Remove python packages from external in Jureca

Update deployment scripts
Update intel build system to support intel-mpi-external

lib/spack/spack/build_systems/intel.py

@@ -821,7 +821,8 @@ def scalapack_libs(self):
               '^intel-parallel-studio' in spec_root):
             blacs_lib = 'libmkl_blacs_intelmpi'
         elif ('^mpt' in spec_root or
-              '^hpe-mpi' in spec_root):
+              '^hpe-mpi' in spec_root or
+              '^intel-mpi-external' in spec_root):
             blacs_lib = 'libmkl_blacs_sgimpt'
         else:
             raise_lib_error('Cannot find a BLACS library for the given MPI.')

sysconfig/daint/deploy_simstack.sh

@@ -46,7 +46,10 @@ spack install --dirty --keep-stage -v neuron %intel ^[email protected] ^mpich
 
 spack spec -I neuron~mpi %intel ^[email protected]
 spack install --dirty --keep-stage -v neuron~mpi %intel ^[email protected]
+
 # PYTHON 3 packages
+module load cray-python/3.6.5.7
+
 spack spec -Il neurodamus-hippocampus+coreneuron %intel ^[email protected] ^synapsetool%gcc
 spack install --dirty --keep-stage neurodamus-hippocampus+coreneuron %intel ^[email protected] ^synapsetool%gcc
 spack install --dirty --keep-stage neurodamus-neocortex+coreneuron %intel ^[email protected] ^synapsetool%gcc
@@ -68,6 +71,9 @@ spack install --dirty --keep-stage py-bluepyopt%gcc ^[email protected] ^zeromq%intel
 
 # Re-generate modules
 spack module tcl refresh --delete-tree -y
+cd $DEPLOYMENT_HOME/install/modules/tcl/cray-cnl7-haswell
+find py* -type f -print0|xargs -0 sed -i '/PYTHONPATH.*\/neuron-/d'
+find neuro* -type f -print0|xargs -0 sed -i '/module load mpich/d'
 
 #ln -s $DEPLOYMENT_HOME/install/modules/tcl/cray-cnl6-haswell $DEPLOYMENT_HOME/modules
 #chmod -R ugo-w $DEPLOYMENT_HOME

sysconfig/jureca-booster/deploy_simstack.sh

@@ -69,6 +69,7 @@ spack install --dirty --keep-stage -v neuron~mpi %intel ^[email protected]
 
 # Python 3 packages
 module load Python/3.6.8
+module load SciPy-Stack/2019a-Python-3.6.8
 module list
 spack spec -Il neurodamus-hippocampus+coreneuron %intel ^coreneuron$cnrn_variant ^[email protected] ^synapsetool%gcc
 spack install --keep-stage --dirty neurodamus-hippocampus+coreneuron %intel ^coreneuron$cnrn_variant ^[email protected] ^synapsetool%gcc
@@ -88,6 +89,8 @@ spack spec -Il py-bluepyopt%gcc ^[email protected] ^zeromq%intel
 spack install --keep-stage --dirty py-bluepyopt%gcc ^[email protected] ^zeromq%intel
 
 spack module tcl refresh --delete-tree -y
+cd $DEPLOYMENT_HOME/modules/tcl/linux-centos7-haswell
+find py* -type f -print0|xargs -0 sed -i '/PYTHONPATH.*\/neuron-/d'
 
 # Create symbolic link
 #mkdir -p $DEPLOYMENT_HOME/../install && cd $DEPLOYMENT_HOME/../install

sysconfig/jureca-booster/packages.yaml

@@ -116,30 +116,10 @@ packages:
             [email protected]: /usr/local/software/jurecabooster/Stages/2019a/software/Python/3.6.8-GCCcore-8.3.0
         version: [2.7.15, 3.6.8]
         buildable: False
-    py-cython:
-        paths:
-            [email protected]: /usr/local/software/jurecabooster/Stages/2019a/software/Python/3.6.8-GCCcore-8.3.0
-        version: [0.29.6]
-        buildable: False
-    py-ipyparallel:
-        paths:
-            [email protected]: /usr/local/software/jurecabooster/Stages/2019a/software/SciPy-Stack/2019a-gcccoremkl-8.3.0-2019.3.199-Python-3.6.8
-        version: [6.1.1]
-        buildable: False
     py-matplotlib:
         paths:
-            [email protected]: /usr/local/software/jurecabooster/Stages/2019a/software/SciPy-Stack/2019a-gcccoremkl-8.3.0-2019.3.199-Python-3.6.8
-        version: [2.2.2]
-        buildable: False
-    py-numpy:
-        paths:
-            [email protected]: /usr/local/software/jurecabooster/Stages/2019a/software/SciPy-Stack/2019a-gcccoremkl-8.3.0-2019.3.199-Python-3.6.8
-        version: [1.15.2]
-        buildable: False
-    py-pandas:
-        paths:
-            [email protected]: /usr/local/software/jurecabooster/Stages/2019a/software/SciPy-Stack/2019a-gcccoremkl-8.3.0-2019.3.199-Python-3.6.8
-        version: [0.24.2]
+            [email protected]: /usr/local/software/jurecabooster/Stages/2019a/software/SciPy-Stack/2019a-gcccoremkl-8.3.0-2019.3.199-Python-3.6.8
+        version: [3.0.3]
         buildable: False
     py-scipy:
         paths:

sysconfig/jureca-cluster/packages.yaml

@@ -96,30 +96,10 @@ packages:
             [email protected]: /usr/local/software/jureca/Stages/2019a/software/Python/3.6.8-GCCcore-8.3.0
         version: [2.7.15, 3.6.8]
         buildable: False    
-    py-cython:
-        paths:
-            [email protected]: /usr/local/software/jureca/Stages/2019a/software/Python/3.6.8-GCCcore-8.3.0
-        version: [0.29.6]
-        buildable: False    
-    py-ipyparallel:
-        paths:
-            [email protected]: /usr/local/software/jureca/Stages/2019a/software/SciPy-Stack/2019a-gcccoremkl-8.3.0-2019.3.199-Python-3.6.8
-        version: [6.1.1]
-        buildable: False
     py-matplotlib:
         paths:
-            [email protected]: /usr/local/software/jureca/Stages/2019a/software/SciPy-Stack/2019a-gcccoremkl-8.3.0-2019.3.199-Python-3.6.8
-        version: [2.2.2]
-        buildable: False
-    py-numpy:
-        paths:
-            [email protected]: /usr/local/software/jureca/Stages/2019a/software/SciPy-Stack/2019a-gcccoremkl-8.3.0-2019.3.199-Python-3.6.8
-        version: [1.15.2]
-        buildable: False
-    py-pandas:
-        paths:
-            [email protected]: /usr/local/software/jureca/Stages/2019a/software/SciPy-Stack/2019a-gcccoremkl-8.3.0-2019.3.199-Python-3.6.8
-        version: [0.24.2]
+            [email protected]: /usr/local/software/jureca/Stages/2019a/software/SciPy-Stack/2019a-gcccoremkl-8.3.0-2019.3.199-Python-3.6.8
+        version: [3.0.3]
         buildable: False
     py-scipy:
         paths: