* gromacs: fix fftw dependency
Only depend on fftw+mpi when gromacs is built with mpi,
and depend on fftw~mpi otherwise.
* gromacs: fix cmake dependency
master branch depends on cmake 3.11 (as specified in CMakeLists.txt
cmake dependency is also bumped to 3.11 when fj compilers are used
in order to fix OpenMP detection.
I get the following error message, if I do not use editline from the system.
```
>> 3090 Undefined symbols for architecture x86_64:
3091 "_tgetent", referenced from:
3092 _terminal_set in libedit.a(terminal.c.o)
3093 "_tgetflag", referenced from:
3094 _terminal_set in libedit.a(terminal.c.o)
3095 "_tgetnum", referenced from:
3096 _terminal_set in libedit.a(terminal.c.o)
...
3110 _terminal_insertwrite in libedit.a(terminal.c.o)
3111 _terminal_clear_EOL in libedit.a(terminal.c.o)
3112 _terminal_clear_screen in libedit.a(terminal.c.o)
3113 _terminal_beep in libedit.a(terminal.c.o)
3114 ...
3115 ld: symbol(s) not found for architecture x86_64
```
Bug fix release:
4.0.4 -- June, 2020
-----------------------
- Fix a memory patcher issue intercepting shmat and shmdt. This was
observed on RHEL 8.x ppc64le (see README for more info).
- Fix an illegal access issue caught using gcc's address sanitizer.
Thanks to Georg Geiser for reporting.
- Add checks to avoid conflicts with a libevent library shipped with LSF.
- Switch to linking against libevent_core rather than libevent, if present.
- Add improved support for UCX 1.9 and later.
- Fix an ABI compatibility issue with the Fortran 2008 bindings.
Thanks to Alastair McKinstry for reporting.
- Fix an issue with rpath of /usr/lib64 when building OMPI on
systems with Lustre. Thanks to David Shrader for reporting.
- Fix a memory leak occurring with certain MPI RMA operations.
- Fix an issue with ORTE's mapping of MPI processes to resources.
Thanks to Alex Margolin for reporting and providing a fix.
- Correct a problem with incorrect error codes being returned
by OMPI MPI_T functions.
- Fix an issue with debugger tools not being able to attach
to mpirun more than once. Thanks to Gregory Lee for reporting.
- Fix an issue with the Fortran compiler wrappers when using
NAG compilers. Thanks to Peter Brady for reporting.
- Fix an issue with the ORTE ssh based process launcher at scale.
Thanks to Benjamín Hernández for reporting.
- Address an issue when using shared MPI I/O operations. OMPIO will
now successfully return from the file open statement but will
raise an error if the file system does not supported shared I/O
operations. Thanks to Romain Hild for reporting.
- Fix an issue with MPI_WIN_DETACH. Thanks to Thomas Naughton for reporting.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* Fix how the Conduit detects that the MPI compiler is the same as the
CC compiler and is more careful when it sets the MPI compilers to be
the Cray PE system compilers.
* Remove unnecessary push of the MPI compilers to the C compilers for Hydrogen.
* Added version 8.2.0, added dependency for documentation build, added variants for documentations
* Renamed variant '+man' to '+html'
Co-authored-by: Alexander Knieps <a.knieps@fz-juelich.de>
- Parallel HDF5 isn't required -- the comment seems to be about a
transitive dependency with pnetcdf.
- Boost usage should respect the variant, not automatically be reenabled
when choosing DTK.
Versions of py-tensorflow between versions 1.1 and 1.14 need a patch to
avoid an import error on the cloud package even if built without support
for the cloud package.
* bazel: Update for use with Fujitsu compiler
* bazel: Fix for use with Fujitsu compiler
* bazel: Fix flake8 error
* bazel: add conflicts setting for use with Fujitsu compiler
* fix flake8 error
* fix flake8 error
In Python 3.8, the reserved "tp_print" slot was changed from a function
pointer to a number, which broke the Python wrapping code in vtk@8
(causing "cannot convert 'std::nullptr_t' to 'Py_ssize_t'" errors in
various places). This is fixed in vtk@9.0.0.
This patch:
1) adds vtk@9.0.0
2) updates depends_on constraints to only use python@3.8: for vtk@9:
vtk@:8 depends on python@2, and vtk@8.0.1:8.9.9 depends on python@:3.7
3) Adds CMake flag VTK_PYTHON_VERSION=3 when using python@3 with vtk@9
* python: adding a distutils fix to improve build compatibility for C++ extension modules (e.g. py-matplotlib)
* python: added C/C++ distutils patches for python@3.6:3.8
Allow Spack to build with ROOT as an external dependency by setting
LD_LIBRARY_PATH: given that the external package was not built by
Spack, dependents would not be able to locate libraries using RPATHs
when running ROOT binaries.
Specified Python to be v2.7 only, as Python3 support is not currently
implemented in chill.
Update chill dependency versions for the following libraries to the
specific versions:
* rose: v0.9.13.0
* bison: v3.4.2
Both rose and iegenlib are build time dependencies, but are also run
time dependencies. Added 'run' to the build type for both dependencies.
cuda: 10.1 and onward, installers will crash if /tmp/cuda-installer.log
exists
Try to help if user owns the file, otherwise try to provide useful
info. Clean up the file post-install to try to avoid the whole issue.
* save edits
* tidy up
* Update var/spack/repos/builtin/packages/py-lmfit/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add python version constraints
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Sinan81 <Sinan81@github>
* Add pygelf Python package
* Update ReFrame package version
* Address styling remarks
* Update var/spack/repos/builtin/packages/reframe/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/reframe/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/reframe/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/reframe/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/reframe/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Address PR remarks
* Remove setuptools runtime dependency
* Address PR remarks
* Address PR remarks
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
bazel uses gcc's -MF option to write dependencies to a
file. Post-compilation, bazel reads this file and makes some
determinations.
"Since gcc is given only relative paths on the command line,
non-system include paths here should never be absolute. If they
are, it's probably due to a non-hermetic #include, & we should stop
the build with an error."
Spack directly injects absolute paths, which appear in this file and
cause bazel to fail the build despite the fact that compilation
succeeded.
This patch disables this failure mode by default, and allows for it
to be turned back on by using the '~nodepfail' variant.
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
#4 0x00007ffff7fa2970 in initscr () from .../lib/libncursesw.so.6
#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.
* Adding a package for wcs.
* Turning on sbml for wcs.
* The cpp flag needs to be available for wcs.
* Wcs needs SBML to properly define the namespace.
* Flake8 fixes.
* Fixing the help string with the description.
* Changing cpp to use the new variant syntax.
* Fixing flake8 errors.
* Forgot to delete one last fixme comment.
* Spack "develop" needs to link to repo "devel"
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Robert Blake <rob.c.blake.3@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Cray: fix Blue Waters support
* pkg-config env vars needed on Blue Waters
* cray platform: fix support for user-build MPI on cray machines
* reintroduce cray environment cleaning behind cnl version guard
* cray platform: fix support for user-build MPI on cray machines
Co-authored-by: Gregory <becker33@llnl.gov>
* Add new package: py-devlib
* Update var/spack/repos/builtin/packages/py-devlib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add depends
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [hsf-cmaketools] add package
* fix formatting
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [hsf-cmaketools] remove cmake_prefix_path which is set already by spack
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
