internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: spack/spack

Issue:
PMIx build fails on aarch64

PMIx up through version 2.1.0 has a bug in its test code that causes problems on strict alignment architectures like aarch64.  (The issue is explained in this commit: pmix/pmix@3a8bc4503a04158e3be072c92eb0253c6c77e534)  The fix is included in the 2.1.1 release.  The issue is exacerbated by building with optimizations turned on (which Spack does by default); it doesn't seem to happen when compiling with ```-O0```.

Since the issue is in test code, the work-around is to just not build that code.
### Expected Result

The install should work.

### Actual Result

The install fails attempting to link pmix_test.

### Steps to reproduce the issue

On an aarch64 machine:
```console
$ spack install -j 56 pmix %gcc@7.3.0
```

### Information on your system

1. HPE (pre-production) Apache servers (w/ Cavium ThunderX2 CPU's)
1. RHEL 7.4
1. GCC 7.3.0 (built by Spack) and GCC 4.8.5 (RHEL 7 default version)



Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/pmix/package.py b/var/spack/repos/builtin/packages/pmix/package.py
--- a/var/spack/repos/builtin/packages/pmix/package.py
+++ b/var/spack/repos/builtin/packages/pmix/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 
 from spack import *
+import spack.architecture
 
 
 class Pmix(AutotoolsPackage):
@@ -48,6 +49,7 @@ class Pmix(AutotoolsPackage):
     homepage = "https://pmix.github.io/pmix"
     url      = "https://github.com/pmix/pmix/releases/download/v2.0.1/pmix-2.0.1.tar.bz2"
 
+    version('2.1.1',    'f9f109421661b757245d5e0bd44a38b3')
     version('2.1.0',    'fc97513b601d78fe7c6bb20c6a21df3c')
     version('2.0.2',    'e3ed1deed87c84f9b43da2621c6ad689')
     version('2.0.1',    'ba3193b485843516e6b4e8641e443b1e')
@@ -61,6 +63,7 @@ class Pmix(AutotoolsPackage):
     depends_on('libevent')
 
     def configure_args(self):
+
         spec = self.spec
         config_args = [
             '--enable-shared',
@@ -71,4 +74,11 @@ def configure_args(self):
         config_args.append(
             '--with-libevent={0}'.format(spec['libevent'].prefix))
 
+        # Versions < 2.1.1 have a bug in the test code that *sometimes*
+        # causes problems on strict alignment architectures such as
+        # aarch64.  Work-around is to just not build the test code.
+        if 'aarch64' in spack.architecture.sys_type() and \
+           self.spec.version < Version('2.1.1'):
+            config_args.append('--without-tests-examples')
+
         return config_args


Test patch:
Repository: spack/spack

Issue:
Kokkos "openmp" feature should be optional, default feature
XCode Clang does not ship with OpenMP support, and in general it would be useful if the Kokkos package could build for compilers without OpenMP (e.g. Kokkos::View is an independently useful concept). Therefore, the `--with-openmp` flag in the Kokkos build should be guarded by an `openmp` feature that can be optionally disabled.

### Expected Result

Successful kokkos install with the default Mac compiler.

### Actual Result
[spack-build.out.txt](https://github.com/spack/spack/files/1944580/spack-build.out.txt)

### Steps to reproduce the issue
```console
$ spack install kokkos %clang@9.0.0-apple
```

### Proposed successful installation

```console
# spack install kokkos -openmp %clang@9.0.0-apple
```

### Information on your system
macOS High Sierra with up-to-date XCode command line tools


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py
--- a/var/spack/repos/builtin/packages/kokkos/package.py
+++ b/var/spack/repos/builtin/packages/kokkos/package.py
@@ -32,10 +32,21 @@ class Kokkos(Package):
     homepage = "https://github.com/kokkos/kokkos"
     url      = "https://github.com/kokkos/kokkos/archive/2.03.00.tar.gz"
 
+    version('2.5.00',  '2db83c56587cb83b772d0c81a3228a21')
+    version('2.04.11', 'd4849cee6eb9001d61c30f1d9fe74336')
+    version('2.04.04', '2c6d1c2569b91c9fcd4117296438e65c')
+    version('2.04.00', 'd99ac790ff5f29545d8eb53de90c0a85')
+    version('2.03.13', '3874a159a517384541ea5b52f85501ba')
+    version('2.03.05', '8727d783453f719eec392e10a36b49fd')
     version('2.03.00', 'f205d659d4304747759fabfba32d43c3')
+    version('2.02.15', 'de41e38f452a50bb03363c519fe20769')
+    version('2.02.07', 'd5baeea70109249f7dca763074ffb202')
+    version('develop', git='https://github.com/kokkos/kokkos',
+            branch='develop')
 
     variant('qthreads', default=False, description="enable Qthreads backend")
     variant('cuda', default=False, description="enable Cuda backend")
+    variant('openmp', default=True, description="enable OpenMP backend")
 
     # Specify that v1.x is required as v2.x has API changes
     depends_on('hwloc@:1')
@@ -49,9 +60,10 @@ def install(self, spec, prefix):
             g_args = [
                 '--prefix=%s' % prefix,
                 '--with-hwloc=%s' % spec['hwloc'].prefix,
-                '--with-serial',
-                '--with-openmp',
+                '--with-serial'
             ]
+            if '+openmp' in spec:
+                g_args.append('--with-openmp')
             if 'qthreads' in spec:
                 g_args.append('--with-qthreads=%s' % spec['qthreads'].prefix)
             if 'cuda' in spec:


Test patch:
Repository: spack/spack

Issue:
laghos cannot be build
```
$ spack install laghos
==> Error: An unsatisfiable version constraint has been detected for spec:

    hypre@2.14.0%gcc@7.2.0~int64+internal-superlu+mpi+shared arch=linux-gentoo2-x86_64


while trying to concretize the partial spec:

    mfem@3.3.2%gcc@7.2.0~conduit~debug~examples~gnutls+gzstream+hypre~lapack~libunwind+metis~miniapps~mpfr+mpi~netcdf~openmp~petsc~shared+static~suite-sparse~sundials~superlu-dist~threadsafe timer=auto arch=linux-gentoo2-x86_64
        ^openmpi@3.0.1%gcc@7.2.0~cuda fabrics= ~java~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-gentoo2-x86_64
            ^hwloc@:1.999
                ^pkgconfig
            ^numactl
                ^autoconf
                    ^m4@1.4.6:
                    ^perl
                        ^gdbm
                            ^readline
                                ^ncurses
                ^automake
                ^libtool
            ^zlib


mfem requires hypre version 2.10.0:2.13.999, but spec asked for 2.14.0
```

Related to #7903 


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
--- a/var/spack/repos/builtin/packages/mfem/package.py
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -163,8 +163,8 @@ class Mfem(Package):
     conflicts('timer=mpi', when='~mpi')
 
     depends_on('mpi', when='+mpi')
-    depends_on('hypre', when='+mpi')
-    depends_on('hypre@2.10.0:2.13.999', when='@:3.3.2')
+    depends_on('hypre@2.10.0:2.13.999', when='@:3.3.999+mpi')
+    depends_on('hypre', when='@3.4:+mpi')
 
     depends_on('metis', when='+metis')
     depends_on('blas', when='+lapack')


Test patch:
Repository: spack/spack

Issue:
Cannot fetch pkgconf@1.4.0
```
$ spack install pkgconfig
==> Installing pkgconf
==> Fetching https://distfiles.dereferenced.org/pkgconf/pkgconf-1.4.0.tar.xz
#=#=-  #       #                                                                                                                                                                                                                                               #=O=#     #        #
curl: (60) SSL certificate problem: certificate has expired
More details here: https://curl.haxx.se/docs/sslcerts.html

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
==> Fetching from https://distfiles.dereferenced.org/pkgconf/pkgconf-1.4.0.tar.xz failed.
==> Error: FetchError: All fetchers failed for pkgconf-1.4.0-lwcki7c6gvhmkysqcr74gqzhs5y646af
FetchError: FetchError: All fetchers failed for pkgconf-1.4.0-lwcki7c6gvhmkysqcr74gqzhs5y646af

/home/junghans/spack/lib/spack/spack/package.py:1028, in do_fetch:
     25                                     self.spec.format('$_$@'), ck_msg)
     26
     27            self.stage.create()
  >> 28            self.stage.fetch(mirror_only)
     29            self._fetch_time = time.time() - start_time
     30
     31            if spack.do_checksum and self.version in self.versions:
```



Discussion:
Had the same issue today, resorted to:
```console
$ spack -k mirror create ...
```
to download it.

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/pkgconf/package.py b/var/spack/repos/builtin/packages/pkgconf/package.py
--- a/var/spack/repos/builtin/packages/pkgconf/package.py
+++ b/var/spack/repos/builtin/packages/pkgconf/package.py
@@ -32,7 +32,7 @@ class Pkgconf(AutotoolsPackage):
     maintaining compatibility."""
 
     homepage = "http://pkgconf.org/"
-    url      = "https://distfiles.dereferenced.org/pkgconf/pkgconf-1.3.10.tar.xz"
+    url      = "http://distfiles.alpinelinux.org/distfiles/pkgconf-1.3.10.tar.xz"
 
     version('1.4.0', 'c509c0dad5a70aa4bc3210557b7eafce')
     version('1.3.10', '9b63707bf6f8da6efb3868101d7525fe')


Test patch:
Repository: spack/spack

Issue:
[libjpeg] Incorrect hash for version 9c
Spack lists the md5 hash for libjpeg 9c as 7794e558c60605424fb1025d836fbf47, but
```
$ curl http://www.ijg.org/files/jpegsrc.v9c.tar.gz | md5sum
93c62597eeef81a84d988bccbda1e990
```
There isn't an official hash or a signature on the ijg.org website, or I would have made a pull request to fix it.


Discussion:
Would you mind contacting the developers and asking them why their checksum changed? 99% of the time, it's a bugfix without a new version number. 1% of the time, the website got hacked and you're downloading a virus.
Sent an email to the jpeg-info address listed in their readme asking about a signature or hash for the archive.

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/libjpeg/package.py b/var/spack/repos/builtin/packages/libjpeg/package.py
--- a/var/spack/repos/builtin/packages/libjpeg/package.py
+++ b/var/spack/repos/builtin/packages/libjpeg/package.py
@@ -33,7 +33,7 @@ class Libjpeg(AutotoolsPackage):
     homepage = "http://www.ijg.org"
     url      = "http://www.ijg.org/files/jpegsrc.v9c.tar.gz"
 
-    version('9c', '7794e558c60605424fb1025d836fbf47')
+    version('9c', '93c62597eeef81a84d988bccbda1e990')
     version('9b', '6a9996ce116ec5c52b4870dbcd6d3ddb')
     version('9a', '3353992aecaee1805ef4109aadd433e7')
 


Test patch:
Repository: spack/spack

Issue:
xsdk@develop has an unsatisfiable version constraint
`xsdk@develop` has an unsatisfiable version constraint

### Expected Result

`spack spec xsdk@develop` concretizes.

### Actual Result

```
$ spack spec xsdk@develop
Input spec
--------------------------------
xsdk@develop

Concretized
--------------------------------
==> Error: An unsatisfiable version constraint has been detected for spec:

    hypre@develop~int64~internal-superlu
        ^blas
        ^lapack


while trying to concretize the partial spec:

    mfem@3.3.2+examples+hypre+miniapps+mpi+petsc+sundials+superlu-dist


mfem requires hypre version 2.10.0:2.13.999, but spec asked for develop
```
That's because `xsdk` has
```
depends_on('mfem@3.3.2+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@develop')
depends_on('hypre@develop~internal-superlu', when='@develop')
```
whereas `mfem` has
```
depends_on('hypre@2.10.0:2.13.999', when='@:3.3.999+mpi')
```
The two are clearly conflicting.

### Steps to reproduce the issue

```console
$ spack spec xsdk@develop
```

Can somebody from `mfem` have a look please?
@goxberry @tzanio @markcmiller86 @acfisher @v-dobrev ping.


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/xsdk/package.py b/var/spack/repos/builtin/packages/xsdk/package.py
--- a/var/spack/repos/builtin/packages/xsdk/package.py
+++ b/var/spack/repos/builtin/packages/xsdk/package.py
@@ -51,7 +51,7 @@ class Xsdk(Package):
     depends_on('hypre@develop~internal-superlu', when='@develop')
 
     depends_on('mfem@3.3.2+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@0.3.0')
-    depends_on('mfem@3.3.2+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@develop')
+    depends_on('mfem@develop+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@develop')
 
     depends_on('superlu-dist@5.2.2', when='@0.3.0')
     depends_on('superlu-dist@xsdk-0.2.0', when='@xsdk-0.2.0')


Test patch:
Repository: spack/spack

Issue:
py-vmd-python "No module named pkg_resources"
Per [Usage](https://github.com/Eigenstate/vmd-python) this should work.


Discussion:
**me@node103[~]$ spack load -r py-vmd-python**

```
> user@node103[~]$ module list
> Currently Loaded Modulefiles:
>   1) libbsd-0.8.6-gcc-6.3.0-ivk7mlv           6) libxml2-2.9.8-gcc-6.3.0-zrdgx44         11) netcdf-4.6.1-gcc-6.3.0-3z5cefi          16) gdbm-1.14.1-gcc-6.3.0-ye56lvz           21) tcl-8.6.8-gcc-6.3.0-igznzsa
>   2) expat-2.2.5-gcc-6.3.0-cxe665y            7) numactl-2.0.11-gcc-6.3.0-dqrr7l5        12) openblas-0.2.20-gcc-6.3.0-oq3x5fo       17) openssl-1-gcc-6.3.0-jfeudwn             22) py-vmd-python-2.0.10-gcc-6.3.0-pz2cxy4
>   3) libpciaccess-0.13.5-gcc-6.3.0-bkmqzbd    8) hwloc-1.11.9-gcc-6.3.0-mq5dzo4          13) bzip2-1.0.6-gcc-6.3.0-x5hwxgo           18) sqlite-3.23.1-gcc-6.3.0-impps3n
>   4) xz-5.2.4-gcc-6.3.0-o2xme3g               9) openmpi-3.1.0-gcc-6.3.0-m2rov3w         14) ncurses-6.1-gcc-6.3.0-rqwrhpn           19) python-2.7.15-gcc-6.3.0-fvf4vy3
>   5) zlib-1.2.11-gcc-6.3.0-rjqs3cq           10) hdf5-1.10.2-gcc-6.3.0-42y7cl5           15) readline-7.0-gcc-6.3.0-gt74ike          20) py-numpy-1.14.2-gcc-6.3.0-a3f3vuz
```

Though I get this error:

```
> me@node103[~]$ python
> Python 2.7.15 (default, May 30 2018, 16:45:15) 
> [GCC 6.3.0] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from vmd import molecule, vmdnumpy
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/pbtech_mounts/softlib001/apps/EL6/spack/opt/spack/linux-rhel6-x86_64/gcc-6.3.0/py-vmd-python-2.0.10-pz2cxy4j5frxqydqzxsuh5di2qf3z5vc/lib/python2.7/site-packages/vmd/__init__.py", line 17, in <module>
>     from pkg_resources import resource_filename
> ImportError: No module named pkg_resources
> 
```
Looks like we need `setuptools`

**spack load -r py-setuptools ^/fvf4vy3**

```
me@node103[~]$ python
Python 2.7.15 (default, May 30 2018, 16:45:15) 
[GCC 6.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from vmd import molecule, vmdnumpy
>>> 
```


Resolving patch:
diff --git a/var/spack/repos/builtin/packages/py-vmd-python/package.py b/var/spack/repos/builtin/packages/py-vmd-python/package.py
--- a/var/spack/repos/builtin/packages/py-vmd-python/package.py
+++ b/var/spack/repos/builtin/packages/py-vmd-python/package.py
@@ -33,8 +33,9 @@ class PyVmdPython(PythonPackage):
 
     version('2.0.10', '8c746d961497a676053b66e3dd692794')
 
-    depends_on('python@2.7:2.8')
-    depends_on('py-numpy')
+    depends_on('python@2.7:2.8', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-setuptools', type='run')
     depends_on('tcl')
     depends_on('netcdf')
     depends_on('expat')


Test patch:
Repository: spack/spack

Issue:
simple feature request to spack arch
To help facilitate script development that involves Spack, could you add two options to Spack arch?

spack arch -o, --operating_system (outputs e.g., centos6)
spack arch -t, --target  (outputs e.g., x86_64)


Discussion:

Resolving patch:
diff --git a/lib/spack/spack/cmd/arch.py b/lib/spack/spack/cmd/arch.py
--- a/lib/spack/spack/cmd/arch.py
+++ b/lib/spack/spack/cmd/arch.py
@@ -35,11 +35,24 @@ def setup_parser(subparser):
     parts = subparser.add_mutually_exclusive_group()
     parts.add_argument(
         '-p', '--platform', action='store_true', default=False,
-        help="print only the platform")
+        help='print only the platform')
+    parts.add_argument(
+        '-o', '--operating-system', action='store_true', default=False,
+        help='print only the operating system')
+    parts.add_argument(
+        '-t', '--target', action='store_true', default=False,
+        help='print only the target')
 
 
 def arch(parser, args):
+    arch = architecture.Arch(
+        architecture.platform(), 'default_os', 'default_target')
+
     if args.platform:
-        print(architecture.platform())
+        print(arch.platform)
+    elif args.operating_system:
+        print(arch.platform_os)
+    elif args.target:
+        print(arch.target)
     else:
-        print(architecture.sys_type())
+        print(arch)
diff --git a/lib/spack/spack/cmd/help.py b/lib/spack/spack/cmd/help.py
--- a/lib/spack/spack/cmd/help.py
+++ b/lib/spack/spack/cmd/help.py
@@ -59,9 +59,9 @@
       @B{variant=value1,value2,value3}  set multi-value <variant> values
 
     architecture variants:
-      @m{target=target}                 specific <target> processor
-      @m{os=operating_system}           specific <operating_system>
       @m{platform=platform}             linux, darwin, cray, bgq, etc.
+      @m{os=operating_system}           specific <operating_system>
+      @m{target=target}                 specific <target> processor
       @m{arch=platform-os-target}       shortcut for all three above
 
     cross-compiling:


Test patch:
diff --git a/lib/spack/spack/test/cmd/arch.py b/lib/spack/spack/test/cmd/arch.py
--- a/lib/spack/spack/test/cmd/arch.py
+++ b/lib/spack/spack/test/cmd/arch.py
@@ -29,6 +29,27 @@
 
 
 def test_arch():
-    """Sanity check the arch command to make sure it works."""
+    """Sanity check ``spack arch`` to make sure it works."""
 
     arch()
+
+
+def test_arch_platform():
+    """Sanity check ``spack arch --platform`` to make sure it works."""
+
+    arch('-p')
+    arch('--platform')
+
+
+def test_arch_operating_system():
+    """Sanity check ``spack arch --operating-system`` to make sure it works."""
+
+    arch('-o')
+    arch('--operating-system')
+
+
+def test_arch_target():
+    """Sanity check ``spack arch --target`` to make sure it works."""
+
+    arch('-t')
+    arch('--target')
Repository: spack/spack

Issue:
simpleMOC checksum has changed 
```
==> Error: ChecksumError: md5 checksum failed for /home/ci/spack/var/spack/stage/simplemoc-1.0-bm3qsbplyedikl75keiqtnibl23rrtud/master.tar.gz
    Expected d8827221a4ae76e9766a32e16d143e60 but got 277fa6cbcf8fc8e2e10575438464cd13
/home/ci/spack/lib/spack/spack/package.py:938, in do_fetch:
        935        self.stage.fetch(mirror_only)
        936        self._fetch_time = time.time() - start_time
        937
  >>    938        if checksum and self.version in self.versions:
        939            self.stage.check()
        940
        941        self.stage.cache_local()
```

/cc @jtramm


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/simplemoc/package.py b/var/spack/repos/builtin/packages/simplemoc/package.py
--- a/var/spack/repos/builtin/packages/simplemoc/package.py
+++ b/var/spack/repos/builtin/packages/simplemoc/package.py
@@ -33,9 +33,9 @@ class Simplemoc(MakefilePackage):
         light water reactor simulation."""
 
     homepage = "https://github.com/ANL-CESAR/SimpleMOC/"
-    url = "https://github.com/ANL-CESAR/SimpleMOC/archive/master.tar.gz"
+    url = "https://github.com/ANL-CESAR/SimpleMOC/archive/v4.tar.gz"
 
-    version('1.0', 'd8827221a4ae76e9766a32e16d143e60')
+    version('4', sha256='a39906014fdb234c43bf26e1919bdc8a13097788812e0b353a492b8e568816a6')
 
     tags = ['proxy-app']
 


Test patch:
Repository: spack/spack

Issue:
bzip.org down
![screenshot from 2018-08-09 09-37-29](https://user-images.githubusercontent.com/14250760/43902396-fe9a826a-9bb7-11e8-9097-44e40c3b65fa.png)



Discussion:
Also [hosted here](https://fossies.org/linux/misc/bzip2-1.0.6.tar.gz) with same checksum
https://lwn.net/Articles/762264/
py-flake8 depends on this...

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py
--- a/var/spack/repos/builtin/packages/bzip2/package.py
+++ b/var/spack/repos/builtin/packages/bzip2/package.py
@@ -32,9 +32,11 @@ class Bzip2(Package):
     compressors), whilst being around twice as fast at compression
     and six times faster at decompression."""
 
-    homepage = "http://www.bzip.org"
-    url      = "http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz"
-    list_url = "http://www.bzip.org/downloads.html"
+    # FIXME: The bzip.org domain has expired:
+    # https://lwn.net/Articles/762264/
+    # This package will need to be updated when a new home is found.
+    homepage = "https://sourceware.org/bzip2/"
+    url      = "https://fossies.org/linux/misc/bzip2-1.0.6.tar.gz"
 
     version('1.0.6', '00b516f4704d4a7cb50a1d97e6e8e15b')
 


Test patch:
Repository: spack/spack

Issue:
Install of Nekbone@17 fails
```
==> Error: FileNotFoundError: [Errno 2] No such file or directory: '../Nekbone'

/home/junghans/spack/var/spack/repos/builtin/packages/nekbone/package.py:65, in install:
         62            cc = spec['mpi'].mpicc
         63
         64        # Install Nekbone in prefix.bin
  >>     65        install_tree("../Nekbone", prefix.bin.Nekbone)
         66
         67        # Install scripts in prefix.bin
         68        nekpmpi = 'test/example1/nekpmpi'
```

@thilinarmtb please have a look!



Discussion:
@adamjstewart 
@adamjstewart: Actually, nevermind.  I thought #8289 was merged already.
@junghans I will have a look.
From looking at the spackage, changing `install_tree("../Nekbone", prefix.bin.Nekbone)` to `install_tree(self.stage.source_path, prefix.bin.Nekbone)` seems to provide the intended behavior. 

But is the intended behavior even "correct"? It looks like it just copies the files and sets it up so that when the examples are run it will use the spack compiler to build the code.

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/nekbone/package.py b/var/spack/repos/builtin/packages/nekbone/package.py
--- a/var/spack/repos/builtin/packages/nekbone/package.py
+++ b/var/spack/repos/builtin/packages/nekbone/package.py
@@ -62,7 +62,7 @@ def install(self, spec, prefix):
             cc = spec['mpi'].mpicc
 
         # Install Nekbone in prefix.bin
-        install_tree("../Nekbone", prefix.bin.Nekbone)
+        install_tree(self.stage.source_path, prefix.bin.Nekbone)
 
         # Install scripts in prefix.bin
         nekpmpi = 'test/example1/nekpmpi'


Test patch: