[[PageOutline]]
Last edited [[Timestamp]]

[[BR]]

'''Author''' : S. Masson 

'''ticket''' : #974

'''Branch''' : [https://forge.ipsl.jussieu.fr/nemo/browser/branches/2012/dev_r3406_LOCEAN4_XIOS      ]  svn+ssh://rblod@forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/branches/2012/dev_r3406_LOCEAN4_XIOS
----

=== Description ===

This is a brand new code so old one (XMLF90 and XML_IOSERVER) can be removed.[[BR]]
XIOS imported from http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk (rev 348) and added under EXTERNAL with the following commands:
NOTE it was update to revision 353 on july 9

{{{
#!/bin/bash

prjname=nemo
userlog=rblod
forge=forge.ipsl.jussieu.fr

rootsrc=${userlog}@${forge}/ipsl/forge/projets/${prjname}/svn

#==========================
# create XIOS vendor
#==========================
#
vendor=XIOS
#
# get it:
svn export http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk XIOS_SRC
# stupid untar
cd XIOS_SRC
for tarname in tools/archive/*.tar.gz; do tar -xzf "$tarname"; done
rm -rf tools/archive/*
rm -rf tools/FCM
cd -

# import it in vendors
svn import XIOS_SRC svn+ssh://${rootsrc}/vendors/${vendor}/current -m "importing initial ${vendor} vendor drop"
revname=r_348
svn copy svn+ssh://${rootsrc}/vendors/${vendor}/current svn+ssh://${rootsrc}/vendors/${vendor}/${revname} -m "tagging ${vendor} ${revname}"
rm -rf XIOS_SRC
#

#==========================
# import in external
#==========================
#svn copy  svn+ssh://rblod@forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/vendors/XIOS_r348 svn+ssh://rblod@forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/branches/2012/dev_r3406_LOCEAN4_XIOS/NEMOGCM/EXTERNAL/XIOS -m "Import XIOS in dev_r3406_LOCEAN4_XIOS"
}}}

=== NEMO code changes ===

Very few, iom.F90 totally modified, nemogcm.F90 for init and finalize, diawri.F90 for new variables, step.F90 for iom_setkt, sbcmod.F90[[BR]]

svn diff OPA_SRC/step.F90 OPA_SRC/nemogcm.F90 OPA_SRC/SBC/sbcmod.F90 OPA_SRC/DIA/diawri.F90
{{{
Index: OPA_SRC/step.F90
===================================================================
--- OPA_SRC/step.F90	(revision 3410)
+++ OPA_SRC/step.F90	(working copy)
@@ -88,7 +88,7 @@
 #endif   
                              indic = 0                ! reset to no error condition
       IF( kstp /= nit000 )   CALL day( kstp )         ! Calendar (day was already called at nit000 in day_init)
-                             CALL iom_setkt( kstp )   ! say to iom that we are at time step kstp
+                             CALL iom_setkt( kstp - nit000 + 1 )   ! say to iom that we are at time step kstp
 
       !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
       ! Update data, open boundaries, surface boundary condition (including sea-ice)
Index: OPA_SRC/nemogcm.F90
===================================================================
--- OPA_SRC/nemogcm.F90	(revision 3410)
+++ OPA_SRC/nemogcm.F90	(working copy)
@@ -72,7 +72,7 @@
 #endif
    USE lib_mpp         ! distributed memory computing
 #if defined key_iomput
-   USE mod_ioclient
+   USE xios
 #endif
 
    IMPLICIT NONE
@@ -183,8 +183,13 @@
       CALL nemo_closefile
 #if defined key_oasis3 || defined key_oasis4
       CALL cpl_prism_finalize           ! end coupling and mpp communications with OASIS
-#else
+# if defined key_iomput
+      IF( Agrif_Root() ) THEN
+         CALL xios_finalize             ! end mpp communications
+      ENDIF
+# else
       IF( lk_mpp )   CALL mppstop       ! end mpp communications
+# endif
 #endif
       !
    END SUBROUTINE nemo_gcm
@@ -218,9 +223,11 @@
 #if defined key_iomput
       IF( Agrif_Root() ) THEN
 # if defined key_oasis3 || defined key_oasis4
-         CALL cpl_prism_init( ilocal_comm )                 ! nemo local communicator given by oasis
+         CALL cpl_prism_init( ilocal_comm )      ! nemo local communicator given by oasis
+         CALL xios_initialize( "oceanx",local_comm=ilocal_comm )
+# else
+         CALL  xios_initialize( "nemo",return_comm=ilocal_comm )
 # endif
-         CALL  init_ioclient( ilocal_comm )                 ! exchange io_server nemo local communicator with the io_server
       ENDIF
       narea = mynode( cltxt, numnam, nstop, ilocal_comm )   ! Nodes selection
 #else
Index: OPA_SRC/SBC/sbcmod.F90
===================================================================
--- OPA_SRC/SBC/sbcmod.F90	(revision 3410)
+++ OPA_SRC/SBC/sbcmod.F90	(working copy)
@@ -240,7 +240,7 @@
       !                                            !        forcing field computation         !
       !                                            ! ---------------------------------------- !
 
-      CALL iom_setkt( kt + nn_fsbc - 1 )                 ! in sbc, iom_put is called every nn_fsbc time step
+!      CALL iom_setkt( kt + nn_fsbc - 1 )                 ! in sbc, iom_put is called every nn_fsbc time step
       !
       IF( ln_apr_dyn ) CALL sbc_apr( kt )                ! atmospheric pressure provided at kt+0.5*nn_fsbc
                                                          ! (caution called before sbc_ssm)
@@ -343,7 +343,7 @@
          IF( nn_ice > 0 )   CALL iom_put( "ice_cover", fr_i )   ! ice fraction 
       ENDIF
       !
-      CALL iom_setkt( kt )           ! iom_put outside of sbc is called at every time step
+!      CALL iom_setkt( kt )           ! iom_put outside of sbc is called at every time step
       !
       CALL iom_put( "utau", utau )   ! i-wind stress   (stress can be updated at 
       CALL iom_put( "vtau", vtau )   ! j-wind stress    each time step in sea-ice)
Index: OPA_SRC/DIA/diawri.F90
===================================================================
--- OPA_SRC/DIA/diawri.F90	(revision 3410)
+++ OPA_SRC/DIA/diawri.F90	(working copy)
@@ -144,7 +144,9 @@
       CALL iom_put( "sss"    , tsn(:,:,1,jp_sal)                     )    ! sea surface salinity
       CALL iom_put( "sss2"   , tsn(:,:,1,jp_sal) * tsn(:,:,1,jp_sal) )    ! square of sea surface salinity
       CALL iom_put( "uoce"   , un                                    )    ! i-current      
+      CALL iom_put( "suoce"  , un(:,:,1)                             )    ! surface i-current      
       CALL iom_put( "voce"   , vn                                    )    ! j-current
+      CALL iom_put( "svoce"  , vn(:,:,1)                             )    ! surface j-current
       
       CALL iom_put( "avt"    , avt                                   )    ! T vert. eddy diff. coef.
       CALL iom_put( "avm"    , avmu                                  )    ! T vert. eddy visc. coef.

}}}

=== Compilation ===

The new code is located under EXTERNAL/XIOS. The old one has none been removed yet but is useless.[[BR]]
 * netcdf has to be version 4 build with hdf5 support (hdf5 installed too)
 * variables for XIOS have been added to arch files. For now, just ARCH/arch-X64_CURIE.fcm. I didn't try to mix options for NEMO and XIOS so there is duplication
 * XIOS is compiled to generate a library under XIOS/lib and a binary under XIOS/bin. So makenemo has few modifications, just 3 lines to before NEMO compilations. For this part -j option is forced to 1
 * TOOLS/COMPILE/bldxag.cfg has been modified to include correct path to XIOS
 * clean option doesn't include cleaning of XIOS, since it takes a while  
 * IOIPSL is still compiled because of sn4 stuff I didn't remove
Note it can't be compiled without key_mpp_mpi, also OASIS case is not treated correctly at compilation. I'm not sure this branch can be compiled with AGRIF or without key_iomput

=== Execution ===

 * file xmlio_server.def is not needed anymore, informations are now included at the end of iodef.xml
 * iodef.xml can be split into szveral files using include files, here we define domain.xml and field.xml wchi shouldn't need to be changed, unless we had a new variables or new zoom








----
=== Testing ===
Testing could consider (where appropriate) other configurations in addition to NVTK].

||NVTK Tested||!'''YES/NO!'''||
||Other model configurations||!'''YES/NO!'''||
||Processor configurations tested||[ Enter processor configs tested here ]||
||If adding new functionality please confirm that the [[BR]]New code doesn't change results when it is switched off [[BR]]and !''works!'' when switched on||!'''YES/NO/NA!'''||

(Answering UNSURE is likely to generate further questions from reviewers.)

'Please add further summary details here'

 * Processor configurations tested
 * etc----

=== Bit Comparability ===
||Does this change preserve answers in your tested standard configurations (to the last bit) ?||!'''YES/NO !'''||
||Does this change bit compare across various processor configurations. (1xM, Nx1 and MxN are recommended)||!'''YES/NO!'''||
||Is this change expected to preserve answers in all possible model configurations?||!'''YES/NO!'''||
||Is this change expected to preserve all diagnostics? [[BR]]!,,!''Preserving answers in model runs does not necessarily imply preserved diagnostics. !''||!'''YES/NO!'''||

If you answered !'''NO!''' to any of the above, please provide further details:

 * Which routine(s) are causing the difference?
 * Why the changes are not protected by a logical switch or new section-version
 * What is needed to achieve regression with the previous model release (e.g. a regression branch, hand-edits etc). If this is not possible, explain why not.
 * What do you expect to see occur in the test harness jobs?
 * Which diagnostics have you altered and why have they changed?Please add details here........

----
=== System Changes ===
||Does your change alter namelists?||!'''YES/NO !'''||
||Does your change require a change in compiler options?||!'''YES/NO !'''||

If any of these apply, please document the changes required here.......

----
=== Resources ===
!''Please !''summarize!'' any changes in runtime or memory use caused by this change......!''

----
=== IPR issues ===
||Has the code been wholly (100%) produced by NEMO developers staff working exclusively on NEMO?||!'''YES/ NO !'''||

If No:

 * Identify the collaboration agreement details
 * Ensure the code routine header is in accordance with the agreement, (Copyright/Redistribution etc).Add further details here if required..........