lots of changes. installed on grace. yet to be tested

abishekg7 · Jul 24, 2021 · 2b27cdb · 2b27cdb
1 parent 83f0f4a
commit 2b27cdb
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Showing 6 changed files with 51 additions and 39 deletions.
diff --git a/Externals.cfg b/Externals.cfg
@@ -29,7 +29,7 @@ required = True
 [ilamb]
 tag = v2.3
 protocol = git
-repo_url = https://bitbucket.org/ncollier/ilamb
+repo_url = https://github.com/rubisco-sfa/ILAMB
 local_path = ilamb/ilamb
 required = True
 

diff --git a/Machines/grace_modules b/Machines/grace_modules
@@ -4,16 +4,21 @@ echo "Loading modules for CESM_postprocessing tool..."
 
 
 ml purge
-export MODULEPATH=/scratch/group/ihesp/software/easybuild/eb/x86_64/mods/all/Core
-ml intel/2019b
-ml NCO
-ml NCL
+export MODULEPATH=/ihesp/software/easybuild/eb/x86_64/mods/all/Core
+ml intel/2020b
+#ml NCO
+#ml NCL
 ml ANTLR
 ml HDF5
+ml netCDF
+ml GSL
+ml UDUNITS
+ml GEOS
+ml PROJ
 #ml NCL/6.6.2
 #ml NCO/4.7.9
 #ml netCDF/4.6.1
-ml Python/2.7.16
+ml Python/2.7.18
 
 #export NCARG_ROOT=/scratch/group/ihesp/software/share/ncl-6.6.2
 #export NCO_PATH=/scratch/group/ihesp/software/share/nco-4.9.4/nco-4.9.7

diff --git a/Machines/machine_postprocess.xml b/Machines/machine_postprocess.xml
@@ -8,29 +8,28 @@
     <ocn_remap_pes  queue="long" nodes="1" pes_per_node="3" wallclock="6:00" memory="18000">3</ocn_remap_pes>
     <mpi_command>mpirun</mpi_command>
     <pythonpath></pythonpath>
-    <f2py fcompiler="gfortran" f77exec="/sw/eb/sw/GCCcore/8.3.0/bin/gfortran">f2py</f2py>
+    <f2py fcompiler="mpiifort" f77exec="mpiifort">f2py</f2py>
     <za>
-      <compiler>gfortran</compiler>
+      <compiler>mpiifort</compiler>
       <flags>-c -g -O2</flags>
-      <include>-I/scratch/group/ihesp/software/share/netcdf-c-4.7.4/install2019b_2/include -I/scratch/group/ihesp/software/share/netcdf-fortran-4.5.3/install2019b_2/include</include>
-      <libs>-L/scratch/group/ihesp/software/share/netcdf-c-4.7.4/install2019b_2/lib -L/scratch/group/ihesp/software/share/netcdf-fortran-4.5.3/install2019b_2/lib -lnetcdff -L/sw/eb/sw/GCCcore/8.3.0/lib64 -L/sw/eb/sw/GCCcore/8.3.0/lib -L/sw/eb/sw/OpenBLAS/0.3.7-GCC-8.3.0/lib -L/sw/eb/sw/ScaLAPACK/2.0.2-gompi-2019b/lib64 -L/sw/eb/sw/FFTW/3.3.8-intel-2019b/lib -lnetcdf -lm -lpthread</libs>
+      <include>-I/sw/eb/sw/netCDF/4.7.4-iimpi-2020b/include -I/sw/eb/sw/netCDF-Fortran/4.5.3-iimpi-2020b/include</include>
+      <libs>-L/sw/eb/sw/netCDF/4.7.4-iimpi-2020b/lib -L/sw/eb/sw/netCDF-Fortran/4.5.3-iimpi-2020b/lib -lnetcdff -L/sw/eb/sw/GCCcore/10.2.0/lib64 -L/sw/eb/sw/iccifort/2020.4.304/compilers_and_libraries_2020.4.304/linux/lib -L/sw/eb/sw/iccifort/2020.4.304/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64 -L/sw/eb/sw/FFTW/3.3.8-intel-2020b/lib -lnetcdf -lm -lpthread</libs>
     </za>
     <reset_modules>
       <module>module purge</module>
     </reset_modules>
     <modules>
-      <module>module load intel/2019b</module>
-      <module>module load ANTLR</module>
-      <module>module load HDF5</module>
-      <module>module load GSL/2.6</module>
-      <module>module load Python/2.7.16</module>
-      <module>export NCARG_ROOT=/scratch/group/ihesp/software/share/ncl-6.6.2</module>
-      <module>export NCO_PATH=/scratch/group/ihesp/software/share/nco-4.9.4/nco-4.9.7/install</module>
-      <module>export NETCDF4_PATH=/scratch/group/ihesp/software/share/netcdf-c-4.7.4/install2019b_2</module>
-      <module>export NETCDFF_PATH=/scratch/group/ihesp/software/share/netcdf-fortran-4.5.3/install2019b_2</module>
+      <module>module load intel/2020b</module>
+      <module>module load NCL</module>
+      <module>module load NCO</module>
+      <module>module load Python/2.7.18</module>
+<!--      <module>export NCARG_ROOT=$EBROOTNCL</module>
+      <module>export NCO_PATH=$EBROOTNCO</module>
+      <module>export NETCDF4_PATH=$EBROOTNETCDF</module>
+      <module>export NETCDFF_PATH=$EBROOTNETCDFMINFORTRAN</module>
       <module>export LD_LIBRARY_PATH=$NCARG_ROOT/lib:$NCO_PATH/lib:$NETCDF4_PATH/lib:$NETCDFF_PATH/lib:$LD_LIBRARY_PATH</module>
-      <module>export PATH=$NCARG_ROOT/bin:$NCO_PATH/bin:$NETCDF4_PATH/bin:$NETCDFF_PATH/bin:$PATH</module>
-      <module>export PYTHONPATH=/scratch/group/iheso/software/CESM_postprocessing/cesm-env2/lib/python2.7/site-packages/PyNIO:$PYTHONPATH</module>
+      <module>export PATH=$NCARG_ROOT/bin:$NCO_PATH/bin:$NETCDF4_PATH/bin:$NETCDFF_PATH/bin:$PATH</module>-->
+      <module>export PYTHONPATH=/ihesp/software/CESM_postprocessing/cesm-env2/lib/python2.7/site-packages/PyNIO:$PYTHONPATH</module>
 <!--      <module>ml NCL/6.6.2-foss-2018b</module>
                 <module>ml NCO/4.7.9-foss-2018b</module>
       <module>ml netCDF/4.6.1-foss-2018b-cdf5</module>
@@ -43,23 +42,23 @@
       	<averages_pes queue="long" nodes="1" pes_per_node="12" wallclock="20:00:00" memory="360000">12</averages_pes>
       	<diagnostics_pes queue="long" nodes="1" pes_per_node="12" wallclock="20:00:00" memory="360000">12</diagnostics_pes>
       	<regrid_pes queue="long" nodes="1" pes_per_node="12" wallclock="20:00:00" memory="360000">12</regrid_pes>
-      	<obs_root>/scratch/group/ihesp/obs_root/amwg/amwg_data</obs_root> 
+      	<obs_root>/ihesp/obs_root/amwg/amwg_data</obs_root> 
       </component>
       <component name="ice">
       	<averages_pes queue="long"  nodes="1" pes_per_node="12" wallclock="20:00:00" memory="360000">12</averages_pes>
       	<diagnostics_pes queue="long"  nodes="1" pes_per_node="12" wallclock="20:00:00" memory="360000">12</diagnostics_pes>
-      	<obs_root>/scratch/group/ihesp/obs_root/pcwg/ice/data</obs_root>
+      	<obs_root>/ihesp/obs_root/pcwg/ice/data</obs_root>
       </component>
       <component name="lnd">
       	<averages_pes queue="long"  nodes="1" pes_per_node="12" wallclock="20:00:00" memory="18000">12</averages_pes>
       	<diagnostics_pes queue="long"  nodes="1" pes_per_node="12" wallclock="20:00:00" memory="18000">12</diagnostics_pes>
       	<regrid_pes queue="long" nodes="1" pes_per_node="12" wallclock="20:00:00" memory="18000">12</regrid_pes>
-      	<obs_root>/scratch/group/ihesp/obs_root/lnd_diag_data</obs_root>
+      	<obs_root>/ihesp/obs_root/lnd_diag_data</obs_root>
       </component>
       <component name="ocn">
       	<averages_pes queue="long"  nodes="1" pes_per_node="12" wallclock="20:00:00" memory="360000">12</averages_pes>
       	<diagnostics_pes queue="long"  nodes="1" pes_per_node="10" wallclock="25:00:00" memory="360000">10</diagnostics_pes>
-      	<obs_root>/scratch/group/ihesp/obs_root</obs_root>
+      	<obs_root>/ihesp/obs_root</obs_root>
       </component>
       <component name="ilamb">
 	<diagnostics_pes queue="mn_small"  nodes="1" pes_per_node="3" wallclock="6:00" memory="18000">3</diagnostics_pes>

diff --git a/create_python_env b/create_python_env
@@ -160,8 +160,9 @@ echo $curdir
 echo "$progname - activating virtual environment in ${pp_dir}/cesm-env2."
 . cesm-env2/bin/activate
 export PATH=${pp_dir}/cesm-env2/bin:$PATH
-
-cesm-env2/bin/pip install -r env_reqs.txt 
+cesm-env2/bin/pip install numpy==1.16.6 --no-cache-dir --ignore-installed
+cesm-env2/bin/pip install configparser --no-cache-dir --ignore-installed
+cesm-env2/bin/pip install -r env_reqs.txt --no-cache-dir --ignore-installed 
 
 #----------------------------------------------------------------------
 # install post processing packages
@@ -208,6 +209,7 @@ echo "---------------------------------------------------------"
 echo "$progname - Compiling ocn diagnostics zonal average tool - za."
 create_ocn_za --machine $machine
 
+export FC=mpiifort F77=mpiifort CC=mpiicc
 cd $pp_dir/ocn_diag/tool_lib/zon_avg
 
 # run the make clean command
@@ -222,32 +224,37 @@ fi
 # link the za compiled code to one level up for the NCL
 ln -sf $pp_dir/ocn_diag/tool_lib/zon_avg/za $pp_dir/ocn_diag/tool_lib/za
 
-
+mkdir -p $pp_dir/src
 cd $pp_dir/src
-export FC=gfortran F77=gfortran CC=gcc
+#export FC=gfortran F77=gfortran CC=gcc
+export FC=mpiifort F77=mpiifort CC=mpiicc
 export PYTHONPATH=$pp_dir/cesm-env2/lib/python2.7/site-packages
 export PYNIOPATH=$pp_dir/cesm-env2/lib/python2.7/site-packages/PyNIO
 export HAS_NETCDF4=1
-export NETCDF4_PREFIX="/scratch/group/ihesp/software/share/netcdf-c-4.7.4/install2019b_2/"
+export NETCDF4_PREFIX=$EBROOTNETCDF # "/scratch/group/ihesp/software/share/netcdf-c-4.7.4/install2019b_2/"
 export HAS_HDF5=1
-export HDF5_PREFIX="/sw/eb/sw/HDF5/1.10.5-iimpi-2019b"
-export F2CLIBS=gfortran
-export F2CLIBS_PREFIX="/sw/eb/sw/GCCcore/8.3.0/bin/gfortran"
+export HDF5_PREFIX=$EBROOTHDF5 #"/sw/eb/sw/HDF5/1.10.5-iimpi-2019b"
+export F2CLIBS=ifcore
+export F2CLIBS_PREFIX=/sw/eb/sw/iccifort/2020.4.304/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64 #"/sw/eb/sw/GCCcore/8.3.0/bin/gfortran"
 
-export NETCDF_PREFIX=/scratch/group/ihesp/software/share/netcdf-c-4.7.4/install2019b_2
+export NETCDF_PREFIX=$EBROOTNETCDF #/scratch/group/ihesp/software/share/netcdf-c-4.7.4/install2019b_2
 rm -rf pynio ASAPPyTools 
 git clone https://github.com/NCAR/pynio.git
 cd pynio
 git checkout 1.5.3
 sed -i '/extra_objects = EXTRA_OBJECTS,/d' setup.py
-FC=gfortran F77=gfortran CC=gcc  $pp_dir/cesm-env2/bin/python setup.py install
+#FC=gfortran F77=gfortran CC=gcc  $pp_dir/cesm-env2/bin/python setup.py install
+FC=ifort F77=ifort CC=icc  $pp_dir/cesm-env2/bin/python setup.py install
+
 
 cd $pp_dir/src
 git clone https://github.com/NCAR/ASAPPyTools.git
 cd ASAPPyTools
 $pp_dir/cesm-env2/bin/python setup.py install
 
 
+
+
 #----------------------------------------------------------------------
 # cleanup and deactivate the virtualenv. 
 #----------------------------------------------------------------------

diff --git a/diagnostics/requirements.txt b/diagnostics/requirements.txt
@@ -1,4 +1,4 @@
 #jinja2>=2.10
-jinja2==2.7.3
-numpy>=1.8.1
-ilamb>=2.1
+#jinja2==2.7.3
+#numpy>=1.8.1
+ilamb==2.3
diff --git a/env_reqs.txt b/env_reqs.txt
@@ -2,10 +2,11 @@ Cython==0.29.21
 scipy==1.2.3
 numpy==1.16.6
 pandas==0.24.2
-netCDF4==1.5.4
+netCDF4==1.5.5.1
 mpi4py==3.0.3
 cf_units==2.1.4
 cftime==1.2.1
 matplotlib==2.2.5
 Jinja2==2.11.2
 sympy==1.5.1
+Cartopy