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' for ', [2]) +('Computing ', 'season average, son', ' for ', 'f11vmr', ' for ', [2]) +('Computing ', 'season average, son', ' for ', 'date', ' for ', [2]) +('Computing ', 'season average, son', ' for ', 'ndcur', ' for ', [2]) +('Computing ', 'season average, son', ' for ', 'co2vmr', ' for ', [2]) +('Computing ', 'season average, son', ' for ', 'ch4vmr', ' for ', [2]) +('Computing ', 'season average, son', ' for ', 'sol_tsi', ' for ', [2]) +('Computing ', 'season average, son', ' for ', 'PRECC', ' for ', [2]) +('Computing ', 'season average, son', ' for ', 'CLDLIQ', ' for ', [2]) +============================================== +COMPLETED SUCCESSFULLY +{'Total Time': 22.741004943847656, 'Define history dictionary': 0.19109296798706055, 'Send Average Time': 0.7136764526367188, 'Create/Define Netcdf File': 0.9775071144104004, 'Write Netcdf Averages': 1.9073071479797363, 'Recv Average Time': 0.0, 'Variable fetch time': 17.824787616729736, 'Time to compute Average': 19.71603798866272} +============================================== diff --git a/averager/pp_tests/runAvg_mpi_atm.sh b/averager/pp_tests/runAvg_mpi_atm.sh new file mode 100755 index 00000000..46776c91 --- /dev/null +++ b/averager/pp_tests/runAvg_mpi_atm.sh @@ -0,0 +1,68 @@ +#!/bin/bash + +#PBS -N atm_averages +#PBS -q regular +#PBS -l select=2:ncpus=9:mpiprocs=9 +#PBS -l walltime=00:05:00 +#PBS -A P93300606 + +source /etc/profile.d/modules.sh + +export MPI_UNBUFFERED_STDIO=true +export TMPDIR=$TMPDIR + + +########## +## +## See https://github.com/NCAR/CESM_postprocessing/wiki for details +## regarding settings for optimal performance for CESM postprocessing tools. +## +########## + +if [ ! -e /gpfs/fs1/work/aliceb/sandboxes/dev/postprocessing_new/cesm-env2/bin ]; then + echo "*************************************************************************************" + echo "CESM atm_averages exiting due to non-existant python virtual environment in" + echo " /gpfs/fs1/work/aliceb/sandboxes/dev/postprocessing_new/cesm-env2/bin" + echo "You must first run:" + echo "$POSTPROCESS_PATH/create_python_env -machine [machine]" + echo "*************************************************************************************" + exit +fi + + +module purge + + + + +## activate the virtualenv that contains all the non-bootstrapped dependencies + +cd /gpfs/fs1/work/aliceb/sandboxes/dev/postprocessing_new/cesm-env2/bin +echo "Running from virtualenv directory:" +pwd +. activate + +## load the boot-strap modules + + +module load python/2.7.14 + +module load intel/17.0.1 + +module load ncarenv + +module load ncarcompilers + +module load mpt/2.15f + +module load netcdf/4.6.1 + +module load nco/4.7.4 + +module load ncl/6.4.0 + +export POSTPROCESS_PATH=/gpfs/fs1/work/aliceb/sandboxes/dev/postprocessing_new + +mpiexec_mpt dplace -s 1 /gpfs/fs1/work/aliceb/sandboxes/dev/postprocessing_new/averager/pp_tests/test_atm_series.py >> /gpfs/fs1/work/aliceb/sandboxes/dev/postprocessing_new/averager/pp_tests/atm_series.log 2>&1 + + diff --git a/averager/pp_tests/test_atm_series.py b/averager/pp_tests/test_atm_series.py new file mode 100755 index 00000000..4c5e7126 --- /dev/null +++ b/averager/pp_tests/test_atm_series.py @@ -0,0 +1,74 @@ +#!/usr/bin/env python2 + +from __future__ import print_function +import sys + +# check the system python version and require 2.7.x or greater +if sys.hexversion < 0x02070000: + print(70 * '*') + print('ERROR: {0} requires python >= 2.7.x. '.format(sys.argv[0])) + print('It appears that you are running python {0}'.format( + '.'.join(str(x) for x in sys.version_info[0:3]))) + print(70 * '*') + sys.exit(1) + +import os + +# +# check the POSTPROCESS_PATH which must be set +# +try: + os.environ["POSTPROCESS_PATH"] +except KeyError: + err_msg = ('create_postprocess ERROR: please set the POSTPROCESS_PATH environment variable.' \ + ' For example on yellowstone: setenv POSTPROCESS_PATH /glade/p/cesm/postprocessing') + raise OSError(err_msg) + +cesm_pp_path = os.environ["POSTPROCESS_PATH"] + +# +# activate the virtual environment that was created by create_python_env +# +if not os.path.isfile('{0}/cesm-env2/bin/activate_this.py'.format(cesm_pp_path)): + err_msg = ('create_postprocess ERROR: the virtual environment cesm-env2 does not exist.' \ + ' Please run $POSTPROCESS_PATH/create_python_env -machine [machine name]') + raise OSError(err_msg) + +execfile('{0}/cesm-env2/bin/activate_this.py'.format(cesm_pp_path), dict(__file__='{0}/cesm-env2/bin/activate_this.py'.format(cesm_pp_path))) + +from pyaverager import PyAverager, specification + +#### User modify #### + +in_dir='/glade/scratch/aliceb/F1850C5_f02_cntrl/atm//proc/tseries/month_1' +out_dir= '/glade/scratch/aliceb/F1850C5_f02_cntrl/atm/proc/climo/F1850C5_f02_cntrl//F1850C5_f02_cntrl.2-5' +pref= 'F1850C5_f02_cntrl.cam.h0' +htype= 'series' +average = ['dep_ann:2:5', 'dep_djf:2:5', 'dep_mam:2:5', 'dep_jja:2:5', 'dep_son:2:5', 'jan:2:5', 'feb:2:5', 'mar:2:5', 'apr:2:5', 'may:2:5', 'jun:2:5', 'jul:2:5', 'aug:2:5', 'sep:2:5', 'oct:2:5', 'nov:2:5', 'dec:2:5'] +collapse_dim = 'lon' +wght= False +ncfrmt = 'netcdfLarge' +serial=False +suffix = 'nc' +clobber = True +date_pattern= 'yyyymm-yyyymm' +var_list = ['CLDLIQ', 'PRECC', 'T', 'TS'] + +#### End user modify #### + +pyAveSpecifier = specification.create_specifier(in_directory=in_dir, + out_directory=out_dir, + prefix=pref, + suffix=suffix, + date_pattern=date_pattern, + hist_type=htype, + avg_list=average, + varlist=var_list, + collapse_dim=collapse_dim, + weighted=wght, + ncformat=ncfrmt, + serial=serial, + clobber=clobber) + +PyAverager.run_pyAverager(pyAveSpecifier) + diff --git a/create_python_env b/create_python_env index c4033164..1ce47ce3 100755 --- a/create_python_env +++ b/create_python_env @@ -15,7 +15,7 @@ function Usage { echo "" echo " This script sets up the python virtual environment (env) for a given supported machine." echo " This script executes the following steps:" - echo " - loads the python modules for this machine necessary to boot-strap the env" + echo " - clones the NCAR Python Library (NPL) for this machine necessary to boot-strap the env" echo " - make env" echo " - activate env" echo " - install post-processing tools into the env" @@ -152,23 +152,15 @@ and rerun this script." exit 0 fi +#---------------------------------------------------------------------- +# install the external tools via the manage_externals/checkout_externals +#---------------------------------------------------------------------- +./manage_externals/checkout_externals + curdir=`pwd` echo $curdir cd $pp_dir -#---------------------------------------------------------------------- -# create the virtual environment. Makefile checks to see if it is -# already setup, so only done once per case. -#---------------------------------------------------------------------- -##echo "$progname - making virtual environment in ${pp_dir}/cesm-env2." -##if [ ${machine} != geyser ]; then -## make env -## if [ $? -ne 0 ]; then -## echo "ERROR: Unable to create virtual environment in ${pp_dir}/cesm-env2. Exiting..." -## exit 1 -## fi -##fi - #---------------------------------------------------------------------- # activate virtualenv for remainder of this script #---------------------------------------------------------------------- diff --git a/diagnostics/diagnostics/ocn/Plots/ecosystem_maps.py b/diagnostics/diagnostics/ocn/Plots/ecosystem_maps.py index de81c465..8faf6e9f 100755 --- a/diagnostics/diagnostics/ocn/Plots/ecosystem_maps.py +++ b/diagnostics/diagnostics/ocn/Plots/ecosystem_maps.py @@ -203,7 +203,7 @@ def __init__(self): self._columns_s2 = [3] self._columns_s3 = [6] - self._columnns = [ self._columns_s1, self._columns_s2, self._columns_s3 ] + self._columns = [ self._columns_s1, self._columns_s2, self._columns_s3 ] self._plotTitles = ['Ecosystem: Maps', 'Ecosystem: Maps at Depth (with obs where applicable)'] self._labels = ['NO3','PO4','SiO3','O2','DIC','ALK','Fe'] diff --git a/diagnostics/diagnostics/ocn/ocn_diags_generator.py b/diagnostics/diagnostics/ocn/ocn_diags_generator.py index 4c873d5f..95e805d5 100755 --- a/diagnostics/diagnostics/ocn/ocn_diags_generator.py +++ b/diagnostics/diagnostics/ocn/ocn_diags_generator.py @@ -109,7 +109,7 @@ def setup_diags(envDict): diag_dict = dict() # ocean bgc being computed by IOMB ## avail_diags = ['MODEL_VS_OBS', 'MODEL_VS_OBS_ECOSYS', 'MODEL_VS_CONTROL', 'MODEL_VS_CONTROL_ECOSYS', 'MODEL_TIMESERIES', 'MODEL_TIMESERIES_ECOSYS'] - avail_diags = ['MODEL_VS_OBS', 'MODEL_VS_CONTROL', 'MODEL_TIMESERIES'] + avail_diags = ['MODEL_VS_OBS', 'MODEL_VS_OBS_ECOSYS', 'MODEL_VS_CONTROL', 'MODEL_TIMESERIES'] for diag in avail_diags: diag_dict[diag] = False for key, value in envDict.iteritems(): diff --git a/ocn_diag/eco_lib/makefile b/ocn_diag/eco_lib/makefile index 8a2af49e..abce0460 100644 --- a/ocn_diag/eco_lib/makefile +++ b/ocn_diag/eco_lib/makefile @@ -1,7 +1,7 @@ all: remap remap: - f2py -c --fcompiler=gfortran --f77exec=/usr/bin/gfortran -m remap remap.f + f2py -c --fcompiler=intelem -m remap remap.f clean: rm -r *.so