Update lmod, miniconda, task modulefiles for Gaea (#353)

* update lmod * update lmod * update hpc-stack and miniconda * fix lmod-setup.sh bug for Gaea * update files to run with new miniconda and MET VX * fix typo * fixed typo * update vx task * Update build_gaea_intel The list of modules to be loaded needs updates. * Update load_modules_run_task.sh Fixed a typo * Update load_modules_run_task.sh * updated vx task Co-authored-by: Parallel Works app-run user <Edward.Snyder@mgmt-edwardsnyder-pclusternoaav2-00061.pw-noaa-us-east-1.pw.local> Co-authored-by: Parallel Works app-run user <Edward.Snyder@mgmt-edwardsnyder-pclusternoaav2-00062.pw-noaa-us-east-1.pw.local> Co-authored-by: Parallel Works app-run user <Edward.Snyder@mgmt-edwardsnyder-pclusternoaav2-00063.pw-noaa-us-east-1.pw.local> Co-authored-by: Parallel Works app-run user <Edward.Snyder@mgmt-edwardsnyder-pclusternoaav2-00064.pw-noaa-us-east-1.pw.local> Co-authored-by: Natalie Perlin <[email protected]>
ufs-community · Sep 28, 2022 · ebe966c · ebe966c
1 parent f6f1717
commit ebe966c
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Showing 16 changed files with 53 additions and 45 deletions.
diff --git a/etc/lmod-setup.csh b/etc/lmod-setup.csh
@@ -27,8 +27,10 @@ else if ( "$L_MACHINE" == singularity ) then
    module purge
 
 else if ( "$L_MACHINE" == gaea ) then
-   set ENV="/lustre/f2/pdata/esrl/gsd/contrib/lua-5.1.4.9/lmod/lmod/init/csh"
-   source $ENV
+   export LMOD_SYSTEM_DEFAULT_MODULES=modules/3.2.11.4
+   export BASH_ENV=/lustre/f2/dev/role.epic/contrib/apps/lmod/lmod/init/profile
+   source $BASH_ENV
+   module --initial_load restore
 
 else if ( "$L_MACHINE" == odin ) then
    module unload modules

diff --git a/etc/lmod-setup.sh b/etc/lmod-setup.sh
@@ -28,9 +28,10 @@ elif [ "$L_MACHINE" = singularity ]; then
    module purge
 
 elif [ "$L_MACHINE" = gaea ]; then
-   export BASH_ENV="/lustre/f2/pdata/esrl/gsd/contrib/lua-5.1.4.9/lmod/lmod/init/bash"
+   export LMOD_SYSTEM_DEFAULT_MODULES=modules/3.2.11.4
+   export BASH_ENV=/lustre/f2/dev/role.epic/contrib/apps/lmod/lmod/init/profile
    source $BASH_ENV
-   module purge
+   module --initial_load restore
 
 elif [ "$L_MACHINE" = odin ]; then
    module unload modules

diff --git a/modulefiles/build_gaea_intel b/modulefiles/build_gaea_intel
@@ -5,30 +5,24 @@ proc ModulesHelp { } {
    puts stderr "the NOAA RDHPC machine Gaea using Intel-2021.3.0"
 }
 
-module-whatis "Loads libraries needed for building SRW on Gaea"
-
-module load PrgEnv-intel/6.0.5
-module rm intel
-module rm cray-mpich
-module rm netcdf
-module load intel/18.0.6.288
-module load cray-mpich/7.7.11
-module load cray-python/3.7.3.2
+module use /lustre/f2/dev/role.epic/contrib/hpc-stack/intel-2021.3.0/modulefiles/stack
+module load hpc/1.2.0
+module load intel/2021.3.0
+module load hpc-intel/2021.3.0
+module load hpc-cray-mpich/7.7.11
 # Needed at runtime:
 module load alps
 #needed for WW3 build
 module load gcc/8.3.0
 
-module use /lustre/f2/pdata/ncep_shared/hpc-stack/modulefiles/stack
-module load hpc/1.1.0
-module load hpc-intel/2021.3.0
-module load hpc-cray-mpich/7.7.11
-
 module load srw_common
+module load libpng/1.6.37
+
+module use /lustre/f2/dev/role.epic/contrib/modulefiles
+module load miniconda3/4.12.0
 
-module use /lustre/f2/pdata/esrl/gsd/contrib/modulefiles
-module load rocoto
 module load cmake/3.20.1
+module load rocoto
 
 setenv CC cc
 setenv FC ftn

diff --git a/modulefiles/module-setup.csh.inc b/modulefiles/module-setup.csh.inc
@@ -28,6 +28,8 @@ else if ( { test -d /lustre -a -d /ncrc } ) then
         # the module command fails.  Hence we actually have to source
         # /etc/csh.login here.
         source /etc/csh.login
+        # initialize Lmod/8.7.12 using a wrapper script
+        source /lustre/f2/dev/role.epic/contrib/Lmod_init.sh
         set __ms_source_etc_csh_login=yes
     else
         set __ms_source_etc_csh_login=no

diff --git a/modulefiles/module-setup.sh.inc b/modulefiles/module-setup.sh.inc
@@ -37,6 +37,8 @@ elif [[ -d /lustre && -d /ncrc ]] ; then
         # the module command fails.  Hence we actually have to source
         # /etc/profile here.
         source /etc/profile
+        # initialize Lmod/8.7.12 using a wrapper script
+        source /lustre/f2/dev/role.epic/contrib/Lmod_init.sh
         __ms_source_etc_profile=yes
     else
         __ms_source_etc_profile=no

diff --git a/modulefiles/tasks/gaea/get_extrn_ics.local b/modulefiles/tasks/gaea/get_extrn_ics.local
@@ -0,0 +1,3 @@
+#%Module
+
+module load miniconda_regional_workflow
diff --git a/modulefiles/tasks/gaea/get_extrn_lbcs.local b/modulefiles/tasks/gaea/get_extrn_lbcs.local
@@ -0,0 +1,3 @@
+#%Module
+
+module load miniconda_regional_workflow
diff --git a/modulefiles/tasks/gaea/make_grid.local b/modulefiles/tasks/gaea/make_grid.local
@@ -1,6 +1,3 @@
 #%Module
-module use /lustre/f2/pdata/esrl/gsd/contrib/modulefiles
-module load rocoto
-module load miniconda3
 
-setenv SRW_ENV regional_workflow
+module load miniconda_regional_workflow
diff --git a/modulefiles/tasks/gaea/make_ics.local b/modulefiles/tasks/gaea/make_ics.local
@@ -1,6 +1,3 @@
 #%Module
-module use /lustre/f2/pdata/esrl/gsd/contrib/modulefiles
-module load rocoto
-module load miniconda3
 
-setenv SRW_ENV regional_workflow
+module load miniconda_regional_workflow
diff --git a/modulefiles/tasks/gaea/make_lbcs.local b/modulefiles/tasks/gaea/make_lbcs.local
@@ -1,6 +1,3 @@
 #%Module
-module use /lustre/f2/pdata/esrl/gsd/contrib/modulefiles
-module load rocoto
-module load miniconda3
 
-setenv SRW_ENV regional_workflow
+module load miniconda_regional_workflow
diff --git a/modulefiles/tasks/gaea/make_orog.local b/modulefiles/tasks/gaea/make_orog.local
@@ -0,0 +1,3 @@
+#%Module
+
+module load miniconda_regional_workflow
diff --git a/modulefiles/tasks/gaea/miniconda_regional_workflow b/modulefiles/tasks/gaea/miniconda_regional_workflow
@@ -0,0 +1,6 @@
+#%Module
+
+module use /lustre/f2/dev/wpo/role.epic/contrib/modulefiles
+module load miniconda3
+
+setenv SRW_ENV regional_workflow
diff --git a/modulefiles/tasks/gaea/run_fcst.local b/modulefiles/tasks/gaea/run_fcst.local
@@ -1,6 +1,3 @@
 #%Module
-module use /lustre/f2/pdata/esrl/gsd/contrib/modulefiles
-module load rocoto
-module load miniconda3
 
-setenv SRW_ENV regional_workflow
+module load miniconda_regional_workflow
diff --git a/modulefiles/tasks/gaea/run_vx.local b/modulefiles/tasks/gaea/run_vx.local
@@ -1,5 +1,5 @@
 #%Module
 
-module use -a /contrib/anaconda/modulefiles
-module load intel/18.0.5.274
-module load anaconda/latest
+module load miniconda_regional_workflow
+
+prepend-path LD_LIBRARY_PATH /ncrc/sw/gaea-cle7/python/3.9/anaconda-base/envs/noaa_py3.9/lib
diff --git a/modulefiles/wflow_gaea b/modulefiles/wflow_gaea
@@ -7,12 +7,14 @@ proc ModulesHelp { } {
 
 module-whatis "Loads libraries needed for running SRW on Gaea"
 
-module use /lustre/f2/pdata/esrl/gsd/contrib/modulefiles
+module use /lustre/f2/dev/role.epic/contrib/modulefiles
 module load rocoto
 module load miniconda3
 
 setenv CONDA_DEFAULT_ENV "regional_workflow"
-setenv PROJ_LIB /lustre/f2/pdata/esrl/gsd/contrib/miniconda3/4.8.3/envs/regional_workflow/share/proj
-#if { [module-info mode load] } {
-#   system "conda activate regional_workflow;"
-#}
+setenv PROJ_LIB /lustre/f2/dev/role.epic/contrib/miniconda3/4.12.0/envs/regional_workflow/share/proj
+
+if { [module-info mode load] } {
+  puts stderr "Please do the following to activate conda:
+       > conda activate regional_workflow"
+}
diff --git a/ush/machine/gaea.sh b/ush/machine/gaea.sh
@@ -19,6 +19,8 @@ function file_location() {
   echo ${location:-}
 }
 
+export PROJ_LIB=/lustre/f2/dev/role.epic/contrib/miniconda3/4.12.0/envs/regional_workflow/share/proj
+export PATH=${PATH}:/lustre/f2/deve/role.epic/contrib/miniconda3/4.12.0/envs/regional_workflow/bin
 
 EXTRN_MDL_SYSBASEDIR_ICS=${EXTRN_MDL_SYSBASEDIR_ICS:-$(file_location \
   ${EXTRN_MDL_NAME_ICS} \
@@ -30,7 +32,7 @@ EXTRN_MDL_SYSBASEDIR_LBCS=${EXTRN_MDL_SYSBASEDIR_LBCS:-$(file_location \
 # System scripts to source to initialize various commands within workflow
 # scripts (e.g. "module").
 if [ -z ${ENV_INIT_SCRIPTS_FPS:-""} ]; then
-  ENV_INIT_SCRIPTS_FPS=( "/etc/profile" )
+  ENV_INIT_SCRIPTS_FPS=( "/etc/profile" "/lustre/f2/dev/role.epic/contrib/Lmod_init.sh")
 fi