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Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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spack config add <value>: add nested value value to the configuration scope specified
spack config remove/rm: remove specified configuration from the relevant scope
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The rose library uses the `strtoflt128` and `quadmath_snprintf`
functions. In order to successfully link the rose library, chill must
also link the GCC libquadmath library to resolve the two functions. This
patch changes the chill build to include this library.
Chill will also not compile unless headers from the gmp and isl
libraries are found in the includes path. Two patches - one each for gmp
and isl - modify the chill build process to add options to specify those
paths. These options follow the similar pattern as seen with BOOSTHOME
and ROSEHOME options which already exist in the chill build process.
Because of the addition of GMPHOME and ISLHOME options, build
requirements for gmp and isl are also added.
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* mdanalysis
* [py-mmtf-python] fixed copyright
Co-authored-by: Andrew Elble <aweits@rit.edu>
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* Update package.py
* edit confliction when add package 'meam'
The USER-MEAMC fully replaces the MEAM package, which has been removed from LAMMPS after the 12 December 2018 version.
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* Add missing dependency on Python for Mono.
At build time
* Adding version 6.8.0.123 for mono
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The lapack-0.3.9-xerbl patch is not needed for versions 0.3.10 and
above.
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* Updated nearly all options to default to OFF
* Fixed imported but unused module flake error
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* Updated MUMPS-5.3.3
* fixed E741 error(l -> ltr)
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Signed-off-by: Adam Moody <moody20@llnl.gov>
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* Add ability to force removal of install failure tracking data through spack clean
* Add clean failures option to packaging guide
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packages. (#8623)
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* 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.
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perl.org still recommends 5.30.3, so keep it as the preferred version.
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* Some minor fixes to set_permissions() in file_permissions.py
The set_permissions() routine claims to prevent users from creating
world writable suid binaries. However, it seems to only be checking
for/preventing group writable suid binaries.
This patch modifies the routine to check for both world and group
writable suid binaries, and complain appropriately.
* permissions.py: Add test to check blocks world writable SUID files
The original test_chmod_rejects_group_writable_suid tested
that the set_permissions() function in
lib/spack/spack/util/file_permissions.py
would raise an exception if changed permission on a file with
both SUID and SGID plus sticky bits is chmod-ed to g+rwx and o+rwx.
I have modified so that more narrowly tests a file with SUID
(and no SGID or sticky bit) set is chmod-ed to g+w.
I have added a second test test_chmod_rejects_world_writable_suid
that checks that exception is raised if an SUID file is chmod-ed
to o+w
* file_permissions.py: Raise exception when try to make sgid file world writable
Updated set_permissions() in file_permissions.py to also raise
an exception if try to make an SGID file world writable. And
added corresponding unit test as well.
* Remove debugging prints from permissions.py
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* Module index should not be unconditionally overwritten
Uncovered after we switched our CI to generate modules for packages
one-by-one rather than in bulk. This overwrote a complete module index
with an index with a single entry, and broke our downstream Spack
instances that needed the upstream module index.
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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
```
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bugfix: fix compiler environment handling to reset environment after
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* Added unit tests to Github Actions
* Set user e-mail and name for git tests to succeed
* Simplify setup.sh logic
* Replicate Travis script on Github Actions
* Update flags since '.' is not allowed
* Added badge, simplified workflow
* Remove pinning of coverage
* Remove unit tests run on Github Actions from Travis
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parallel-netcdf's buildiface script needs perl during build.
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Co-authored-by: Andrew Elble <aweits@rit.edu>
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Bug fix release:
4.0.4 -- June, 2020
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- 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>
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(#17182)
See https://gitlab.cern.ch/hepmc/HepMC3/-/commit/ba38f14d8f56c16cc4105d98f6d4540c928c6150, which is included in master and released as of hepmc3@3.2.2
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PR #17108 broke the build. Spack's ncurses package does not provide a
libtermcap, so we need to use libtinfow.
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* add package evtgen
fix formatting
add evtgen dependencies and update pythia8
fix formatting
* [evtgen] update versions
* [pythia8] add 'without-PACKAGE' args
* fix formatting
* Add LHAPDF
Co-authored-by: iarspider
* Add package whizard
fix formatting
* [pyhtia8, evtgen] add conflict msg re: circular dependencies
* [pyhtia8, evtgen] fix conflicts
* [pyhtia8, evtgen] fix msg string
* Set pythia8 default to ~evtgen
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* [py-macs2] Combined commit
- Added version 2.1.3.3
- added dependency py-cython
Author: Jen Herting <jen@herting.cc>
Date: Tue May 26 16:41:28 2020 -0400
[py-macs2] added sha256=
Author: Andrew Elble <aweits@rit.edu>
Date: Tue Oct 29 10:34:33 2019 -0400
migrated repos
* [py-macs2] fixed copyright
* [py-macs2] py-cython is build dependency
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