As of v15.7, the PGI Fortran compiler does not properly support how
Open MPI uses the "USE ... ONLY" Fortran syntax to include modules
with conflicting symbol definitions (interestingly, pgfortran only has
a problem with this when compiling with -g).
In short, OMPI uses "USE :: module_aaa, ONLY: foo" and "USE ::
module_bbb, ONLY: bar" to use modules aaa and bbb, even though they
contain conflicting definitions for some symbols. However, the use of
the ONLY clause should preclude the inclusion of the conflicting
symbols -- as the word implies, it should direct the compiler to
*only* use the symbols identified by the clause (i.e., foo and bar, in
this example).
This commit adds a configure test for this capability. If the
compiler fails to build a simple test that mimics this behavior, then
disable the mpi_f08 bindings.
Fixesopen-mpi/ompi#857
After long debugging, I found last week the reason this optimization originally broke
some hdf5 tests. We now pass the hdf5 test suite with the optimization being actively used.
Specifically:
- reduce the number of realloc's and malloc's by moving
some arrays out of the cycle loop, if we know that there
size is not changing
- store the rank of the aggregator in a separate variable to avoid
continuous dereferencing
- change the wait_all logic in write_all to use a fix number of requests
(even if they are MPI_REQUEST_NULL)
- fix the timing to considere the two initial allgather and the one
allgatherv operation to be a part of it
- add more comments.
- MPI_Compare_and_swap
- MPI_Fetch_and_op
- MPI_Raccumulate
- MPI_Win_detach
Thanks to Michael Knobloch and Takahiro Kawashima for bringing this
to our attention
Bring Slurm PMI-1 component online
Bring the s2 component online
Little cleanup - let the various PMIx modules set the process name during init, and then just raise it up to the ORTE level. Required as the different PMI environments all pass the jobid in different ways.
Bring the OMPI pubsub/pmi component online
Get comm_spawn working again
Ensure we always provide a cpuset, even if it is NULL
pmix/cray: adjust cray pmix component for pmix
Make changes so cray pmix can work within the integrated
ompi/pmix framework.
Bring singletons back online. Implement the comm_spawn operation using pmix - not tested yet
Cleanup comm_spawn - procs now starting, error in connect_accept
Complete integration
In an abort situation, just bail out immediately -- don't try to
invoke any atexit()/on_exit()-registered functions.
This is similar rationale to
open-mpi/ompi@17846411c3.
Ensure to define ompi/pompi versions for platforms that don't have
weak symbols. Also make fortran/mpif-h/profile build a separate
sizeof library, just like fortran/mpifh-h does.
Per http://www.open-mpi.org/community/lists/devel/2015/08/17775.php,
some compilers don't like it when there's a .f90 file that only
contains comments (and no actual Fortran code). So if OMPI determines
that the Fortran compiler does not support enough Fortran mojo to
support MPI_SIZEOF, generate at least one dummy Fortran subroutine
that can be compiled in an otherwise barren Fortran landscape that is
devoid of life and hope.
This pull request adds an arraylist of type Buffer to
the Request class. Whenever a request object is created
that has associated buffers, the buffers should be added
to this array list so the java garbage collector does
not dispose of the buffers prematurely.
This is a more robust expansion on the idea first proposed by
@ggouaillardet
Fixes#369
Signed-off-by: Nathaniel Graham <ngraham@lanl.gov>
Portals4 supports atomic ops on datatypes less than or equal to
max_fetch_atomic_size bytes. This commit fixes a bug that required
the datatype to be less than max_fetch_atomic_size bytes.
Fortran uses objects (ompi_f08_mpi_comm_world, mpi_fortran_bottom,, ...) that are defined in C.
Some compilers have different requirements on how these objects should be aligned.
Smaller alignment in C can lead to several confusing warnings from the linker, so try to
find the alignment expected by Fortran compiler, and inform the C compiler.
The libmpi_*.la fortran libraries make some direct calls to
libopen-pal.la. In many (most?) cases, having libmpi_* link
against libmpi is sufficient (because libmpi pulls in libopen-pal).
But when building RPMs on SLES, some compiler/linker flags are used
that seem to make this implicit linking not sufficient -- we get
missing opal symbols when creating libmpi_mpifh.la. So link in
open-pal directly (vs. indirectly), which solves the problem.
On some OSs (e.g., Ubuntu 14.04.2 LTS), the linker is configured such
that the symbols of library dependencies are not available to the
application. Hence, we need to explicitly list such dependencies when
creating the executable.
For this commit, these tests are use OPAL function calls, so we must
explicitly link in libopen-pal.so.
- make the internal structure follow the Open MPI naming convention
- provide a single flag/macro which controls the compilation/utilization of this
feature, to avoid that somebody using this has to modify every single
fcoll component. A configure option could be added later if desired.
configury: fix hcoll, fca and mxm detection and revamp yalla Makefile.am
Thanks to David Shrader and Ake Sandgren for bringing this issue to our attention
* do not add -I/.../include/fca -I /.../include/fca_core to CPPFLAGS
* allow configure --with-fca
* search fca libs in both DIR/lib and DIR/lib64
* fix the description of the --with-fca option
* do not add -I/.../include/hcoll -I /.../include/hcoll/api to CPPFLAGS
* allow configure --with-hcoll
* search hcoll libs in both DIR/lib and DIR/lib64
* fix the description of the --with-hcoll option
mtl_ofi_provider_include (resp. mtl_ofi_provider_exclude) can be used
to specify which provider(s) the OFI MTL can select (resp. ignore).
e.g. --mca mtl_ofi_provider_include "psm,sockets"
By default, mtl_ofi_provider_exclude is set to "sockets,mxm".
This deprecates the old MCA var named "mtl_ofi_provider".
This commit does the following:
* s/ompi_check_treematch/ompi_topo_treematch/ (i.e., abide by the
prefix rule)
* change the value of ompi_topo_treematch_happy from yes/no to 0/1, so
that we can use -eq for numerical comparisons (vs. string
comparisons). It's the little things in life, no?
* Check the valueo f $OPAL_HAVE_HWLOC to ensure that hwloc support is
enabled. If not, disqualify treematch from building.
* Fixes a few places that were underquoted
* Convert from "test ... -a ..." to "test ... && test ..."
Fixesopen-mpi/ompi#797
The prior code was checking string constants (which are #defines from
configure) against NULL. They can never be NULL, so the checks were
overly-defensive. If the preprocessor macros do not exist, we'll get
a different compiler error. So remove the dead code.
This fixes CID 72349.
A helper method in Request.java could cause a crash
if the request array that was passed contained nulls.
Signed-off-by: Nathaniel Graham <ngraham@lanl.gov>
This commit rewrites parts of libnbc to fix issues identified by
coverity and myself. The changes are as follows:
- libnbc function would return invalid error codes (internal to
libnbc) to the mpi layer. These codes names are of the form
NBC_. They do not match up with the error codes expected by the mpi
layer. I purged the use of all these error codes with the exception
of NBC_OK and NBC_CONTINUE in progress. These codes are used to
identify when a request handle is complete.
- Handles and schedules were leaked by all collective routines on
error. A new routine was added to return a collective handle
(NBC_Return_handle).
- Temporary buffers containting in/out neighbors for neighborhood
collectives were always leaked.
- Neigborhood collectives contained code to handle MPI_IN_PLACE which
is never a valid input for the send or receive buffer. Stipped this
code out.
- Files were inconsistently named. Most are nbc_isomething.c but one
was named coll_libnbc_ireduce_scatter_block.c.
- Made the NBC_Schedule "structure" and object so it can be
retained/released. This may enable the use of schedule caching at a
later time. More testing will be needed to ensure the caching code
works. If it doesn't the code should be stripped out completely.
- Added code to simply common case of scheduling send/recv +
barrier.
- Code cleanup for readability.
The code now passes the clang static analyzer.
Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
Some OFI providers such as "sockets" are used for debugging
purposes mostly. For these providers, other components usually
offer better performance -- e.g. for sockets, the BTL/TCP would
be a better choice.
Thus, we chose to ignore some providers unless explicitly asked
by the user on the command line:
e.g. --mca mtl_ofi_provider sockets
Added Cloneable to the implemented interface list as per
Coverity suggestion. The required methods were already
implemented, but it was not explicitly stated. This is
an intent revealing change.
Signed-off-by: Nathaniel Graham <ngraham@lanl.gov>
When configured with --enable-picky
topo_base_lazy_init.c compiles with a warning:
CC base/topo_base_lazy_init.lo
base/topo_base_lazy_init.c:46:67: warning: implicit conversion from enumeration type 'enum mca_base_register_flag_t' to different enumeration type 'mca_base_open_flag_t' (aka 'enum mca_base_open_flag_t') [-Wenum-conversion]
err = mca_base_framework_open (&ompi_topo_base_framework, MCA_BASE_REGISTER_DEFAULT);
This commit fixes this implicit conversion problem.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
our optimized default file view. Otherwise, performance will suffer. file_get_view should still return the correct filetype, not our optimized default file view
Includes java bindings for MPI_GET_ELEMENTS_X and
MPI_STATUS_SET_ELEMENTS_X. This PR also adds the
Count object which represents MPI_Count.
Signed-off-by: Nathaniel Graham <ngraham@lanl.gov>
