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manifestoso merged 897 commits intoDeepThoughtHPC:developfrom
spack:develop
Mar 22, 2020
Merged

sync#1
manifestoso merged 897 commits intoDeepThoughtHPC:developfrom
spack:develop

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sync develop

pat-s and others added 30 commits March 3, 2020 11:02
* @develop needs the full git repo to use "git describe"
  properly

* If not specifying the cxxstd variant, let cmake use its
  default

* Improve fmt dependencies: fairlogger < 1.6.2 does not
  work with fmt >= 6.

* Small other stuff
…alii to GO int, to make it compile again (#15288)

Co-authored-by: Andrey Prokopenko <[email protected]>
…15293)

and found when using the RelWithDebInfo build type.  Change protobuf
to only support Release and Debug build types.
Increase the connect timeout for elfutils to 60 sec.  Elfutils (and
bzip2) tar files are on sourceware.org which is often slow to respond.
* added UQTk package

* Add missing expat dependency to uqtk
Spack's fflags are meant for both f77 and fc. Therefore, they must
be passed as FFLAGS and FCFLAGS to the configure scripts of
Autotools-based packages.
fixes #15184

GraphBLAS depends on m4 according to CMake error message
Do not use INSTALL= when compiling the library
…15338)

* use os.sep instead of null byte to pad replacement paths in binaries

* Prefix the pading os.sep's
Removed the code that was converting the old index.yaml format into
index.json. Since the change happened in #2189 it should be
considered safe to drop this (untested) code.
Since 1.9.0 is broken for Darwin, which impacts many developers, and
the fix is still a RC, let's keep the previous release as default.

This avoids distruption for OSX developers and CI.
This recovers the old behavior of replace_prefix_bin that was
modified to work with elf binaries by prefixing os.sep to new prefix
until length is the same as old prefix.
Add the python dependency and CMake hints when build with tests.
`spack install --tests=root adios2`
* ADIOS2: Version `master`

Rename branch version to supported, real development branch `master`.
The old name is legacy Spack when alternative development branch
names were not yet supported.

* ADIOS: Simplify via spec Variable

use the already defined local variable `spec` to shorten
lines
Testing the install StopIteration exception resulted in an attribute error:

AttributeError: 'StopIteration' object has no attribute 'message'

This PR adds a unit test and resolves that error.
* [opensubdiv] created stub for opensubdiv

* [opensubdiv] added homepage and description

* [opensubdiv] removed boilerplate

* [opensubdiv] working on dependencies and variants

* [opensubdiv] fixed syntax error

* [opensubdiv] defined spec

* [opensubdiv] added dev version

* [opensubdiv] building on CudaPackage

* [opensubdiv] always build with open gl and depends_on('gl')

* [opensubdiv] applying cuda flags

* [opensubdiv] worked on doc variant

* [opensubdiv] added some x11 libraries

* [opensubdiv] depends on glfw

* [opensubdiv] locating glew

* [opensubdiv] added openmp variant

* [opensubdiv] flake8 fixing

* [opensubdiv] fixed develop version name

* [opensubdiv] fixed description to not need @
Add package for ripgrep:

    ripgrep is a line-oriented search tool that recursively searches
    your current directory for a regex pattern.  ripgrep is similar to
    other popular search tools like The Silver Searcher, ack and grep.
* New package: fd-find

Add package for fd-find:

    A simple, fast and user-friendly alternative to 'find'.

* Update copyright date
becker33 and others added 26 commits March 20, 2020 11:47
Bug: Spack hangs on some Cray machines

Reason: The TERM environment variable is necessary to run bash -lc "echo $CRAY_CPU_TARGET", but we run that command within env -i, which wipes the environment.

Fix: Manually forward the TERM environment variable to env -i /bin/bash -lc "echo $CRAY_CPU_TARGET"
This makes sure that a package's fetch_options are used when fetching
new versions to checksum. This allows working around problems with
slow servers or those requiring a cookie to be set.
Spack currently cannot run as a background process uninterrupted because some of the logging functions used in the install method (especially to create the dynamic verbosity toggle with the v key) cause the OS to issue a SIGTTOU to Spack when it's backgrounded.

This PR puts the necessary gatekeeping in place so that Spack doesn't do anything that will cause a signal to stop the process when operating as a background process.
Spack currently cannot run as a background process uninterrupted because some of the logging functions used in the install method (especially to create the dynamic verbosity toggle with the v key) cause the OS to issue a SIGTTOU to Spack when it's backgrounded.

This PR puts the necessary gatekeeping in place so that Spack doesn't do anything that will cause a signal to stop the process when operating as a background process.
* Add Ceres Solver version 1.14.0

* Add variants for Ceres Solver
* Add gmsh v4.5.4 with new options

This adds OpenCASCADE as an alternative to the oce package.
A new variant 'privateapi' is added to enable the gmsh private API.

* Make oce conflict with opencascade in gmsh
* freeipmi: Initial commit

Added freeipmi package. Configure and build work fine, install only as root,
thus added warning and added reference to issue #4432 .

* freeipmi: fixed change requests
Reading the database repeatedly can be quite slow.  We need a way to speed
up Spack when it reads the DB multiple times, but the DB has not been
modified between reads (which is nearly all the time).

- [x] Add a file containing a unique uuid that is regenerated at database
    write time. Use this uuid to suppress re-parsing the database
    contents if we know a previous uuid and the uuid has not changed.

- [x] Fix mutable_database fixture so that it resets the last seen
    verifier when it resets.

- [x] Enable not rereading the database immediately after a write. Make
    the tests reset the last seen verifier in between tests that use the
    database fixture.

- [x] make presence of uuid module optional
* add new pacakge: nfs-ganesha

* refine package.py

* update bison & flex as build depends
…ent (#15577)

* Put bindist.py on it's own branch

* Working on SL7 with python 3.6

* Flake8

* Put back clearing of compiler cache
* davix: add cxxstd variant

Davix is written in C++, so add this variant to allow dependents to specify
this so a consistent ABI is used.

* davix: fix flake8 errors
Update WarpX for recent developments:
- add openPMD I/O (default: ON)
- remove electro-static solver option (now a runtime option)
- enable tiny profiler by default
- depend on new CXX std support in make scripts for C++14
- WarpX only supports 2D and 3D in cartesian dims
`spack test` has a spurious '[+] ' in the output:

```
lib/spack/spack/test/install.py .........[+] ......
```

Output is properly suppressed:

```
lib/spack/spack/test/install.py ...............
```
@manifestoso manifestoso merged commit 94a8ae6 into DeepThoughtHPC:develop Mar 22, 2020
manifestoso pushed a commit that referenced this pull request Jun 19, 2020
Whenever attempting to use any ncurses functionality within cscope, a
page fault would result within the ncurses library.

    Program received signal SIGSEGV, Segmentation fault.
    0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    (gdb) bt
    #0  0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    #1  0x00007ffff7faa794 in _nc_setupscreen_sp () from .../lib/libncursesw.so.6
    #2  0x00007ffff7fa614c in newterm_sp () from .../lib/libncursesw.so.6
    #3  0x00007ffff7fa65b9 in newterm () from .../lib/libncursesw.so.6
    spack#4  0x00007ffff7fa2970 in initscr () from .../lib/libncursesw.so.6
    spack#5  0x0000000000403dc2 in main (argc=<optimized out>, argv=0x7fffffffcea8) at main.c:574

This is due to a conflict between libtinfo.so and libtinfow.so. Both are
linked into cscope:

    $ ldd $(which cscope)
    /bin/bash: .../lib/libtinfo.so.6: no version information available (required by /bin/bash)
        linux-vdso.so.1 (0x00007fff5dbcb000)
        libncursesw.so.6 => .../lib/libncursesw.so.6 (0x00007f435cc69000)
        libtinfo.so.6 => .../lib/libtinfo.so.6 (0x00007f435cc2c000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f435ca29000)
        libtinfow.so.6 => .../lib/libtinfow.so.6 (0x00007f435c9e8000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f435cca7000)

Specifically linking libtinfow.so instead of libtinfo.so resolves the
issue.

All instances of '...' above represent the path to the installed ncurses
for Spack.
manifestoso pushed a commit that referenced this pull request Jun 19, 2020
Whenever attempting to use any ncurses functionality within cscope, a
page fault would result within the ncurses library.

    Program received signal SIGSEGV, Segmentation fault.
    0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    (gdb) bt
    #0  0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    #1  0x00007ffff7faa794 in _nc_setupscreen_sp () from .../lib/libncursesw.so.6
    #2  0x00007ffff7fa614c in newterm_sp () from .../lib/libncursesw.so.6
    #3  0x00007ffff7fa65b9 in newterm () from .../lib/libncursesw.so.6
    spack#4  0x00007ffff7fa2970 in initscr () from .../lib/libncursesw.so.6
    spack#5  0x0000000000403dc2 in main (argc=<optimized out>, argv=0x7fffffffcea8) at main.c:574

This is due to a conflict between libtinfo.so and libtinfow.so. Both are
linked into cscope:

    $ ldd $(which cscope)
    /bin/bash: .../lib/libtinfo.so.6: no version information available (required by /bin/bash)
        linux-vdso.so.1 (0x00007fff5dbcb000)
        libncursesw.so.6 => .../lib/libncursesw.so.6 (0x00007f435cc69000)
        libtinfo.so.6 => .../lib/libtinfo.so.6 (0x00007f435cc2c000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f435ca29000)
        libtinfow.so.6 => .../lib/libtinfow.so.6 (0x00007f435c9e8000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f435cca7000)

Specifically linking libtinfow.so instead of libtinfo.so resolves the
issue.

All instances of '...' above represent the path to the installed ncurses
for Spack.
manifestoso pushed a commit that referenced this pull request Oct 16, 2020
The r-devtools package was not installable due to a few issues.

- The rstudioapi spec was for 0.11.0 but the rstudioapi version is
  actually 0.11. This caused an error during concretization.
- Set r-usethis to depend on [email protected]: rather than [email protected].
- Set r-usethis to depend on [email protected]: rather than [email protected].
- Added version r-gh-1.1.0 as it is not currently present in spack.
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