ORcompDCAO DCAO - Historial de revisiones

Lluis.fita: /* Installation steps using modipsl */

2019-10-02T12:21:37Z

Installation steps using modipsl

← Revisión anterior		Revisión del 12:21 2 oct 2019
Línea 25:		Línea 25:
	* Getting IOIPSL:		* Getting IOIPSL:
	<pre>$ mkdir -p IOIPSL/src		<pre>$ mkdir -p IOIPSL/src
	$ svn co https://forge.ipsl.jussieu.fr/igcmg/svn/IOIPSL/tags/~~v2_2_2~~/src IOIPSL/src</pre>		$ svn co https://forge.ipsl.jussieu.fr/igcmg/svn/IOIPSL/tags/v2_2_4/src IOIPSL/src</pre>
	* Getting XIOS library		* Getting XIOS library
	<pre>$ svn co -r 1043 https://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk XIOS</pre>		<pre>$ svn co -r 1043 https://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk XIOS</pre>

Lluis.fita: /* Installation steps using modipsl */

2019-07-23T12:54:13Z

Installation steps using modipsl

← Revisión anterior		Revisión del 12:54 23 jul 2019
Línea 3:		Línea 3:
	= Installation steps using modipsl =		= Installation steps using modipsl =
	* Required packages:		* Required packages:
	<pre># apt-get install subversion git libnetcdf-dev libnetcdff-dev netcdf-bin make ncview ksh csh mpi mpich vim </pre>		<pre># apt-get install subversion git libnetcdf-dev libnetcdff-dev netcdf-bin make
			ncview ksh csh mpi mpich vim
			</pre>
	* Additional for python and netcdf (not required by ORCHIDEE)		* Additional for python and netcdf (not required by ORCHIDEE)
	<pre># apt-get install python-matplotlib python-matplotlib-data python-matplotlib-doc python-mpltoolkits.basemap		<pre># apt-get install python-matplotlib python-matplotlib-data python-matplotlib-doc
	python-mpltoolkits.basemap-data dvipng python-netcdf4</pre>		python-mpltoolkits.basemap python-mpltoolkits.basemap-data dvipng python-netcdf4
			</pre>
	* And fake gmake (Ubunutu)		* And fake gmake (Ubunutu)
	<pre>ln -s /usr/bin/make /usr/bin/gmake</pre>		<pre>ln -s /usr/bin/make /usr/bin/gmake</pre>

Lluis.fita: /* Installation steps using modipsl */

2019-07-23T12:53:46Z

Installation steps using modipsl

← Revisión anterior		Revisión del 12:53 23 jul 2019
Línea 3:		Línea 3:
	= Installation steps using modipsl =		= Installation steps using modipsl =
	* Required packages:		* Required packages:
	<pre># apt-get install subversion git libnetcdf-dev libnetcdff-dev make ncview ksh csh mpi mpich vim </pre>		<pre># apt-get install subversion git libnetcdf-dev libnetcdff-dev netcdf-bin make ncview ksh csh mpi mpich vim </pre>
	* Additional for python and netcdf (not required by ORCHIDEE)		* Additional for python and netcdf (not required by ORCHIDEE)
	<pre># apt-get install python-matplotlib python-matplotlib-data python-matplotlib-doc python-mpltoolkits.basemap		<pre># apt-get install python-matplotlib python-matplotlib-data python-matplotlib-doc python-mpltoolkits.basemap
Línea 176:		Línea 176:
	$ ls ../../bin/		$ ls ../../bin/
	orchideedriver orchidee_ol </pre>		orchideedriver orchidee_ol </pre>


	= Compiling rebuild =		= Compiling rebuild =

Lluis.fita: /* Compiling rebuild */

2019-07-16T13:27:16Z

Compiling rebuild

← Revisión anterior		Revisión del 13:27 16 jul 2019
Línea 182:		Línea 182:
	Due to the fact that <code>hydra</code> does not have the netcdf libraries compiled in parallel, ORCHDEE output is written with multiple files being a file for each process. In order to overcome this output. IPSL does prepare a tool to join the files and provide the expected output. This tool is called <code>rebuild</code> (a Kornshell script which encapsulates de exacutable <code>flio_rbld</code>) and it comes with the <code>IOIPSL</code> libraries. The IOIPSL libraries, are a set of old libraries developed by the IPSL (M. A. Foujuls, J. Polcher among others) to deal with the netCDF data access for all the models developed at the IOIPSL. Compiling IOIPSL (following [http://lmdz.lmd.jussieu.fr/utilisateurs/faq-en/installation/comment-installer-ioipsl-et-loutil-rebuild install rebuild]. It has to be compiled independently. Here it is explained how it has to be done.		Due to the fact that <code>hydra</code> does not have the netcdf libraries compiled in parallel, ORCHDEE output is written with multiple files being a file for each process. In order to overcome this output. IPSL does prepare a tool to join the files and provide the expected output. This tool is called <code>rebuild</code> (a Kornshell script which encapsulates de exacutable <code>flio_rbld</code>) and it comes with the <code>IOIPSL</code> libraries. The IOIPSL libraries, are a set of old libraries developed by the IPSL (M. A. Foujuls, J. Polcher among others) to deal with the netCDF data access for all the models developed at the IOIPSL. Compiling IOIPSL (following [http://lmdz.lmd.jussieu.fr/utilisateurs/faq-en/installation/comment-installer-ioipsl-et-loutil-rebuild install rebuild]. It has to be compiled independently. Here it is explained how it has to be done.

	* Go to the instalation directory <code>[INSTALLDIR]</code> ~~(at hydra <code>share</code>)~~		* Go to the instalation directory <code>[INSTALLDIR]</code>
	<pre>$ cd [INSTALLDIR]</pre>		<pre>$ cd [INSTALLDIR]</pre>
	* getting the last version of the code		* getting the last version of the code

Lluis.fita en 13:25 16 jul 2019

2019-07-16T13:25:33Z

← Revisión anterior		Revisión del 13:25 16 jul 2019
Línea 176:		Línea 176:
	$ ls ../../bin/		$ ls ../../bin/
	orchideedriver orchidee_ol </pre>		orchideedriver orchidee_ol </pre>


			= Compiling rebuild =

			Due to the fact that <code>hydra</code> does not have the netcdf libraries compiled in parallel, ORCHDEE output is written with multiple files being a file for each process. In order to overcome this output. IPSL does prepare a tool to join the files and provide the expected output. This tool is called <code>rebuild</code> (a Kornshell script which encapsulates de exacutable <code>flio_rbld</code>) and it comes with the <code>IOIPSL</code> libraries. The IOIPSL libraries, are a set of old libraries developed by the IPSL (M. A. Foujuls, J. Polcher among others) to deal with the netCDF data access for all the models developed at the IOIPSL. Compiling IOIPSL (following [http://lmdz.lmd.jussieu.fr/utilisateurs/faq-en/installation/comment-installer-ioipsl-et-loutil-rebuild install rebuild]. It has to be compiled independently. Here it is explained how it has to be done.

			* Go to the instalation directory <code>[INSTALLDIR]</code> (at hydra <code>share</code>)
			<pre>$ cd [INSTALLDIR]</pre>
			* getting the last version of the code
			<pre>$ svn co https://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl_IOIPSLtools</pre>
			* going to prepare compilation/installation
			<pre>$ cd modipsl_IOIPSLtools/util</pre>
			* preparing environment
			<pre>./model IOIPSL_PLUS</pre>
			* We got some issues with the ports, thus, it needs to be manually done:
			<pre>$ cd ../modeles</pre>
			* Getting IOIPSL ('''NOTE:''' notice the difference in library's version from the previous one):
			<pre>$ svn co https://forge.ipsl.jussieu.fr/igcmg/svn/IOIPSL/tags/v2_2_3 IOIPSL</pre>
			* Comming back to the <code>util</code> folder
			<pre>$ cd ../util</pre>
			* Creation of the compilation environment for <code>`DCAO'</code> using <code>'gfortran'</code> inside <code>AA_make.gdef</code> as in the full compilation
			<pre>$ cp ../../modipsl/util/AA_make.gdef ./</pre>
			* Preparing makefiles
			<pre>$ ./ins_make -t "DCAO_gfortran" -p I4R8</pre>
			* going to src folder to compile
			<pre>$ cd ../modeles/IOIPSL/src</pre>
			* cleaning (you never know...)
			<pre>$ make clean</pre>
			* compiling
			<pre>$ make >& run_make.log</pre>
			* Checking no errors:
			<pre>$ cat -n run_make.log \| grep Error</pre>
			* compilation of tools (file concatenation)
			<pre>$ cd ../tools </pre>
			* cleaning (you never know...)
			<pre>$ make clean</pre>
			* compiling
			<pre>$ make >& run_make.log</pre>
			* Checking no errors:
			<pre>$ cat -n run_make.log \| grep Error</pre>
			* One should have:
			<pre>$ ls ../../../bin/
			flio_rbld rebuild</pre>

			= debug Instalation =
			Getting a debugging copy for test purposes

			== Instalation steps using modipsl ==
			* Go to the instalation directory <code>[INSTALLDIR]</code>
			<pre>$ cd [INSTALLDIR]</pre>
			* Getting the IPSL-models suite (r 3379)
			<pre>$ svn co https://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl_dbg</pre>
			* Once we got the codes, we need to copy the specificities of the installation for <code>hydra</code>
			<pre>$ cp ../../modipsl/util/AA_make.gdef ./
			$ cp ../../modipsl/modeles/XIOS/arch/hydra ../modeles/XIOS/arch/
			$ cp ../../modipsl/modeles/ORCHIDEE/arch/hydra ../modeles/ORCHIDEE/arch/</pre>
			* Everything is the same as for the installation, except that we need to indicate debugging compilation:
			<pre>./ins_make -t DCAO_gfortran -d >& run_ins_make.log</pre>
			* And on <code>Makefile</code> from <code>config/ORCHIDEE_OL</code>, change all the <code>-prod</code> by <code>-debug</code>
			<pre>(...)
			xios :
			(cd ../../modeles/XIOS ; ./make_xios --netcdf_lib netcdf4_seq \
			--debug --arch ${FCM_ARCH} --job 8 ; cp bin/xios_server.exe ../../bin/. ; )
			(...)
			driver :
			(cd ../../modeles/ORCHIDEE ; ./makeorchidee_fcm -j 8 -parallel mpi -debug -arch ${FCM_ARCH} -driver ; )
			(...)
			driver_xios :
			(cd ../../modeles/ORCHIDEE ; ./makeorchidee_fcm -xios2 -j 8 -parallel mpi -debug -arch ${FCM_ARCH} -driver ; )
			(...)</pre>
			* Compiling:
			<pre>$ gmake >& run_gmake.log</pre>
			* Checking if everything went fine:
			<pre>$ cat -n run_gmake.log \| grep Error
			$ cat -n run_gmake.log \| grep undefined
			$ ls ../../bin/
			orchidee_ol xios_server.exe</pre>

Lluis.fita: /* Installation steps using modipsl */

2019-07-16T13:21:56Z

Installation steps using modipsl

← Revisión anterior		Revisión del 13:21 16 jul 2019
Línea 3:		Línea 3:
	= Installation steps using modipsl =		= Installation steps using modipsl =
	* Required packages:		* Required packages:
	<pre># apt-get install subversion git libnetcdf-dev libnetcdff-dev make ncview ksh csh mpi mpich vim		<pre># apt-get install subversion git libnetcdf-dev libnetcdff-dev make ncview ksh csh mpi mpich vim </pre>
	python-matplotlib python-matplotlib-data python-matplotlib-doc python-mpltoolkits.basemap		* Additional for python and netcdf (not required by ORCHIDEE)
			<pre># apt-get install python-matplotlib python-matplotlib-data python-matplotlib-doc python-mpltoolkits.basemap
	python-mpltoolkits.basemap-data dvipng python-netcdf4</pre>		python-mpltoolkits.basemap-data dvipng python-netcdf4</pre>
	* And fake gmake (Ubunutu)		* And fake gmake (Ubunutu)

Lluis.fita: /* Building & compiling */

2019-07-10T15:23:14Z

Building & compiling

← Revisión anterior		Revisión del 15:23 10 jul 2019
Línea 161:		Línea 161:

	== Building & compiling ==		== Building & compiling ==
	** Going back to <code>util</code> to proceed
	~~<pre>$ cd ../../../util</pre>~~
	** Installing the code:		** Installing the code:
	<pre>$ ./ins_make -t DCAO_gfortran >& run_ins_make.log</pre>		<pre>$ ./ins_make -t DCAO_gfortran >& run_ins_make.log</pre>

Lluis.fita: /* Installation steps using modipsl */

2019-07-10T15:22:25Z

Installation steps using modipsl

← Revisión anterior		Revisión del 15:22 10 jul 2019
Línea 70:		Línea 70:

	== XIOS ==		== XIOS ==
	** ~~going there:~~		** Creation of 'fcm' compilation environtment file for <code>DCAO_gfortran</code>
	<~~pre~~>~~$ cd ../modeles/XIOS/arch~~</~~pre~~>
	** Using generic gcc compilation as reference
	<pre>$ vim ../modeles/XIOS/arch/arch-DCAO_gfortran.fcm</pre>		<pre>$ vim ../modeles/XIOS/arch/arch-DCAO_gfortran.fcm</pre>
			** values:
	<pre>################################################################################		<pre>################################################################################
	################### Projet XIOS ###################		################### Projet XIOS ###################
Línea 98:		Línea 97:
	%FPP cpp -P		%FPP cpp -P
	%MAKE gmake</pre>		%MAKE gmake</pre>
	** ~~Getting paths:~~		** Creation of 'path' compilation environtment file for <code>DCAO_gfortran</code>
	<pre>$ cp arch~~-GCC_LINUX.path~~ arch-DCAO_gfortran.path</pre>		<pre>$ vim ../modeles/XIOS/arch/arch-DCAO_gfortran.path</pre>
	** ~~Adapting~~ values:		** values:
	<pre>NETCDF_INCDIR="-I $NETCDF_INC_DIR"		<pre>NETCDF_INCDIR="-I $NETCDF_INC_DIR"
	NETCDF_LIBDIR="-L $NETCDF_LIB_DIR"		NETCDF_LIBDIR="-L $NETCDF_LIB_DIR"
Línea 117:		Línea 116:
	#OASIS_LIB="-lpsmile.MPI1 -lscrip -lmct -lmpeu"</pre>		#OASIS_LIB="-lpsmile.MPI1 -lscrip -lmct -lmpeu"</pre>

	** ~~Getting environment:~~		** Creation of 'env' compilation environtment file for <code>DCAO_gfortran</code>
	<pre>$ cp arch~~-GCC_LINUX.env~~ arch-DCAO_gfortran.env</pre>		<pre>$ vim ../modeles/XIOS/arch/arch-DCAO_gfortran.env</pre>

	** ~~Adapting~~ values:		** values:
	<pre>export HDF5_INC_DIR=/usr/include		<pre>export HDF5_INC_DIR=/usr/include
	export HDF5_LIB_DIR=/usr/lib/x86_64-linux-gnu		export HDF5_LIB_DIR=/usr/lib/x86_64-linux-gnu
Línea 128:		Línea 127:

	== ORCHIDEE ==		== ORCHIDEE ==
	** ~~Going there~~		** Creation of 'fcm' compilation environtment file for <code>DCAO_gfortran</code>
	<pre>$ cd ../../ORCHIDEE/arch</~~pre>~~		<pre>$ vim ../modeles/ORCHIDEE/arch/arch-DCAO_gfortran.fcm</pre>
	** Using gfotran compilation as reference		** values:
	~~<pre>$ cp arch-gfortran.fcm~~ arch-DCAO_gfortran.fcm</pre>
	** ~~Adapting~~ values:
	<pre>%COMPILER /usr/bin/mpicc		<pre>%COMPILER /usr/bin/mpicc
	%LINK /usr/bin/mpif90		%LINK /usr/bin/mpif90
Línea 148:		Línea 145:
	%MPI_LD		%MPI_LD
	%OMP_LD -openmp</pre>		%OMP_LD -openmp</pre>
	** ~~getting paths~~		** Creation of 'path' compilation environtment file for <code>DCAO_gfortran</code>
	<pre>$ cp arch~~-gfortran.path~~ arch-DCAO_gfortran.path</pre>		<pre>$ vim ../modeles/ORCHIDEE/arch/arch-DCAO_gfortran.path</pre>
	** ~~Adapting~~ values:		** values:
	<pre>NETCDF_INCDIR="-I/usr/include"		<pre>NETCDF_INCDIR="-I/usr/include"
	NETCDF_LIBDIR="-L/usr/lib/x86_64-linux-gnu"		NETCDF_LIBDIR="-L/usr/lib/x86_64-linux-gnu"

Lluis.fita: /* Installation steps using modipsl */

2019-07-10T15:15:45Z

Installation steps using modipsl

← Revisión anterior		Revisión del 15:15 10 jul 2019
Línea 73:		Línea 73:
	<pre>$ cd ../modeles/XIOS/arch</pre>		<pre>$ cd ../modeles/XIOS/arch</pre>
	** Using generic gcc compilation as reference		** Using generic gcc compilation as reference
	<pre>$ cp arch~~-GCC_LINUX.fcm~~ arch-DCAO_gfortran.fcm</pre>		<pre>$ vim ../modeles/XIOS/arch/arch-DCAO_gfortran.fcm</pre>
	<pre>################################################################################		<pre>################################################################################
	################### Projet XIOS ###################		################### Projet XIOS ###################

Lluis.fita: /* Installation steps using modipsl */

2019-07-10T14:33:56Z

Installation steps using modipsl

← Revisión anterior		Revisión del 14:33 10 jul 2019
Línea 15:		Línea 15:
	<pre>$ cd modipsl/util</pre>		<pre>$ cd modipsl/util</pre>
	* Getting the off-line version of ORCHIDEE		* Getting the off-line version of ORCHIDEE
	<pre>$ ./model ORCHIDEE_trunk >& run_get_model.log</pre>		<!--pre>$ ./model ORCHIDEE_trunk >& run_get_model.log</pre-->
			<pre>$ ./model ORCHIDEE_trunk</pre>
	* We got some issues with the ports, thus, it needs to be manually done:		* We got some issues with the ports, thus, it needs to be manually done:
	<pre>$ cd ../modeles</pre>		<pre>$ cd ../modeles</pre>