compiled''' with {{{palmbuild}}}. This would not make sense because your user-interface may differ among your PALM runs, so you would need different {{{MAKE_DEPOSITORIES}}} depending on the run-identifier (option {{{-r}}}). Therefore, {{{palmrun}}} compiles the user-interface each time you call the script. Strictly speaking, {{{palmrun}}} internally calls {{{palmbuild}}} with special options, and {{{palmbuild}}} then compiles the user-interface and generates the {{{SOURCES_FOR_RUN}}} folder (see above).
+It is important to know, that in general the modified user-interface files cannot be pre-compiled with {{{palmbuild}}}. This would not make sense because your user-interface may differ among your PALM runs, so you would need different {{{MAKE_DEPOSITORIES}}} depending on the run-identifier (option {{{-r}}}). Therefore, {{{palmrun}}} compiles the user-interface each time you call the script. Strictly speaking, {{{palmrun}}} internally calls {{{palmbuild}}} with special options, and {{{palmbuild}}} then compiles the user-interface and generates the {{{SOURCES_FOR_RUN}}} folder (see above).
 
-In case you carry out a large number of test runs and don't want the user-interface to be compiled each time again (because it may take a lot of time, and you didn't change it), you can suppress compilation by adding {{{palmrun}}} option {{{-V}}}. Then, {{{palmrun}}}/{{{palmbuild}}} tries to re-use the compiled interface from the last call of {{{palmrun}}} with same configuration identifier and run identifier (given by options {{{-c}}} and {{{-r}}}), by re-using the respective {{{SOURCES_FOR_RUN}}} folder that has been generated by the previous run. Automatically generated calls of {{{palmrun}}} (restart runs in job chains) use the same method, so they do not need to compile the user-interface again. \\\\
-
-For debugging user-defined code, see section [../../intdbg Debugging]. 
-
+In case you carry out a large number of test runs and you **don't want the user-interface to be compiled each time** again (because it may take a lot of time, and you didn't change it), you can suppress compilation by adding {{{palmrun}}} option {{{-V}}}. Then, {{{palmrun}}}/{{{palmbuild}}} tries to re-use the compiled interface from the last call of {{{palmrun}}} with same configuration identifier and run identifier (given by options {{{-c}}} and {{{-r}}}), by re-using the respective {{{SOURCES_FOR_RUN}}} folder that has been generated by the previous run. Automatically generated calls of {{{palmrun}}} (restart runs in job chains) use the same method, so they do not need to compile the user-interface again. \\\\