Merge branch 'feature/trunk/testing' into 'trunk2master' :

small changes in testing to compile xios with same env file than dynamico 
port testing from jean-zay to irene

arch/arch-X64_IRENE.env

@@ -2,11 +2,12 @@
 # module feature/openmpi/mpi_compiler/intel is made necessary by c++/gnu
 
 module purge
+module load flavor/buildcompiler/intel/17
 module load feature/openmpi/mpi_compiler/intel
 module load c++/gnu/7.3.0
 module load intel/17.0.6.256
 module load mpi/openmpi/2.0.4
 module load flavor/hdf5/parallel
+module load hdf5/1.8.20
 module load netcdf-fortran/4.4.4
 module load mkl/17.0.6.256
-module load hdf5/1.8.20

param_sets/dcmip2012/run21.def

@@ -92,6 +92,9 @@ write_period = 50000
 # Scale factor for small planet experiment : real (default=1.)
 scale_factor = 500
 
+# Time style : [none|dcmip] (default=dcmip)
+time_style = dcmip
+
 # Initial state : 
 #   [jablonowsky06|academic|dcmip[1-4]|heldsz|dcmip2_schaer_noshear] (default=jablonowsky06)
 etat0 = dcmip2_schaer_noshear

param_sets/dcmip2012/run3.def

@@ -81,10 +81,10 @@ niterdivgrad = 2
 #---------------- Time ----------------
 
 # Run length in s : real (default=??)
-run_length = 4.5e5
+run_length = 3600
 
 # Interval in s between two outputs : integer (default=??)
-write_period = 12500
+write_period = 7500
 
 
 #---------------- Physical parameters ----------------
@@ -92,6 +92,9 @@ write_period = 12500
 # Scale factor for small planet experiment : real (default=1.)
 scale_factor = 125
 
+# Time style : [none|dcmip] (default=dcmip)
+time_style = dcmip
+
 # Initial state : 
 #   [jablonowsky06|academic|dcmip[1-4]|heldsz|dcmip2_schaer_noshear] (default=jablonowsky06)
 etat0 = dcmip3

param_sets/dcmip2012/run41.def

@@ -25,19 +25,19 @@ nsplit_j = 1
 dt = 600
 
 # Dissipation time for grad(div) : real (default=5000)
-tau_graddiv = 9000
+tau_graddiv = 21600
 
 # Exponent of grad(div) disspation : integer (default=1)
 nitergdiv = 2
 
 # Dissipation time for curl(curl) : real (default=5000)
-tau_gradrot = 9000
+tau_gradrot = 50000
 
 # Exponent of curl(curl) disspation : integer (default=1)
 nitergrot = 2
 
 # Dissipation time for div(grad) : real (default=5000)
-tau_divgrad = 9000
+tau_divgrad = 50000
 
 # Exponent of div(grad) disspation : integer (default=1)
 niterdivgrad = 2
@@ -63,3 +63,4 @@ etat0 = dcmip4
 
 # DCMIP 4 Test case : [1|2] (default=1)
 dcmip4_testcase = 1
+

param_sets/dcmip2012/run42.def

@@ -3,7 +3,7 @@ INCLUDEDEF = const.def
 #---------------- Mesh ----------------
 
 # Number of subdivisions on a main triangle : integer (default=40)
-nbp = 80
+nbp = 32
 
 # Number of vertical layers : integer (default=19)
 llm = 30
@@ -15,29 +15,29 @@ disvert = ncarl30
 optim_it = 100
 
 # Sub splitting of main rhombus : integer (default=1)
-nsplit_i = 2
-nsplit_j = 2
+nsplit_i = 1
+nsplit_j = 1
 
 
 #---------------- Numerics ----------------
 
 # Time step in s : real (default=480)
-dt = 240
+dt = 600
 
 # Dissipation time for grad(div) : real (default=5000)
-tau_graddiv = 9000
+tau_graddiv = 21600
 
 # Exponent of grad(div) disspation : integer (default=1)
 nitergdiv = 2
 
 # Dissipation time for curl(curl) : real (default=5000)
-tau_gradrot = 9000
+tau_gradrot = 50000
 
 # Exponent of curl(curl) disspation : integer (default=1)
 nitergrot = 2
 
 # Dissipation time for div(grad) : real (default=5000)
-tau_divgrad = 9000
+tau_divgrad = 50000
 
 # Exponent of div(grad) disspation : integer (default=1)
 niterdivgrad = 2
@@ -46,7 +46,7 @@ niterdivgrad = 2
 #---------------- Time ----------------
 
 # Run length in s : real (default=??)
-run_length = 3.6e6
+run_length = 864000
 
 # Interval in s between two outputs : integer (default=??)
 write_period = 21600

param_sets/make_rundefs.sh

@@ -219,7 +219,7 @@ function dcmip21
     group 'Numerics' time_step 300
     dissip64
     group 'Time' run_length 3.6e6 write_period 50000
-    group 'Physical parameters' scale_factor 500  etat0 dcmip2_schaer_noshear rayleigh_friction_tau 12500 rayleigh_friction_type dcmip2_schaer_noshear
+    group 'Physical parameters' scale_factor 500 time_style dcmip etat0 dcmip2_schaer_noshear rayleigh_friction_tau 12500 rayleigh_friction_type dcmip2_schaer_noshear
 }
 
 function dcmip3
@@ -228,8 +228,8 @@ function dcmip3
     group 'Mesh' nbp 80 llm 10 disvert ncar ncar_dz 1000 optim_it 100 ; split 2 2
     group 'Numerics' time_step 240
     dissip80
-    group 'Time' run_length 4.5e5 write_period 12500
-    group 'Physical parameters' scale_factor 125 etat0 dcmip3
+    group 'Time' run_length 3600 write_period 7500
+    group 'Physical parameters' scale_factor 125 time_style dcmip etat0 dcmip3
 }
 
 # Next DCMIP test cases have rotation
@@ -237,10 +237,10 @@ function dcmip3
 function dcmip4x
 {
     echo 'INCLUDEDEF = const.def'
-    group 'Mesh' nbp 80 llm 30 disvert ncarl30 optim_it 100 ; split 2 2
-    group 'Numerics' time_step 240
-    dissip80
-    group 'Time' run_length 3.6e6 write_period 21600
+    group 'Mesh' nbp 32 llm 30 disvert ncarl30 optim_it 100 ; split 1 1
+    group 'Numerics' time_step 600
+    dissip32
+    group 'Time' run_length 864000 write_period 21600
     group 'Physical parameters' nqtot 2 etat0 dcmip4 dcmip4_testcase $1
 }
 
@@ -266,7 +266,8 @@ function mkcd { cd $ROOT ; mkdir -p $1 ; cd $1
 }
 
 set -o errexit
-ROOT=$PWD
+ROOT=$(dirname $0)
+ROOT=$(cd -P $ROOT ; pwd)
 
 mkcd climate/Held_Suarez
 held_suarez > run.def

src/dcmip/dcmip_initial_conditions_test_1_2_3_v5.f90

@@ -139,7 +139,7 @@ IMPLICIT NONE
       real(rstd) :: height							! The height of the model levels
       real(rstd) :: ptop							! Model top in p
       real(rstd) :: sin_tmp, cos_tmp, sin_tmp2, cos_tmp2			! Calculate great circle distances
-      real(rstd) :: d1, d2, r, r2					! For tracer calculations 
+      real(rstd) :: d1, d2, r, r2, d3, d4					! For tracer calculations 
       real(rstd) :: s, bs							! Shape function, and parameter
       real(rstd) :: lonp							! Translational longitude, depends on time
       real(rstd) :: ud							! Divergent part of u
@@ -1235,7 +1235,7 @@ IMPLICIT NONE
 			    	Peq     = 100000.d0,		&	! Reference PS at Equator
                             	ztop    = 10000.d0,		&	! Model Top       
 				lambdac = 2.d0*pi/3.d0, 	& 	! Lon of Pert Center
-				d       = 5000.d0, 		& 	! Width for Pert
+				d       = 625000.d0, 		& 	! Width for Pert for X=1
 				phic    = 0.d0,	 		& 	! Lat of Pert Center
 				delta_theta = 1.d0, 		& 	! Max Amplitude of Pert
 				Lz      = 20000.d0, 		& 	! Vertical Wavelength of Pert
@@ -1332,7 +1332,7 @@ IMPLICIT NONE
 
 	r  = as * ACOS (sin_tmp + cos_tmp*cos(lon-lambdac)) 
 
-	s = (d**2)/(d**2 + r**2)
+	s = ((d/X)**2)/((d/X)**2 + r**2)
 
 	theta_pert = delta_theta*s*sin(2.d0*pi*height/Lz)
 

test/bash/arch-X64_IRENE.sh

+#!/bin/bash
+
+# This script provides site-specific functions
+# called by the site-independent scripts
+# create_runs.sh and submit.sh
+
+# NB : we must use the queue 'normal' because there seems to be a limit
+# on the number of jobs that can be submitted to queue 'test'
+
+#----------------------------- split_XXX ----------------------------
+
+function split_mpi_32() {
+    setvar nbp 32 nsplit_i 2 nsplit_j 4
+}
+function split_serial_40() {
+    setvar nbp 40 nsplit_i 2 nsplit_j 2
+}
+function split_mpi_40() {
+    setvar nbp 40 nsplit_i 2 nsplit_j 2
+}
+function split_mpi_80() {
+    setvar nbp 80 nsplit_i 4 nsplit_j 2
+}
+function split_mpi_omp_40() {
+    setvar nbp 40 nsplit_i 2 nsplit_j 2 omp_level_size 4
+}
+
+#----------------- job submission ------------------
+
+function submit_job_X64_IRENE() # $1=script $* = SLURM OPTIONS
+{
+    TMP=$(mktemp)
+    ccc_msub $1 > $TMP
+    cat $TMP 1>&2
+    cat $TMP | awk '{print $NF }'
+    rm -f $TMP
+}
+
+#------------------------------ job_XXX -----------------------------
+
+# Serial jobs
+function job_serial() { # EXP_NAME
+    job_X64_IRENE $1 1 1 "./gcm.exe"
+}
+function job_serial_40() { # EXP_NAME
+    job_serial $1
+}
+
+# MPI jobs
+function job_mpi() { #EXP_NAME NB_MPI
+    job_X64_IRENE $1 $2 1 "ccc_mprun ./gcm.exe"
+}
+function job_mpi_32() { # EXP_NAME
+    job_mpi $1 80
+}
+function job_mpi_40() { # EXP_NAME
+    job_mpi $1 40
+}
+function job_mpi_80() { # EXP_NAME
+    job_mpi $1 80
+}
+
+# MPI-OMP jobs
+function job_mpi_omp() { #EXP_NAME NB_MPI NB_OMP
+    job_X64_IRENE $1 $2 $3 "ccc_mprun ./gcm.exe"
+}
+function job_mpi_omp_40() { # EXP_NAME
+    job_mpi_omp $1 40 4
+}
+
+# Generic
+function job_X64_IRENE() { # EXP_NAME MPI_TASKS OMP_TASKS MPIRUN
+    cat <<EOF
+#!/bin/bash
+## Request name
+#MSUB -r $1
+## Number of tasks (=MPI processes) to use
+#MSUB -n $2
+## Number of OpenMP threads
+#MSUB -c $3
+## Elapsed time limit in seconds
+#MSUB -T 300
+# account, partition (Xeon/KNL)
+#MSUB -A $project
+#MSUB -q skylake
+# Mount $WORK on compute node
+#MSUB -m work
+## Quality of Service required (long [3 days], normal [1 day], test [30 min])
+#MSUB -Q normal
+
+export OMP_NUM_THREADS=$3
+export OMP_STACKSIZE=128M
+ulimit -s unlimited
+
+cd \${BRIDGE_MSUB_PWD} 
+
+$(cat $ROOT/DYNAMICO/arch/arch-X64_IRENE.env)
+module list
+
+rm -rf gcm.log logs *.nc netcdf
+date > gcm.log
+ulimit -s unlimited
+$4 >> gcm.log
+date >> gcm.log
+
+mkdir -p netcdf
+cp gcm.log *.def netcdf
+mv *.nc netcdf
+
+mkdir -p logs
+cp *.xml logs
+cp -pr $(readlink -e gcm.exe) logs
+cp -pr $(readlink -e build/src) logs
+mv xios_client_*.err xios_client_*.out gcm.log logs
+
+EOF
+}
+
+#------------------------------ post-processing job -----------------------------
+
+function job_post_X64_IRENE() # LIST
+{
+    DEPLIST=afterany
+    for ID in $* ; do
+	DEPLIST="$DEPLIST:$ID"
+    done
+    cat <<EOF
+#!/bin/bash
+## Request name
+#MSUB -r testing
+#MSUB -n 1
+## Elapsed time limit in seconds
+#MSUB -T 600
+#MSUB -q standard 
+#MSUB -A $project
+#MSUB -q skylake
+#MSUB -m work
+#MSUB -E "--dependency=$DEPLIST"
+## Number of tasks (=MPI processes) to use
+## Quality of Service required (long [3 days], normal [1 day], test [30 min])
+#MSUB -Q normal
+
+export OMP_NUM_THREADS=1
+# this script is submitted from $ROOT/logs
+cd \${BRIDGE_MSUB_PWD}/..
+
+$(cat $ROOT/DYNAMICO/arch/arch-X64_IRENE.env)
+module load python
+
+bash/post.sh
+EOF
+}

test/bash/arch-X64_JEANZAY.sh

@@ -10,19 +10,19 @@
 #----------------------------- split_XXX ----------------------------
 
 function split_mpi_32() {
-    setvar nbp 33 nsplit_i 2 nsplit_j 4
+    setvar nbp 32 nsplit_i 2 nsplit_j 4
 }
 function split_serial_40() {
-    setvar nbp 41 nsplit_i 2 nsplit_j 2
+    setvar nbp 40 nsplit_i 2 nsplit_j 2
 }
 function split_mpi_40() {
-    setvar nbp 41 nsplit_i 2 nsplit_j 2
+    setvar nbp 40 nsplit_i 2 nsplit_j 2
 }
 function split_mpi_80() {
-    setvar nbp 81 nsplit_i 4 nsplit_j 2
+    setvar nbp 80 nsplit_i 4 nsplit_j 2
 }
 function split_mpi_omp_40() {
-    setvar nbp 41 nsplit_i 2 nsplit_j 2 omp_level_size 4
+    setvar nbp 40 nsplit_i 2 nsplit_j 2 omp_level_size 4
 }
 
 #----------------- job submission ------------------
@@ -79,8 +79,6 @@ function job_X64_JEANZAY() { # EXP_NAME MPI_TASKS OMP_TASKS MPIRUN
 ## Number of OpenMP threads
 #SBATCH --cpus-per-task=$3
 
-## computing project
-#SBATCH -A wuu@cpu
 ## QoS for short jobs
 #SBATCH --qos=qos_cpu-dev
 ## Elapsed time limit HH:MM:SS

test/bash/build.sh

@@ -28,12 +28,14 @@ function build_xios()
     LOGFILE=$1 ; shift
     echo '# command used to build XIOS :' >> logs/build.sh
     echo "./make_xios $*" >> logs/build.sh
-    
+
+    ln -s $ROOT/DYNAMICO/arch/arch-${arch}.env $ROOT/.
+
     cd -P $ROOT/XIOS
     echo "In $PWD : Building XIOS"
     echo "To watch build progress : tail -f $LOGFILE"
     echo "./make_xios $*"
-    ./make_xios $* > $LOGFILE 2>&1
+    ./make_xios $* --full --arch_path $ROOT > $LOGFILE 2>&1
 }
 
 function main()

test/bash/create_runs.sh

@@ -118,7 +118,7 @@ function rundef_DCMIP21() { # NBP TAU
     setvar dysl_caldyn_vert .TRUE. caldyn_vert conservative
     setvar omega 0. llm 60 disvert ncar ncar_T0 300 ncar_p0 1e5 ncar_disvert_c 1 ncar_dz 500 
     setvar tau_graddiv $TAU tau_gradrot $TAU tau_divgrad $TAU 
-    setvar scale_factor 500 write_period 50000 run_length 1.8e6 etat0 dcmip2_schaer_noshear
+    setvar scale_factor 500 time_style dcmip write_period 50000 run_length 1.8e6 etat0 dcmip2_schaer_noshear
     setvar rayleigh_friction_type dcmip2_schaer_noshear rayleigh_friction_tau 12500
 }
 
@@ -128,7 +128,7 @@ function rundef_DCMIP31() { # NBP TAU HYDRO
     setvar dysl .TRUE. hydrostatic $3
     setvar omega 0. llm 10 disvert ncar ncar_T0 300 ncar_p0 1e5 ncar_disvert_c 1 ncar_dz 1118
     setvar tau_graddiv $TAU tau_gradrot $TAU tau_divgrad $TAU 
-    setvar scale_factor 125 write_period 7500 run_length 4.5e5 etat0 dcmip3
+    setvar scale_factor 125 time_style dcmip write_period 7500 run_length 3600 etat0 dcmip3
 }
 
 function rundef_DCMIP41() { # NBP TAU
@@ -173,7 +173,7 @@ function rundef_bubble() { # NBP TAU
     setvar llm 50 disvert ncar ncar_dz 20 ncar_T0 300 ncar_p0 1e5
 #    setvar time_scheme ARK2.3
     setvar nitergdiv 2 nitergrot 2 niterdivgrad 2 tau_graddiv $TAU tau_gradrot $TAU tau_divgrad $TAU
-    setvar radius 5e6 scale_factor 10000  g 9.80616 kappa 0.2857143 cpp 1004.5 preff 1e5 omega 0.
+    setvar radius 5e6 scale_factor 10000 time_style dcmip g 9.80616 kappa 0.2857143 cpp 1004.5 preff 1e5 omega 0.
 }
 function job_bubble() { # EXEC NBP
     job_$1_$2 Bubble_$1
@@ -238,7 +238,7 @@ function main()
 {
 # the number associated to each run.def parameter is used to sort the lines and order them in a logical way
     declare -A idx
-    order 100 radius omega g cpp kappa preff scale_factor
+    order 100 radius omega g cpp kappa preff scale_factor time_style
     order 200 boussinesq hydrostatic
     order 300 nbp optim_it nsplit_i nsplit_j llm omp_level_size disvert ncar_disvert_c ncar_dz ncar_T0 ncar_p0
     order 400 caldyn_eta time_scheme caldyn_conserv dt nqtot itau_adv dysl dysl_caldyn_vert caldyn_vert