From 07847174530c301a85b70e766b56c5a2718b6df6 Mon Sep 17 00:00:00 2001
From: Christopher Enochs Kees <cekees@lightning07.afrl.hpc.mil>
Date: Wed, 25 Mar 2015 00:48:06 -0400
Subject: [PATCH 01/29] lightning.afrl changes

---
 examples/proteus.garnet.gnu.yaml |  6 +++---
 pkgs/numpy/numpy.yaml            | 10 +++++-----
 pkgs/scipy/scipy-crayxe6.yaml    | 10 +++++-----
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/examples/proteus.garnet.gnu.yaml b/examples/proteus.garnet.gnu.yaml
index 88aa9825b..d7aa8fbc5 100644
--- a/examples/proteus.garnet.gnu.yaml
+++ b/examples/proteus.garnet.gnu.yaml
@@ -23,7 +23,7 @@ parameters:
   PATH: |
     /usr/bin:/bin:/usr/sbin:/sbin
   PROLOGUE: |
-    source /opt/modules/default/init/bash; export MODULEPATH=/opt/cray/gem/modulefiles:/opt/cray/xt-asyncpe/default/modulefiles:/opt/modulefiles:/opt/cray/modulefiles:/cm/local/modulefiles:/cm/shared/modulefiles:/usr/local/modulefiles/COTS:/usr/local/modulefiles/unsupported; export MODULESHOME=/opt/modules/3.2.6.7; export MODULE_VERSION=3.2.6.7; export MODULE_VERSION_STACK=3.2.6.7; echo "unloading modules"; module unload PrgEnv-pgi; echo "loading modules"; module load PrgEnv-gnu/4.2.34; module load cray-mpich/6.0.0; module unload cray-libsci; module load acml/5.3.1; echo "setting default compilers"; export CC=gcc; export CXX=g++; export FC=gfortran; export F77=gfortran; export F90=gfortran; export CPP=cpp;
+    unset RCLOCAL_PRGENV; source /etc/bash.bashrc; source  /etc/bash.bashrc.local; module swap PrgEnv-cray PrgEnv-gnu; module load cray-mpich; module list; echo "setting default compilers"; export CC=gcc; export CXX=g++; export FC=gfortran; export F77=gfortran; export F90=gfortran; export CPP=cpp;
   DYNAMIC_EXE_LINKER_FLAGS: -dynamic
 
 packages:
@@ -34,9 +34,9 @@ packages:
     build_with: |
       openssl,bzip2,sqlite
   blas:
-    use: host-acml-blas
+    use: host-libsci-blas
   lapack:
-    use: host-acml-lapack
+    use: host-libsci-lapack
   daetk:
   mpi:
     use: host-mpi
diff --git a/pkgs/numpy/numpy.yaml b/pkgs/numpy/numpy.yaml
index 8e29b6f2b..e8e00f815 100644
--- a/pkgs/numpy/numpy.yaml
+++ b/pkgs/numpy/numpy.yaml
@@ -38,8 +38,8 @@ build_stages:
     bash: |
       cat > site.cfg << EOF
       [DEFAULT]
-      library_dirs = ${ACML_DIR}/gfortran64/lib
-      libraries = acml
+      library_dirs = ${CRAY_LIBSCI_PREFIX_DIR}/lib
+      libraries = sci_gnu
       EOF
 
   - when: machine == 'CrayXE6'
@@ -48,9 +48,9 @@ build_stages:
     before: install
     handler: bash
     bash: |
-      export LDFLAGS="-shared -Wl,-rpath=${PYTHON_DIR}/lib -Wl,-rpath=${ACML_DIR}/gfortran64/lib $(${PYTHON_DIR}/bin/python-config --ldflags)"
-      export LAPACK=acml
-      export BLAS=acml
+      export LDFLAGS="-shared -Wl,-rpath=${PYTHON_DIR}/lib -Wl,-rpath=${CRAY_LIBSCI_PREFIX_DIR}/lib $(${PYTHON_DIR}/bin/python-config --ldflags)"
+      export LAPACK=sci_gnu
+      export BLAS=sci_gnu
       export ATLAS=None
 
   - when: platform == 'Cygwin'
diff --git a/pkgs/scipy/scipy-crayxe6.yaml b/pkgs/scipy/scipy-crayxe6.yaml
index c39039c4e..fe307d043 100644
--- a/pkgs/scipy/scipy-crayxe6.yaml
+++ b/pkgs/scipy/scipy-crayxe6.yaml
@@ -17,8 +17,8 @@ build_stages:
     bash: |
       cat > site.cfg << EOF
       [DEFAULT]
-      library_dirs = ${ACML_DIR}/gfortran64/lib
-      libraries = acml
+      library_dirs = ${CRAY_LIBSCI_PREFIX_DIR}/lib
+      libraries = sci_gnu
       EOF
 
   - name: set-LDFLAGS
@@ -26,8 +26,8 @@ build_stages:
     before: install
     handler: bash
     bash: |
-      export LDFLAGS="-shared -Wl,-rpath=${PYTHON_DIR}/lib -Wl,-rpath=${ACML_DIR}/gfortran64/lib $(${PYTHON_DIR}/bin/python-config --ldflags)"
+      export LDFLAGS="-shared -Wl,-rpath=${PYTHON_DIR}/lib -Wl,-rpath=${CRAY_LIBSCI_PREFIX_DIR}/lib $(${PYTHON_DIR}/bin/python-config --ldflags)"
       export ATLAS=None
-      export LAPACK=acml
-      export BLAS=acml
+      export LAPACK=sci_gnu
+      export BLAS=sci_gnu
 

From b226d41050700e5cc7f5377c0408f9d9e4294446 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Wed, 25 Mar 2015 00:49:54 -0400
Subject: [PATCH 02/29] added some host packages

---
 pkgs/host-openblas-blas.yaml   | 2 ++
 pkgs/host-openblas-lapack.yaml | 2 ++
 2 files changed, 4 insertions(+)
 create mode 100644 pkgs/host-openblas-blas.yaml
 create mode 100644 pkgs/host-openblas-lapack.yaml

diff --git a/pkgs/host-openblas-blas.yaml b/pkgs/host-openblas-blas.yaml
new file mode 100644
index 000000000..3a845f318
--- /dev/null
+++ b/pkgs/host-openblas-blas.yaml
@@ -0,0 +1,2 @@
+when_build_dependency:
+  - {set: 'BLAS_LDFLAGS', value: '-lopenblas'}
\ No newline at end of file
diff --git a/pkgs/host-openblas-lapack.yaml b/pkgs/host-openblas-lapack.yaml
new file mode 100644
index 000000000..f7c50dc43
--- /dev/null
+++ b/pkgs/host-openblas-lapack.yaml
@@ -0,0 +1,2 @@
+when_build_dependency:
+  - {set: 'LAPACK_LDFLAGS', value: '-lopenblas'}
\ No newline at end of file

From ac0e31f108e8b85799540450e2d6c5779c2029f3 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Thu, 21 May 2015 12:33:12 -0400
Subject: [PATCH 03/29] added lightning profile

---
 examples/proteus.lightning.gnu.yaml | 73 +++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 examples/proteus.lightning.gnu.yaml

diff --git a/examples/proteus.lightning.gnu.yaml b/examples/proteus.lightning.gnu.yaml
new file mode 100644
index 000000000..d7aa8fbc5
--- /dev/null
+++ b/examples/proteus.lightning.gnu.yaml
@@ -0,0 +1,73 @@
+# This profile file controls your <#> (HashDist) build environment.
+
+# In the future, we'll provide better incorporation of
+# automatic environment detection.  For now, have a look
+# at the YAML files in the top-level directory and choose
+# the most *specific* file that matches your environment.
+
+extends:
+- file: suse.yaml
+
+# The packages list specifies all the packages that you
+# require installed.  <#> will ensure that all packages
+# and their dependencies are installed when you build this
+# profile.
+
+parameters:
+  machine: CrayXE6
+  HOST_MPICC: cc
+  HOST_MPICXX: CC
+  HOST_MPIF77: ftn
+  HOST_MPIF90: ftn
+  HOST_MPIEXEC: aprun
+  PATH: |
+    /usr/bin:/bin:/usr/sbin:/sbin
+  PROLOGUE: |
+    unset RCLOCAL_PRGENV; source /etc/bash.bashrc; source  /etc/bash.bashrc.local; module swap PrgEnv-cray PrgEnv-gnu; module load cray-mpich; module list; echo "setting default compilers"; export CC=gcc; export CXX=g++; export FC=gfortran; export F77=gfortran; export F90=gfortran; export CPP=cpp;
+  DYNAMIC_EXE_LINKER_FLAGS: -dynamic
+
+packages:
+  launcher:
+  cmake:
+  python:
+    host: false
+    build_with: |
+      openssl,bzip2,sqlite
+  blas:
+    use: host-libsci-blas
+  lapack:
+    use: host-libsci-lapack
+  daetk:
+  mpi:
+    use: host-mpi
+  mpi4py:
+  nose:
+  hdf5:
+  ipython:
+  matplotlib:
+  parmetis:
+    without_check: true
+  petsc:
+    build_with: |
+      parmetis
+    download: |
+      ptscotch, superlu, superlu_dist, spooles, hypre, blacs, scalapack, mumps
+    coptflags: -O2
+    link: shared
+    debug: false
+  petsc4py:
+    with_conf: true
+  pytables:
+  sphinx:
+  superlu:
+  sympy:
+  tetgen:
+  triangle:
+  memory_profiler:
+  scipy:
+  netcdf4f:
+  python-netcdf4:
+ # ode:
+ # pyode:
+ # vtk:
+ # pyvtk:

From 9df2e03871c475af87bbe27dfd99142afffc8123 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Thu, 21 May 2015 12:33:40 -0400
Subject: [PATCH 04/29] added host-openblas.yaml for lightning

---
 pkgs/host-openblas.yaml | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 pkgs/host-openblas.yaml

diff --git a/pkgs/host-openblas.yaml b/pkgs/host-openblas.yaml
new file mode 100644
index 000000000..fdbc77c8f
--- /dev/null
+++ b/pkgs/host-openblas.yaml
@@ -0,0 +1,2 @@
+when_build_dependency:
+  - {set: 'BLAS_LDFLAGS', value: '-lacml'}
\ No newline at end of file

From 1efcb3068891a544c5fbeca8f01b5d8e186b5883 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Thu, 21 May 2015 16:30:40 -0400
Subject: [PATCH 05/29] support  for lightning.afrl

---
 examples/proteus.garnet.gnu.yaml | 6 +++---
 pkgs/ncurses/ncurses.yaml        | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/examples/proteus.garnet.gnu.yaml b/examples/proteus.garnet.gnu.yaml
index d7aa8fbc5..88aa9825b 100644
--- a/examples/proteus.garnet.gnu.yaml
+++ b/examples/proteus.garnet.gnu.yaml
@@ -23,7 +23,7 @@ parameters:
   PATH: |
     /usr/bin:/bin:/usr/sbin:/sbin
   PROLOGUE: |
-    unset RCLOCAL_PRGENV; source /etc/bash.bashrc; source  /etc/bash.bashrc.local; module swap PrgEnv-cray PrgEnv-gnu; module load cray-mpich; module list; echo "setting default compilers"; export CC=gcc; export CXX=g++; export FC=gfortran; export F77=gfortran; export F90=gfortran; export CPP=cpp;
+    source /opt/modules/default/init/bash; export MODULEPATH=/opt/cray/gem/modulefiles:/opt/cray/xt-asyncpe/default/modulefiles:/opt/modulefiles:/opt/cray/modulefiles:/cm/local/modulefiles:/cm/shared/modulefiles:/usr/local/modulefiles/COTS:/usr/local/modulefiles/unsupported; export MODULESHOME=/opt/modules/3.2.6.7; export MODULE_VERSION=3.2.6.7; export MODULE_VERSION_STACK=3.2.6.7; echo "unloading modules"; module unload PrgEnv-pgi; echo "loading modules"; module load PrgEnv-gnu/4.2.34; module load cray-mpich/6.0.0; module unload cray-libsci; module load acml/5.3.1; echo "setting default compilers"; export CC=gcc; export CXX=g++; export FC=gfortran; export F77=gfortran; export F90=gfortran; export CPP=cpp;
   DYNAMIC_EXE_LINKER_FLAGS: -dynamic
 
 packages:
@@ -34,9 +34,9 @@ packages:
     build_with: |
       openssl,bzip2,sqlite
   blas:
-    use: host-libsci-blas
+    use: host-acml-blas
   lapack:
-    use: host-libsci-lapack
+    use: host-acml-lapack
   daetk:
   mpi:
     use: host-mpi
diff --git a/pkgs/ncurses/ncurses.yaml b/pkgs/ncurses/ncurses.yaml
index 8ab8292a1..3a7aa7e66 100644
--- a/pkgs/ncurses/ncurses.yaml
+++ b/pkgs/ncurses/ncurses.yaml
@@ -2,7 +2,7 @@ extends: [autotools_package]
 
 sources:
   - key: git:2031c7bde2dfb2189b9c724946f19c089596eac4
-    url: https://github.com/hashdist/pkg-ncurses
+    url: git@github.com:hashdist/pkg-ncurses
 
 defaults:
   relocatable: false

From 5240c6e31fa5b5630085cb61da9ccfc645f77f63 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Fri, 12 Jun 2015 18:09:54 +0100
Subject: [PATCH 06/29] added insert_location step for non-relocatable packages

---
 base/base_package.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/base/base_package.yaml b/base/base_package.yaml
index bba0ffdf7..45e44ab60 100644
--- a/base/base_package.yaml
+++ b/base/base_package.yaml
@@ -44,6 +44,12 @@ post_process:
       - "check-ignore=.*\\.pyc\\$"
       - "check-ignore=.*\\.pyo\\$"
 
+  - name: insert_location
+    when: relocatable !=  True
+    after: [default]
+    hit:
+      - insert-location
+
 profile_links:
   - when: platform == 'Cygwin'
     name: copy_dlls

From 6d458ee0eb8727fb887d3f8bdf1345392bfd6ec0 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Tue, 7 Jul 2015 12:08:01 +0100
Subject: [PATCH 07/29] updating proteus stacks

---
 examples/proteus.Darwin.yaml | 3 ++-
 examples/proteus.linux2.yaml | 3 +++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/examples/proteus.Darwin.yaml b/examples/proteus.Darwin.yaml
index 1bdaea30e..a19fd09c7 100644
--- a/examples/proteus.Darwin.yaml
+++ b/examples/proteus.Darwin.yaml
@@ -53,4 +53,5 @@ packages:
   tetgen:
   memory_profiler:
   ipdb:
-  pip:
\ No newline at end of file
+  pip:
+  doxygen:
diff --git a/examples/proteus.linux2.yaml b/examples/proteus.linux2.yaml
index 4ae9108cf..80e724fb9 100644
--- a/examples/proteus.linux2.yaml
+++ b/examples/proteus.linux2.yaml
@@ -53,3 +53,6 @@ packages:
   memory_profiler:
   ipdb:
   pip:
+  scipy:
+  ode:
+  h5py:

From c3b54ea3df5132e34e2379e3e118a36e044cce67 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Tue, 7 Jul 2015 12:21:02 +0100
Subject: [PATCH 08/29] adding h5py, netcdf, ode to  default stack

---
 examples/proteus.Darwin.yaml | 10 ++++++++--
 examples/proteus.linux2.yaml |  4 ++++
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/examples/proteus.Darwin.yaml b/examples/proteus.Darwin.yaml
index a19fd09c7..43864fa51 100644
--- a/examples/proteus.Darwin.yaml
+++ b/examples/proteus.Darwin.yaml
@@ -27,13 +27,13 @@ packages:
   blas:
     use: host-osx-framework-accelerate
   daetk:
-  matplotlib:
   mpi:
     use: mpich
   mpi4py:
   nose:
   hdf5:
   ipython:
+  matplotlib:
   petsc:
     build_with: |
       parmetis      
@@ -49,9 +49,15 @@ packages:
   sphinx:
   superlu:
   sympy:
-  triangle:
   tetgen:
+  triangle:
   memory_profiler:
   ipdb:
   pip:
   doxygen:
+  scipy:
+  ode:
+  h5py:
+  netcdf4:
+  netcdf4f:
+  netcdf4cpp:
diff --git a/examples/proteus.linux2.yaml b/examples/proteus.linux2.yaml
index 80e724fb9..e07621ceb 100644
--- a/examples/proteus.linux2.yaml
+++ b/examples/proteus.linux2.yaml
@@ -53,6 +53,10 @@ packages:
   memory_profiler:
   ipdb:
   pip:
+  doxygen:
   scipy:
   ode:
   h5py:
+  netcdf4:
+  netcdf4f:
+  netcdf4cpp:

From 5e3b73aae13c012d94e163e3e40b6c24d727ea55 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Thu, 9 Jul 2015 15:42:18 +0100
Subject: [PATCH 09/29] added python-netscdf4

---
 examples/proteus.Darwin.yaml | 2 ++
 examples/proteus.linux2.yaml | 1 +
 2 files changed, 3 insertions(+)

diff --git a/examples/proteus.Darwin.yaml b/examples/proteus.Darwin.yaml
index 43864fa51..edded2a95 100644
--- a/examples/proteus.Darwin.yaml
+++ b/examples/proteus.Darwin.yaml
@@ -61,3 +61,5 @@ packages:
   netcdf4:
   netcdf4f:
   netcdf4cpp:
+  python-netcdf4:
+
diff --git a/examples/proteus.linux2.yaml b/examples/proteus.linux2.yaml
index e07621ceb..101b19cf7 100644
--- a/examples/proteus.linux2.yaml
+++ b/examples/proteus.linux2.yaml
@@ -60,3 +60,4 @@ packages:
   netcdf4:
   netcdf4f:
   netcdf4cpp:
+  python-netcdf4:

From 1bfd4cd1411bdf24ef9da3229cb7a5db1040a948 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Mon, 20 Jul 2015 16:08:36 +0100
Subject: [PATCH 10/29] added h5py and ode deps to proteus stacks

---
 examples/proteus.Cygwin.yaml     | 4 +++-
 examples/proteus.Darwin.yaml     | 4 +++-
 examples/proteus.centos.yaml     | 2 ++
 examples/proteus.garnet.gnu.yaml | 3 ++-
 examples/proteus.host-arch.yaml  | 2 ++
 examples/proteus.linux2.yaml     | 2 ++
 6 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/examples/proteus.Cygwin.yaml b/examples/proteus.Cygwin.yaml
index f41ba028d..799a24a6e 100755
--- a/examples/proteus.Cygwin.yaml
+++ b/examples/proteus.Cygwin.yaml
@@ -53,4 +53,6 @@ packages:
   zmq: 
   memory_profiler:
   ipdb:
-  pip:
\ No newline at end of file
+  pip:
+  h5py:
+  ode:
diff --git a/examples/proteus.Darwin.yaml b/examples/proteus.Darwin.yaml
index 1bdaea30e..a7f0a987d 100644
--- a/examples/proteus.Darwin.yaml
+++ b/examples/proteus.Darwin.yaml
@@ -53,4 +53,6 @@ packages:
   tetgen:
   memory_profiler:
   ipdb:
-  pip:
\ No newline at end of file
+  pip:
+  h5py:
+  ode:
diff --git a/examples/proteus.centos.yaml b/examples/proteus.centos.yaml
index 54d178029..bb9f26575 100644
--- a/examples/proteus.centos.yaml
+++ b/examples/proteus.centos.yaml
@@ -61,3 +61,5 @@ packages:
   tetgen:
   triangle:
   memory_profiler:
+  h5py:
+  ode:
diff --git a/examples/proteus.garnet.gnu.yaml b/examples/proteus.garnet.gnu.yaml
index 88aa9825b..ebcb0495a 100644
--- a/examples/proteus.garnet.gnu.yaml
+++ b/examples/proteus.garnet.gnu.yaml
@@ -67,7 +67,8 @@ packages:
   scipy:
   netcdf4f:
   python-netcdf4:
- # ode:
+  h5py:
+  ode:
  # pyode:
  # vtk:
  # pyvtk:
diff --git a/examples/proteus.host-arch.yaml b/examples/proteus.host-arch.yaml
index e77a8d7ff..e283d978d 100644
--- a/examples/proteus.host-arch.yaml
+++ b/examples/proteus.host-arch.yaml
@@ -59,3 +59,5 @@ packages:
     use: host-pytables
   tetgen:
   triangle:
+  h5py:
+  ode:
diff --git a/examples/proteus.linux2.yaml b/examples/proteus.linux2.yaml
index 4ae9108cf..fe8e854d2 100644
--- a/examples/proteus.linux2.yaml
+++ b/examples/proteus.linux2.yaml
@@ -53,3 +53,5 @@ packages:
   memory_profiler:
   ipdb:
   pip:
+  h5py:
+  ode:

From 805c2fa281be624ec81b0a26f3a9aa3a36e914d4 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Tue, 21 Jul 2015 14:17:44 +0100
Subject: [PATCH 11/29] updating linux2 stack

---
 examples/proteus.linux2.yaml | 33 ++++++++++++++++++++++++++-------
 1 file changed, 26 insertions(+), 7 deletions(-)

diff --git a/examples/proteus.linux2.yaml b/examples/proteus.linux2.yaml
index c5e4a7dcd..6e61bccc1 100644
--- a/examples/proteus.linux2.yaml
+++ b/examples/proteus.linux2.yaml
@@ -14,7 +14,7 @@ extends:
 # profile.
 
 packages:
-
+  clawpack:
   launcher:
   cmake:
     use: host-cmake
@@ -25,13 +25,15 @@ packages:
       bzip2, sqlite
   blas:
     use: host-blas
+  lapack:
+    use: host-lapack
   daetk:
   mpi:
     use: mpich
   mpi4py:
   nose:
+  coverage:
   hdf5:
-  ipython:
   matplotlib:
   petsc:
     build_with: |
@@ -51,13 +53,30 @@ packages:
   tetgen:
   triangle:
   memory_profiler:
-  ipdb:
-  pip:
-  doxygen:
-  scipy:
+  boost:
+    toolset: gcc
+    address_model: 64
+    build_with: |
+      python
   netcdf4:
+  python-netcdf4:
   netcdf4f:
   netcdf4cpp:
-  python-netcdf4:
+  jasper:
+  grib_api:
+  pyproj:
+  pygrib:
+  scipy:
+  ipython:
+  terminado:
   h5py:
+  pydap:
+  leafletwidget:
+  geojson:
+  rdp:
+  rtree:
   ode:
+  ipdb:
+  pip:
+  pexpect:
+  doxygen:
\ No newline at end of file

From d51a47b42def5d5cf971db276c1af6c7d1267463 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Tue, 21 Jul 2015 22:34:14 +0100
Subject: [PATCH 12/29] add pcs_api

---
 examples/proteus.linux2.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/examples/proteus.linux2.yaml b/examples/proteus.linux2.yaml
index fe8e854d2..c13885e9b 100644
--- a/examples/proteus.linux2.yaml
+++ b/examples/proteus.linux2.yaml
@@ -55,3 +55,4 @@ packages:
   pip:
   h5py:
   ode:
+  pcs_api:

From 1331d75e167a543694b803a76a1f42685275264f Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Wed, 22 Jul 2015 10:28:03 +0100
Subject: [PATCH 13/29] updated jupyter-pip and pythreejs

---
 examples/proteus.linux2.yaml | 2 ++
 pkgs/jupyter-pip.yaml        | 4 ++--
 pkgs/pythreejs.yaml          | 9 +++++++++
 3 files changed, 13 insertions(+), 2 deletions(-)
 create mode 100644 pkgs/pythreejs.yaml

diff --git a/examples/proteus.linux2.yaml b/examples/proteus.linux2.yaml
index 90fc7a24d..841f69a5a 100644
--- a/examples/proteus.linux2.yaml
+++ b/examples/proteus.linux2.yaml
@@ -81,3 +81,5 @@ packages:
   pexpect:
   doxygen:
   pcs_api:
+  jupyter-pip:
+  pythreejs:
diff --git a/pkgs/jupyter-pip.yaml b/pkgs/jupyter-pip.yaml
index de0d9c37e..ec747c8ff 100644
--- a/pkgs/jupyter-pip.yaml
+++ b/pkgs/jupyter-pip.yaml
@@ -5,5 +5,5 @@ dependencies:
   run: []
 
 sources:
- - key: tar.gz:wxla2vqnbs3zhqn3l6kafwyhobj6ppak
-   url: https://pypi.python.org/packages/source/j/jupyter-pip/jupyter-pip-0.1.tar.gz
+ - key: git:9fe7ab80870b2c7de8380ab8013fbb33df7ee847
+   url: https://github.com/jdfreder/jupyter-pip.git
diff --git a/pkgs/pythreejs.yaml b/pkgs/pythreejs.yaml
new file mode 100644
index 000000000..8db3e4bc7
--- /dev/null
+++ b/pkgs/pythreejs.yaml
@@ -0,0 +1,9 @@
+extends: [setuptools_package]
+
+dependencies:
+  build: [ipython,pip,jupyter-pip]
+
+sources:
+  - url: https://github.com/jasongrout/pythreejs
+    key: git:ac189124bb54fe5a5e65ad6299a21becfbab94c7
+

From 0355f7b5f92e8a226441e9560f89c36165625b07 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Thu, 10 Sep 2015 18:54:03 -0500
Subject: [PATCH 14/29] removed host cmake dependency

---
 examples/proteus.linux2.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/examples/proteus.linux2.yaml b/examples/proteus.linux2.yaml
index 841f69a5a..78368b0cf 100644
--- a/examples/proteus.linux2.yaml
+++ b/examples/proteus.linux2.yaml
@@ -17,7 +17,6 @@ packages:
   clawpack:
   launcher:
   cmake:
-    use: host-cmake
   python:
     host: false
     link: shared
@@ -79,7 +78,6 @@ packages:
   ipdb:
   pip:
   pexpect:
-  doxygen:
   pcs_api:
   jupyter-pip:
   pythreejs:

From 7808dd3ccd5b110dbb627a3e01c21ff900a46365 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Fri, 11 Sep 2015 16:03:51 -0400
Subject: [PATCH 15/29] added ode and h5py

---
 examples/proteus.lightning.gnu.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/examples/proteus.lightning.gnu.yaml b/examples/proteus.lightning.gnu.yaml
index d7aa8fbc5..7599861a5 100644
--- a/examples/proteus.lightning.gnu.yaml
+++ b/examples/proteus.lightning.gnu.yaml
@@ -67,7 +67,8 @@ packages:
   scipy:
   netcdf4f:
   python-netcdf4:
- # ode:
+  h5py:
+  ode:
  # pyode:
  # vtk:
  # pyvtk:

From acf9d9d5a25a58d68be47b6cad0e9b8a49060e30 Mon Sep 17 00:00:00 2001
From: cekees <cekees@gmail.com>
Date: Sat, 3 Oct 2015 17:55:53 -0400
Subject: [PATCH 16/29] corrected machine type to XC30

---
 examples/proteus.lightning.gnu.yaml |  5 ++++-
 pkgs/hdf5/hdf5.yaml                 |  4 ++--
 pkgs/netcdf4/netcdf4.yaml           |  2 +-
 pkgs/numpy/numpy.yaml               |  4 ++--
 pkgs/petsc/petsc.py                 | 31 +++++++++++++++++++++++++++
 pkgs/scipy/scipy-crayxc30.yaml      | 33 +++++++++++++++++++++++++++++
 6 files changed, 73 insertions(+), 6 deletions(-)
 create mode 100644 pkgs/scipy/scipy-crayxc30.yaml

diff --git a/examples/proteus.lightning.gnu.yaml b/examples/proteus.lightning.gnu.yaml
index 7599861a5..c8294f38c 100644
--- a/examples/proteus.lightning.gnu.yaml
+++ b/examples/proteus.lightning.gnu.yaml
@@ -14,7 +14,7 @@ extends:
 # profile.
 
 parameters:
-  machine: CrayXE6
+  machine: CrayXC30
   HOST_MPICC: cc
   HOST_MPICXX: CC
   HOST_MPIF77: ftn
@@ -48,6 +48,7 @@ packages:
   parmetis:
     without_check: true
   petsc:
+    version: 3.6.1
     build_with: |
       parmetis
     download: |
@@ -56,6 +57,7 @@ packages:
     link: shared
     debug: false
   petsc4py:
+    version: 3.6.0
     with_conf: true
   pytables:
   sphinx:
@@ -69,6 +71,7 @@ packages:
   python-netcdf4:
   h5py:
   ode:
+  pip:
  # pyode:
  # vtk:
  # pyvtk:
diff --git a/pkgs/hdf5/hdf5.yaml b/pkgs/hdf5/hdf5.yaml
index a9d97475f..f29fd5b97 100644
--- a/pkgs/hdf5/hdf5.yaml
+++ b/pkgs/hdf5/hdf5.yaml
@@ -18,7 +18,7 @@ build_stages:
   bash: |
     export CC=${MPICC}
 
-- when: machine == 'CrayXE6'
+- when: machine == 'CrayXE6' or machine == 'CrayXC30'
   name: make_exe_builds_static
   handler: bash
   after: configure
@@ -40,7 +40,7 @@ build_stages:
           '--enable-largefile=yes',
           '--with-default-api-version=v18']
 
-- when: machine == 'CrayXE6'
+- when: machine == 'CrayXE6' or machine == 'CrayXC30'
   name: configure
   extra: ['--enable-static-exec',
           '--with-zlib=${ZLIB_DIR}',
diff --git a/pkgs/netcdf4/netcdf4.yaml b/pkgs/netcdf4/netcdf4.yaml
index c7159ee24..173dd6258 100644
--- a/pkgs/netcdf4/netcdf4.yaml
+++ b/pkgs/netcdf4/netcdf4.yaml
@@ -19,7 +19,7 @@ build_stages:
   bash: |
     export CC=$MPICC
 
-- when: machine == 'CrayXE6'
+- when: machine == 'CrayXE6' or machine == 'CrayXC30'
   name: configure
   mode: override
   append: {LDFLAGS: {{DYNAMIC_EXE_LINKER_FLAGS}}}
diff --git a/pkgs/numpy/numpy.yaml b/pkgs/numpy/numpy.yaml
index 50cfec591..549ebc68f 100644
--- a/pkgs/numpy/numpy.yaml
+++ b/pkgs/numpy/numpy.yaml
@@ -53,7 +53,7 @@ build_stages:
       export BLAS=None
       export ATLAS=None
 
-  - when: machine == 'CrayXE6'
+  - when: machine == 'CrayXC30'
     name: create-site.cfg
     after: prologue
     before: install
@@ -65,7 +65,7 @@ build_stages:
       libraries = sci_gnu
       EOF
 
-  - when: machine == 'CrayXE6'
+  - when: machine == 'CrayXC30'
     name: set-LDFLAGS
     after: prologue
     before: install
diff --git a/pkgs/petsc/petsc.py b/pkgs/petsc/petsc.py
index ba0d5bdae..2cd2dcb07 100644
--- a/pkgs/petsc/petsc.py
+++ b/pkgs/petsc/petsc.py
@@ -4,6 +4,35 @@ def preConfigureCrayXE6(ctx, conf_lines):
     conf_lines += ['LDFLAGS=' + ctx.parameters['DYNAMIC_EXE_LINKER_FLAGS'],
                '--known-mpi-shared-libraries=1',
                '--with-batch',
+               '--known-sdot-returns-double=0',
+               '--known-snrm2-returns-double=0',
+               '--known-level1-dcache-size=16384',
+               '--known-level1-dcache-linesize=64',
+               '--known-level1-dcache-assoc=4',
+               '--known-memcmp-ok=1',
+               '--known-sizeof-char=1',
+               '--known-sizeof-void-p=8',
+               '--known-sizeof-short=2',
+               '--known-sizeof-int=4',
+               '--known-sizeof-long=8',
+               '--known-sizeof-long-long=8',
+               '--known-sizeof-float=4',
+               '--known-sizeof-double=8',
+               '--known-sizeof-size_t=8',
+               '--known-bits-per-byte=8',
+               '--known-sizeof-MPI_Comm=4',
+               '--known-sizeof-MPI_Fint=4',
+               '--known-mpi-long-double=1',
+               '--known-mpi-c-double-complex=1',
+               '--known-mpi-int64_t=1',
+               '--with-pthread=1']
+
+def preConfigureCrayXC30(ctx, conf_lines):
+    conf_lines += ['LDFLAGS=' + ctx.parameters['DYNAMIC_EXE_LINKER_FLAGS'],
+               '--known-mpi-shared-libraries=1',
+               '--with-batch',
+               '--known-sdot-returns-double=0',
+               '--known-snrm2-returns-double=0',
                '--known-level1-dcache-size=16384',
                '--known-level1-dcache-linesize=64',
                '--known-level1-dcache-assoc=4',
@@ -87,6 +116,8 @@ def configure(ctx, stage_args):
 
     if ctx.parameters.get('machine','') == 'CrayXE6':
         preConfigureCrayXE6(ctx, conf_lines)
+    elif ctx.parameters.get('machine','') == 'CrayXC30':
+        preConfigureCrayXC30(ctx, conf_lines)
     elif ctx.parameters.get('machine','') == 'SGIICEX':
         preConfigureSGIICEX(ctx, conf_lines)
 
diff --git a/pkgs/scipy/scipy-crayxc30.yaml b/pkgs/scipy/scipy-crayxc30.yaml
new file mode 100644
index 000000000..33c1a77a7
--- /dev/null
+++ b/pkgs/scipy/scipy-crayxc30.yaml
@@ -0,0 +1,33 @@
+when: machine == 'CrayXC30'
+
+extends: [distutils_package]
+dependencies:
+  build: [blas, lapack, numpy]
+  run: [blas, lapack, numpy]
+
+sources:
+  - url: http://downloads.sourceforge.net/scipy/scipy-0.13.3.tar.gz
+    key: tar.gz:vhrty7xamdbvzvog5y5mtzpjxo4zegox
+
+build_stages:
+  - name: create-site.cfg
+    after: prologue
+    before: install
+    handler: bash
+    bash: |
+      cat > site.cfg << EOF
+      [DEFAULT]
+      library_dirs = ${CRAY_LIBSCI_PREFIX_DIR}/lib
+      libraries = sci_gnu
+      EOF
+
+  - name: set-LDFLAGS
+    after: prologue
+    before: install
+    handler: bash
+    bash: |
+      export LDFLAGS="-shared -Wl,-rpath=${PYTHON_DIR}/lib -Wl,-rpath=${CRAY_LIBSCI_PREFIX_DIR}/lib $(${PYTHON_DIR}/bin/python-config --ldflags)"
+      export ATLAS=None
+      export LAPACK=sci_gnu
+      export BLAS=sci_gnu
+

From 6a6deeb773275bc064fce73613b371aa97d8486c Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Fri, 30 Oct 2015 17:12:25 +0000
Subject: [PATCH 17/29] Added support for ARCHER (Cray XC30).

---
 archer.yaml                  |  2 +
 examples/proteus.archer.yaml | 75 ++++++++++++++++++++++++++++++++++++
 pkgs/hdf5/hdf5.yaml          |  7 ++--
 3 files changed, 81 insertions(+), 3 deletions(-)
 create mode 100644 archer.yaml
 create mode 100644 examples/proteus.archer.yaml

diff --git a/archer.yaml b/archer.yaml
new file mode 100644
index 000000000..5b3158be5
--- /dev/null
+++ b/archer.yaml
@@ -0,0 +1,2 @@
+extends:
+  - file: linux.yaml
diff --git a/examples/proteus.archer.yaml b/examples/proteus.archer.yaml
new file mode 100644
index 000000000..9b177b510
--- /dev/null
+++ b/examples/proteus.archer.yaml
@@ -0,0 +1,75 @@
+# This profile file controls your <#> (HashDist) build environment.
+
+# In the future, we'll provide better incorporation of
+# automatic environment detection.  For now, have a look
+# at the YAML files in the top-level directory and choose
+# the most *specific* file that matches your environment.
+
+extends:
+- file: archer.yaml
+
+# The packages list specifies all the packages that you
+# require installed.  <#> will ensure that all packages
+# and their dependencies are installed when you build this
+# profile.
+
+parameters:
+  machine: CrayXC30
+  HOST_MPICC: cc
+  HOST_MPICXX: CC
+  HOST_MPIF77: ftn
+  HOST_MPIF90: ftn
+  HOST_MPIEXEC: aprun
+  PATH: |
+    /usr/bin:/bin:/usr/sbin:/sbin
+  PROLOGUE: |
+    source /opt/modules/default/init/bash; export MODULEPATH=/opt/cray/craype/default/modulefiles:/opt/cray/ari/modulefiles:/opt/cray/modulefiles:/opt/modulefiles:/cm/local/modulefiles:/cm/shared/modulefiles:/opt/modules/packages-archer; export MODULESHOME=/opt/modules/default; export MODULE_VERSION=3.2.10; export MODULE_VERSION_STACK=3.2.10; export CRAY_CPU_TARGET=ivybridge; echo "unloading modules"; module unload PrgEnv-cray; echo "loading modules"; module load PrgEnv-gnu; module load cray-mpich; module load cray-libsci; module load cray-tpsl; echo "setting default compilers"; export CC=gcc; export CXX=g++; export FC=gfortran; export F77=gfortran; export F90=gfortran; export CPP=cpp;
+  DYNAMIC_EXE_LINKER_FLAGS: -dynamic
+
+packages:
+  launcher:
+  cmake:
+  python:
+    host: false
+    build_with: |
+      openssl,bzip2,sqlite
+  blas:
+    use: openblas
+  lapack:
+#    use: host-acml-lapack
+  daetk:
+  mpi:
+    use: host-mpi
+  mpi4py:
+  nose:
+  hdf5:
+  ipython:
+  matplotlib:
+  parmetis:
+    without_check: true
+  petsc:
+    build_with: |
+      parmetis
+    download: |
+      ptscotch, superlu, superlu_dist, spooles, hypre, blacs, scalapack, mumps
+    coptflags: -O2
+    link: shared
+    debug: false
+  petsc4py:
+    with_conf: true
+  pytables:
+  sphinx:
+  superlu:
+  sympy:
+  tetgen:
+  triangle:
+  memory_profiler:
+  scipy:
+#  netcdf4f:
+#  python-netcdf4:
+  h5py:
+  ode:
+ # pyode:
+ # vtk:
+ # pyvtk:
+
diff --git a/pkgs/hdf5/hdf5.yaml b/pkgs/hdf5/hdf5.yaml
index a9d97475f..6f610b0af 100644
--- a/pkgs/hdf5/hdf5.yaml
+++ b/pkgs/hdf5/hdf5.yaml
@@ -18,15 +18,16 @@ build_stages:
   bash: |
     export CC=${MPICC}
 
-- when: machine == 'CrayXE6'
+- when: machine == 'CrayXC30'
   name: make_exe_builds_static
   handler: bash
   after: configure
   before: make
   bash: |
-    for f in {test,testpar,tools/*,perform,hl/*,hl/*/*}/Makefile 
+    for f in {src,test,testpar,tools/*,perform,hl/*,hl/*/*}/Makefile 
     do 
       sed -i 's/CCLD = $(CC)/CCLD = $(CC) -static/g' $f
+      sed -i "s/sed -e 's\/-L\/:\/g' -e 's\/ \/\/g'/sed -e 's\/-L\/:\/g' -e 's\/-rpath=\/:\/g' -e 's\/-Wl,\/\/g' -e 's\/ \/\/g'/g" $f
     done
 
 - name: configure
@@ -40,7 +41,7 @@ build_stages:
           '--enable-largefile=yes',
           '--with-default-api-version=v18']
 
-- when: machine == 'CrayXE6'
+- when: machine == 'CrayXC30'
   name: configure
   extra: ['--enable-static-exec',
           '--with-zlib=${ZLIB_DIR}',

From 02cfd0fac4c04d2f253b1f18803305609e0b1d7e Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Tue, 3 Nov 2015 11:57:39 +0000
Subject: [PATCH 18/29] Added specific version numbers for petsc and petsc4py.

---
 examples/proteus.archer.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/examples/proteus.archer.yaml b/examples/proteus.archer.yaml
index 9b177b510..c2a8e5533 100644
--- a/examples/proteus.archer.yaml
+++ b/examples/proteus.archer.yaml
@@ -48,6 +48,8 @@ packages:
   parmetis:
     without_check: true
   petsc:
+    version: 3.6.1
+    without_check: true
     build_with: |
       parmetis
     download: |
@@ -56,6 +58,7 @@ packages:
     link: shared
     debug: false
   petsc4py:
+    version: 3.6.0
     with_conf: true
   pytables:
   sphinx:

From b2276b116c8aac4b4a33ff6130d8f94b7b90e4f8 Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Tue, 3 Nov 2015 11:58:57 +0000
Subject: [PATCH 19/29] Restored backward compatibility for CrayXE6.

---
 pkgs/hdf5/hdf5.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/hdf5/hdf5.yaml b/pkgs/hdf5/hdf5.yaml
index 6f610b0af..40cbdb7a7 100644
--- a/pkgs/hdf5/hdf5.yaml
+++ b/pkgs/hdf5/hdf5.yaml
@@ -18,7 +18,7 @@ build_stages:
   bash: |
     export CC=${MPICC}
 
-- when: machine == 'CrayXC30'
+- when: machine == 'CrayXE6' or machine == 'CrayXC30'
   name: make_exe_builds_static
   handler: bash
   after: configure
@@ -41,7 +41,7 @@ build_stages:
           '--enable-largefile=yes',
           '--with-default-api-version=v18']
 
-- when: machine == 'CrayXC30'
+- when: machine == 'CrayXE6' or machine == 'CrayXC30'
   name: configure
   extra: ['--enable-static-exec',
           '--with-zlib=${ZLIB_DIR}',

From bb922b8b53a91f07b50f3e2e40d7cccc2140a5c0 Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Fri, 6 Nov 2015 21:52:33 +0000
Subject: [PATCH 20/29] host-libsci-blas used by blas and scipy modules, and
 host-libsci-lapack used by lapack

---
 examples/proteus.archer.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/examples/proteus.archer.yaml b/examples/proteus.archer.yaml
index c2a8e5533..cf2ce14b9 100644
--- a/examples/proteus.archer.yaml
+++ b/examples/proteus.archer.yaml
@@ -34,9 +34,9 @@ packages:
     build_with: |
       openssl,bzip2,sqlite
   blas:
-    use: openblas
+    use: host-libsci-blas
   lapack:
-#    use: host-acml-lapack
+    use: host-libsci-lapack
   daetk:
   mpi:
     use: host-mpi
@@ -68,6 +68,7 @@ packages:
   triangle:
   memory_profiler:
   scipy:
+    use: host-libsci-blas
 #  netcdf4f:
 #  python-netcdf4:
   h5py:

From 8cf79e089807e712ddb9e78249a1865353ddaa45 Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Fri, 6 Nov 2015 21:56:13 +0000
Subject: [PATCH 21/29] placed patch for sed command in separate loop as per
 the fix on fix_hdf5_sed branch

---
 pkgs/hdf5/hdf5.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pkgs/hdf5/hdf5.yaml b/pkgs/hdf5/hdf5.yaml
index 40cbdb7a7..8f543eb3d 100644
--- a/pkgs/hdf5/hdf5.yaml
+++ b/pkgs/hdf5/hdf5.yaml
@@ -24,9 +24,12 @@ build_stages:
   after: configure
   before: make
   bash: |
-    for f in {src,test,testpar,tools/*,perform,hl/*,hl/*/*}/Makefile 
+    for f in {test,testpar,tools/*,perform,hl/*,hl/*/*}/Makefile 
     do 
       sed -i 's/CCLD = $(CC)/CCLD = $(CC) -static/g' $f
+    done
+    for f in {src,test,testpar,tools/*,perform,hl/*,hl/*/*}/Makefile 
+    do 
       sed -i "s/sed -e 's\/-L\/:\/g' -e 's\/ \/\/g'/sed -e 's\/-L\/:\/g' -e 's\/-rpath=\/:\/g' -e 's\/-Wl,\/\/g' -e 's\/ \/\/g'/g" $f
     done
 

From 4ed653a9f3781e1c2596881459b28c6494ff15b5 Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Fri, 6 Nov 2015 21:58:10 +0000
Subject: [PATCH 22/29] modified make command such that MAKE_NP is set

---
 pkgs/petsc/petsc.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/petsc/petsc.yaml b/pkgs/petsc/petsc.yaml
index 45fe482ad..14d54aee3 100644
--- a/pkgs/petsc/petsc.yaml
+++ b/pkgs/petsc/petsc.yaml
@@ -43,8 +43,8 @@ build_stages:
    handler: bash
    after: configure
    bash: |
-     make
- 
+     make MAKE_NP=${HASHDIST_CPU_COUNT}
+
 -  name: install
    mode: replace
    handler: bash

From fe76e07e30bd0544864bcc4a4bda8d0cb7ffbbd9 Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Fri, 13 Nov 2015 09:02:53 +0000
Subject: [PATCH 23/29] Added pip package to allow make develop.

---
 examples/proteus.archer.yaml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/examples/proteus.archer.yaml b/examples/proteus.archer.yaml
index cf2ce14b9..785849a62 100644
--- a/examples/proteus.archer.yaml
+++ b/examples/proteus.archer.yaml
@@ -27,6 +27,7 @@ parameters:
   DYNAMIC_EXE_LINKER_FLAGS: -dynamic
 
 packages:
+  pip:
   launcher:
   cmake:
   python:
@@ -69,11 +70,5 @@ packages:
   memory_profiler:
   scipy:
     use: host-libsci-blas
-#  netcdf4f:
-#  python-netcdf4:
   h5py:
   ode:
- # pyode:
- # vtk:
- # pyvtk:
-

From f780c7f1e499daeee44cbad0d9f209ba44cc2b6f Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Fri, 13 Nov 2015 09:50:43 +0000
Subject: [PATCH 24/29] Added sections to allow customised build paths.

---
 config.yaml | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/config.yaml b/config.yaml
index 64b388f63..12d9dddb2 100644
--- a/config.yaml
+++ b/config.yaml
@@ -5,6 +5,38 @@ package_dirs:
 hook_import_dirs:
 - base
 
+build_stores:
+ - dir: ./bld
+
+
+## Location where temporary directories for building software are created.
+## Such directories are by default removed again once the build is done.
+
+build_temp: ./tmp
+
+
+## Locations of downloaded tarballs and git repositories.  A location
+## can either be a local filesystem, or a URL to an online, read-only
+## mirror. Only the first location, which should be a local directory,
+## will be written to.
+
+source_caches:
+ - dir: ./src
+## For additional source cache mirror:
+## - url: https://some.server.org/hashdist/src
+
+
+## The cache directory is used for misc. caching (e.g., probing of host
+## system).  The contents can always be wiped without resulting in rebuilds.
+
+cache: ./cache
+
+## The roots directory contains links to (links to) profiles. Anything
+## pointed to through here will not be deleted when garbage-collected.
+
+gc_roots: ./gcroots
+
+
 parameters:
   BASH: /bin/bash
   PROLOGUE: | # by default, PROLOGUE is a no-op

From 531cfbd35a9569f0014262debcd849ce69927b46 Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Fri, 13 Nov 2015 12:35:43 +0000
Subject: [PATCH 25/29] Removed pip module.

---
 examples/proteus.archer.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/examples/proteus.archer.yaml b/examples/proteus.archer.yaml
index 785849a62..dcb32eb74 100644
--- a/examples/proteus.archer.yaml
+++ b/examples/proteus.archer.yaml
@@ -27,7 +27,6 @@ parameters:
   DYNAMIC_EXE_LINKER_FLAGS: -dynamic
 
 packages:
-  pip:
   launcher:
   cmake:
   python:

From d390e9fbe10f6d87d820325ff798441150276a17 Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Fri, 13 Nov 2015 12:36:21 +0000
Subject: [PATCH 26/29] Added CrayXC30 section.

---
 pkgs/numpy/numpy.yaml | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/pkgs/numpy/numpy.yaml b/pkgs/numpy/numpy.yaml
index 7e544e86c..838ea1299 100644
--- a/pkgs/numpy/numpy.yaml
+++ b/pkgs/numpy/numpy.yaml
@@ -76,6 +76,29 @@ build_stages:
       export BLAS=acml
       export ATLAS=None
 
+  - when: machine == 'CrayXC30'
+    name: create-site.cfg
+    after: prologue
+    before: install
+    handler: bash
+    bash: |
+      cat > site.cfg << EOF
+      [DEFAULT]
+      library_dirs = ${CRAY_LIBSCI_PREFIX_DIR}/lib
+      libraries = sci_gnu
+      EOF
+
+  - when: machine == 'CrayXC30'
+    name: set-LDFLAGS
+    after: prologue
+    before: install
+    handler: bash
+    bash: |
+      export LDFLAGS="-shared -Wl,-rpath=${PYTHON_DIR}/lib -Wl,-rpath=${CRAY_LIBSCI_PREFIX_DIR}/lib $(${PYTHON_DIR}/bin/python-config --ldflags)"
+      export LAPACK=sci_gnu
+      export BLAS=sci_gnu
+      export ATLAS=None
+
   - when: platform == 'Cygwin'
     name: set-LDFLAGS
     before: install

From d8ad2c42538f43fe2ebd2eac9b7060d29763ac01 Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Fri, 13 Nov 2015 12:36:55 +0000
Subject: [PATCH 27/29] Added CrayXC30 section.

---
 pkgs/petsc/petsc.py | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/pkgs/petsc/petsc.py b/pkgs/petsc/petsc.py
index ba0d5bdae..82cad6b92 100644
--- a/pkgs/petsc/petsc.py
+++ b/pkgs/petsc/petsc.py
@@ -25,6 +25,33 @@ def preConfigureCrayXE6(ctx, conf_lines):
                '--known-mpi-int64_t=1',
                '--with-pthread=1']
 
+def preConfigureCrayXC30(ctx, conf_lines):
+    conf_lines += ['LDFLAGS=' + ctx.parameters['DYNAMIC_EXE_LINKER_FLAGS'],
+               '--known-mpi-shared-libraries=1',
+               '--with-batch',
+               '--known-sdot-returns-double=0',
+               '--known-snrm2-returns-double=0',
+               '--known-level1-dcache-size=16384',
+               '--known-level1-dcache-linesize=64',
+               '--known-level1-dcache-assoc=4',
+               '--known-memcmp-ok=1',
+               '--known-sizeof-char=1',
+               '--known-sizeof-void-p=8',
+               '--known-sizeof-short=2',
+               '--known-sizeof-int=4',
+               '--known-sizeof-long=8',
+               '--known-sizeof-long-long=8',
+               '--known-sizeof-float=4',
+               '--known-sizeof-double=8',
+               '--known-sizeof-size_t=8',
+               '--known-bits-per-byte=8',
+               '--known-sizeof-MPI_Comm=4',
+               '--known-sizeof-MPI_Fint=4',
+               '--known-mpi-long-double=1',
+               '--known-mpi-c-double-complex=1',
+               '--known-mpi-int64_t=1',
+               '--with-pthread=1']
+
 def preConfigureSGIICEX(ctx, conf_lines):
     conf_lines += ['LDFLAGS=' + ctx.parameters['DYNAMIC_EXE_LINKER_FLAGS'],
                '--known-mpi-shared-libraries=1',

From 9a023428b6499fcd9d81ae00b2b61fc3dc98b2ba Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Mon, 16 Nov 2015 09:24:00 +0000
Subject: [PATCH 28/29] Removed redundant preConfigureCrayXC30 def.

---
 pkgs/petsc/petsc.py | 27 ---------------------------
 1 file changed, 27 deletions(-)

diff --git a/pkgs/petsc/petsc.py b/pkgs/petsc/petsc.py
index caa8fd72f..2cd2dcb07 100644
--- a/pkgs/petsc/petsc.py
+++ b/pkgs/petsc/petsc.py
@@ -54,33 +54,6 @@ def preConfigureCrayXC30(ctx, conf_lines):
                '--known-mpi-int64_t=1',
                '--with-pthread=1']
 
-def preConfigureCrayXC30(ctx, conf_lines):
-    conf_lines += ['LDFLAGS=' + ctx.parameters['DYNAMIC_EXE_LINKER_FLAGS'],
-               '--known-mpi-shared-libraries=1',
-               '--with-batch',
-               '--known-sdot-returns-double=0',
-               '--known-snrm2-returns-double=0',
-               '--known-level1-dcache-size=16384',
-               '--known-level1-dcache-linesize=64',
-               '--known-level1-dcache-assoc=4',
-               '--known-memcmp-ok=1',
-               '--known-sizeof-char=1',
-               '--known-sizeof-void-p=8',
-               '--known-sizeof-short=2',
-               '--known-sizeof-int=4',
-               '--known-sizeof-long=8',
-               '--known-sizeof-long-long=8',
-               '--known-sizeof-float=4',
-               '--known-sizeof-double=8',
-               '--known-sizeof-size_t=8',
-               '--known-bits-per-byte=8',
-               '--known-sizeof-MPI_Comm=4',
-               '--known-sizeof-MPI_Fint=4',
-               '--known-mpi-long-double=1',
-               '--known-mpi-c-double-complex=1',
-               '--known-mpi-int64_t=1',
-               '--with-pthread=1']
-
 def preConfigureSGIICEX(ctx, conf_lines):
     conf_lines += ['LDFLAGS=' + ctx.parameters['DYNAMIC_EXE_LINKER_FLAGS'],
                '--known-mpi-shared-libraries=1',

From b3e1a2e938ba333b28be17cebea121aae51e7c70 Mon Sep 17 00:00:00 2001
From: Michael Bareford <michael.bareford@epcc.ed.ac.uk>
Date: Mon, 16 Nov 2015 14:44:35 +0000
Subject: [PATCH 29/29] Reinstated https link to github repository.

---
 pkgs/ncurses/ncurses.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/ncurses/ncurses.yaml b/pkgs/ncurses/ncurses.yaml
index 3a7aa7e66..8ab8292a1 100644
--- a/pkgs/ncurses/ncurses.yaml
+++ b/pkgs/ncurses/ncurses.yaml
@@ -2,7 +2,7 @@ extends: [autotools_package]
 
 sources:
   - key: git:2031c7bde2dfb2189b9c724946f19c089596eac4
-    url: git@github.com:hashdist/pkg-ncurses
+    url: https://github.com/hashdist/pkg-ncurses
 
 defaults:
   relocatable: false