Merge pull request #65 from ACCESS-NRI/update_env

Try this

environments/access-med/config.sh

@@ -9,9 +9,9 @@
 
 
 ### Optional config for custom deploy script
-export VERSION_TO_MODIFY=0.4
+export VERSION_TO_MODIFY=0.6
 export STABLE_VERSION=0.3
-export UNSTABLE_VERSION=0.4
+export UNSTABLE_VERSION=0.6
 
 ### Version settings
 export ENVIRONMENT=access-med

environments/access-med/environment.yml

@@ -55,7 +55,7 @@ dependencies:
 - objgraph ### Unlisted dependency of greenlet
 - asyncssh
 - gevent
-- openmpi
+- openmpi==4.1.5
 - mpi4py
 - esmf>=8.0.1=mpi_openmpi*
 - esmpy>=8.0.1=mpi_openmpi*
@@ -71,6 +71,7 @@ dependencies:
 - pip:
   - railroad-diagrams ### Unlisted dependency of pip and pyparsing
   - access-med-utils==0.1.6
+
 
 # Julia (dependencies installed by separate script)
 - julia

environments/access-med/testconfig.yml

@@ -50,6 +50,8 @@ skip:
 - esmf_regrid
 - esmvaltool.diag_scripts
 - med_diagnostics
+- numba
+- urllib3
 
 # Preload these modules before testing to avoid weird python issues
 preload:

scripts/build.sh

@@ -64,14 +64,16 @@ function inner() {
 
     pushd "${ENV_INSTALLATION_PATH}"
     ### Get rid of stuff from packages we don't want
-    for dir in bin lib etc libexec include; do 
-        pushd $dir
-        for i in $( rpm -qli "${rpms_to_remove[@]}" ); do 
-            fn=$( basename $i )
-            [[ -f $fn ]] && rm $fn
-            [[ -d $fn ]] && rm -rf $fn
-        done
-        popd
+    for dir in bin lib etc libexec include; do
+	if [[ -d "${dir}" ]]; then
+            pushd $dir
+            for i in $( rpm -qli "${rpms_to_remove[@]}" ); do
+                fn=$( basename $i )
+                [[ -f $fn ]] && rm $fn
+                [[ -d $fn ]] && rm -rf $fn
+            done
+            popd
+	fi
     done
 
     ### Replace things from apps

scripts/functions.sh

@@ -206,11 +206,20 @@ function initialise_tmp_dirs() {
     if [[ "${PBS_JOBFS}" ]]; then
         relink_cmds=""
         for dir in "$@"; do
-            relink_cmds="${relink_cmds}rm ~/${dir}; ln -s $( readlink ~/${dir} ) ~/${dir}; "
-            rm ~/"${dir}"
-            mkdir -p "${PBS_JOBFS}"/"${dir}"
-            ln -s "${PBS_JOBFS}"/"${dir}" ~
-            ### Race condition
+            if [[ -h ~/"${dir}" ]]; then
+                relink_cmds="${relink_cmds}rm ~/${dir}; ln -s $( readlink ~/${dir} ) ~/${dir}; "
+                rm ~/"${dir}"
+                mkdir -p "${PBS_JOBFS}"/"${dir}"
+                ln -s "${PBS_JOBFS}"/"${dir}" ~
+                ### Race condition
+            elif [[ -d ~/"${dir}" ]]; then
+                echo "Warning! ~/${dir} is a directory (not a symlink). This can significantly increase "
+                echo "installation time of conda environments."
+            else
+                relink_cmds="${relink_cmds}rm ~/${dir}; "
+                mkdir -p "${PBS_JOBFS}"/"${dir}"
+                ln -s "${PBS_JOBFS}"/"${dir}" ~
+            fi
         done
         trap "${relink_cmds}" EXIT
     fi