Changes between Version 3 and Version 4 of Doc/ComputingCenters/LocalPC

Timestamp:

10/11/19 15:46:04 (5 years ago)

Author:

nillod

Comment:

--

Doc/ComputingCenters/LocalPC

@@ -9 +9 @@
 # Compiling # 
 ## Test installation of XIOS ##
-It is recommended to first make a test installation of XIOS following the guide here: http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation 
-Then use the same libraries and compiler versions for all components as for XIOS.
+It is recommended to first make a test installation of [wiki:Doc/Tools#XIOS XIOS] following the guide here: http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation. [[BR]]
+Then use the same libraries and compiler versions for all components as for [wiki:Doc/Tools#XIOS XIOS].
 
-Note: the netcdf4 library can be parallel or sequential, depending on the version. If the sequential netcdf4 library is used, some functionalities in XIOS can not be used such us using several servers. To link XIOS to the sequential library, the argument --netcdf_lib netcdf4_seq must be set when compiling XIOS. This is added in the main makefile or the main script for compilaton just after ./make_xios --netcdf_lib netcdf4_seq ...
+Note: the netcdf4 library can be parallel or sequential, depending on the version. If the sequential netcdf4 library is used, some functionalities in [wiki:Doc/Tools#XIOS XIOS] can not be used such as using several servers. To link [wiki:Doc/Tools#XIOS XIOS] to the sequential library, the argument `--netcdf_lib netcdf4_seq` must be set when compiling [wiki:Doc/Tools#XIOS XIOS]. This is added in the main Makefile or the main script for compilaton just after `./make_xios --netcdf_lib netcdf4_seq` ...
 
 
-Some configurations can be installed without XIOS.
+Some configurations can be installed without [wiki:Doc/Tools#XIOS XIOS].
 
 ## Choose a target in AA_make.gdef ##
-The ins_make script from modipsl will not recognize your local PC to create makefiles. You must specify an existing target or create a new target in the util/AA_make.gdef file. Adapt this target to your computing environment (compiler, options, path to netcdf, etc), and create a new makefile specifying this target: 
+The `ins_make` script from modipsl will not recognize your local PC to create makefiles. You must specify an existing target or create a new target in the `util/AA_make`.gdef file. Adapt this target to your computing environment (compiler, options, path to netcdf, etc), and create a new makefile specifying this target: 
 {{{
 ./ins_make -t new_target
 }}}
 
-One of the important variables given is FCM_ARCH. Set for example FCM_ARCH=NEW-ARCH. FCM_ARCH gives the name of the arch files used for the different models, see next section. 
+One of the important variables given is `FCM_ARCH`. Set for example `FCM_ARCH=NEW-ARCH`. `FCM_ARCH` gives the name of the arch files used for the different models, see next section. 
 
 ## Adapt compilation for each model ##
 Please refer to the model managers of your model configuration to learn more about how to compile the IPSL models on a local PC and which compilers can be used with the specific models you need. See some information here below.
 
-Most of the IPSL models uses compilation based on fcm ([wiki:Doc/Compile#Compilingenvironment for more informations on fcm]) and the compiling options are set in arch files. Depending on the version of the models and between the models the file arch-target.path might have different syntaxes. For each model, take as example one existing target machine and adapt for your PC. The files are stored in the folder modipsl/modeles/MODEL/arch/arch-NEW_ARCH.fcm/.path/.env. The name NEW_ARCH can be changed but must be the same for all modeles and set in AA_make.gdef.
+Most of the IPSL models uses compilation based on fcm ([wiki:Doc/Compile#Compilingenvironment for more informations on fcm]) and the compiling options are set in arch files. Depending on the version of the models and between the models the file `arch-target.path` might have different syntaxes. For each model, take as example one existing target machine and adapt for your PC. The files are stored in the folder `modipsl/modeles/MODEL/arch/arch-NEW_ARCH.fcm/.path/.env`. The name `NEW_ARCH` can be changed but must be the same for all modeles and set in AA_make.gdef.
 
 ## Example for installing ORCHIDEE offline ##
-Before installing ORCHIDEE, make a test installation of XIOS, see guide here: http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation . If this fails, it is still possible to install ORCHIDEE without XIOS, see notes below. 
+Before installing [wiki:Doc/Models/ORCHIDEE ORCHIDEE], make a test installation of [wiki:Doc/Tools#XIOS XIOS], see guide here: http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation . If this fails, it is still possible to install [wiki:Doc/Models/ORCHIDEE ORCHIDEE] without [wiki:Doc/Tools#XIOS XIOS], see notes below. 
 
 {{{
@@ -57 +57 @@
  modipsl/modeles/XIOS/arch/arch_NEW_ARCH.env
 
-# Note: the netcdf4 library can be parallel or sequential, depending on the version. If the sequential netcdf4 library is used, some functionalities in XIOS can not be used such us using several servers. To link XIOS to the sequantial library, the argument --netcdf_lib netcdf4_seq when compiling XIOS. This should be added in modipsl/config/ORCHIDEE_OL/AA_make just after ./make_xios --netcdf_lib netcdf4_seq ...
+# Note: the netcdf4 library can be parallel or sequential, depending on the version. If the sequential netcdf4 library is used,
+#       some functionalities in XIOS can not be used such us using several servers. To link XIOS to the sequantial library, the 
+#       argument --netcdf_lib netcdf4_seq when compiling XIOS. This should be added in modipsl/config/ORCHIDEE_OL/AA_make just 
+#       after ./make_xios --netcdf_lib netcdf4_seq ...
 
 
@@ -77 +80 @@
 }}}
 Notes:
-* The name NEW_ARCH can be changed to another name but needs to be same everywhere 
-* All arch_NEW_ARCH.* files and AA_make.gdef must be coherent for the libraries and options choosen 
-* It is still possible to install without XIOS. For that case, you do not need to do 3b above and the compilation is done using '''gmake without_xios''' 
+* The name `NEW_ARCH` can be changed to another name but needs to be same everywhere 
+* All `arch_NEW_ARCH.*` files and `AA_make.gdef` must be coherent for the libraries and options choosen 
+* It is still possible to install without [wiki:Doc/Tools#XIOS XIOS]. For that case, you do not need to do 3b above and the compilation is done using '''gmake without_xios''' 
 
 
@@ -107 +110 @@
 
 
-Note 1: for installing in parallel mode with MPI, do as above but adapt the files arch-gfortran.path, arch-gfortran.fcm and AA_make.gef with suitable compile options. You can use target gfortran_CICLAD in AA_make.gdef as example. Do not do point 3 above. [[BR]]
+Note 1: for installing in parallel mode with MPI, do as above but adapt the files `arch-gfortran.path`, `arch-gfortran.fcm` and `AA_make.gef` with suitable compile options. You can use target `gfortran_CICLAD` in `AA_make.gdef` as example. Do not do point 3 above. [[BR]]
 
-Note 2: for older version of ORCHIDEE, such as in LMDZOR_v5, the files in modeles/ORCHIDEE/arch do not exist. Compile options in AA_make.gdef is used for ORCHIDEE in this case.
+Note 2: for older version of [wiki:Doc/Models/ORCHIDEE ORCHIDEE], such as in LMDZOR_v5, the files in modeles/ORCHIDEE/arch do not exist. Compile options in `AA_make.gdef` is used for [wiki:Doc/Models/ORCHIDEE ORCHIDEE] in this case.
 
-[[NoteBox(note,The v6 configurations cannot be compiled in sequential mode because XIOS do not compile or run without the MPI library., 600px)]]
+[[NoteBox(note,The v6 configurations cannot be compiled in sequential mode because [wiki:Doc/Tools#XIOS XIOS] do not compile or run without the MPI library., 600px)]]
 
 
 # Simulation with libIGCM #
-When using libIGCM on a local PC, the parameters of the default system described in the libIGCM_sys/libIGCM_sys_default.ksh file will be used. You may have to change this file to match your system. [[BR]]
+When using [wiki:Doc/Tools#libIGCM libIGCM] on a local PC, the parameters of the default system described in the `libIGCM_sys/libIGCM_sys_default.ksh` file will be used. You may have to change this file to match your system. [[BR]]
 
-A minimum subset of files located on the shared IGCM account must be downloaded and installed. This directory is called R_IN in libIGCM_sys_default.ksh and it has the default path /home/${LOGIN}/IGCM.
+A minimum subset of files located on the shared IGCM account must be downloaded and installed. This directory is called `R_IN` in `libIGCM_sys_default.ksh` and it has the default path `/home/${LOGIN}/IGCM`.
 
 # Installing rebuild #
 The output of old version of the models (ORCHIDEE, LMDZ, INCA, REPROBUS) must be recombined to the total horizontal domain when simulation is done in parallel mode. 
 
-The tool for this is called ''rebuild''. The rebuild tool is called in the post-processing phase by libIGCM. rebuild is a fortran code included in IOIPSL. rebuild must be installed and compiled on the local machine. The rebuild can then be used interactively outside libIGCM or in the post-processing phase. 
+The tool for this is called ''rebuild''. The rebuild tool is called in the post-processing phase by [wiki:Doc/Tools#libIGCM libIGCM]. Rebuild is a Fortran code included in [wiki:Doc/Tools#IOIPSLandREBUILD IOIPSL]. rebuild must be installed and compiled on the local machine. The rebuild can then be used interactively outside libIGCM or in the post-processing phase. 
 
 '''Installation''' 
@@ -136 +139 @@
 
 
-For use with libIGCM, add the path to your rebuild in libIGCM_sys/libIGCM_sys_default.ksh. 
+For use with [wiki:Doc/Tools#libIGCM libIGCM], add the path to your rebuild in `libIGCM_sys/libIGCM_sys_default.ksh`.
 
 '''Use in interactive mode'''[[BR]]
 
-rebuild can also be used interactively. For example create the global file sechiba_history.nc as following :
+rebuild can also be used interactively. For example create the global file `sechiba_history.nc` as following :
 
 {{{